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a/.doctrees/snippets/status-warning.doctree and /dev/null differ diff --git a/_downloads/07f4b1b69497c93530bbe772d7eb535a/smooth.py b/_downloads/07f4b1b69497c93530bbe772d7eb535a/smooth.py index f9b969b5..316d9444 100644 --- a/_downloads/07f4b1b69497c93530bbe772d7eb535a/smooth.py +++ b/_downloads/07f4b1b69497c93530bbe772d7eb535a/smooth.py @@ -109,7 +109,7 @@ def plot_raw_and_smooth_timeseries_and_psd( # Smoothing with a median filter # ------------------------------ # Using the -# :py:meth:`median_filter()\ +# :meth:`median_filter()\ # ` # method of the ``move`` accessor, # we apply a rolling window median filter over a 0.1-second window @@ -125,13 +125,13 @@ def plot_raw_and_smooth_timeseries_and_psd( # %% # .. note:: -# The ``move`` accessor :py:meth:`median_filter()\ +# The ``move`` accessor :meth:`median_filter()\ # ` # method is a convenience method that applies -# :py:func:`movement.filtering.median_filter` +# :func:`movement.filtering.median_filter` # to the ``position`` data variable. # The equivalent function call using the -# :py:mod:`movement.filtering` module would be: +# :mod:`movement.filtering` module would be: # # .. code-block:: python # @@ -249,11 +249,11 @@ def plot_raw_and_smooth_timeseries_and_psd( # Smoothing with a Savitzky-Golay filter # -------------------------------------- # Here we use the -# :py:meth:`savgol_filter()\ +# :meth:`savgol_filter()\ # ` # method of the ``move`` accessor, which is a convenience method that applies -# :py:func:`movement.filtering.savgol_filter` -# (a wrapper around :py:func:`scipy.signal.savgol_filter`), +# :func:`movement.filtering.savgol_filter` +# (a wrapper around :func:`scipy.signal.savgol_filter`), # to the ``position`` data variable. # The Savitzky-Golay filter is a polynomial smoothing filter that can be # applied to time series data on a rolling window basis. diff --git a/_downloads/085258163d1f42f74bf76da18a848b11/compute_kinematics.ipynb b/_downloads/085258163d1f42f74bf76da18a848b11/compute_kinematics.ipynb index d787743a..4c040a10 100644 --- a/_downloads/085258163d1f42f74bf76da18a848b11/compute_kinematics.ipynb +++ b/_downloads/085258163d1f42f74bf76da18a848b11/compute_kinematics.ipynb @@ -22,7 +22,7 @@ }, "outputs": [], "source": [ - "import numpy as np\n\n# For interactive plots: install ipympl with `pip install ipympl` and uncomment\n# the following line in your notebook\n# %matplotlib widget\nfrom matplotlib import pyplot as plt\n\nfrom movement import sample_data" + "# For interactive plots: install ipympl with `pip install ipympl` and uncomment\n# the following line in your notebook\n# %matplotlib widget\nfrom matplotlib import pyplot as plt\n\nfrom movement import sample_data\nfrom movement.utils.vector import compute_norm" ] }, { @@ -122,7 +122,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "We can also easily plot the components of the position vector against time\nusing ``xarray``'s built-in plotting methods. We use\n:py:meth:`xarray.DataArray.squeeze` to\nremove the dimension of length 1 from the data (the ``keypoints`` dimension).\n\n" + "We can also easily plot the components of the position vector against time\nusing ``xarray``'s built-in plotting methods. We use\n:meth:`xarray.DataArray.squeeze` to\nremove the dimension of length 1 from the data (the ``keypoints`` dimension).\n\n" ] }, { @@ -172,7 +172,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Notice that we could also compute the displacement (and all the other\nkinematic variables) using the :py:mod:`movement.analysis.kinematics` module:\n\n" + "Notice that we could also compute the displacement (and all the other\nkinematic variables) using the :mod:`movement.analysis.kinematics` module:\n\n" ] }, { @@ -283,7 +283,7 @@ }, "outputs": [], "source": [ - "# length of each displacement vector\ndisplacement_vectors_lengths = np.linalg.norm(\n displacement.sel(individuals=mouse_name, space=[\"x\", \"y\"]).squeeze(),\n axis=1,\n)\n\n# sum of all displacement vectors\ntotal_displacement = np.sum(displacement_vectors_lengths, axis=0) # in pixels\n\nprint(\n f\"The mouse {mouse_name}'s trajectory is {total_displacement:.2f} \"\n \"pixels long\"\n)" + "# length of each displacement vector\ndisplacement_vectors_lengths = compute_norm(\n displacement.sel(individuals=mouse_name)\n)\n\n# sum the lengths of all displacement vectors (in pixels)\ntotal_displacement = displacement_vectors_lengths.sum(dim=\"time\").values[0]\n\nprint(\n f\"The mouse {mouse_name}'s trajectory is {total_displacement:.2f} \"\n \"pixels long\"\n)" ] }, { @@ -315,7 +315,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "We can plot the components of the velocity vector against time\nusing ``xarray``'s built-in plotting methods. We use\n:py:meth:`xarray.DataArray.squeeze` to\nremove the dimension of length 1 from the data (the ``keypoints`` dimension).\n\n" + "We can plot the components of the velocity vector against time\nusing ``xarray``'s built-in plotting methods. We use\n:meth:`xarray.DataArray.squeeze` to\nremove the dimension of length 1 from the data (the ``keypoints`` dimension).\n\n" ] }, { @@ -340,7 +340,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "We can also visualise the speed, as the norm of the velocity vector:\n\n" + "We can also visualise the speed, as the magnitude (norm)\nof the velocity vector:\n\n" ] }, { @@ -351,7 +351,7 @@ }, "outputs": [], "source": [ - "fig, axes = plt.subplots(3, 1, sharex=True, sharey=True)\nfor mouse_name, ax in zip(velocity.individuals.values, axes, strict=False):\n # compute the norm of the velocity vector for one mouse\n speed_one_mouse = np.linalg.norm(\n velocity.sel(individuals=mouse_name, space=[\"x\", \"y\"]).squeeze(),\n axis=1,\n )\n # plot speed against time\n ax.plot(speed_one_mouse)\n ax.set_title(mouse_name)\n ax.set_xlabel(\"time (s)\")\n ax.set_ylabel(\"speed (px/s)\")\nfig.tight_layout()" + "fig, axes = plt.subplots(3, 1, sharex=True, sharey=True)\nfor mouse_name, ax in zip(velocity.individuals.values, axes, strict=False):\n # compute the magnitude of the velocity vector for one mouse\n speed_one_mouse = compute_norm(velocity.sel(individuals=mouse_name))\n # plot speed against time\n ax.plot(speed_one_mouse)\n ax.set_title(mouse_name)\n ax.set_xlabel(\"time (s)\")\n ax.set_ylabel(\"speed (px/s)\")\nfig.tight_layout()" ] }, { @@ -419,7 +419,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "The norm of the acceleration vector is the magnitude of the\nacceleration.\nWe can also represent this for each individual.\n\n" + "The can also represent the magnitude (norm) of the acceleration vector\nfor each individual:\n\n" ] }, { @@ -430,7 +430,7 @@ }, "outputs": [], "source": [ - "fig, axes = plt.subplots(3, 1, sharex=True, sharey=True)\nfor mouse_name, ax in zip(accel.individuals.values, axes, strict=False):\n # compute norm of the acceleration vector for one mouse\n accel_one_mouse = np.linalg.norm(\n accel.sel(individuals=mouse_name, space=[\"x\", \"y\"]).squeeze(),\n axis=1,\n )\n\n # plot acceleration against time\n ax.plot(accel_one_mouse)\n ax.set_title(mouse_name)\n ax.set_xlabel(\"time (s)\")\n ax.set_ylabel(\"accel (px/s**2)\")\nfig.tight_layout()" + "fig, axes = plt.subplots(3, 1, sharex=True, sharey=True)\nfor mouse_name, ax in zip(accel.individuals.values, axes, strict=False):\n # compute magnitude of the acceleration vector for one mouse\n accel_one_mouse = compute_norm(accel.sel(individuals=mouse_name))\n\n # plot acceleration against time\n ax.plot(accel_one_mouse)\n ax.set_title(mouse_name)\n ax.set_xlabel(\"time (s)\")\n ax.set_ylabel(\"accel (px/s**2)\")\nfig.tight_layout()" ] } ], diff --git a/_downloads/122338c6db2328ed9eeb5e9961344704/filter_and_interpolate.ipynb b/_downloads/122338c6db2328ed9eeb5e9961344704/filter_and_interpolate.ipynb index 2e6eb7a4..b4b46fc5 100644 --- a/_downloads/122338c6db2328ed9eeb5e9961344704/filter_and_interpolate.ipynb +++ b/_downloads/122338c6db2328ed9eeb5e9961344704/filter_and_interpolate.ipynb @@ -54,7 +54,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "## Visualise the pose tracks\nSince the data contains only a single wasp, we use\n:py:meth:`xarray.DataArray.squeeze` to remove\nthe dimension of length 1 from the data (the ``individuals`` dimension).\n\n" + "## Visualise the pose tracks\nSince the data contains only a single wasp, we use\n:meth:`xarray.DataArray.squeeze` to remove\nthe dimension of length 1 from the data (the ``individuals`` dimension).\n\n" ] }, { @@ -79,7 +79,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "## Visualise confidence scores\nThe confidence scores are stored in the ``confidence`` data variable.\nSince the predicted poses in this example have been generated by DeepLabCut,\nthe confidence scores should be likelihood values between 0 and 1.\nThat said, confidence scores are not standardised across pose\nestimation frameworks, and their ranges can vary. Therefore,\nit's always a good idea to inspect the actual confidence values in the data.\n\nLet's first look at a histogram of the confidence scores. As before, we use\n:py:meth:`xarray.DataArray.squeeze` to remove the ``individuals`` dimension\nfrom the data.\n\n" + "## Visualise confidence scores\nThe confidence scores are stored in the ``confidence`` data variable.\nSince the predicted poses in this example have been generated by DeepLabCut,\nthe confidence scores should be likelihood values between 0 and 1.\nThat said, confidence scores are not standardised across pose\nestimation frameworks, and their ranges can vary. Therefore,\nit's always a good idea to inspect the actual confidence values in the data.\n\nLet's first look at a histogram of the confidence scores. As before, we use\n:meth:`xarray.DataArray.squeeze` to remove the ``individuals`` dimension\nfrom the data.\n\n" ] }, { @@ -122,7 +122,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "## Filter out points with low confidence\nUsing the\n:py:meth:`filter_by_confidence()\\\n`\nmethod of the ``move`` accessor,\nwe can filter out points with confidence scores below a certain threshold.\nThe default ``threshold=0.6`` will be used when ``threshold`` is not\nprovided.\nThis method will also report the number of NaN values in the dataset before\nand after the filtering operation by default (``print_report=True``).\nWe will use :py:meth:`xarray.Dataset.update` to update ``ds`` in-place\nwith the filtered ``position``.\n\n" + "## Filter out points with low confidence\nUsing the\n:meth:`filter_by_confidence()\\\n`\nmethod of the ``move`` accessor,\nwe can filter out points with confidence scores below a certain threshold.\nThe default ``threshold=0.6`` will be used when ``threshold`` is not\nprovided.\nThis method will also report the number of NaN values in the dataset before\nand after the filtering operation by default (``print_report=True``).\nWe will use :meth:`xarray.Dataset.update` to update ``ds`` in-place\nwith the filtered ``position``.\n\n" ] }, { @@ -140,7 +140,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "

Note

The ``move`` accessor :py:meth:`filter_by_confidence()\\\n `\n method is a convenience method that applies\n :py:func:`movement.filtering.filter_by_confidence`,\n which takes ``position`` and ``confidence`` as arguments.\n The equivalent function call using the\n :py:mod:`movement.filtering` module would be:\n\n```python\nfrom movement.filtering import filter_by_confidence\n\nds.update({\"position\": filter_by_confidence(position, confidence)})

\n```\n" + "

Note

The ``move`` accessor :meth:`filter_by_confidence()\\\n `\n method is a convenience method that applies\n :func:`movement.filtering.filter_by_confidence`,\n which takes ``position`` and ``confidence`` as arguments.\n The equivalent function call using the\n :mod:`movement.filtering` module would be:\n\n```python\nfrom movement.filtering import filter_by_confidence\n\nds.update({\"position\": filter_by_confidence(position, confidence)})

\n```\n" ] }, { @@ -172,7 +172,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "## Interpolate over missing values\nUsing the\n:py:meth:`interpolate_over_time()\\\n`\nmethod of the ``move`` accessor,\nwe can interpolate over the gaps we've introduced in the pose tracks.\nHere we use the default linear interpolation method (``method=linear``)\nand interpolate over gaps of 40 frames or less (``max_gap=40``).\nThe default ``max_gap=None`` would interpolate over all gaps, regardless of\ntheir length, but this should be used with caution as it can introduce\nspurious data. The ``print_report`` argument acts as described above.\n\n" + "## Interpolate over missing values\nUsing the\n:meth:`interpolate_over_time()\\\n`\nmethod of the ``move`` accessor,\nwe can interpolate over the gaps we've introduced in the pose tracks.\nHere we use the default linear interpolation method (``method=linear``)\nand interpolate over gaps of 40 frames or less (``max_gap=40``).\nThe default ``max_gap=None`` would interpolate over all gaps, regardless of\ntheir length, but this should be used with caution as it can introduce\nspurious data. The ``print_report`` argument acts as described above.\n\n" ] }, { @@ -190,7 +190,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "

Note

The ``move`` accessor :py:meth:`interpolate_over_time()\\\n `\n is also a convenience method that applies\n :py:func:`movement.filtering.interpolate_over_time`\n to the ``position`` data variable.\n The equivalent function call using the\n :py:mod:`movement.filtering` module would be:\n\n```python\nfrom movement.filtering import interpolate_over_time\n\nds.update({\"position\": interpolate_over_time(\n position_filtered, max_gap=40\n)})

\n```\n" + "

Note

The ``move`` accessor :meth:`interpolate_over_time()\\\n `\n is also a convenience method that applies\n :func:`movement.filtering.interpolate_over_time`\n to the ``position`` data variable.\n The equivalent function call using the\n :mod:`movement.filtering` module would be:\n\n```python\nfrom movement.filtering import interpolate_over_time\n\nds.update({\"position\": interpolate_over_time(\n position_filtered, max_gap=40\n)})

\n```\n" ] }, { @@ -233,7 +233,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "## Filtering multiple data variables\nAll :py:mod:`movement.filtering` functions are available via the\n``move`` accessor. These ``move`` accessor methods operate on the\n``position`` data variable in the dataset ``ds`` by default.\nThere is also an additional argument ``data_vars`` that allows us to\nspecify which data variables in ``ds`` to filter.\nWhen multiple data variable names are specified in ``data_vars``,\nthe method will return a dictionary with the data variable names as keys\nand the filtered DataArrays as values, otherwise it will return a single\nDataArray that is the filtered data.\nThis is useful when we want to apply the same filtering operation to\nmultiple data variables in ``ds`` at the same time.\n\nFor instance, to filter both ``position`` and ``velocity`` data variables\nin ``ds``, based on the confidence scores, we can specify\n``data_vars=[\"position\", \"velocity\"]`` in the method call.\nAs the filtered data variables are returned as a dictionary, we can once\nagain use :py:meth:`xarray.Dataset.update` to update ``ds`` in-place\nwith the filtered data variables.\n\n" + "## Filtering multiple data variables\nAll :mod:`movement.filtering` functions are available via the\n``move`` accessor. These ``move`` accessor methods operate on the\n``position`` data variable in the dataset ``ds`` by default.\nThere is also an additional argument ``data_vars`` that allows us to\nspecify which data variables in ``ds`` to filter.\nWhen multiple data variable names are specified in ``data_vars``,\nthe method will return a dictionary with the data variable names as keys\nand the filtered DataArrays as values, otherwise it will return a single\nDataArray that is the filtered data.\nThis is useful when we want to apply the same filtering operation to\nmultiple data variables in ``ds`` at the same time.\n\nFor instance, to filter both ``position`` and ``velocity`` data variables\nin ``ds``, based on the confidence scores, we can specify\n``data_vars=[\"position\", \"velocity\"]`` in the method call.\nAs the filtered data variables are returned as a dictionary, we can once\nagain use :meth:`xarray.Dataset.update` to update ``ds`` in-place\nwith the filtered data variables.\n\n" ] }, { diff --git a/_downloads/441eab1669614b55b79b26c34c5789c0/filter_and_interpolate.zip b/_downloads/441eab1669614b55b79b26c34c5789c0/filter_and_interpolate.zip new file mode 100644 index 00000000..a744e072 Binary files /dev/null and b/_downloads/441eab1669614b55b79b26c34c5789c0/filter_and_interpolate.zip differ diff --git a/_downloads/67c42b92a18ad7782039430d00e41877/load_and_explore_poses.zip b/_downloads/67c42b92a18ad7782039430d00e41877/load_and_explore_poses.zip new file mode 100644 index 00000000..d9116ead Binary files /dev/null and b/_downloads/67c42b92a18ad7782039430d00e41877/load_and_explore_poses.zip differ diff --git a/_downloads/8187ecfe17e4bd1029ff7f254a6773c3/smooth.zip b/_downloads/8187ecfe17e4bd1029ff7f254a6773c3/smooth.zip new file mode 100644 index 00000000..012f87a5 Binary files /dev/null and b/_downloads/8187ecfe17e4bd1029ff7f254a6773c3/smooth.zip differ diff --git a/_downloads/844e74b700fac354e52a59dbe7329a84/smooth.ipynb b/_downloads/844e74b700fac354e52a59dbe7329a84/smooth.ipynb index f77fcfd4..c86b500a 100644 --- a/_downloads/844e74b700fac354e52a59dbe7329a84/smooth.ipynb +++ b/_downloads/844e74b700fac354e52a59dbe7329a84/smooth.ipynb @@ -72,7 +72,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "## Smoothing with a median filter\nUsing the\n:py:meth:`median_filter()\\\n`\nmethod of the ``move`` accessor,\nwe apply a rolling window median filter over a 0.1-second window\n(4 frames) to the wasp dataset.\nAs the ``window`` parameter is defined in *number of observations*,\nwe can simply multiply the desired time window by the frame rate\nof the video. We will also create a copy of the dataset to avoid\nmodifying the original data.\n\n" + "## Smoothing with a median filter\nUsing the\n:meth:`median_filter()\\\n`\nmethod of the ``move`` accessor,\nwe apply a rolling window median filter over a 0.1-second window\n(4 frames) to the wasp dataset.\nAs the ``window`` parameter is defined in *number of observations*,\nwe can simply multiply the desired time window by the frame rate\nof the video. We will also create a copy of the dataset to avoid\nmodifying the original data.\n\n" ] }, { @@ -90,7 +90,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "

Note

The ``move`` accessor :py:meth:`median_filter()\\\n `\n method is a convenience method that applies\n :py:func:`movement.filtering.median_filter`\n to the ``position`` data variable.\n The equivalent function call using the\n :py:mod:`movement.filtering` module would be:\n\n```python\nfrom movement.filtering import median_filter\n\nds_wasp_smooth.update({\"position\": median_filter(position, window)})

\n```\n" + "

Note

The ``move`` accessor :meth:`median_filter()\\\n `\n method is a convenience method that applies\n :func:`movement.filtering.median_filter`\n to the ``position`` data variable.\n The equivalent function call using the\n :mod:`movement.filtering` module would be:\n\n```python\nfrom movement.filtering import median_filter\n\nds_wasp_smooth.update({\"position\": median_filter(position, window)})

\n```\n" ] }, { @@ -237,7 +237,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "## Smoothing with a Savitzky-Golay filter\nHere we use the\n:py:meth:`savgol_filter()\\\n`\nmethod of the ``move`` accessor, which is a convenience method that applies\n:py:func:`movement.filtering.savgol_filter`\n(a wrapper around :py:func:`scipy.signal.savgol_filter`),\nto the ``position`` data variable.\nThe Savitzky-Golay filter is a polynomial smoothing filter that can be\napplied to time series data on a rolling window basis.\nA polynomial with a degree specified by ``polyorder`` is applied to each\ndata segment defined by the size ``window``.\nThe value of the polynomial at the midpoint of each ``window`` is then\nused as the output value.\n\nLet's try it on the mouse dataset, this time using a 0.2-second\nwindow (i.e. 6 frames) and the default ``polyorder=2`` for smoothing.\nAs before, we first compute the corresponding number of observations\nto be used as the ``window`` size.\n\n" + "## Smoothing with a Savitzky-Golay filter\nHere we use the\n:meth:`savgol_filter()\\\n`\nmethod of the ``move`` accessor, which is a convenience method that applies\n:func:`movement.filtering.savgol_filter`\n(a wrapper around :func:`scipy.signal.savgol_filter`),\nto the ``position`` data variable.\nThe Savitzky-Golay filter is a polynomial smoothing filter that can be\napplied to time series data on a rolling window basis.\nA polynomial with a degree specified by ``polyorder`` is applied to each\ndata segment defined by the size ``window``.\nThe value of the polynomial at the midpoint of each ``window`` is then\nused as the output value.\n\nLet's try it on the mouse dataset, this time using a 0.2-second\nwindow (i.e. 6 frames) and the default ``polyorder=2`` for smoothing.\nAs before, we first compute the corresponding number of observations\nto be used as the ``window`` size.\n\n" ] }, { diff --git a/_downloads/8616797cd8df925412b19674f364ffea/filter_and_interpolate.py b/_downloads/8616797cd8df925412b19674f364ffea/filter_and_interpolate.py index dbe33044..71384ca7 100644 --- a/_downloads/8616797cd8df925412b19674f364ffea/filter_and_interpolate.py +++ b/_downloads/8616797cd8df925412b19674f364ffea/filter_and_interpolate.py @@ -27,7 +27,7 @@ # Visualise the pose tracks # ------------------------- # Since the data contains only a single wasp, we use -# :py:meth:`xarray.DataArray.squeeze` to remove +# :meth:`xarray.DataArray.squeeze` to remove # the dimension of length 1 from the data (the ``individuals`` dimension). ds.position.squeeze().plot.line( @@ -51,7 +51,7 @@ # it's always a good idea to inspect the actual confidence values in the data. # # Let's first look at a histogram of the confidence scores. As before, we use -# :py:meth:`xarray.DataArray.squeeze` to remove the ``individuals`` dimension +# :meth:`xarray.DataArray.squeeze` to remove the ``individuals`` dimension # from the data. ds.confidence.squeeze().plot.hist(bins=20) @@ -74,7 +74,7 @@ # Filter out points with low confidence # ------------------------------------- # Using the -# :py:meth:`filter_by_confidence()\ +# :meth:`filter_by_confidence()\ # ` # method of the ``move`` accessor, # we can filter out points with confidence scores below a certain threshold. @@ -82,20 +82,20 @@ # provided. # This method will also report the number of NaN values in the dataset before # and after the filtering operation by default (``print_report=True``). -# We will use :py:meth:`xarray.Dataset.update` to update ``ds`` in-place +# We will use :meth:`xarray.Dataset.update` to update ``ds`` in-place # with the filtered ``position``. ds.update({"position": ds.move.filter_by_confidence()}) # %% # .. note:: -# The ``move`` accessor :py:meth:`filter_by_confidence()\ +# The ``move`` accessor :meth:`filter_by_confidence()\ # ` # method is a convenience method that applies -# :py:func:`movement.filtering.filter_by_confidence`, +# :func:`movement.filtering.filter_by_confidence`, # which takes ``position`` and ``confidence`` as arguments. # The equivalent function call using the -# :py:mod:`movement.filtering` module would be: +# :mod:`movement.filtering` module would be: # # .. code-block:: python # @@ -121,7 +121,7 @@ # Interpolate over missing values # ------------------------------- # Using the -# :py:meth:`interpolate_over_time()\ +# :meth:`interpolate_over_time()\ # ` # method of the ``move`` accessor, # we can interpolate over the gaps we've introduced in the pose tracks. @@ -135,13 +135,13 @@ # %% # .. note:: -# The ``move`` accessor :py:meth:`interpolate_over_time()\ +# The ``move`` accessor :meth:`interpolate_over_time()\ # ` # is also a convenience method that applies -# :py:func:`movement.filtering.interpolate_over_time` +# :func:`movement.filtering.interpolate_over_time` # to the ``position`` data variable. # The equivalent function call using the -# :py:mod:`movement.filtering` module would be: +# :mod:`movement.filtering` module would be: # # .. code-block:: python # @@ -176,7 +176,7 @@ # %% # Filtering multiple data variables # --------------------------------- -# All :py:mod:`movement.filtering` functions are available via the +# All :mod:`movement.filtering` functions are available via the # ``move`` accessor. These ``move`` accessor methods operate on the # ``position`` data variable in the dataset ``ds`` by default. # There is also an additional argument ``data_vars`` that allows us to @@ -192,7 +192,7 @@ # in ``ds``, based on the confidence scores, we can specify # ``data_vars=["position", "velocity"]`` in the method call. # As the filtered data variables are returned as a dictionary, we can once -# again use :py:meth:`xarray.Dataset.update` to update ``ds`` in-place +# again use :meth:`xarray.Dataset.update` to update ``ds`` in-place # with the filtered data variables. ds["velocity"] = ds.move.compute_velocity() diff --git a/_downloads/a98cbac755c506fe52bb526be923dd06/compute_polar_coordinates.zip b/_downloads/a98cbac755c506fe52bb526be923dd06/compute_polar_coordinates.zip new file mode 100644 index 00000000..9abd8887 Binary files /dev/null and b/_downloads/a98cbac755c506fe52bb526be923dd06/compute_polar_coordinates.zip differ diff --git a/_downloads/b14755a378a13dd501d6f42af59fe770/compute_kinematics.py b/_downloads/b14755a378a13dd501d6f42af59fe770/compute_kinematics.py index 8cea0912..b3fefd4a 100644 --- a/_downloads/b14755a378a13dd501d6f42af59fe770/compute_kinematics.py +++ b/_downloads/b14755a378a13dd501d6f42af59fe770/compute_kinematics.py @@ -10,14 +10,13 @@ # Imports # ------- -import numpy as np - # For interactive plots: install ipympl with `pip install ipympl` and uncomment # the following line in your notebook # %matplotlib widget from matplotlib import pyplot as plt from movement import sample_data +from movement.utils.vector import compute_norm # %% # Load sample dataset @@ -105,7 +104,7 @@ # %% # We can also easily plot the components of the position vector against time # using ``xarray``'s built-in plotting methods. We use -# :py:meth:`xarray.DataArray.squeeze` to +# :meth:`xarray.DataArray.squeeze` to # remove the dimension of length 1 from the data (the ``keypoints`` dimension). position.squeeze().plot.line(x="time", row="individuals", aspect=2, size=2.5) plt.gcf().show() @@ -131,7 +130,7 @@ # %% # Notice that we could also compute the displacement (and all the other -# kinematic variables) using the :py:mod:`movement.analysis.kinematics` module: +# kinematic variables) using the :mod:`movement.analysis.kinematics` module: # %% import movement.analysis.kinematics as kin @@ -255,13 +254,12 @@ # mouse along its trajectory. # length of each displacement vector -displacement_vectors_lengths = np.linalg.norm( - displacement.sel(individuals=mouse_name, space=["x", "y"]).squeeze(), - axis=1, +displacement_vectors_lengths = compute_norm( + displacement.sel(individuals=mouse_name) ) -# sum of all displacement vectors -total_displacement = np.sum(displacement_vectors_lengths, axis=0) # in pixels +# sum the lengths of all displacement vectors (in pixels) +total_displacement = displacement_vectors_lengths.sum(dim="time").values[0] print( f"The mouse {mouse_name}'s trajectory is {total_displacement:.2f} " @@ -284,7 +282,7 @@ # %% # We can plot the components of the velocity vector against time # using ``xarray``'s built-in plotting methods. We use -# :py:meth:`xarray.DataArray.squeeze` to +# :meth:`xarray.DataArray.squeeze` to # remove the dimension of length 1 from the data (the ``keypoints`` dimension). velocity.squeeze().plot.line(x="time", row="individuals", aspect=2, size=2.5) @@ -299,14 +297,12 @@ # uses second order central differences. # %% -# We can also visualise the speed, as the norm of the velocity vector: +# We can also visualise the speed, as the magnitude (norm) +# of the velocity vector: fig, axes = plt.subplots(3, 1, sharex=True, sharey=True) for mouse_name, ax in zip(velocity.individuals.values, axes, strict=False): - # compute the norm of the velocity vector for one mouse - speed_one_mouse = np.linalg.norm( - velocity.sel(individuals=mouse_name, space=["x", "y"]).squeeze(), - axis=1, - ) + # compute the magnitude of the velocity vector for one mouse + speed_one_mouse = compute_norm(velocity.sel(individuals=mouse_name)) # plot speed against time ax.plot(speed_one_mouse) ax.set_title(mouse_name) @@ -379,16 +375,12 @@ fig.tight_layout() # %% -# The norm of the acceleration vector is the magnitude of the -# acceleration. -# We can also represent this for each individual. +# The can also represent the magnitude (norm) of the acceleration vector +# for each individual: fig, axes = plt.subplots(3, 1, sharex=True, sharey=True) for mouse_name, ax in zip(accel.individuals.values, axes, strict=False): - # compute norm of the acceleration vector for one mouse - accel_one_mouse = np.linalg.norm( - accel.sel(individuals=mouse_name, space=["x", "y"]).squeeze(), - axis=1, - ) + # compute magnitude of the acceleration vector for one mouse + accel_one_mouse = compute_norm(accel.sel(individuals=mouse_name)) # plot acceleration against time ax.plot(accel_one_mouse) diff --git a/_downloads/bc82bea3a5dd7bdba60b65220891d9e5/examples_python.zip b/_downloads/bc82bea3a5dd7bdba60b65220891d9e5/examples_python.zip index 2ef134f7..6a5d9bd1 100644 Binary files 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a/_modules/index.html +++ b/_modules/index.html @@ -27,20 +27,20 @@ - + - + - + - + @@ -125,7 +125,7 @@ -

movement v0.0.19

+

movement v0.0.20

@@ -409,6 +409,7 @@

All modules for which code is available

  • movement.analysis.kinematics
  • movement.filtering
    • +
  • movement.io.load_bboxes
  • movement.io.load_poses
  • movement.io.save_poses
  • movement.move_accessor
    • @@ -456,7 +457,7 @@

    All modules for which code is available

    - Created using Sphinx 7.4.5. + Created using Sphinx 8.0.2.

    diff --git a/_modules/movement/analysis/kinematics.html b/_modules/movement/analysis/kinematics.html index 237bc3ef..a8ef7a87 100644 --- a/_modules/movement/analysis/kinematics.html +++ b/_modules/movement/analysis/kinematics.html @@ -27,20 +27,20 @@ - + - + - + - + @@ -125,7 +125,7 @@ -

    movement v0.0.19

    +

    movement v0.0.20

    @@ -412,7 +412,6 @@

    Source code for movement.analysis.kinematics

     """Compute kinematic variables like velocity and acceleration."""
 
-import numpy as np
 import xarray as xr
 
 from movement.utils.logging import log_error
@@ -421,22 +420,40 @@ 
    Source code for movement.analysis.kinematics
     [docs]
 def compute_displacement(data: xr.DataArray) -> xr.DataArray:
-    """Compute displacement between consecutive positions.
+    """Compute displacement array in cartesian coordinates.
 
-    This is the difference between consecutive positions of each keypoint for
-    each individual across time. At each time point ``t``, it's defined as a
-    vector in cartesian ``(x,y)`` coordinates, pointing from the previous
-    ``(t-1)`` to the current ``(t)`` position.
+    The displacement array is defined as the difference between the position
+    array at time point ``t`` and the position array at time point ``t-1``.
+
+    As a result, for a given individual and keypoint, the displacement vector
+    at time point ``t``, is the vector pointing from the previous
+    ``(t-1)`` to the current ``(t)`` position, in cartesian coordinates.
 
     Parameters
     ----------
     data : xarray.DataArray
-        The input data containing ``time`` as a dimension.
+        The input data array containing position vectors in cartesian
+        coordinates, with ``time`` as a dimension.
 
     Returns
     -------
     xarray.DataArray
-        An xarray DataArray containing the computed displacement.
+        An xarray DataArray containing displacement vectors in cartesian
+        coordinates.
+
+    Notes
+    -----
+    For the ``position`` array of a ``poses`` dataset, the ``displacement``
+    array will hold the displacement vectors for every keypoint and every
+    individual.
+
+    For the ``position`` array of a ``bboxes`` dataset, the ``displacement``
+    array will hold the displacement vectors for the centroid of every
+    individual bounding box.
+
+    For the ``shape`` array of a ``bboxes`` dataset, the
+    ``displacement`` array will hold vectors with the change in width and
+    height per bounding box, between consecutive time points.
 
     """
     _validate_time_dimension(data)
@@ -449,70 +466,105 @@ 
    Source code for movement.analysis.kinematics
     [docs]
 def compute_velocity(data: xr.DataArray) -> xr.DataArray:
-    """Compute the velocity in cartesian ``(x,y)`` coordinates.
+    """Compute velocity array in cartesian coordinates.
 
-    Velocity is the first derivative of position for each keypoint
-    and individual across time. It's computed using numerical differentiation
-    and assumes equidistant time spacing.
+    The velocity array is the first time-derivative of the position
+    array. It is computed by applying the second-order accurate central
+    differences method on the position array.
 
     Parameters
     ----------
     data : xarray.DataArray
-        The input data containing ``time`` as a dimension.
+        The input data array containing position vectors in cartesian
+        coordinates, with ``time`` as a dimension.
 
     Returns
     -------
     xarray.DataArray
-        An xarray DataArray containing the computed velocity.
+        An xarray DataArray containing velocity vectors in cartesian
+        coordinates.
+
+    Notes
+    -----
+    For the ``position`` array of a ``poses`` dataset, the ``velocity`` array
+    will hold the velocity vectors for every keypoint and every individual.
+
+    For the ``position`` array of a ``bboxes`` dataset, the ``velocity`` array
+    will hold the velocity vectors for the centroid of every individual
+    bounding box.
+
+    See Also
+    --------
+    :meth:`xarray.DataArray.differentiate` : The underlying method used.
 
     """
-    return _compute_approximate_derivative(data, order=1)
    
+    return _compute_approximate_time_derivative(data, order=1)
    
 
 
 
 
    
 [docs]
 def compute_acceleration(data: xr.DataArray) -> xr.DataArray:
-    """Compute acceleration in cartesian ``(x,y)`` coordinates.
+    """Compute acceleration array in cartesian coordinates.
 
-    Acceleration represents the second derivative of position for each keypoint
-    and individual across time. It's computed using numerical differentiation
-    and assumes equidistant time spacing.
+    The acceleration array is the second time-derivative of the
+    position array. It is computed by applying the second-order accurate
+    central differences method on the velocity array.
 
     Parameters
     ----------
     data : xarray.DataArray
-        The input data containing ``time`` as a dimension.
+        The input data array containing position vectors in cartesian
+        coordinates, with``time`` as a dimension.
 
     Returns
     -------
     xarray.DataArray
-        An xarray DataArray containing the computed acceleration.
+        An xarray DataArray containing acceleration vectors in cartesian
+        coordinates.
+
+    Notes
+    -----
+    For the ``position`` array of a ``poses`` dataset, the ``acceleration``
+    array will hold the acceleration vectors for every keypoint and every
+    individual.
+
+    For the ``position`` array of a ``bboxes`` dataset, the ``acceleration``
+    array will hold the acceleration vectors for the centroid of every
+    individual bounding box.
+
+    See Also
+    --------
+    :meth:`xarray.DataArray.differentiate` : The underlying method used.
 
     """
-    return _compute_approximate_derivative(data, order=2)
    
+    return _compute_approximate_time_derivative(data, order=2)
    -def _compute_approximate_derivative( +def _compute_approximate_time_derivative( data: xr.DataArray, order: int ) -> xr.DataArray: - """Compute the derivative using numerical differentiation. + """Compute the time-derivative of an array using numerical differentiation. - This assumes equidistant time spacing. + This function uses :meth:`xarray.DataArray.differentiate`, + which differentiates the array with the second-order + accurate central differences method. Parameters ---------- data : xarray.DataArray - The input data containing ``time`` as a dimension. + The input data array containing ``time`` as a dimension. order : int - The order of the derivative. 1 for velocity, 2 for - acceleration. Value must be a positive integer. + The order of the time-derivative. For an input containing position + data, use 1 to compute velocity, and 2 to compute acceleration. Value + must be a positive integer. Returns ------- xarray.DataArray - An xarray DataArray containing the derived variable. + An xarray DataArray containing the time-derivative of the + input data. """ if not isinstance(order, int): @@ -521,17 +573,12 @@

    Source code for movement.analysis.kinematics

    )
     if order <= 0:
         raise log_error(ValueError, "Order must be a positive integer.")
+
     _validate_time_dimension(data)
+
     result = data
-    dt = data["time"].values[1] - data["time"].values[0]
     for _ in range(order):
-        result = xr.apply_ufunc(
-            np.gradient,
-            result,
-            dt,
-            kwargs={"axis": 0},
-        )
-    result = result.reindex_like(data)
+        result = result.differentiate("time")
     return result
 
 
@@ -545,13 +592,13 @@ 
    Source code for movement.analysis.kinematics
        Raises
     ------
-    AttributeError
+    ValueError
         If the input data does not contain a ``time`` dimension.
 
     """
     if "time" not in data.dims:
         raise log_error(
-            AttributeError, "Input data must contain 'time' as a dimension."
+            ValueError, "Input data must contain 'time' as a dimension."
         )
 
    
 
@@ -591,7 +638,7 @@ 
    Source code for movement.analysis.kinematics
           
         
    
-    Created using Sphinx 7.4.5.
+    Created using Sphinx 8.0.2.
     
    
     
    
     
    
diff --git a/_modules/movement/filtering.html b/_modules/movement/filtering.html
index 96637bca..da445a91 100644
--- a/_modules/movement/filtering.html
+++ b/_modules/movement/filtering.html
@@ -27,20 +27,20 @@
 
 
 
-    
+    
     
-    
+    
     
     
     
-    
+    
   
   
   
 
   
 
-    
+    
     
     
     
@@ -125,7 +125,7 @@
   
   
   
-    
    movement v0.0.19
    
+    
    movement v0.0.20
    
   
 
    
     
@@ -410,7 +410,7 @@
                 
    
                   
   
    Source code for movement.filtering
    -"""Filter and interpolate  pose tracks in ``movement`` datasets."""
+"""Filter and interpolate tracks in ``movement`` datasets."""
 
 import xarray as xr
 from scipy import signal
@@ -454,14 +454,14 @@ 
    Source code for movement.filtering
     
     Notes
     -----
-    The point-wise confidence values reported by various pose estimation
-    frameworks are not standardised, and the range of values can vary.
-    For example, DeepLabCut reports a likelihood value between 0 and 1, whereas
-    the point confidence reported by SLEAP can range above 1.
-    Therefore, the default threshold value will not be appropriate for all
-    datasets and does not have the same meaning across pose estimation
-    frameworks. We advise users to inspect the confidence values
-    in their dataset and adjust the threshold accordingly.
+    For the poses dataset case, note that the point-wise confidence values
+    reported by various pose estimation frameworks are not standardised, and
+    the range of values can vary. For example, DeepLabCut reports a likelihood
+    value between 0 and 1, whereas the point confidence reported by SLEAP can
+    range above 1. Therefore, the default threshold value will not be
+    appropriate for all datasets and does not have the same meaning across
+    pose estimation frameworks. We advise users to inspect the confidence
+    values in their dataset and adjust the threshold accordingly.
 
     """
     data_filtered = data.where(confidence >= threshold)
@@ -483,7 +483,7 @@ 
    Source code for movement.filtering
     ) -> xr.DataArray:
     """Fill in NaN values by interpolating over the ``time`` dimension.
 
-    This method uses :py:meth:`xarray.DataArray.interpolate_na` under the
+    This method uses :meth:`xarray.DataArray.interpolate_na` under the
     hood and passes the ``method`` and ``max_gap`` parameters to it.
     See the xarray documentation for more details on these parameters.
 
@@ -505,14 +505,14 @@ 
    Source code for movement.filtering
     
     Returns
     -------
-    xr.DataArray
+    xarray.DataArray
         The data where NaN values have been interpolated over
         using the parameters provided.
 
     Notes
     -----
     The ``max_gap`` parameter differs slightly from that in
-    :py:meth:`xarray.DataArray.interpolate_na`, in which the gap size
+    :meth:`xarray.DataArray.interpolate_na`, in which the gap size
     is defined as the difference between the ``time`` coordinate values
     at the first data point after a gap and the last value before a gap.
 
@@ -547,17 +547,17 @@ 
    Source code for movement.filtering
         data : xarray.DataArray
         The input data to be smoothed.
     window : int
-        The size of the filter window, representing the fixed number
+        The size of the smoothing window, representing the fixed number
         of observations used for each window.
     min_periods : int
         Minimum number of observations in the window required to have
         a value (otherwise result is NaN). The default, None, is
         equivalent to setting ``min_periods`` equal to the size of the window.
         This argument is directly  passed to the ``min_periods`` parameter of
-        :py:meth:`xarray.DataArray.rolling`.
+        :meth:`xarray.DataArray.rolling`.
     print_report : bool
         Whether to print a report on the number of NaNs in the dataset
-        before and after filtering. Default is ``True``.
+        before and after smoothing. Default is ``True``.
 
     Returns
     -------
@@ -566,7 +566,7 @@ 
    Source code for movement.filtering
     
     Notes
     -----
-    By default, whenever one or more NaNs are present in the filter window,
+    By default, whenever one or more NaNs are present in the smoothing window,
     a NaN is returned to the output array. As a result, any
     stretch of NaNs present in the input data will be propagated
     proportionally to the size of the window  (specifically, by
@@ -617,7 +617,7 @@ 
    Source code for movement.filtering
         data : xarray.DataArray
         The input data to be smoothed.
     window : int
-        The size of the filter window, representing the fixed number
+        The size of the smoothing window, representing the fixed number
         of observations used for each window.
     polyorder : int
         The order of the polynomial used to fit the samples. Must be
@@ -625,10 +625,10 @@ 
    Source code for movement.filtering
             2 is used.
     print_report : bool
         Whether to print a report on the number of NaNs in the dataset
-        before and after filtering. Default is ``True``.
+        before and after smoothing. Default is ``True``.
     **kwargs : dict
         Additional keyword arguments are passed to
-        :py:func:`scipy.signal.savgol_filter`.
+        :func:`scipy.signal.savgol_filter`.
         Note that the ``axis`` keyword argument may not be overridden.
 
 
@@ -640,15 +640,15 @@ 
    Source code for movement.filtering
     
     Notes
     -----
-    Uses the :py:func:`scipy.signal.savgol_filter` function to apply a
+    Uses the :func:`scipy.signal.savgol_filter` function to apply a
     Savitzky-Golay filter to the input data.
     See the SciPy documentation for more information on that function.
-    Whenever one or more NaNs are present in a filter window of the
+    Whenever one or more NaNs are present in a smoothing window of the
     input data, a NaN is returned to the output array. As a result, any
     stretch of NaNs present in the input data will be propagated
     proportionally to the size of the window (specifically, by
     ``floor(window/2)``). Note that, unlike
-    :py:func:`movement.filtering.median_filter()`, there is no ``min_periods``
+    :func:`movement.filtering.median_filter`, there is no ``min_periods``
     option to control this behaviour.
 
     """
@@ -707,7 +707,7 @@ 
    Source code for movement.filtering
         
    
       
         
    
-    Created using Sphinx 7.4.5.
+    Created using Sphinx 8.0.2.
     
    
     
    
     
    
diff --git a/_modules/movement/io/load_bboxes.html b/_modules/movement/io/load_bboxes.html
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+  
    Source code for movement.io.load_bboxes
    +"""Load bounding boxes' tracking data into ``movement``."""
+
+import ast
+import logging
+import re
+from collections.abc import Callable
+from pathlib import Path
+from typing import Literal
+
+import numpy as np
+import pandas as pd
+import xarray as xr
+
+from movement import MovementDataset
+from movement.utils.logging import log_error
+from movement.validators.datasets import ValidBboxesDataset
+from movement.validators.files import ValidFile, ValidVIATracksCSV
+
+logger = logging.getLogger(__name__)
+
+
+
    
+[docs]
+def from_numpy(
+    position_array: np.ndarray,
+    shape_array: np.ndarray,
+    confidence_array: np.ndarray | None = None,
+    individual_names: list[str] | None = None,
+    frame_array: np.ndarray | None = None,
+    fps: float | None = None,
+    source_software: str | None = None,
+) -> xr.Dataset:
+    """Create a ``movement`` bounding boxes dataset from NumPy arrays.
+
+    Parameters
+    ----------
+    position_array : np.ndarray
+        Array of shape (n_frames, n_individuals, n_space)
+        containing the tracks of the bounding boxes' centroids.
+        It will be converted to a :class:`xarray.DataArray` object
+        named "position".
+    shape_array : np.ndarray
+        Array of shape (n_frames, n_individuals, n_space)
+        containing the shape of the bounding boxes. The shape of a bounding
+        box is its width (extent along the x-axis of the image) and height
+        (extent along the y-axis of the image). It will be converted to a
+        :class:`xarray.DataArray` object named "shape".
+    confidence_array : np.ndarray, optional
+        Array of shape (n_frames, n_individuals) containing
+        the confidence scores of the bounding boxes. If None (default), the
+        confidence scores are set to an array of NaNs. It will be converted
+        to a :class:`xarray.DataArray` object named "confidence".
+    individual_names : list of str, optional
+        List of individual names for the tracked bounding boxes in the video.
+        If None (default), bounding boxes are assigned names based on the size
+        of the ``position_array``. The names will be in the format of
+        ``id_<N>``, where <N>  is an integer from 0 to
+        ``position_array.shape[1]-1`` (i.e., "id_0", "id_1"...).
+    frame_array : np.ndarray, optional
+        Array of shape (n_frames, 1) containing the frame numbers for which
+        bounding boxes are defined. If None (default), frame numbers will
+        be assigned based on the first dimension of the ``position_array``,
+        starting from 0. If a specific array of frame numbers is provided,
+        these need to be consecutive integers.
+    fps : float, optional
+        The video sampling rate. If None (default), the ``time`` coordinates
+        of the resulting ``movement`` dataset will be in frame numbers. If
+        ``fps`` is provided, the ``time`` coordinates  will be in seconds. If
+        the ``time`` coordinates are in seconds, they will indicate the
+        elapsed time from the capture of the first frame (assumed to be frame
+        0).
+    source_software : str, optional
+        Name of the software that generated the data. Defaults to None.
+
+    Returns
+    -------
+    xarray.Dataset
+        ``movement`` dataset containing the position, shape, and confidence
+        scores of the tracked bounding boxes, and any associated metadata.
+
+    Examples
+    --------
+    Create random position data for two bounding boxes, ``id_0`` and ``id_1``,
+    with the same width (40 pixels) and height (30 pixels). These are tracked
+    in 2D space for 100 frames, which are numbered from the start frame 1200
+    to the end frame 1299. The confidence score for all bounding boxes is set
+    to 0.5.
+
+    >>> import numpy as np
+    >>> from movement.io import load_bboxes
+    >>> ds = load_bboxes.from_numpy(
+    ...     position_array=np.random.rand(100, 2, 2),
+    ...     shape_array=np.ones((100, 2, 2)) * [40, 30],
+    ...     confidence_array=np.ones((100, 2)) * 0.5,
+    ...     individual_names=["id_0", "id_1"],
+    ...     frame_array=np.arange(1200, 1300).reshape(-1, 1),
+    ... )
+
+    Create a dataset with the same data as above, but with the time
+    coordinates in seconds. We use a video sampling rate of 60 fps. The time
+    coordinates in the resulting dataset will indicate the elapsed time from
+    the capture of the 0th frame. So for the frames 1200, 1201, 1203,... 1299
+    the corresponding time coordinates in seconds will be 20, 20.0167,
+    20.033,... 21.65 s.
+
+    >>> ds = load_bboxes.from_numpy(
+    ...     position_array=np.random.rand(100, 2, 2),
+    ...     shape_array=np.ones((100, 2, 2)) * [40, 30],
+    ...     confidence_array=np.ones((100, 2)) * 0.5,
+    ...     individual_names=["id_0", "id_1"],
+    ...     frame_array=np.arange(1200, 1300).reshape(-1, 1),
+    ...     fps=60,
+    ... )
+
+    Create a dataset with the same data as above, but express the time
+    coordinate in frames, and assume the first tracked frame is frame 0.
+    To do this, we simply omit the ``frame_array`` input argument.
+
+    >>> ds = load_bboxes.from_numpy(
+    ...     position_array=np.random.rand(100, 2, 2),
+    ...     shape_array=np.ones((100, 2, 2)) * [40, 30],
+    ...     confidence_array=np.ones((100, 2)) * 0.5,
+    ...     individual_names=["id_0", "id_1"],
+    ... )
+
+    Create a dataset with the same data as above, but express the time
+    coordinate in seconds, and assume the first tracked frame is captured
+    at time = 0 seconds. To do this, we omit the ``frame_array`` input argument
+    and pass an ``fps`` value.
+
+    >>> ds = load_bboxes.from_numpy(
+    ...     position_array=np.random.rand(100, 2, 2),
+    ...     shape_array=np.ones((100, 2, 2)) * [40, 30],
+    ...     confidence_array=np.ones((100, 2)) * 0.5,
+    ...     individual_names=["id_0", "id_1"],
+    ...     fps=60,
+    ... )
+
+    """
+    valid_bboxes_data = ValidBboxesDataset(
+        position_array=position_array,
+        shape_array=shape_array,
+        confidence_array=confidence_array,
+        individual_names=individual_names,
+        frame_array=frame_array,
+        fps=fps,
+        source_software=source_software,
+    )
+    return _ds_from_valid_data(valid_bboxes_data)
    
+
+
+
+
    
+[docs]
+def from_file(
+    file_path: Path | str,
+    source_software: Literal["VIA-tracks"],
+    fps: float | None = None,
+    use_frame_numbers_from_file: bool = False,
+) -> xr.Dataset:
+    """Create a ``movement`` bounding boxes dataset from a supported file.
+
+    At the moment, we only support VIA-tracks .csv files.
+
+    Parameters
+    ----------
+    file_path : pathlib.Path or str
+        Path to the file containing the tracked bounding boxes. Currently
+        only VIA-tracks .csv files are supported.
+    source_software : "VIA-tracks".
+        The source software of the file. Currently only files from the
+        VIA 2.0.12 annotator [1]_ ("VIA-tracks") are supported.
+        See .
+    fps : float, optional
+        The video sampling rate. If None (default), the ``time`` coordinates
+        of the resulting ``movement`` dataset will be in frame numbers. If
+        ``fps`` is provided, the ``time`` coordinates  will be in seconds. If
+        the ``time`` coordinates are in seconds, they will indicate the
+        elapsed time from the capture of the first frame (assumed to be frame
+        0).
+    use_frame_numbers_from_file : bool, optional
+        If True, the frame numbers in the resulting dataset are
+        the same as the ones specified for each tracked bounding box in the
+        input file. This may be useful if the bounding boxes are tracked for a
+        subset of frames in a video, but you want to maintain the start of the
+        full video as the time origin. If False (default), the frame numbers
+        in the VIA tracks .csv file are instead mapped to a 0-based sequence of
+        consecutive integers.
+
+    Returns
+    -------
+    xarray.Dataset
+        ``movement`` dataset containing the position, shape, and confidence
+        scores of the tracked bounding boxes, and any associated metadata.
+
+    See Also
+    --------
+    movement.io.load_bboxes.from_via_tracks_file
+
+    References
+    ----------
+    .. [1] https://www.robots.ox.ac.uk/~vgg/software/via/
+
+    Examples
+    --------
+    Create a dataset from the VIA tracks .csv file at "path/to/file.csv", with
+    the time coordinates in seconds, and assuming t = 0 seconds corresponds to
+    the first tracked frame in the file.
+
+    >>> from movement.io import load_bboxes
+    >>> ds = load_bboxes.from_file(
+    >>>     "path/to/file.csv",
+    >>>     source_software="VIA-tracks",
+    >>>     fps=30,
+    >>> )
+
+    """
+    if source_software == "VIA-tracks":
+        return from_via_tracks_file(
+            file_path,
+            fps,
+            use_frame_numbers_from_file=use_frame_numbers_from_file,
+        )
+    else:
+        raise log_error(
+            ValueError, f"Unsupported source software: {source_software}"
+        )
    
+
+
+
+
    
+[docs]
+def from_via_tracks_file(
+    file_path: Path | str,
+    fps: float | None = None,
+    use_frame_numbers_from_file: bool = False,
+) -> xr.Dataset:
+    """Create a ``movement`` dataset from a VIA tracks .csv file.
+
+    Parameters
+    ----------
+    file_path : pathlib.Path or str
+        Path to the VIA tracks .csv file with the tracked bounding boxes.
+        For more information on the VIA tracks .csv file format, see the VIA
+        tutorial for tracking [1]_.
+    fps : float, optional
+        The video sampling rate. If None (default), the ``time`` coordinates
+        of the resulting ``movement`` dataset will be in frame numbers. If
+        ``fps`` is provided, the ``time`` coordinates  will be in seconds. If
+        the ``time`` coordinates are in seconds, they will indicate the
+        elapsed time from the capture of the first frame (assumed to be frame
+        0).
+    use_frame_numbers_from_file : bool, optional
+        If True, the frame numbers in the resulting dataset are
+        the same as the ones in the VIA tracks .csv file. This may be useful if
+        the bounding boxes are tracked for a subset of frames in a video,
+        but you want to maintain the start of the full video as the time
+        origin. If False (default), the frame numbers in the VIA tracks .csv
+        file are instead mapped to a 0-based sequence of consecutive integers.
+
+    Returns
+    -------
+    xarray.Dataset
+        ``movement`` dataset containing the position, shape, and confidence
+        scores of the tracked bounding boxes, and any associated metadata.
+
+    Notes
+    -----
+    The bounding boxes' IDs specified in the "track" field of the VIA
+    tracks .csv file are mapped to the "individual_name" column of the
+    ``movement`` dataset. The individual names follow the format ``id_<N>``,
+    with N being the bounding box ID.
+
+    References
+    ----------
+    .. [1] https://www.robots.ox.ac.uk/~vgg/software/via/docs/face_track_annotation.html
+
+    Examples
+    --------
+    Create a dataset from the VIA tracks .csv file at "path/to/file.csv", with
+    the time coordinates in frames, and setting the first tracked frame in the
+    file as frame 0.
+
+    >>> from movement.io import load_bboxes
+    >>> ds = load_bboxes.from_via_tracks_file(
+    ...     "path/to/file.csv",
+    ... )
+
+    Create a dataset from the VIA tracks .csv file at "path/to/file.csv", with
+    the time coordinates in seconds, and assuming t = 0 seconds corresponds to
+    the first tracked frame in the file.
+
+    >>> from movement.io import load_bboxes
+    >>> ds = load_bboxes.from_via_tracks_file(
+    ...     "path/to/file.csv",
+    ...     fps=30,
+    ... )
+
+    Create a dataset from the VIA tracks .csv file at "path/to/file.csv", with
+    the time coordinates in frames, and using the same frame numbers as
+    in the VIA tracks .csv file.
+
+    >>> from movement.io import load_bboxes
+    >>> ds = load_bboxes.from_via_tracks_file(
+    ...     "path/to/file.csv",
+    ...     use_frame_numbers_from_file=True.
+    ... )
+
+    Create a dataset from the VIA tracks .csv file at "path/to/file.csv", with
+    the time coordinates in seconds, and assuming t = 0 seconds corresponds to
+    the 0th frame in the full video.
+
+    >>> from movement.io import load_bboxes
+    >>> ds = load_bboxes.from_via_tracks_file(
+    ...     "path/to/file.csv",
+    ...     fps=30,
+    ...     use_frame_numbers_from_file=True,
+    ... )
+
+
+    """
+    # General file validation
+    file = ValidFile(
+        file_path, expected_permission="r", expected_suffix=[".csv"]
+    )
+
+    # Specific VIA-tracks .csv file validation
+    via_file = ValidVIATracksCSV(file.path)
+    logger.debug(f"Validated VIA tracks .csv file {via_file.path}.")
+
+    # Create an xarray.Dataset from the data
+    bboxes_arrays = _numpy_arrays_from_via_tracks_file(via_file.path)
+    ds = from_numpy(
+        position_array=bboxes_arrays["position_array"],
+        shape_array=bboxes_arrays["shape_array"],
+        confidence_array=bboxes_arrays["confidence_array"],
+        individual_names=[
+            f"id_{id}" for id in bboxes_arrays["ID_array"].squeeze()
+        ],
+        frame_array=(
+            bboxes_arrays["frame_array"]
+            if use_frame_numbers_from_file
+            else None
+        ),
+        fps=fps,
+        source_software="VIA-tracks",
+    )  # it validates the dataset via ValidBboxesDataset
+
+    # Add metadata as attributes
+    ds.attrs["source_software"] = "VIA-tracks"
+    ds.attrs["source_file"] = file.path.as_posix()
+
+    logger.info(f"Loaded tracks of the bounding boxes from {via_file.path}:")
+    logger.info(ds)
+    return ds
    
+
+
+
+def _numpy_arrays_from_via_tracks_file(file_path: Path) -> dict:
+    """Extract numpy arrays from the input VIA tracks .csv file.
+
+    The extracted numpy arrays are returned in a dictionary with the following
+    keys:
+
+    - position_array (n_frames, n_individuals, n_space):
+        contains the trajectories of the bounding boxes' centroids.
+    - shape_array (n_frames, n_individuals, n_space):
+        contains the shape of the bounding boxes (width and height).
+    - confidence_array (n_frames, n_individuals):
+        contains the confidence score of each bounding box.
+        If no confidence scores are provided, they are set to an array of NaNs.
+    - ID_array (n_individuals, 1):
+        contains the integer IDs of the tracked bounding boxes.
+    - frame_array (n_frames, 1):
+        contains the frame numbers.
+
+    Parameters
+    ----------
+    file_path : pathlib.Path
+        Path to the VIA tracks .csv file containing the bounding boxes' tracks.
+
+    Returns
+    -------
+    dict
+        The validated bounding boxes' arrays.
+
+    """
+    # Extract 2D dataframe from input data
+    # (sort data by ID and frame number, and
+    # fill empty frame-ID pairs with nans)
+    df = _df_from_via_tracks_file(file_path)
+
+    # Compute indices of the rows where the IDs switch
+    bool_id_diff_from_prev = df["ID"].ne(df["ID"].shift())  # pandas series
+    indices_id_switch = (
+        bool_id_diff_from_prev.loc[lambda x: x].index[1:].to_numpy()
+    )
+
+    # Stack position, shape and confidence arrays along ID axis
+    map_key_to_columns = {
+        "position_array": ["x", "y"],
+        "shape_array": ["w", "h"],
+        "confidence_array": ["confidence"],
+    }
+    array_dict = {}
+    for key in map_key_to_columns:
+        list_arrays = np.split(
+            df[map_key_to_columns[key]].to_numpy(),
+            indices_id_switch,  # indices along axis=0
+        )
+
+        array_dict[key] = np.stack(list_arrays, axis=1).squeeze()
+
+    # Add remaining arrays to dict
+    array_dict["ID_array"] = df["ID"].unique().reshape(-1, 1)
+    array_dict["frame_array"] = df["frame_number"].unique().reshape(-1, 1)
+
+    return array_dict
+
+
+def _df_from_via_tracks_file(file_path: Path) -> pd.DataFrame:
+    """Load VIA tracks .csv file as a dataframe.
+
+    Read the VIA tracks .csv file as a pandas dataframe with columns:
+    - ID: the integer ID of the tracked bounding box.
+    - frame_number: the frame number of the tracked bounding box.
+    - x: the x-coordinate of the tracked bounding box centroid.
+    - y: the y-coordinate of the tracked bounding box centroid.
+    - w: the width of the tracked bounding box.
+    - h: the height of the tracked bounding box.
+    - confidence: the confidence score of the tracked bounding box.
+
+    The dataframe is sorted by ID and frame number, and for each ID,
+    empty frames are filled in with NaNs.
+    """
+    # Read VIA tracks .csv file as a pandas dataframe
+    df_file = pd.read_csv(file_path, sep=",", header=0)
+
+    # Format to a 2D dataframe
+    df = pd.DataFrame(
+        {
+            "ID": _via_attribute_column_to_numpy(
+                df_file, "region_attributes", ["track"], int
+            ),
+            "frame_number": _extract_frame_number_from_via_tracks_df(df_file),
+            "x": _via_attribute_column_to_numpy(
+                df_file, "region_shape_attributes", ["x"], float
+            ),
+            "y": _via_attribute_column_to_numpy(
+                df_file, "region_shape_attributes", ["y"], float
+            ),
+            "w": _via_attribute_column_to_numpy(
+                df_file, "region_shape_attributes", ["width"], float
+            ),
+            "h": _via_attribute_column_to_numpy(
+                df_file, "region_shape_attributes", ["height"], float
+            ),
+            "confidence": _extract_confidence_from_via_tracks_df(df_file),
+        }
+    )
+
+    # Sort dataframe by ID and frame number
+    df = df.sort_values(by=["ID", "frame_number"]).reset_index(drop=True)
+
+    # Fill in empty frames with nans
+    multi_index = pd.MultiIndex.from_product(
+        [df["ID"].unique(), df["frame_number"].unique()],
+        names=["ID", "frame_number"],
+    )  # desired index: all combinations of ID and frame number
+
+    # Set index to (ID, frame number), fill in values with nans and
+    # reset to original index
+    df = (
+        df.set_index(["ID", "frame_number"]).reindex(multi_index).reset_index()
+    )
+    return df
+
+
+def _extract_confidence_from_via_tracks_df(df) -> np.ndarray:
+    """Extract confidence scores from the VIA tracks input dataframe.
+
+    Parameters
+    ----------
+    df : pd.DataFrame
+        The VIA tracks input dataframe is the one obtained from
+        ``df = pd.read_csv(file_path, sep=",", header=0)``.
+
+    Returns
+    -------
+    np.ndarray
+        A numpy array of size (n_bboxes, ) containing the bounding boxes
+        confidence scores.
+
+    """
+    region_attributes_dicts = [
+        ast.literal_eval(d) for d in df.region_attributes
+    ]
+
+    # Check if confidence is defined as a region attribute, else set to NaN
+    if all(["confidence" in d for d in region_attributes_dicts]):
+        bbox_confidence = _via_attribute_column_to_numpy(
+            df, "region_attributes", ["confidence"], float
+        )
+    else:
+        bbox_confidence = np.full((df.shape[0], 1), np.nan).squeeze()
+
+    return bbox_confidence
+
+
+def _extract_frame_number_from_via_tracks_df(df) -> np.ndarray:
+    """Extract frame numbers from the VIA tracks input dataframe.
+
+    Parameters
+    ----------
+    df : pd.DataFrame
+        The VIA tracks input dataframe is the one obtained from
+        ``df = pd.read_csv(file_path, sep=",", header=0)``.
+
+    Returns
+    -------
+    np.ndarray
+        A numpy array of size (n_frames, ) containing the frame numbers.
+        In the VIA tracks .csv file, the frame number is expected to be
+        defined as a 'file_attribute' , or encoded in the filename as an
+        integer number led by at least one zero, between "_" and ".", followed
+        by the file extension.
+
+    """
+    # Extract frame number from file_attributes if exists
+    file_attributes_dicts = [ast.literal_eval(d) for d in df.file_attributes]
+    if all(["frame" in d for d in file_attributes_dicts]):
+        frame_array = _via_attribute_column_to_numpy(
+            df,
+            via_column_name="file_attributes",
+            list_keys=["frame"],
+            cast_fn=int,
+        )
+    # Else extract from filename
+    else:
+        pattern = r"_(0\d*)\.\w+$"
+        list_frame_numbers = [
+            int(re.search(pattern, f).group(1))  # type: ignore
+            if re.search(pattern, f)
+            else np.nan
+            for f in df["filename"]
+        ]
+
+        frame_array = np.array(list_frame_numbers)
+
+    return frame_array
+
+
+def _via_attribute_column_to_numpy(
+    df: pd.DataFrame,
+    via_column_name: str,
+    list_keys: list[str],
+    cast_fn: Callable = float,
+) -> np.ndarray:
+    """Convert values from VIA attribute-type column to a numpy array.
+
+    In the VIA tracks .csv file, the attribute-type columns are the columns
+    whose name includes the word ``attributes`` (i.e. ``file_attributes``,
+    ``region_shape_attributes`` or ``region_attributes``). These columns hold
+    dictionary data.
+
+    Parameters
+    ----------
+    df : pd.DataFrame
+        The pandas DataFrame containing the data from the VIA tracks .csv file.
+        This is the dataframe obtained from running
+        ``df = pd.read_csv(file_path, sep=",", header=0)``.
+    via_column_name : str
+        The name of a column in the VIA tracks .csv file whose values are
+        literal dictionaries (i.e. ``file_attributes``,
+        ``region_shape_attributes`` or ``region_attributes``).
+    list_keys : list[str]
+        The list of keys whose values we want to extract from the literal
+        dictionaries in the ``via_column_name`` column.
+    cast_fn : type, optional
+        The type function to cast the values to. By default ``float``.
+
+    Returns
+    -------
+    np.ndarray
+        A numpy array holding the extracted values. If ``len(list_keys) > 1``
+        the array is two-dimensional with shape ``(N, len(list_keys))``, where
+        ``N`` is the number of rows in the input dataframe ``df``. If
+        ``len(list_keys) == 1``, the resulting array will be one-dimensional,
+        with shape (N, ). Note that the computed array is squeezed before
+        returning.
+
+    """
+    list_bbox_attr = []
+    for _, row in df.iterrows():
+        row_dict_data = ast.literal_eval(row[via_column_name])
+        list_bbox_attr.append(
+            tuple(cast_fn(row_dict_data[reg]) for reg in list_keys)
+        )
+
+    bbox_attr_array = np.array(list_bbox_attr)
+
+    return bbox_attr_array.squeeze()
+
+
+def _ds_from_valid_data(data: ValidBboxesDataset) -> xr.Dataset:
+    """Convert a validated bounding boxes dataset to an xarray Dataset.
+
+    Parameters
+    ----------
+    data : movement.validators.datasets.ValidBboxesDataset
+        The validated bounding boxes dataset object.
+
+    Returns
+    -------
+    bounding boxes dataset containing the boxes tracks,
+        boxes shapes, confidence scores and associated metadata.
+
+    """
+    # Create the time coordinate
+    time_coords = data.frame_array.squeeze()  # type: ignore
+    time_unit = "frames"
+    # if fps is provided:
+    # time_coords is expressed in seconds, with the time origin
+    # set as frame 0 == time 0 seconds
+    if data.fps:
+        # Compute elapsed time from frame 0.
+        # Ignoring type error because `data.frame_array` is not None after
+        # ValidBboxesDataset.__attrs_post_init__()  # type: ignore
+        time_coords = np.array(
+            [frame / data.fps for frame in data.frame_array.squeeze()]  # type: ignore
+        )
+        time_unit = "seconds"
+
+    # Convert data to an xarray.Dataset
+    # with dimensions ('time', 'individuals', 'space')
+    DIM_NAMES = MovementDataset.dim_names["bboxes"]
+    n_space = data.position_array.shape[-1]
+    return xr.Dataset(
+        data_vars={
+            "position": xr.DataArray(data.position_array, dims=DIM_NAMES),
+            "shape": xr.DataArray(data.shape_array, dims=DIM_NAMES),
+            "confidence": xr.DataArray(
+                data.confidence_array, dims=DIM_NAMES[:-1]
+            ),
+        },
+        coords={
+            DIM_NAMES[0]: time_coords,
+            DIM_NAMES[1]: data.individual_names,
+            DIM_NAMES[2]: ["x", "y", "z"][:n_space],
+        },
+        attrs={
+            "fps": data.fps,
+            "time_unit": time_unit,
+            "source_software": data.source_software,
+            "source_file": None,
+            "ds_type": "bboxes",
+        },
+    )
+
    
+
+                
    
+              
+              
+              
+              
+              
+                
    
+                  
+
    
+
    
+                
    
+              
+            
    
+            
+            
+              
+            
+          
    
+          
    
+            
+          
    
+        
+      
    
+    
    
+  
    
+  
+  
+  
+
+
+  
+  
+
\ No newline at end of file
diff --git a/_modules/movement/io/load_poses.html b/_modules/movement/io/load_poses.html
index b4452b44..f36a06e1 100644
--- a/_modules/movement/io/load_poses.html
+++ b/_modules/movement/io/load_poses.html
@@ -27,20 +27,20 @@
 
 
 
-    
+    
     
-    
+    
     
     
     
-    
+    
   
   
   
 
   
 
-    
+    
     
     
     
@@ -125,7 +125,7 @@
   
   
   
-    
    movement v0.0.19
    
+    
    movement v0.0.20
    
   
 
    
     
@@ -441,18 +441,18 @@ 
    Source code for movement.io.load_poses
         fps: float | None = None,
     source_software: str | None = None,
 ) -> xr.Dataset:
-    """Create a ``movement`` dataset from NumPy arrays.
+    """Create a ``movement`` poses dataset from NumPy arrays.
 
     Parameters
     ----------
     position_array : np.ndarray
         Array of shape (n_frames, n_individuals, n_keypoints, n_space)
         containing the poses. It will be converted to a
-        :py:class:`xarray.DataArray` object named "position".
+        :class:`xarray.DataArray` object named "position".
     confidence_array : np.ndarray, optional
         Array of shape (n_frames, n_individuals, n_keypoints) containing
         the point-wise confidence scores. It will be converted to a
-        :py:class:`xarray.DataArray` object named "confidence".
+        :class:`xarray.DataArray` object named "confidence".
         If None (default), the scores will be set to an array of NaNs.
     individual_names : list of str, optional
         List of unique names for the individuals in the video. If None
@@ -512,7 +512,7 @@ 
    Source code for movement.io.load_poses
         source_software: Literal["DeepLabCut", "SLEAP", "LightningPose"],
     fps: float | None = None,
 ) -> xr.Dataset:
-    """Create a ``movement`` dataset from any supported file.
+    """Create a ``movement`` poses dataset from any supported file.
 
     Parameters
     ----------
@@ -568,7 +568,7 @@ 
    Source code for movement.io.load_poses
         fps: float | None = None,
     source_software: Literal["DeepLabCut", "LightningPose"] = "DeepLabCut",
 ) -> xr.Dataset:
-    """Create a ``movement`` dataset from a DeepLabCut-style DataFrame.
+    """Create a ``movement`` poses dataset from a DeepLabCut-style DataFrame.
 
     Parameters
     ----------
@@ -637,7 +637,7 @@ 
    Source code for movement.io.load_poses
     def from_sleap_file(
     file_path: Path | str, fps: float | None = None
 ) -> xr.Dataset:
-    """Create a ``movement`` dataset from a SLEAP file.
+    """Create a ``movement`` poses dataset from a SLEAP file.
 
     Parameters
     ----------
@@ -716,7 +716,7 @@ 
    Source code for movement.io.load_poses
     def from_lp_file(
     file_path: Path | str, fps: float | None = None
 ) -> xr.Dataset:
-    """Create a ``movement`` dataset from a LightningPose file.
+    """Create a ``movement`` poses dataset from a LightningPose file.
 
     Parameters
     ----------
@@ -749,7 +749,7 @@ 
    Source code for movement.io.load_poses
     def from_dlc_file(
     file_path: Path | str, fps: float | None = None
 ) -> xr.Dataset:
-    """Create a ``movement`` dataset from a DeepLabCut file.
+    """Create a ``movement`` poses dataset from a DeepLabCut file.
 
     Parameters
     ----------
@@ -787,7 +787,7 @@ 
    Source code for movement.io.load_poses
         source_software: Literal["LightningPose", "DeepLabCut"],
     fps: float | None = None,
 ) -> xr.Dataset:
-    """Create a ``movement`` dataset from a LightningPose or DeepLabCut file.
+    """Create a ``movement`` poses dataset from a LightningPose or DLC file.
 
     Parameters
     ----------
@@ -836,7 +836,7 @@ 
    Source code for movement.io.load_poses
     def _ds_from_sleap_analysis_file(
     file_path: Path, fps: float | None
 ) -> xr.Dataset:
-    """Create a ``movement`` dataset from a SLEAP analysis (.h5) file.
+    """Create a ``movement`` poses dataset from a SLEAP analysis (.h5) file.
 
     Parameters
     ----------
@@ -884,7 +884,7 @@ 
    Source code for movement.io.load_poses
     def _ds_from_sleap_labels_file(
     file_path: Path, fps: float | None
 ) -> xr.Dataset:
-    """Create a ``movement`` dataset from a SLEAP labels (.slp) file.
+    """Create a ``movement`` poses dataset from a SLEAP labels (.slp) file.
 
     Parameters
     ----------
@@ -1060,7 +1060,7 @@ 
    Source code for movement.io.load_poses
     
 
 def _ds_from_valid_data(data: ValidPosesDataset) -> xr.Dataset:
-    """Create a ``movement`` dataset from validated pose tracking data.
+    """Create a ``movement`` poses dataset from validated pose tracking data.
 
     Parameters
     ----------
@@ -1084,7 +1084,7 @@ 
    Source code for movement.io.load_poses
             time_coords = time_coords / data.fps
         time_unit = "seconds"
 
-    DIM_NAMES = MovementDataset.dim_names
+    DIM_NAMES = MovementDataset.dim_names["poses"]
     # Convert data to an xarray.Dataset
     return xr.Dataset(
         data_vars={
@@ -1104,6 +1104,7 @@ 
    Source code for movement.io.load_poses
                 "time_unit": time_unit,
             "source_software": data.source_software,
             "source_file": None,
+            "ds_type": "poses",
         },
     )
 
    
@@ -1144,7 +1145,7 @@ 
    Source code for movement.io.load_poses
         
    
       
         
    
-    Created using Sphinx 7.4.5.
+    Created using Sphinx 8.0.2.
     
    
     
    
     
    
diff --git a/_modules/movement/io/save_poses.html b/_modules/movement/io/save_poses.html
index b1a40298..9d86cbb7 100644
--- a/_modules/movement/io/save_poses.html
+++ b/_modules/movement/io/save_poses.html
@@ -27,20 +27,20 @@
 
 
 
-    
+    
     
-    
+    
     
     
     
-    
+    
   
   
   
 
   
 
-    
+    
     
     
     
@@ -125,7 +125,7 @@
   
   
   
-    
    movement v0.0.19
    
+    
    movement v0.0.20
    
   
 
    
     
@@ -661,7 +661,7 @@ 
    Source code for movement.io.save_poses
         -----
     LightningPose saves pose estimation outputs as .csv files, using the same
     format as single-animal DeepLabCut projects. Therefore, under the hood,
-    this function calls :py:func:`movement.io.save_poses.to_dlc_file`
+    this function calls :func:`movement.io.save_poses.to_dlc_file`
     with ``split_individuals=True``. This setting means that each individual
     is saved to a separate file, with the individual's name appended to the
     file path, just before the file extension,
@@ -895,7 +895,7 @@ 
    Source code for movement.io.save_poses
         
    
       
         
    
-    Created using Sphinx 7.4.5.
+    Created using Sphinx 8.0.2.
     
    
     
    
     
    
diff --git a/_modules/movement/move_accessor.html b/_modules/movement/move_accessor.html
index cf301ea6..b390d93e 100644
--- a/_modules/movement/move_accessor.html
+++ b/_modules/movement/move_accessor.html
@@ -27,20 +27,20 @@
 
 
 
-    
+    
     
-    
+    
     
     
     
-    
+    
   
   
   
 
   
 
-    
+    
     
     
     
@@ -125,7 +125,7 @@
   
   
   
-    
    movement v0.0.19
    
+    
    movement v0.0.20
    
   
 
    
     
@@ -410,7 +410,7 @@
                 
    
                   
   
    Source code for movement.move_accessor
    -"""Accessor for extending :py:class:`xarray.Dataset` objects."""
+"""Accessor for extending :class:`xarray.Dataset` objects."""
 
 import logging
 from typing import ClassVar
@@ -420,7 +420,7 @@ 
    Source code for movement.move_accessor
     from movement import filtering
 from movement.analysis import kinematics
 from movement.utils.logging import log_error
-from movement.validators.datasets import ValidPosesDataset
+from movement.validators.datasets import ValidBboxesDataset, ValidPosesDataset
 
 logger = logging.getLogger(__name__)
 
@@ -432,11 +432,11 @@ 
    Source code for movement.move_accessor
     [docs]
 @xr.register_dataset_accessor("move")
 class MovementDataset:
-    """An :py:class:`xarray.Dataset` accessor for pose tracking data.
+    """An :class:`xarray.Dataset` accessor for ``movement`` data.
 
-    A ``movement`` dataset is an :py:class:`xarray.Dataset` with a specific
-    structure to represent pose tracks, associated confidence scores and
-    relevant metadata.
+    A ``movement`` dataset is an :class:`xarray.Dataset` with a specific
+    structure to represent pose tracks or bounding boxes data,
+    associated confidence scores and relevant metadata.
 
     Methods/properties that extend the standard ``xarray`` functionality are
     defined in this class. To avoid conflicts with ``xarray``'s namespace,
@@ -445,10 +445,12 @@ 
    Source code for movement.move_accessor
     
     Attributes
     ----------
-    dim_names : tuple
-        Names of the expected dimensions in the dataset.
-    var_names : tuple
-        Names of the expected data variables in the dataset.
+    dim_names : dict
+        A dictionary with the names of the expected dimensions in the dataset,
+        for each dataset type (``"poses"`` or ``"bboxes"``).
+    var_names : dict
+        A dictionary with the expected data variables in the dataset, for each
+        dataset type (``"poses"`` or ``"bboxes"``).
 
     References
     ----------
@@ -456,29 +458,30 @@ 
    Source code for movement.move_accessor
     
     """
 
-    dim_names: ClassVar[tuple] = (
-        "time",
-        "individuals",
-        "keypoints",
-        "space",
-    )
-
-    var_names: ClassVar[tuple] = (
-        "position",
-        "confidence",
-    )
+    # Set class attributes for expected dimensions and data variables
+    dim_names: ClassVar[dict] = {
+        "poses": ("time", "individuals", "keypoints", "space"),
+        "bboxes": ("time", "individuals", "space"),
+    }
+    var_names: ClassVar[dict] = {
+        "poses": ("position", "confidence"),
+        "bboxes": ("position", "shape", "confidence"),
+    }
 
     def __init__(self, ds: xr.Dataset):
         """Initialize the MovementDataset."""
         self._obj = ds
+        # Set instance attributes based on dataset type
+        self.dim_names_instance = self.dim_names[self._obj.ds_type]
+        self.var_names_instance = self.var_names[self._obj.ds_type]
 
     def __getattr__(self, name: str) -> xr.DataArray:
         """Forward requested but undefined attributes to relevant modules.
 
         This method currently only forwards kinematic property computation
         and filtering operations to the respective functions in
-        :py:mod:`movement.analysis.kinematics` and
-        :py:mod:`movement.filtering`.
+        :mod:`movement.analysis.kinematics` and
+        :mod:`movement.filtering`.
 
         Parameters
         ----------
@@ -519,7 +522,7 @@ 
    Source code for movement.move_accessor
             """Provide convenience method for computing kinematic properties.
 
         This method forwards kinematic property computation
-        to the respective functions in :py:mod:`movement.analysis.kinematics`.
+        to the respective functions in :mod:`movement.analysis.kinematics`.
 
         Parameters
         ----------
@@ -577,7 +580,7 @@ 
    Source code for movement.move_accessor
             """Provide convenience method for filtering data variables.
 
         This method forwards filtering and/or smoothing to the respective
-        functions in :py:mod:`movement.filtering`. The data variables to
+        functions in :mod:`movement.filtering`. The data variables to
         filter can be specified in ``data_vars``. If ``data_vars`` is not
         specified, the ``position`` data variable is selected by default.
 
@@ -662,33 +665,64 @@ 
    Source code for movement.move_accessor
     
         This method checks if the dataset contains the expected dimensions,
         data variables, and metadata attributes. It also ensures that the
-        dataset contains valid poses.
+        dataset contains valid poses or bounding boxes data.
+
+        Raises
+        ------
+        ValueError
+            If the dataset is missing required dimensions, data variables,
+            or contains invalid poses or bounding boxes data.
+
         """
         fps = self._obj.attrs.get("fps", None)
         source_software = self._obj.attrs.get("source_software", None)
         try:
-            missing_dims = set(self.dim_names) - set(self._obj.dims)
-            missing_vars = set(self.var_names) - set(self._obj.data_vars)
-            if missing_dims:
-                raise ValueError(
-                    f"Missing required dimensions: {missing_dims}"
+            self._validate_dims()
+            self._validate_data_vars()
+            if self._obj.ds_type == "poses":
+                ValidPosesDataset(
+                    position_array=self._obj["position"].values,
+                    confidence_array=self._obj["confidence"].values,
+                    individual_names=self._obj.coords["individuals"].values,
+                    keypoint_names=self._obj.coords["keypoints"].values,
+                    fps=fps,
+                    source_software=source_software,
                 )
-            if missing_vars:
-                raise ValueError(
-                    f"Missing required data variables: {missing_vars}"
+            elif self._obj.ds_type == "bboxes":
+                # Define frame_array.
+                # Recover from time axis in seconds if necessary.
+                frame_array = self._obj.coords["time"].values.reshape(-1, 1)
+                if self._obj.attrs["time_unit"] == "seconds":
+                    frame_array *= fps
+                ValidBboxesDataset(
+                    position_array=self._obj["position"].values,
+                    shape_array=self._obj["shape"].values,
+                    confidence_array=self._obj["confidence"].values,
+                    individual_names=self._obj.coords["individuals"].values,
+                    frame_array=frame_array,
+                    fps=fps,
+                    source_software=source_software,
                 )
-            ValidPosesDataset(
-                position_array=self._obj[self.var_names[0]].values,
-                confidence_array=self._obj[self.var_names[1]].values,
-                individual_names=self._obj.coords[self.dim_names[1]].values,
-                keypoint_names=self._obj.coords[self.dim_names[2]].values,
-                fps=fps,
-                source_software=source_software,
-            )
         except Exception as e:
-            error_msg = "The dataset does not contain valid poses. " + str(e)
+            error_msg = (
+                f"The dataset does not contain valid {self._obj.ds_type}. {e}"
+            )
             raise log_error(ValueError, error_msg) from e
    
-
    
+
+
+    def _validate_dims(self) -> None:
+        missing_dims = set(self.dim_names_instance) - set(self._obj.dims)
+        if missing_dims:
+            raise ValueError(
+                f"Missing required dimensions: {sorted(missing_dims)}"
+            )  # sort for a reproducible error message
+
+    def _validate_data_vars(self) -> None:
+        missing_vars = set(self.var_names_instance) - set(self._obj.data_vars)
+        if missing_vars:
+            raise ValueError(
+                f"Missing required data variables: {sorted(missing_vars)}"
+            )  # sort for a reproducible error message
    
 
 
    
 
@@ -728,7 +762,7 @@ 
    Source code for movement.move_accessor
         
    
       
         
    
-    Created using Sphinx 7.4.5.
+    Created using Sphinx 8.0.2.
     
    
     
    
     
    
diff --git a/_modules/movement/sample_data.html b/_modules/movement/sample_data.html
index c679bb42..ec99ab23 100644
--- a/_modules/movement/sample_data.html
+++ b/_modules/movement/sample_data.html
@@ -27,20 +27,20 @@
 
 
 
-    
+    
     
-    
+    
     
     
     
-    
+    
   
   
   
 
   
 
-    
+    
     
     
     
@@ -125,7 +125,7 @@
   
   
   
-    
    movement v0.0.19
    
+    
    movement v0.0.20
    
   
 
    
     
@@ -426,7 +426,7 @@ 
    Source code for movement.sample_data
     import yaml
 from requests.exceptions import RequestException
 
-from movement.io import load_poses
+from movement.io import load_bboxes, load_poses
 from movement.utils.logging import log_error, log_warning
 
 logger = logging.getLogger(__name__)
@@ -709,14 +709,15 @@ 
    Source code for movement.sample_data
         """
     file_paths = fetch_dataset_paths(filename, with_video=with_video)
 
-    ds = load_poses.from_file(
-        file_paths["poses"],
-        source_software=metadata[filename]["source_software"],
-        fps=metadata[filename]["fps"],
-    )
-
-    # TODO: Add support for loading bounding boxes data.
-    # Implemented in PR 229: https://github.com/neuroinformatics-unit/movement/pull/229
+    for key, load_module in zip(
+        ["poses", "bboxes"], [load_poses, load_bboxes], strict=False
+    ):
+        if file_paths.get(key):
+            ds = load_module.from_file(
+                file_paths[key],
+                source_software=metadata[filename]["source_software"],
+                fps=metadata[filename]["fps"],
+            )
 
     ds.attrs["frame_path"] = file_paths["frame"]
     ds.attrs["video_path"] = file_paths["video"]
@@ -761,7 +762,7 @@ 
    Source code for movement.sample_data
         
    
       
         
    
-    Created using Sphinx 7.4.5.
+    Created using Sphinx 8.0.2.
     
    
     
    
     
    
diff --git a/_modules/movement/utils/logging.html b/_modules/movement/utils/logging.html
index 0493e5f8..ab148d8b 100644
--- a/_modules/movement/utils/logging.html
+++ b/_modules/movement/utils/logging.html
@@ -27,20 +27,20 @@
 
 
 
-    
+    
     
-    
+    
     
     
     
-    
+    
   
   
   
 
   
 
-    
+    
     
     
     
@@ -125,7 +125,7 @@
   
   
   
-    
    movement v0.0.19
    
+    
    movement v0.0.20
    
   
 
    
     
@@ -536,8 +536,8 @@ 
    Source code for movement.utils.logging
         """Log the operation performed by the wrapped function.
 
     This decorator appends log entries to the data's ``log``
-    attribute. The wrapped function must accept an :py:class:`xarray.Dataset`
-    or :py:class:`xarray.DataArray` as its first argument and return an
+    attribute. The wrapped function must accept an :class:`xarray.Dataset`
+    or :class:`xarray.DataArray` as its first argument and return an
     object of the same type.
     """
 
@@ -600,7 +600,7 @@ 
    Source code for movement.utils.logging
         
    
       
         
    
-    Created using Sphinx 7.4.5.
+    Created using Sphinx 8.0.2.
     
    
     
    
     
    
diff --git a/_modules/movement/utils/reports.html b/_modules/movement/utils/reports.html
index 735001f2..1609d1f5 100644
--- a/_modules/movement/utils/reports.html
+++ b/_modules/movement/utils/reports.html
@@ -27,20 +27,20 @@
 
 
 
-    
+    
     
-    
+    
     
     
     
-    
+    
   
   
   
 
   
 
-    
+    
     
     
     
@@ -125,7 +125,7 @@
   
   
   
-    
    movement v0.0.19
    
+    
    movement v0.0.20
    
   
 
    
     
@@ -549,7 +549,7 @@ 
    Source code for movement.utils.reports
         
    
       
         
    
-    Created using Sphinx 7.4.5.
+    Created using Sphinx 8.0.2.
     
    
     
    
     
    
diff --git a/_modules/movement/utils/vector.html b/_modules/movement/utils/vector.html
index 31ba1ac8..f6c360a8 100644
--- a/_modules/movement/utils/vector.html
+++ b/_modules/movement/utils/vector.html
@@ -27,20 +27,20 @@
 
 
 
-    
+    
     
-    
+    
     
     
     
-    
+    
   
   
   
 
   
 
-    
+    
     
     
     
@@ -125,7 +125,7 @@
   
   
   
-    
    movement v0.0.19
    
+    
    movement v0.0.20
    
   
 
    
     
@@ -418,6 +418,99 @@ 
    Source code for movement.utils.vector
     from movement.utils.logging import log_error
 
 
+
    
+[docs]
+def compute_norm(data: xr.DataArray) -> xr.DataArray:
+    """Compute the norm of the vectors along the spatial dimension.
+
+    The norm of a vector is its magnitude, also called Euclidean norm, 2-norm
+    or Euclidean length. Note that if the input data is expressed in polar
+    coordinates, the magnitude of a vector is the same as its radial coordinate
+    ``rho``.
+
+    Parameters
+    ----------
+    data : xarray.DataArray
+        The input data array containing either ``space`` or ``space_pol``
+        as a dimension.
+
+    Returns
+    -------
+    xarray.DataArray
+         A data array holding the norm of the input vectors.
+         Note that this output array has no spatial dimension but preserves
+         all other dimensions of the input data array (see Notes).
+
+    Notes
+    -----
+    If the input data array is a ``position`` array, this function will compute
+    the magnitude of the position vectors, for every individual and keypoint,
+    at every timestep. If the input data array is a ``shape`` array of a
+    bounding boxes dataset, it will compute the magnitude of the shape
+    vectors (i.e., the diagonal of the bounding box),
+    for every individual and at every timestep.
+
+
+    """
+    if "space" in data.dims:
+        _validate_dimension_coordinates(data, {"space": ["x", "y"]})
+        return xr.apply_ufunc(
+            np.linalg.norm,
+            data,
+            input_core_dims=[["space"]],
+            kwargs={"axis": -1},
+        )
+    elif "space_pol" in data.dims:
+        _validate_dimension_coordinates(data, {"space_pol": ["rho", "phi"]})
+        return data.sel(space_pol="rho", drop=True)
+    else:
+        _raise_error_for_missing_spatial_dim()
    
+
+
+
+
    
+[docs]
+def convert_to_unit(data: xr.DataArray) -> xr.DataArray:
+    """Convert the vectors along the spatial dimension into unit vectors.
+
+    A unit vector is a vector pointing in the same direction as the original
+    vector but with norm = 1.
+
+    Parameters
+    ----------
+    data : xarray.DataArray
+        The input data array containing either ``space`` or ``space_pol``
+        as a dimension.
+
+    Returns
+    -------
+    xarray.DataArray
+        A data array holding the unit vectors of the input data array
+        (all input dimensions are preserved).
+
+    Notes
+    -----
+    Note that the unit vector for the null vector is undefined, since the null
+    vector has 0 norm and no direction associated with it.
+
+    """
+    if "space" in data.dims:
+        _validate_dimension_coordinates(data, {"space": ["x", "y"]})
+        return data / compute_norm(data)
+    elif "space_pol" in data.dims:
+        _validate_dimension_coordinates(data, {"space_pol": ["rho", "phi"]})
+        # Set both rho and phi values to NaN at null vectors (where rho = 0)
+        new_data = xr.where(data.sel(space_pol="rho") == 0, np.nan, data)
+        # Set the rho values to 1 for non-null vectors (phi is preserved)
+        new_data.loc[{"space_pol": "rho"}] = xr.where(
+            new_data.sel(space_pol="rho").isnull(), np.nan, 1
+        )
+        return new_data
+    else:
+        _raise_error_for_missing_spatial_dim()
    
+
+
+
 
    
 [docs]
 def cart2pol(data: xr.DataArray) -> xr.DataArray:
@@ -439,12 +532,7 @@ 
    Source code for movement.utils.vector
     
     """
     _validate_dimension_coordinates(data, {"space": ["x", "y"]})
-    rho = xr.apply_ufunc(
-        np.linalg.norm,
-        data,
-        input_core_dims=[["space"]],
-        kwargs={"axis": -1},
-    )
+    rho = compute_norm(data)
     phi = xr.apply_ufunc(
         np.arctan2,
         data.sel(space="y"),
@@ -540,6 +628,14 @@ 
    Source code for movement.utils.vector
                 )
     if error_message:
         raise log_error(ValueError, error_message)
+
+
+def _raise_error_for_missing_spatial_dim() -> None:
+    raise log_error(
+        ValueError,
+        "Input data array must contain either 'space' or 'space_pol' "
+        "as dimensions.",
+    )
 
    
 
                 
    
@@ -578,7 +674,7 @@ 
    Source code for movement.utils.vector
         
    
       
         
    
-    Created using Sphinx 7.4.5.
+    Created using Sphinx 8.0.2.
     
    
     
    
     
    
diff --git a/_modules/movement/validators/datasets.html b/_modules/movement/validators/datasets.html
index 7045d8d1..2dd43193 100644
--- a/_modules/movement/validators/datasets.html
+++ b/_modules/movement/validators/datasets.html
@@ -27,20 +27,20 @@
 
 
 
-    
+    
     
-    
+    
     
     
     
-    
+    
   
   
   
 
   
 
-    
+    
     
     
     
@@ -125,7 +125,7 @@
   
   
   
-    
    movement v0.0.19
    
+    
    movement v0.0.20
    
   
 
    
     
@@ -415,13 +415,14 @@ 
    Source code for movement.validators.datasets
    from collections.abc import Iterable
 from typing import Any
 
+import attrs
 import numpy as np
 from attrs import converters, define, field, validators
 
 from movement.utils.logging import log_error, log_warning
 
 
-def _list_of_str(value: str | Iterable[Any]) -> list[str]:
+def _convert_to_list_of_str(value: str | Iterable[Any]) -> list[str]:
     """Try to coerce the value into a list of strings."""
     if isinstance(value, str):
         log_warning(
@@ -437,15 +438,7 @@ 
    Source code for movement.validators.datasets
    )
 
 
-def _ensure_type_ndarray(value: Any) -> None:
-    """Raise ValueError the value is a not numpy array."""
-    if not isinstance(value, np.ndarray):
-        raise log_error(
-            ValueError, f"Expected a numpy array, but got {type(value)}."
-        )
-
-
-def _set_fps_to_none_if_invalid(fps: float | None) -> float | None:
+def _convert_fps_to_none_if_invalid(fps: float | None) -> float | None:
     """Set fps to None if a non-positive float is passed."""
     if fps is not None and fps <= 0:
         log_warning(
@@ -456,7 +449,29 @@ 
    Source code for movement.validators.datasets
    return fps
 
 
-def _validate_list_length(attribute, value: list | None, expected_length: int):
+def _validate_type_ndarray(value: Any) -> None:
+    """Raise ValueError the value is a not numpy array."""
+    if not isinstance(value, np.ndarray):
+        raise log_error(
+            ValueError, f"Expected a numpy array, but got {type(value)}."
+        )
+
+
+def _validate_array_shape(
+    attribute: attrs.Attribute, value: np.ndarray, expected_shape: tuple
+):
+    """Raise ValueError if the value does not have the expected shape."""
+    if value.shape != expected_shape:
+        raise log_error(
+            ValueError,
+            f"Expected '{attribute.name}' to have shape {expected_shape}, "
+            f"but got {value.shape}.",
+        )
+
+
+def _validate_list_length(
+    attribute: attrs.Attribute, value: list | None, expected_length: int
+):
     """Raise a ValueError if the list does not have the expected length."""
     if (value is not None) and (len(value) != expected_length):
         raise log_error(
@@ -470,7 +485,21 @@ 
    Source code for movement.validators.datasets
    [docs]
 @define(kw_only=True)
 class ValidPosesDataset:
-    """Class for validating data intended for a ``movement`` dataset.
+    """Class for validating poses data intended for a ``movement`` dataset.
+
+    The validator ensures that within the ``movement poses`` dataset:
+
+    - The required ``position_array`` is a numpy array
+      with the last dimension containing 2 or 3 spatial coordinates.
+    - The optional ``confidence_array``, if provided, is a numpy array
+      with its shape matching the first three dimensions of the
+      ``position_array``; otherwise, it defaults to an array of NaNs.
+    - The optional ``individual_names`` and ``keypoint_names``,
+      if provided, match the number of individuals and keypoints
+      in the dataset, respectively; otherwise, default names are assigned.
+    - The optional ``fps`` is a positive float; otherwise, it defaults to None.
+    - The optional ``source_software`` is a string; otherwise,
+      it defaults to None.
 
     Attributes
     ----------
@@ -495,23 +524,31 @@ 
    Source code for movement.validators.datasets
            Name of the software from which the poses were loaded.
         Defaults to None.
 
+    Raises
+    ------
+    ValueError
+        If the dataset does not meet the ``movement poses``
+        dataset requirements.
+
     """
 
-    # Define class attributes
+    # Required attributes
     position_array: np.ndarray = field()
+
+    # Optional attributes
     confidence_array: np.ndarray | None = field(default=None)
     individual_names: list[str] | None = field(
         default=None,
-        converter=converters.optional(_list_of_str),
+        converter=converters.optional(_convert_to_list_of_str),
     )
     keypoint_names: list[str] | None = field(
         default=None,
-        converter=converters.optional(_list_of_str),
+        converter=converters.optional(_convert_to_list_of_str),
     )
     fps: float | None = field(
         default=None,
         converter=converters.pipe(  # type: ignore
-            converters.optional(float), _set_fps_to_none_if_invalid
+            converters.optional(float), _convert_fps_to_none_if_invalid
         ),
     )
     source_software: str | None = field(
@@ -522,7 +559,7 @@ 
    Source code for movement.validators.datasets
    # Add validators
     @position_array.validator
     def _validate_position_array(self, attribute, value):
-        _ensure_type_ndarray(value)
+        _validate_type_ndarray(value)
         if value.ndim != 4:
             raise log_error(
                 ValueError,
@@ -539,14 +576,10 @@ 
    Source code for movement.validators.datasets
    @confidence_array.validator
     def _validate_confidence_array(self, attribute, value):
         if value is not None:
-            _ensure_type_ndarray(value)
-            expected_shape = self.position_array.shape[:-1]
-            if value.shape != expected_shape:
-                raise log_error(
-                    ValueError,
-                    f"Expected '{attribute.name}' to have shape "
-                    f"{expected_shape}, but got {value.shape}.",
-                )
+            _validate_type_ndarray(value)
+            _validate_array_shape(
+                attribute, value, expected_shape=self.position_array.shape[:-1]
+            )
 
     @individual_names.validator
     def _validate_individual_names(self, attribute, value):
@@ -597,32 +630,59 @@ 
    Source code for movement.validators.datasets
    class ValidBboxesDataset:
     """Class for validating bounding boxes' data for a ``movement`` dataset.
 
-    We consider 2D bounding boxes only.
+    The validator considers 2D bounding boxes only. It ensures that
+    within the ``movement bboxes`` dataset:
+
+    - The required ``position_array`` and ``shape_array`` are numpy arrays,
+      with the last dimension containing 2 spatial coordinates.
+    - The optional ``confidence_array``, if provided, is a numpy array
+      with its shape matching the first two dimensions of the
+      ``position_array``; otherwise, it defaults to an array of NaNs.
+    - The optional ``individual_names``, if provided, match the number of
+      individuals in the dataset; otherwise, default names are assigned.
+    - The optional ``frame_array``, if provided, is a column vector
+      with the frame numbers; otherwise, it defaults to an array of
+      0-based integers.
+    - The optional ``fps`` is a positive float; otherwise, it defaults to None.
+    - The optional ``source_software`` is a string; otherwise, it defaults to
+      None.
 
     Attributes
     ----------
     position_array : np.ndarray
-        Array of shape (n_frames, n_individual_names, n_space)
-        containing the bounding boxes' centroid positions.
+        Array of shape (n_frames, n_individuals, n_space)
+        containing the tracks of the bounding boxes' centroids.
     shape_array : np.ndarray
-        Array of shape (n_frames, n_individual_names, n_space)
-        containing the bounding boxes' width (extent along the
-        x-axis) and height (extent along the y-axis).
+        Array of shape (n_frames, n_individuals, n_space)
+        containing the shape of the bounding boxes. The shape of a bounding
+        box is its width (extent along the x-axis of the image) and height
+        (extent along the y-axis of the image).
     confidence_array : np.ndarray, optional
-        Array of shape (n_frames, n_individuals, n_keypoints) containing
-        the bounding boxes' confidence scores. If None (default), the
-        confidence scores will be set to an array of NaNs.
+        Array of shape (n_frames, n_individuals) containing
+        the confidence scores of the bounding boxes. If None (default), the
+        confidence scores are set to an array of NaNs.
     individual_names : list of str, optional
         List of individual names for the tracked bounding boxes in the video.
         If None (default), bounding boxes are assigned names based on the size
-        of the `position_array`. The names will be in the format of `id_<N>`,
-        where <N>  is an integer from 1 to `position_array.shape[1]`.
+        of the ``position_array``. The names will be in the format of
+        ``id_<N>``, where <N>  is an integer from 0 to
+        ``position_array.shape[1]-1``.
+    frame_array : np.ndarray, optional
+        Array of shape (n_frames, 1) containing the frame numbers for which
+        bounding boxes are defined. If None (default), frame numbers will
+        be assigned based on the first dimension of the ``position_array``,
+        starting from 0.
     fps : float, optional
         Frames per second defining the sampling rate of the data.
         Defaults to None.
     source_software : str, optional
-        Name of the software from which the bounding boxes were loaded.
-        Defaults to None.
+        Name of the software that generated the data. Defaults to None.
+
+    Raises
+    ------
+    ValueError
+        If the dataset does not meet the ``movement bboxes`` dataset
+        requirements.
 
     """
 
@@ -635,13 +695,14 @@ 
    Source code for movement.validators.datasets
    individual_names: list[str] | None = field(
         default=None,
         converter=converters.optional(
-            _list_of_str
+            _convert_to_list_of_str
         ),  # force into list of strings if not
     )
+    frame_array: np.ndarray | None = field(default=None)
     fps: float | None = field(
         default=None,
         converter=converters.pipe(  # type: ignore
-            converters.optional(float), _set_fps_to_none_if_invalid
+            converters.optional(float), _convert_fps_to_none_if_invalid
         ),
     )
     source_software: str | None = field(
@@ -653,8 +714,7 @@ 
    Source code for movement.validators.datasets
    @position_array.validator
     @shape_array.validator
     def _validate_position_and_shape_arrays(self, attribute, value):
-        _ensure_type_ndarray(value)
-
+        _validate_type_ndarray(value)
         # check last dimension (spatial) has 2 coordinates
         n_expected_spatial_coordinates = 2
         if value.shape[-1] != n_expected_spatial_coordinates:
@@ -670,7 +730,6 @@ 
    Source code for movement.validators.datasets
    _validate_list_length(
                 attribute, value, self.position_array.shape[1]
             )
-
             # check n_individual_names are unique
             # NOTE: combined with the requirement above, we are enforcing
             # unique IDs per frame
@@ -685,14 +744,26 @@ 
    Source code for movement.validators.datasets
    @confidence_array.validator
     def _validate_confidence_array(self, attribute, value):
         if value is not None:
-            _ensure_type_ndarray(value)
+            _validate_type_ndarray(value)
+            _validate_array_shape(
+                attribute, value, expected_shape=self.position_array.shape[:-1]
+            )
 
-            expected_shape = self.position_array.shape[:-1]
-            if value.shape != expected_shape:
+    @frame_array.validator
+    def _validate_frame_array(self, attribute, value):
+        if value is not None:
+            _validate_type_ndarray(value)
+            # should be a column vector (n_frames, 1)
+            _validate_array_shape(
+                attribute,
+                value,
+                expected_shape=(self.position_array.shape[0], 1),
+            )
+            # check frames are continuous: exactly one frame number per row
+            if not np.all(np.diff(value, axis=0) == 1):
                 raise log_error(
                     ValueError,
-                    f"Expected '{attribute.name}' to have shape "
-                    f"{expected_shape}, but got {value.shape}.",
+                    f"Frame numbers in {attribute.name} are not continuous.",
                 )
 
     # Define defaults
@@ -701,8 +772,9 @@ 
    Source code for movement.validators.datasets
            If no confidence_array is provided, set it to an array of NaNs.
         If no individual names are provided, assign them unique IDs per frame,
-        starting with 1 ("id_1")
+        starting with 0 ("id_0").
         """
+        # assign default confidence_array
         if self.confidence_array is None:
             self.confidence_array = np.full(
                 (self.position_array.shape[:-1]),
@@ -710,19 +782,27 @@ 
    Source code for movement.validators.datasets
    dtype="float32",
             )
             log_warning(
-                "Confidence array was not provided."
+                "Confidence array was not provided. "
                 "Setting to an array of NaNs."
             )
-
+        # assign default individual_names
         if self.individual_names is None:
             self.individual_names = [
-                f"id_{i+1}" for i in range(self.position_array.shape[1])
+                f"id_{i}" for i in range(self.position_array.shape[1])
             ]
             log_warning(
                 "Individual names for the bounding boxes "
                 "were not provided. "
-                "Setting to 1-based IDs that are unique per frame: \n"
+                "Setting to 0-based IDs that are unique per frame: \n"
                 f"{self.individual_names}.\n"
+            )
+        # assign default frame_array
+        if self.frame_array is None:
+            n_frames = self.position_array.shape[0]
+            self.frame_array = np.arange(n_frames).reshape(-1, 1)
+            log_warning(
+                "Frame numbers were not provided. "
+                "Setting to an array of 0-based integers."
             )
    
 
 
    
@@ -763,7 +843,7 @@ 
    Source code for movement.validators.datasets
           
         
    
-    Created using Sphinx 7.4.5.
+    Created using Sphinx 8.0.2.
     
    
     
    
     
    
diff --git a/_modules/movement/validators/files.html b/_modules/movement/validators/files.html
index d89cd622..c09e434f 100644
--- a/_modules/movement/validators/files.html
+++ b/_modules/movement/validators/files.html
@@ -27,20 +27,20 @@
 
 
 
-    
+    
     
-    
+    
     
     
     
-    
+    
   
   
   
 
   
 
-    
+    
     
     
     
@@ -125,7 +125,7 @@
   
   
   
-    
    movement v0.0.19
    
+    
    movement v0.0.20
    
   
 
    
     
@@ -412,11 +412,14 @@
   
    Source code for movement.validators.files
     """``attrs`` classes for validating file paths."""
 
+import ast
 import os
+import re
 from pathlib import Path
 from typing import Literal
 
 import h5py
+import pandas as pd
 from attrs import define, field, validators
 
 from movement.utils.logging import log_error
@@ -428,6 +431,14 @@ 
    Source code for movement.validators.files
     class ValidFile:
     """Class for validating file paths.
 
+    The validator ensures that the file:
+
+    - is not a directory,
+    - exists if it is meant to be read,
+    - does not exist if it is meant to be written,
+    - has the expected access permission(s), and
+    - has one of the expected suffix(es).
+
     Attributes
     ----------
     path : str or pathlib.Path
@@ -448,9 +459,9 @@ 
    Source code for movement.validators.files
         PermissionError
         If the file does not have the expected access permission(s).
     FileNotFoundError
-        If the file does not exist when `expected_permission` is "r" or "rw".
+        If the file does not exist when ``expected_permission`` is "r" or "rw".
     FileExistsError
-        If the file exists when `expected_permission` is "w".
+        If the file exists when ``expected_permission`` is "w".
     ValueError
         If the file does not have one of the expected suffix(es).
 
@@ -527,6 +538,11 @@ 
    Source code for movement.validators.files
     class ValidHDF5:
     """Class for validating HDF5 files.
 
+    The validator ensures that the file:
+
+    - is in HDF5 format, and
+    - contains the expected datasets.
+
     Attributes
     ----------
     path : pathlib.Path
@@ -579,6 +595,9 @@ 
    Source code for movement.validators.files
     class ValidDeepLabCutCSV:
     """Class for validating DeepLabCut-style .csv files.
 
+    The validator ensures that the file contains the
+    expected index column levels.
+
     Attributes
     ----------
     path : pathlib.Path
@@ -595,7 +614,7 @@ 
    Source code for movement.validators.files
         path: Path = field(validator=validators.instance_of(Path))
 
     @path.validator
-    def _csv_file_contains_expected_levels(self, attribute, value):
+    def _file_contains_expected_levels(self, attribute, value):
         """Ensure that the .csv file contains the expected index column levels.
 
         These are to be found among the top 4 rows of the file.
@@ -619,6 +638,225 @@ 
    Source code for movement.validators.files
                         "DeepLabCut pose estimation output files.",
                 )
    
 
+
+
+
    
+[docs]
+@define
+class ValidVIATracksCSV:
+    """Class for validating VIA tracks .csv files.
+
+    The validator ensures that the file:
+
+    - contains the expected header,
+    - contains valid frame numbers,
+    - contains tracked bounding boxes, and
+    - defines bounding boxes whose IDs are unique per image file.
+
+    Attributes
+    ----------
+    path : pathlib.Path
+        Path to the VIA tracks .csv file.
+
+    Raises
+    ------
+    ValueError
+        If the file does not match the VIA tracks .csv file requirements.
+
+    """
+
+    path: Path = field(validator=validators.instance_of(Path))
+
+    @path.validator
+    def _file_contains_valid_header(self, attribute, value):
+        """Ensure the VIA tracks .csv file contains the expected header."""
+        expected_header = [
+            "filename",
+            "file_size",
+            "file_attributes",
+            "region_count",
+            "region_id",
+            "region_shape_attributes",
+            "region_attributes",
+        ]
+
+        with open(value) as f:
+            header = f.readline().strip("\n").split(",")
+
+            if header != expected_header:
+                raise log_error(
+                    ValueError,
+                    ".csv header row does not match the known format for "
+                    "VIA tracks .csv files. "
+                    f"Expected {expected_header} but got {header}.",
+                )
+
+    @path.validator
+    def _file_contains_valid_frame_numbers(self, attribute, value):
+        """Ensure that the VIA tracks .csv file contains valid frame numbers.
+
+        This involves:
+
+        - Checking that frame numbers are included in ``file_attributes`` or
+          encoded in the image file ``filename``.
+        - Checking the frame number can be cast as an integer.
+        - Checking that there are as many unique frame numbers as unique image
+          files.
+
+        If the frame number is included as part of the image file name, then
+        it is expected as an integer led by at least one zero, between "_" and
+        ".", followed by the file extension.
+
+        """
+        df = pd.read_csv(value, sep=",", header=0)
+
+        # Extract list of file attributes (dicts)
+        file_attributes_dicts = [
+            ast.literal_eval(d) for d in df.file_attributes
+        ]
+
+        # If 'frame' is a file_attribute for all files:
+        # extract frame number
+        list_frame_numbers = []
+        if all(["frame" in d for d in file_attributes_dicts]):
+            for k_i, k in enumerate(file_attributes_dicts):
+                try:
+                    list_frame_numbers.append(int(k["frame"]))
+                except Exception as e:
+                    raise log_error(
+                        ValueError,
+                        f"{df.filename.iloc[k_i]} (row {k_i}): "
+                        "'frame' file attribute cannot be cast as an integer. "
+                        f"Please review the file attributes: {k}.",
+                    ) from e
+
+        # else: extract frame number from filename.
+        else:
+            pattern = r"_(0\d*)\.\w+$"
+
+            for f_i, f in enumerate(df["filename"]):
+                regex_match = re.search(pattern, f)
+                if regex_match:  # if there is a pattern match
+                    list_frame_numbers.append(
+                        int(regex_match.group(1))  # type: ignore
+                        # the match will always be castable as integer
+                    )
+                else:
+                    raise log_error(
+                        ValueError,
+                        f"{f} (row {f_i}): "
+                        "a frame number could not be extracted from the "
+                        "filename. If included in the filename, the frame "
+                        "number is expected as a zero-padded integer between "
+                        "an underscore '_' and the file extension "
+                        "(e.g. img_00234.png).",
+                    )
+
+        # Check we have as many unique frame numbers as unique image files
+        if len(set(list_frame_numbers)) != len(df.filename.unique()):
+            raise log_error(
+                ValueError,
+                "The number of unique frame numbers does not match the number "
+                "of unique image files. Please review the VIA tracks .csv "
+                "file and ensure a unique frame number is defined for each "
+                "file. ",
+            )
+
+    @path.validator
+    def _file_contains_tracked_bboxes(self, attribute, value):
+        """Ensure that the VIA tracks .csv contains tracked bounding boxes.
+
+        This involves:
+
+        - Checking that the bounding boxes are defined as rectangles.
+        - Checking that the bounding boxes have all geometric parameters
+          (``["x", "y", "width", "height"]``).
+        - Checking that the bounding boxes have a track ID defined.
+        - Checking that the track ID can be cast as an integer.
+        """
+        df = pd.read_csv(value, sep=",", header=0)
+
+        for row in df.itertuples():
+            row_region_shape_attrs = ast.literal_eval(
+                row.region_shape_attributes
+            )
+            row_region_attrs = ast.literal_eval(row.region_attributes)
+
+            # check annotation is a rectangle
+            if row_region_shape_attrs["name"] != "rect":
+                raise log_error(
+                    ValueError,
+                    f"{row.filename} (row {row.Index}): "
+                    "bounding box shape must be 'rect' (rectangular) "
+                    "but instead got "
+                    f"'{row_region_shape_attrs['name']}'.",
+                )
+
+            # check all geometric parameters for the box are defined
+            if not all(
+                [
+                    key in row_region_shape_attrs
+                    for key in ["x", "y", "width", "height"]
+                ]
+            ):
+                raise log_error(
+                    ValueError,
+                    f"{row.filename} (row {row.Index}): "
+                    f"at least one bounding box shape parameter is missing. "
+                    "Expected 'x', 'y', 'width', 'height' to exist as "
+                    "'region_shape_attributes', but got "
+                    f"'{list(row_region_shape_attrs.keys())}'.",
+                )
+
+            # check track ID is defined
+            if "track" not in row_region_attrs:
+                raise log_error(
+                    ValueError,
+                    f"{row.filename} (row {row.Index}): "
+                    "bounding box does not have a 'track' attribute defined "
+                    "under 'region_attributes'. "
+                    "Please review the VIA tracks .csv file.",
+                )
+
+            # check track ID is castable as an integer
+            try:
+                int(row_region_attrs["track"])
+            except Exception as e:
+                raise log_error(
+                    ValueError,
+                    f"{row.filename} (row {row.Index}): "
+                    "the track ID for the bounding box cannot be cast "
+                    "as an integer. Please review the VIA tracks .csv file.",
+                ) from e
+
+    @path.validator
+    def _file_contains_unique_track_ids_per_filename(self, attribute, value):
+        """Ensure the VIA tracks .csv contains unique track IDs per filename.
+
+        It checks that bounding boxes IDs are defined once per image file.
+        """
+        df = pd.read_csv(value, sep=",", header=0)
+
+        list_unique_filenames = list(set(df.filename))
+        for file in list_unique_filenames:
+            df_one_filename = df.loc[df["filename"] == file]
+
+            list_track_ids_one_filename = [
+                int(ast.literal_eval(row.region_attributes)["track"])
+                for row in df_one_filename.itertuples()
+            ]
+
+            if len(set(list_track_ids_one_filename)) != len(
+                list_track_ids_one_filename
+            ):
+                raise log_error(
+                    ValueError,
+                    f"{file}: "
+                    "multiple bounding boxes in this file "
+                    "have the same track ID. "
+                    "Please review the VIA tracks .csv file.",
+                )
    
+
 
    
 
                 
    
@@ -657,7 +895,7 @@ 
    Source code for movement.validators.files
         
    
       
         
    
-    Created using Sphinx 7.4.5.
+    Created using Sphinx 8.0.2.
     
    
     
    
     
    
diff --git a/_sources/api/movement.io.load_bboxes.from_file.rst.txt b/_sources/api/movement.io.load_bboxes.from_file.rst.txt
new file mode 100644
index 00000000..050c3de4
--- /dev/null
+++ b/_sources/api/movement.io.load_bboxes.from_file.rst.txt
@@ -0,0 +1,6 @@
+from\_file
+==========
+
+.. currentmodule:: movement.io.load_bboxes
+
+.. autofunction:: from_file
\ No newline at end of file
diff --git a/_sources/api/movement.io.load_bboxes.from_numpy.rst.txt b/_sources/api/movement.io.load_bboxes.from_numpy.rst.txt
new file mode 100644
index 00000000..1dfbea89
--- /dev/null
+++ b/_sources/api/movement.io.load_bboxes.from_numpy.rst.txt
@@ -0,0 +1,6 @@
+from\_numpy
+===========
+
+.. currentmodule:: movement.io.load_bboxes
+
+.. autofunction:: from_numpy
\ No newline at end of file
diff --git a/_sources/api/movement.io.load_bboxes.from_via_tracks_file.rst.txt b/_sources/api/movement.io.load_bboxes.from_via_tracks_file.rst.txt
new file mode 100644
index 00000000..bc8a889c
--- /dev/null
+++ b/_sources/api/movement.io.load_bboxes.from_via_tracks_file.rst.txt
@@ -0,0 +1,6 @@
+from\_via\_tracks\_file
+=======================
+
+.. currentmodule:: movement.io.load_bboxes
+
+.. autofunction:: from_via_tracks_file
\ No newline at end of file
diff --git a/_sources/api/movement.io.load_bboxes.rst.txt b/_sources/api/movement.io.load_bboxes.rst.txt
new file mode 100644
index 00000000..00e55cb4
--- /dev/null
+++ b/_sources/api/movement.io.load_bboxes.rst.txt
@@ -0,0 +1,25 @@
+movement.io.load\_bboxes
+========================
+
+.. rubric:: Description
+
+.. automodule:: movement.io.load_bboxes
+
+.. currentmodule:: movement.io.load_bboxes
+
+
+
+
+.. rubric:: Functions
+
+.. autosummary::
+    :toctree: .
+    :nosignatures:
+    
+    from_file
+    
+    from_numpy
+    
+    from_via_tracks_file
+    
+
diff --git a/_sources/api/movement.utils.vector.compute_norm.rst.txt b/_sources/api/movement.utils.vector.compute_norm.rst.txt
new file mode 100644
index 00000000..7a4df4b6
--- /dev/null
+++ b/_sources/api/movement.utils.vector.compute_norm.rst.txt
@@ -0,0 +1,6 @@
+compute\_norm
+=============
+
+.. currentmodule:: movement.utils.vector
+
+.. autofunction:: compute_norm
\ No newline at end of file
diff --git a/_sources/api/movement.utils.vector.convert_to_unit.rst.txt b/_sources/api/movement.utils.vector.convert_to_unit.rst.txt
new file mode 100644
index 00000000..a79aa2a7
--- /dev/null
+++ b/_sources/api/movement.utils.vector.convert_to_unit.rst.txt
@@ -0,0 +1,6 @@
+convert\_to\_unit
+=================
+
+.. currentmodule:: movement.utils.vector
+
+.. autofunction:: convert_to_unit
\ No newline at end of file
diff --git a/_sources/api/movement.utils.vector.rst.txt b/_sources/api/movement.utils.vector.rst.txt
index 50944565..3db0d4ea 100644
--- a/_sources/api/movement.utils.vector.rst.txt
+++ b/_sources/api/movement.utils.vector.rst.txt
@@ -18,6 +18,10 @@
     
     cart2pol
     
+    compute_norm
+    
+    convert_to_unit
+    
     pol2cart
     
 
diff --git a/_sources/api/movement.validators.files.ValidVIATracksCSV.rst.txt b/_sources/api/movement.validators.files.ValidVIATracksCSV.rst.txt
new file mode 100644
index 00000000..945f1021
--- /dev/null
+++ b/_sources/api/movement.validators.files.ValidVIATracksCSV.rst.txt
@@ -0,0 +1,20 @@
+ValidVIATracksCSV
+=================
+
+.. currentmodule:: movement.validators.files
+
+.. autoclass:: ValidVIATracksCSV
+   :members:
+   :show-inheritance:
+   :inherited-members:
+
+   
+   
+
+   
+   
+   
+   
+
+   
+   
\ No newline at end of file
diff --git a/_sources/api/movement.validators.files.rst.txt b/_sources/api/movement.validators.files.rst.txt
index aa053320..01bfaf36 100644
--- a/_sources/api/movement.validators.files.rst.txt
+++ b/_sources/api/movement.validators.files.rst.txt
@@ -20,6 +20,8 @@
     
     ValidHDF5
     
+    ValidVIATracksCSV
+    
 
 
 
diff --git a/_sources/api_index.rst.txt b/_sources/api_index.rst.txt
index 3960acf1..428d2515 100644
--- a/_sources/api_index.rst.txt
+++ b/_sources/api_index.rst.txt
@@ -1,3 +1,6 @@
+..
+  This file is auto-generated.
+
 .. _target-api:
 
 API Reference
@@ -12,14 +15,15 @@ Information on specific functions, classes, and methods.
     :recursive:
     :nosignatures:
 
-    movement.move_accessor
-    movement.io.load_poses
-    movement.io.save_poses
     movement.filtering
-    movement.analysis.kinematics
-    movement.utils.vector
+    movement.move_accessor
+    movement.sample_data
     movement.utils.logging
     movement.utils.reports
-    movement.sample_data
-    movement.validators.files
+    movement.utils.vector
+    movement.analysis.kinematics
     movement.validators.datasets
+    movement.validators.files
+    movement.io.load_bboxes
+    movement.io.load_poses
+    movement.io.save_poses
diff --git a/_sources/community/roadmaps.md.txt b/_sources/community/roadmaps.md.txt
index 69b6000e..78b1bd67 100644
--- a/_sources/community/roadmaps.md.txt
+++ b/_sources/community/roadmaps.md.txt
@@ -24,5 +24,5 @@ We plan to release version `v0.1` of movement in early 2024, providing a minimal
 - [x] Ability to compute velocity and acceleration from pose tracks.
 - [x] Public website with [documentation](target-movement).
 - [x] Package released on [PyPI](https://pypi.org/project/movement/).
-- [ ] Package released on [conda-forge](https://conda-forge.org/).
+- [x] Package released on [conda-forge](https://anaconda.org/conda-forge/movement).
 - [ ] Ability to visualise pose tracks using [napari](napari:). We aim to represent pose tracks via napari's [Points](napari:howtos/layers/points) and [Tracks](napari:howtos/layers/tracks) layers and overlay them on video frames.
diff --git a/_sources/examples/compute_kinematics.rst.txt b/_sources/examples/compute_kinematics.rst.txt
index c3ffa6c8..c6e0d0cf 100644
--- a/_sources/examples/compute_kinematics.rst.txt
+++ b/_sources/examples/compute_kinematics.rst.txt
@@ -28,19 +28,18 @@ visualise the results.
 Imports
 -------
 
-.. GENERATED FROM PYTHON SOURCE LINES 12-22
+.. GENERATED FROM PYTHON SOURCE LINES 12-21
 
 .. code-block:: Python
 
 
-    import numpy as np
-
     # For interactive plots: install ipympl with `pip install ipympl` and uncomment
     # the following line in your notebook
     # %matplotlib widget
     from matplotlib import pyplot as plt
 
     from movement import sample_data
+    from movement.utils.vector import compute_norm
 
 
 
@@ -49,14 +48,14 @@ Imports
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 23-27
+.. GENERATED FROM PYTHON SOURCE LINES 22-26
 
 Load sample dataset
 ------------------------
 First, we load an example dataset. In this case, we select the
 ``SLEAP_three-mice_Aeon_proofread`` sample data.
 
-.. GENERATED FROM PYTHON SOURCE LINES 27-33
+.. GENERATED FROM PYTHON SOURCE LINES 26-32
 
 .. code-block:: Python
 
@@ -89,13 +88,14 @@ First, we load an example dataset. In this case, we select the
         time_unit:        seconds
         source_software:  SLEAP
         source_file:      /home/runner/.movement/data/poses/SLEAP_three-mice_Aeon...
+        ds_type:          poses
         frame_path:       /home/runner/.movement/data/frames/three-mice_Aeon_fram...
         video_path:       None
 
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 34-39
+.. GENERATED FROM PYTHON SOURCE LINES 33-38
 
 We can see in the printed description of the dataset ``ds`` that
 the data was acquired at 50 fps, and the time axis is expressed in seconds.
@@ -103,14 +103,14 @@ It includes data for three individuals(``AEON3B_NTP``, ``AEON3B_TP1``,
 and ``AEON3B_TP2``), and only one keypoint called ``centroid`` was tracked
 in ``x`` and ``y`` dimensions.
 
-.. GENERATED FROM PYTHON SOURCE LINES 41-45
+.. GENERATED FROM PYTHON SOURCE LINES 40-44
 
 The loaded dataset ``ds`` contains two data arrays:
 ``position`` and ``confidence``.
 To compute displacement, velocity and acceleration, we will need the
 ``position`` one:
 
-.. GENERATED FROM PYTHON SOURCE LINES 45-48
+.. GENERATED FROM PYTHON SOURCE LINES 44-47
 
 .. code-block:: Python
 
@@ -124,14 +124,14 @@ To compute displacement, velocity and acceleration, we will need the
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 49-53
+.. GENERATED FROM PYTHON SOURCE LINES 48-52
 
 Visualise the data
 ---------------------------
 First, let's visualise the trajectories of the mice in the XY plane,
 colouring them by individual.
 
-.. GENERATED FROM PYTHON SOURCE LINES 53-74
+.. GENERATED FROM PYTHON SOURCE LINES 52-73
 
 .. code-block:: Python
 
@@ -168,18 +168,18 @@ colouring them by individual.
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 75-79
+.. GENERATED FROM PYTHON SOURCE LINES 74-78
 
 We can see that the trajectories of the three mice are close to a circular
 arc. Notice that the x and y axes are set to equal scales, and that the
 origin of the coordinate system is at the top left of the image. This
 follows the convention for SLEAP and most image processing tools.
 
-.. GENERATED FROM PYTHON SOURCE LINES 81-82
+.. GENERATED FROM PYTHON SOURCE LINES 80-81
 
 We can also color the data points based on their timestamps:
 
-.. GENERATED FROM PYTHON SOURCE LINES 82-99
+.. GENERATED FROM PYTHON SOURCE LINES 81-98
 
 .. code-block:: Python
 
@@ -212,21 +212,21 @@ We can also color the data points based on their timestamps:
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 100-104
+.. GENERATED FROM PYTHON SOURCE LINES 99-103
 
 These plots show that for this snippet of the data,
 two of the mice (``AEON3B_NTP`` and ``AEON3B_TP1``)
 moved around the circle in clockwise direction, and
 the third mouse (``AEON3B_TP2``) followed an anti-clockwise direction.
 
-.. GENERATED FROM PYTHON SOURCE LINES 106-110
+.. GENERATED FROM PYTHON SOURCE LINES 105-109
 
 We can also easily plot the components of the position vector against time
 using ``xarray``'s built-in plotting methods. We use
-:py:meth:`xarray.DataArray.squeeze` to
+:meth:`xarray.DataArray.squeeze` to
 remove the dimension of length 1 from the data (the ``keypoints`` dimension).
 
-.. GENERATED FROM PYTHON SOURCE LINES 110-113
+.. GENERATED FROM PYTHON SOURCE LINES 109-112
 
 .. code-block:: Python
 
@@ -245,13 +245,13 @@ remove the dimension of length 1 from the data (the ``keypoints`` dimension).
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 114-117
+.. GENERATED FROM PYTHON SOURCE LINES 113-116
 
 If we use ``xarray``'s plotting function, the axes units are automatically
 taken from the data array. In our case, ``time`` is expressed in seconds,
 and the ``x`` and ``y`` coordinates of the ``position`` are in pixels.
 
-.. GENERATED FROM PYTHON SOURCE LINES 119-125
+.. GENERATED FROM PYTHON SOURCE LINES 118-124
 
 Compute displacement
 ---------------------
@@ -260,7 +260,7 @@ their trajectories.
 For this, we can use the ``compute_displacement`` method of the
 ``move`` accessor.
 
-.. GENERATED FROM PYTHON SOURCE LINES 125-127
+.. GENERATED FROM PYTHON SOURCE LINES 124-126
 
 .. code-block:: Python
 
@@ -273,18 +273,18 @@ For this, we can use the ``compute_displacement`` method of the
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 128-131
+.. GENERATED FROM PYTHON SOURCE LINES 127-130
 
 This method will return a data array equivalent to the ``position`` one,
 but holding displacement data along the ``space`` axis, rather than
 position data.
 
-.. GENERATED FROM PYTHON SOURCE LINES 133-135
+.. GENERATED FROM PYTHON SOURCE LINES 132-134
 
 Notice that we could also compute the displacement (and all the other
-kinematic variables) using the :py:mod:`movement.analysis.kinematics` module:
+kinematic variables) using the :mod:`movement.analysis.kinematics` module:
 
-.. GENERATED FROM PYTHON SOURCE LINES 137-141
+.. GENERATED FROM PYTHON SOURCE LINES 136-140
 
 .. code-block:: Python
 
@@ -299,20 +299,20 @@ kinematic variables) using the :py:mod:`movement.analysis.kinematics` module:
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 142-145
+.. GENERATED FROM PYTHON SOURCE LINES 141-144
 
 The ``displacement`` data array holds, for a given individual and keypoint
 at timestep ``t``, the vector that goes from its previous position at time
 ``t-1`` to its current position at time ``t``.
 
-.. GENERATED FROM PYTHON SOURCE LINES 147-151
+.. GENERATED FROM PYTHON SOURCE LINES 146-150
 
 And what happens at ``t=0``, since there is no previous timestep?
 We define the displacement vector at time ``t=0`` to be the zero vector.
 This way the shape of the ``displacement`` data array is the
 same as the  ``position`` array:
 
-.. GENERATED FROM PYTHON SOURCE LINES 151-154
+.. GENERATED FROM PYTHON SOURCE LINES 150-153
 
 .. code-block:: Python
 
@@ -333,12 +333,12 @@ same as the  ``position`` array:
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 155-157
+.. GENERATED FROM PYTHON SOURCE LINES 154-156
 
 We can visualise these displacement vectors with a quiver plot. In this case
 we focus on the mouse ``AEON3B_TP2``:
 
-.. GENERATED FROM PYTHON SOURCE LINES 157-194
+.. GENERATED FROM PYTHON SOURCE LINES 156-193
 
 .. code-block:: Python
 
@@ -393,18 +393,18 @@ we focus on the mouse ``AEON3B_TP2``:
  .. code-block:: none
 
 
-    
+    
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 195-199
+.. GENERATED FROM PYTHON SOURCE LINES 194-198
 
 Notice that this figure is not very useful as a visual check:
 we can see that there are vectors defined for each point in
 the trajectory, but we have no easy way to verify they are indeed
 the displacement vectors from ``t-1`` to ``t``.
 
-.. GENERATED FROM PYTHON SOURCE LINES 201-208
+.. GENERATED FROM PYTHON SOURCE LINES 200-207
 
 If instead we plot
 the opposite of the displacement vector, we will see that at every time
@@ -414,12 +414,12 @@ time ``t``, that goes from the previous position ``t-1`` to the
 current position at ``t``. Therefore, the opposite vector will point
 from the position point at ``t``, to the position point at ``t-1``.
 
-.. GENERATED FROM PYTHON SOURCE LINES 210-212
+.. GENERATED FROM PYTHON SOURCE LINES 209-211
 
 We can easily do this by flipping the sign of the displacement vector in
 the plot above:
 
-.. GENERATED FROM PYTHON SOURCE LINES 212-249
+.. GENERATED FROM PYTHON SOURCE LINES 211-248
 
 .. code-block:: Python
 
@@ -474,33 +474,32 @@ the plot above:
  .. code-block:: none
 
 
-    
+    
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 250-252
+.. GENERATED FROM PYTHON SOURCE LINES 249-251
 
 Now we can visually verify that indeed the displacement vector
 connects the previous and current positions as expected.
 
-.. GENERATED FROM PYTHON SOURCE LINES 254-256
+.. GENERATED FROM PYTHON SOURCE LINES 253-255
 
 With the displacement data we can compute the distance travelled by the
 mouse along its trajectory.
 
-.. GENERATED FROM PYTHON SOURCE LINES 256-271
+.. GENERATED FROM PYTHON SOURCE LINES 255-269
 
 .. code-block:: Python
 
 
     # length of each displacement vector
-    displacement_vectors_lengths = np.linalg.norm(
-        displacement.sel(individuals=mouse_name, space=["x", "y"]).squeeze(),
-        axis=1,
+    displacement_vectors_lengths = compute_norm(
+        displacement.sel(individuals=mouse_name)
     )
 
-    # sum of all displacement vectors
-    total_displacement = np.sum(displacement_vectors_lengths, axis=0)  # in pixels
+    # sum the lengths of all displacement vectors (in pixels)
+    total_displacement = displacement_vectors_lengths.sum(dim="time").values[0]
 
     print(
         f"The mouse {mouse_name}'s trajectory is {total_displacement:.2f} "
@@ -520,14 +519,14 @@ mouse along its trajectory.
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 272-276
+.. GENERATED FROM PYTHON SOURCE LINES 270-274
 
 Compute velocity
 ----------------
 We can easily compute the velocity vectors for all individuals in our data
 array:
 
-.. GENERATED FROM PYTHON SOURCE LINES 276-278
+.. GENERATED FROM PYTHON SOURCE LINES 274-276
 
 .. code-block:: Python
 
@@ -540,21 +539,21 @@ array:
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 279-283
+.. GENERATED FROM PYTHON SOURCE LINES 277-281
 
 The ``velocity`` method will return a data array equivalent to the
 ``position`` one, but holding velocity data along the ``space`` axis, rather
 than position data. Notice how ``xarray`` nicely deals with the different
 individuals and spatial dimensions for us! ✨
 
-.. GENERATED FROM PYTHON SOURCE LINES 285-289
+.. GENERATED FROM PYTHON SOURCE LINES 283-287
 
 We can plot the components of the velocity vector against time
 using ``xarray``'s built-in plotting methods. We use
-:py:meth:`xarray.DataArray.squeeze` to
+:meth:`xarray.DataArray.squeeze` to
 remove the dimension of length 1 from the data (the ``keypoints`` dimension).
 
-.. GENERATED FROM PYTHON SOURCE LINES 289-293
+.. GENERATED FROM PYTHON SOURCE LINES 287-291
 
 .. code-block:: Python
 
@@ -574,7 +573,7 @@ remove the dimension of length 1 from the data (the ``keypoints`` dimension).
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 294-300
+.. GENERATED FROM PYTHON SOURCE LINES 292-298
 
 The components of the velocity vector seem noisier than the components of
 the position vector.
@@ -583,21 +582,19 @@ position (which is somewhat noisy), over small stepsizes.
 More specifically, we use numpy's gradient implementation, which
 uses second order central differences.
 
-.. GENERATED FROM PYTHON SOURCE LINES 302-303
+.. GENERATED FROM PYTHON SOURCE LINES 300-302
 
-We can also visualise the speed, as the norm of the velocity vector:
+We can also visualise the speed, as the magnitude (norm)
+of the velocity vector:
 
-.. GENERATED FROM PYTHON SOURCE LINES 303-317
+.. GENERATED FROM PYTHON SOURCE LINES 302-313
 
 .. code-block:: Python
 
     fig, axes = plt.subplots(3, 1, sharex=True, sharey=True)
     for mouse_name, ax in zip(velocity.individuals.values, axes, strict=False):
-        # compute the norm of the velocity vector for one mouse
-        speed_one_mouse = np.linalg.norm(
-            velocity.sel(individuals=mouse_name, space=["x", "y"]).squeeze(),
-            axis=1,
-        )
+        # compute the magnitude of the velocity vector for one mouse
+        speed_one_mouse = compute_norm(velocity.sel(individuals=mouse_name))
         # plot speed against time
         ax.plot(speed_one_mouse)
         ax.set_title(mouse_name)
@@ -617,12 +614,12 @@ We can also visualise the speed, as the norm of the velocity vector:
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 318-320
+.. GENERATED FROM PYTHON SOURCE LINES 314-316
 
 To visualise the direction of the velocity vector at each timestep, we can
 use a quiver plot:
 
-.. GENERATED FROM PYTHON SOURCE LINES 320-350
+.. GENERATED FROM PYTHON SOURCE LINES 316-346
 
 .. code-block:: Python
 
@@ -668,18 +665,18 @@ use a quiver plot:
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 351-353
+.. GENERATED FROM PYTHON SOURCE LINES 347-349
 
 Here we scaled the length of vectors to half of their actual value
 (``scale=2``) for easier visualisation.
 
-.. GENERATED FROM PYTHON SOURCE LINES 355-358
+.. GENERATED FROM PYTHON SOURCE LINES 351-354
 
 Compute acceleration
 ---------------------
 We can compute the acceleration of the data with an equivalent method:
 
-.. GENERATED FROM PYTHON SOURCE LINES 358-360
+.. GENERATED FROM PYTHON SOURCE LINES 354-356
 
 .. code-block:: Python
 
@@ -692,12 +689,12 @@ We can compute the acceleration of the data with an equivalent method:
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 361-363
+.. GENERATED FROM PYTHON SOURCE LINES 357-359
 
 and plot of the components of the acceleration vector ``ax``, ``ay`` per
 individual:
 
-.. GENERATED FROM PYTHON SOURCE LINES 363-381
+.. GENERATED FROM PYTHON SOURCE LINES 359-377
 
 .. code-block:: Python
 
@@ -731,23 +728,19 @@ individual:
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 382-385
+.. GENERATED FROM PYTHON SOURCE LINES 378-380
 
-The norm of the acceleration vector is the magnitude of the
-acceleration.
-We can also represent this for each individual.
+The can also represent the magnitude (norm) of the acceleration vector
+for each individual:
 
-.. GENERATED FROM PYTHON SOURCE LINES 385-399
+.. GENERATED FROM PYTHON SOURCE LINES 380-391
 
 .. code-block:: Python
 
     fig, axes = plt.subplots(3, 1, sharex=True, sharey=True)
     for mouse_name, ax in zip(accel.individuals.values, axes, strict=False):
-        # compute norm of the acceleration vector for one mouse
-        accel_one_mouse = np.linalg.norm(
-            accel.sel(individuals=mouse_name, space=["x", "y"]).squeeze(),
-            axis=1,
-        )
+        # compute magnitude of the acceleration vector for one mouse
+        accel_one_mouse = compute_norm(accel.sel(individuals=mouse_name))
 
         # plot acceleration against time
         ax.plot(accel_one_mouse)
@@ -770,7 +763,7 @@ We can also represent this for each individual.
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 2.105 seconds)
+   **Total running time of the script:** (0 minutes 2.379 seconds)
 
 
 .. _sphx_glr_download_examples_compute_kinematics.py:
@@ -794,6 +787,10 @@ We can also represent this for each individual.
 
       :download:`Download Python source code: compute_kinematics.py `
 
+    .. container:: sphx-glr-download sphx-glr-download-zip
+
+      :download:`Download zipped: compute_kinematics.zip `
+
 
 .. only:: html
 
diff --git a/_sources/examples/compute_polar_coordinates.rst.txt b/_sources/examples/compute_polar_coordinates.rst.txt
index 6860fe28..94bec878 100644
--- a/_sources/examples/compute_polar_coordinates.rst.txt
+++ b/_sources/examples/compute_polar_coordinates.rst.txt
@@ -96,6 +96,7 @@ In this tutorial, we will use a sample dataset with a single individual
         time_unit:        frames
         source_software:  SLEAP
         source_file:      /home/runner/.movement/data/poses/SLEAP_single-mouse_EP...
+        ds_type:          poses
     -----------------------------
     Individuals: ['individual_0']
     Keypoints: ['snout' 'left_ear' 'right_ear' 'centre' 'tail_base' 'tail_end']
@@ -674,7 +675,7 @@ with two coordinates: ``x`` and ``y``.
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 16.520 seconds)
+   **Total running time of the script:** (0 minutes 16.565 seconds)
 
 
 .. _sphx_glr_download_examples_compute_polar_coordinates.py:
@@ -698,6 +699,10 @@ with two coordinates: ``x`` and ``y``.
 
       :download:`Download Python source code: compute_polar_coordinates.py `
 
+    .. container:: sphx-glr-download sphx-glr-download-zip
+
+      :download:`Download zipped: compute_polar_coordinates.zip `
+
 
 .. only:: html
 
diff --git a/_sources/examples/filter_and_interpolate.rst.txt b/_sources/examples/filter_and_interpolate.rst.txt
index 1dc9704c..820f759f 100644
--- a/_sources/examples/filter_and_interpolate.rst.txt
+++ b/_sources/examples/filter_and_interpolate.rst.txt
@@ -77,6 +77,7 @@ Load a sample dataset
         time_unit:        seconds
         source_software:  DeepLabCut
         source_file:      /home/runner/.movement/data/poses/DLC_single-wasp.predi...
+        ds_type:          poses
         frame_path:       /home/runner/.movement/data/frames/single-wasp_frame-10...
         video_path:       None
 
@@ -95,7 +96,7 @@ lasts for approximately 27 seconds.
 Visualise the pose tracks
 -------------------------
 Since the data contains only a single wasp, we use
-:py:meth:`xarray.DataArray.squeeze` to remove
+:meth:`xarray.DataArray.squeeze` to remove
 the dimension of length 1 from the data (the ``individuals`` dimension).
 
 .. GENERATED FROM PYTHON SOURCE LINES 32-37
@@ -121,7 +122,7 @@ the dimension of length 1 from the data (the ``individuals`` dimension).
  .. code-block:: none
 
 
-    
+    
 
 
 
@@ -144,7 +145,7 @@ estimation frameworks, and their ranges can vary. Therefore,
 it's always a good idea to inspect the actual confidence values in the data.
 
 Let's first look at a histogram of the confidence scores. As before, we use
-:py:meth:`xarray.DataArray.squeeze` to remove the ``individuals`` dimension
+:meth:`xarray.DataArray.squeeze` to remove the ``individuals`` dimension
 from the data.
 
 .. GENERATED FROM PYTHON SOURCE LINES 56-59
@@ -207,7 +208,7 @@ they evolve over time.
  .. code-block:: none
 
 
-    
+    
 
 
 
@@ -222,7 +223,7 @@ We can use that to our advantage.
 Filter out points with low confidence
 -------------------------------------
 Using the
-:py:meth:`filter_by_confidence()\
+:meth:`filter_by_confidence()\
 `
 method of the ``move`` accessor,
 we can filter out points with confidence scores below a certain threshold.
@@ -230,7 +231,7 @@ The default ``threshold=0.6`` will be used when ``threshold`` is not
 provided.
 This method will also report the number of NaN values in the dataset before
 and after the filtering operation by default (``print_report=True``).
-We will use :py:meth:`xarray.Dataset.update` to update ``ds`` in-place
+We will use :meth:`xarray.Dataset.update` to update ``ds`` in-place
 with the filtered ``position``.
 
 .. GENERATED FROM PYTHON SOURCE LINES 87-90
@@ -294,6 +295,7 @@ with the filtered ``position``.
     }
 
     html[theme=dark],
+    html[data-theme=dark],
     body[data-theme=dark],
     body.vscode-dark {
       --xr-font-color0: rgba(255, 255, 255, 1);
@@ -641,9 +643,10 @@ with the filtered ``position``.
         time_unit:        seconds
         source_software:  DeepLabCut
         source_file:      /home/runner/.movement/data/poses/DLC_single-wasp.predi...
+        ds_type:          poses
         frame_path:       /home/runner/.movement/data/frames/single-wasp_frame-10...
-        video_path:       None
  • confidence
    (time, individuals, keypoints)
    float64
    0.05305 0.07366 0.03532 ... 0.0 0.0
    array([[[0.05305099, 0.07366323]],
+             [nan, nan]]]])
  • confidence
    (time, individuals, keypoints)
    float64
    0.05305 0.07366 0.03532 ... 0.0 0.0
    array([[[0.05305099, 0.07366323]],
 
            [[0.03531652, 0.03293059]],
 
@@ -684,12 +687,12 @@ with the filtered ``position``.
 
            [[0.        , 0.        ]],
 
-           [[0.        , 0.        ]]])
    • time
      PandasIndex
      PandasIndex(Index([   0.0,  0.025,   0.05,  0.075,    0.1,  0.125,   0.15,  0.175,    0.2,
+           [[0.        , 0.        ]]])
    • time
      PandasIndex
      PandasIndex(Index([   0.0,  0.025,   0.05,  0.075,    0.1,  0.125,   0.15,  0.175,    0.2,
             0.225,
            ...
            26.875,   26.9, 26.925,  26.95, 26.975,   27.0, 27.025,  27.05, 27.075,
              27.1],
-          dtype='float64', name='time', length=1085))
    • individuals
      PandasIndex
      PandasIndex(Index(['individual_0'], dtype='object', name='individuals'))
    • keypoints
      PandasIndex
      PandasIndex(Index(['head', 'stinger'], dtype='object', name='keypoints'))
    • space
      PandasIndex
      PandasIndex(Index(['x', 'y'], dtype='object', name='space'))
  • fps :
    40.0
    time_unit :
    seconds
    source_software :
    DeepLabCut
    source_file :
    /home/runner/.movement/data/poses/DLC_single-wasp.predictions.h5
    frame_path :
    /home/runner/.movement/data/frames/single-wasp_frame-10sec.png
    video_path :
    None
    • + dtype='float64', name='time', length=1085))
  • individuals
    PandasIndex
    PandasIndex(Index(['individual_0'], dtype='object', name='individuals'))
  • keypoints
    PandasIndex
    PandasIndex(Index(['head', 'stinger'], dtype='object', name='keypoints'))
  • space
    PandasIndex
    PandasIndex(Index(['x', 'y'], dtype='object', name='space'))
  • fps :
    40.0
    time_unit :
    seconds
    source_software :
    DeepLabCut
    source_file :
    /home/runner/.movement/data/poses/DLC_single-wasp.predictions.h5
    ds_type :
    poses
    frame_path :
    /home/runner/.movement/data/frames/single-wasp_frame-10sec.png
    video_path :
    None


    • @@ -697,13 +700,13 @@ with the filtered ``position``. .. GENERATED FROM PYTHON SOURCE LINES 91-105 .. note:: - The ``move`` accessor :py:meth:`filter_by_confidence()\ + The ``move`` accessor :meth:`filter_by_confidence()\ ` method is a convenience method that applies - :py:func:`movement.filtering.filter_by_confidence`, + :func:`movement.filtering.filter_by_confidence`, which takes ``position`` and ``confidence`` as arguments. The equivalent function call using the - :py:mod:`movement.filtering` module would be: + :mod:`movement.filtering` module would be: .. code-block:: python @@ -739,7 +742,7 @@ We can see that the filtering operation has introduced NaN values in the .. code-block:: none - + @@ -755,7 +758,7 @@ lasting < 1 second (or 40 frames). Interpolate over missing values ------------------------------- Using the -:py:meth:`interpolate_over_time()\ +:meth:`interpolate_over_time()\ ` method of the ``move`` accessor, we can interpolate over the gaps we've introduced in the pose tracks. @@ -826,6 +829,7 @@ spurious data. The ``print_report`` argument acts as described above. } html[theme=dark], + html[data-theme=dark], body[data-theme=dark], body.vscode-dark { --xr-font-color0: rgba(255, 255, 255, 1); @@ -1173,14 +1177,15 @@ spurious data. The ``print_report`` argument acts as described above. time_unit: seconds source_software: DeepLabCut source_file: /home/runner/.movement/data/poses/DLC_single-wasp.predi... + ds_type: poses frame_path: /home/runner/.movement/data/frames/single-wasp_frame-10... - video_path: None + dtype='float64', name='time', length=1085))
  • individuals
    PandasIndex
    PandasIndex(Index(['individual_0'], dtype='object', name='individuals'))
  • keypoints
    PandasIndex
    PandasIndex(Index(['head', 'stinger'], dtype='object', name='keypoints'))
  • space
    PandasIndex
    PandasIndex(Index(['x', 'y'], dtype='object', name='space'))
  • fps :
    40.0
    time_unit :
    seconds
    source_software :
    DeepLabCut
    source_file :
    /home/runner/.movement/data/poses/DLC_single-wasp.predictions.h5
    ds_type :
    poses
    frame_path :
    /home/runner/.movement/data/frames/single-wasp_frame-10sec.png
    video_path :
    None


    • @@ -1229,13 +1234,13 @@ spurious data. The ``print_report`` argument acts as described above. .. GENERATED FROM PYTHON SOURCE LINES 137-153 .. note:: - The ``move`` accessor :py:meth:`interpolate_over_time()\ + The ``move`` accessor :meth:`interpolate_over_time()\ ` is also a convenience method that applies - :py:func:`movement.filtering.interpolate_over_time` + :func:`movement.filtering.interpolate_over_time` to the ``position`` data variable. The equivalent function call using the - :py:mod:`movement.filtering` module would be: + :mod:`movement.filtering` module would be: .. code-block:: python @@ -1274,7 +1279,7 @@ Let's visualise the interpolated pose tracks. .. code-block:: none - + @@ -1305,13 +1310,13 @@ applied to the data. Let's inspect the log entries. .. code-block:: none - {'operation': 'filter_by_confidence', 'datetime': '2024-07-17 10:15:49.445284', 'confidence': Size: 17kB + {'operation': 'filter_by_confidence', 'datetime': '2024-09-06 12:30:55.519032', 'confidence': Size: 17kB 0.05305 0.07366 0.03532 0.03293 0.01707 0.01022 ... 0.0 0.0 0.0 0.0 0.0 0.0 Coordinates: * time (time) float64 9kB 0.0 0.025 0.05 0.075 ... 27.05 27.07 27.1 * individuals (individuals)
  • fps :
    40.0
    time_unit :
    seconds
    source_software :
    DeepLabCut
    source_file :
    /home/runner/.movement/data/poses/DLC_single-wasp.predictions.h5
    ds_type :
    poses
    frame_path :
    /home/runner/.movement/data/frames/single-wasp_frame-10sec.png
    video_path :
    None


    • @@ -1856,7 +1858,7 @@ with the filtered data variables. .. rst-class:: sphx-glr-timing - **Total running time of the script:** (0 minutes 3.496 seconds) + **Total running time of the script:** (0 minutes 2.401 seconds) .. _sphx_glr_download_examples_filter_and_interpolate.py: @@ -1880,6 +1882,10 @@ with the filtered data variables. :download:`Download Python source code: filter_and_interpolate.py ` + .. container:: sphx-glr-download sphx-glr-download-zip + + :download:`Download zipped: filter_and_interpolate.zip ` + .. only:: html diff --git a/_sources/examples/load_and_explore_poses.rst.txt b/_sources/examples/load_and_explore_poses.rst.txt index aa7d823a..6c6b03e0 100644 --- a/_sources/examples/load_and_explore_poses.rst.txt +++ b/_sources/examples/load_and_explore_poses.rst.txt @@ -130,6 +130,7 @@ Load the data into movement time_unit: seconds source_software: SLEAP source_file: /home/runner/.movement/data/poses/SLEAP_three-mice_Aeon... + ds_type: poses @@ -213,7 +214,7 @@ using ``xarray``'s built-in plotting methods: .. code-block:: none - + @@ -244,7 +245,7 @@ for all individuals: .. code-block:: none - + @@ -288,14 +289,14 @@ For example, we can use ``matplotlib`` to plot trajectories .. code-block:: none - + .. rst-class:: sphx-glr-timing - **Total running time of the script:** (0 minutes 0.637 seconds) + **Total running time of the script:** (0 minutes 0.713 seconds) .. _sphx_glr_download_examples_load_and_explore_poses.py: @@ -319,6 +320,10 @@ For example, we can use ``matplotlib`` to plot trajectories :download:`Download Python source code: load_and_explore_poses.py ` + .. container:: sphx-glr-download sphx-glr-download-zip + + :download:`Download zipped: load_and_explore_poses.zip ` + .. only:: html diff --git a/_sources/examples/sg_execution_times.rst.txt b/_sources/examples/sg_execution_times.rst.txt index 358d6c21..07704d23 100644 --- a/_sources/examples/sg_execution_times.rst.txt +++ b/_sources/examples/sg_execution_times.rst.txt @@ -6,7 +6,7 @@ Computation times ================= -**00:24.360** total execution time for 5 files **from examples**: +**00:23.826** total execution time for 5 files **from examples**: .. container:: @@ -33,17 +33,17 @@ Computation times - Time - Mem (MB) * - :ref:`sphx_glr_examples_compute_polar_coordinates.py` (``compute_polar_coordinates.py``) - - 00:16.520 + - 00:16.565 - 0.0 * - :ref:`sphx_glr_examples_filter_and_interpolate.py` (``filter_and_interpolate.py``) - - 00:03.496 + - 00:02.401 - 0.0 * - :ref:`sphx_glr_examples_compute_kinematics.py` (``compute_kinematics.py``) - - 00:02.105 + - 00:02.379 - 0.0 * - :ref:`sphx_glr_examples_smooth.py` (``smooth.py``) - - 00:01.601 + - 00:01.767 - 0.0 * - :ref:`sphx_glr_examples_load_and_explore_poses.py` (``load_and_explore_poses.py``) - - 00:00.637 + - 00:00.713 - 0.0 diff --git a/_sources/examples/smooth.rst.txt b/_sources/examples/smooth.rst.txt index 829b2c4f..3cacf54f 100644 --- a/_sources/examples/smooth.rst.txt +++ b/_sources/examples/smooth.rst.txt @@ -84,6 +84,7 @@ display of the dataset's contents. time_unit: seconds source_software: DeepLabCut source_file: /home/runner/.movement/data/poses/DLC_single-wasp.predi... + ds_type: poses frame_path: /home/runner/.movement/data/frames/single-wasp_frame-10... video_path: None @@ -190,7 +191,7 @@ specify the spatial coordinate (``x`` or ``y``) and a time range to focus on. Smoothing with a median filter ------------------------------ Using the -:py:meth:`median_filter()\ +:meth:`median_filter()\ ` method of the ``move`` accessor, we apply a rolling window median filter over a 0.1-second window @@ -263,6 +264,7 @@ modifying the original data. } html[theme=dark], + html[data-theme=dark], body[data-theme=dark], body.vscode-dark { --xr-font-color0: rgba(255, 255, 255, 1); @@ -610,9 +612,10 @@ modifying the original data. time_unit: seconds source_software: DeepLabCut source_file: /home/runner/.movement/data/poses/DLC_single-wasp.predi... + ds_type: poses frame_path: /home/runner/.movement/data/frames/single-wasp_frame-10... - video_path: None
  • fps :
    40.0
    time_unit :
    seconds
    source_software :
    DeepLabCut
    source_file :
    /home/runner/.movement/data/poses/DLC_single-wasp.predictions.h5
    ds_type :
    poses
    frame_path :
    /home/runner/.movement/data/frames/single-wasp_frame-10sec.png
    video_path :
    None


    • @@ -661,13 +664,13 @@ modifying the original data. .. GENERATED FROM PYTHON SOURCE LINES 127-141 .. note:: - The ``move`` accessor :py:meth:`median_filter()\ + The ``move`` accessor :meth:`median_filter()\ ` method is a convenience method that applies - :py:func:`movement.filtering.median_filter` + :func:`movement.filtering.median_filter` to the ``position`` data variable. The equivalent function call using the - :py:mod:`movement.filtering` module would be: + :mod:`movement.filtering` module would be: .. code-block:: python @@ -755,6 +758,7 @@ dataset that contains missing values. time_unit: seconds source_software: SLEAP source_file: /home/runner/.movement/data/poses/SLEAP_single-mouse_EP... + ds_type: poses frame_path: /home/runner/.movement/data/frames/single-mouse_EPM_fra... video_path: None @@ -843,6 +847,7 @@ to the dataset. } html[theme=dark], + html[data-theme=dark], body[data-theme=dark], body.vscode-dark { --xr-font-color0: rgba(255, 255, 255, 1); @@ -1190,10 +1195,11 @@ to the dataset. time_unit: seconds source_software: SLEAP source_file: /home/runner/.movement/data/poses/SLEAP_single-mouse_EP... + ds_type: poses frame_path: /home/runner/.movement/data/frames/single-mouse_EPM_fra... - video_path: None
  • fps :
    30.0
    time_unit :
    seconds
    source_software :
    SLEAP
    source_file :
    /home/runner/.movement/data/poses/SLEAP_single-mouse_EPM.analysis.h5
    ds_type :
    poses
    frame_path :
    /home/runner/.movement/data/frames/single-mouse_EPM_frame-20sec.png
    video_path :
    None


    • @@ -1350,6 +1356,7 @@ window are sufficient for the median to be calculated. Let's try this. } html[theme=dark], + html[data-theme=dark], body[data-theme=dark], body.vscode-dark { --xr-font-color0: rgba(255, 255, 255, 1); @@ -1697,10 +1704,11 @@ window are sufficient for the median to be calculated. Let's try this. time_unit: seconds source_software: SLEAP source_file: /home/runner/.movement/data/poses/SLEAP_single-mouse_EP... + ds_type: poses frame_path: /home/runner/.movement/data/frames/single-mouse_EPM_fra... - video_path: None
  • fps :
    30.0
    time_unit :
    seconds
    source_software :
    SLEAP
    source_file :
    /home/runner/.movement/data/poses/SLEAP_single-mouse_EPM.analysis.h5
    ds_type :
    poses
    frame_path :
    /home/runner/.movement/data/frames/single-mouse_EPM_frame-20sec.png
    video_path :
    None


    • @@ -1881,6 +1889,7 @@ What happens if we increase the ``window`` to 2 seconds (60 frames)? } html[theme=dark], + html[data-theme=dark], body[data-theme=dark], body.vscode-dark { --xr-font-color0: rgba(255, 255, 255, 1); @@ -2228,10 +2237,11 @@ What happens if we increase the ``window`` to 2 seconds (60 frames)? time_unit: seconds source_software: SLEAP source_file: /home/runner/.movement/data/poses/SLEAP_single-mouse_EP... + ds_type: poses frame_path: /home/runner/.movement/data/frames/single-mouse_EPM_fra... - video_path: None
  • fps :
    30.0
    time_unit :
    seconds
    source_software :
    SLEAP
    source_file :
    /home/runner/.movement/data/poses/SLEAP_single-mouse_EPM.analysis.h5
    ds_type :
    poses
    frame_path :
    /home/runner/.movement/data/frames/single-mouse_EPM_frame-20sec.png
    video_path :
    None


    • @@ -2347,11 +2357,11 @@ that the filter is not removing important features. Smoothing with a Savitzky-Golay filter -------------------------------------- Here we use the -:py:meth:`savgol_filter()\ +:meth:`savgol_filter()\ ` method of the ``move`` accessor, which is a convenience method that applies -:py:func:`movement.filtering.savgol_filter` -(a wrapper around :py:func:`scipy.signal.savgol_filter`), +:func:`movement.filtering.savgol_filter` +(a wrapper around :func:`scipy.signal.savgol_filter`), to the ``position`` data variable. The Savitzky-Golay filter is a polynomial smoothing filter that can be applied to time series data on a rolling window basis. @@ -2435,6 +2445,7 @@ to be used as the ``window`` size. } html[theme=dark], + html[data-theme=dark], body[data-theme=dark], body.vscode-dark { --xr-font-color0: rgba(255, 255, 255, 1); @@ -2782,10 +2793,11 @@ to be used as the ``window`` size. time_unit: seconds source_software: SLEAP source_file: /home/runner/.movement/data/poses/SLEAP_single-mouse_EP... + ds_type: poses frame_path: /home/runner/.movement/data/frames/single-mouse_EPM_fra... - video_path: None
  • fps :
    30.0
    time_unit :
    seconds
    source_software :
    SLEAP
    source_file :
    /home/runner/.movement/data/poses/SLEAP_single-mouse_EPM.analysis.h5
    ds_type :
    poses
    frame_path :
    /home/runner/.movement/data/frames/single-mouse_EPM_frame-20sec.png
    video_path :
    None


    • @@ -2957,6 +2969,7 @@ Now let's apply the same Savitzky-Golay filter to the wasp dataset. } html[theme=dark], + html[data-theme=dark], body[data-theme=dark], body.vscode-dark { --xr-font-color0: rgba(255, 255, 255, 1); @@ -3304,9 +3317,10 @@ Now let's apply the same Savitzky-Golay filter to the wasp dataset. time_unit: seconds source_software: DeepLabCut source_file: /home/runner/.movement/data/poses/DLC_single-wasp.predi... + ds_type: poses frame_path: /home/runner/.movement/data/frames/single-wasp_frame-10... - video_path: None
  • fps :
    40.0
    time_unit :
    seconds
    source_software :
    DeepLabCut
    source_file :
    /home/runner/.movement/data/poses/DLC_single-wasp.predictions.h5
    ds_type :
    poses
    frame_path :
    /home/runner/.movement/data/frames/single-wasp_frame-10sec.png
    video_path :
    None


    • @@ -3466,6 +3480,7 @@ First, we will apply the median filter. } html[theme=dark], + html[data-theme=dark], body[data-theme=dark], body.vscode-dark { --xr-font-color0: rgba(255, 255, 255, 1); @@ -3813,10 +3828,11 @@ First, we will apply the median filter. time_unit: seconds source_software: SLEAP source_file: /home/runner/.movement/data/poses/SLEAP_single-mouse_EP... + ds_type: poses frame_path: /home/runner/.movement/data/frames/single-mouse_EPM_fra... - video_path: None
  • fps :
    30.0
    time_unit :
    seconds
    source_software :
    SLEAP
    source_file :
    /home/runner/.movement/data/poses/SLEAP_single-mouse_EPM.analysis.h5
    ds_type :
    poses
    frame_path :
    /home/runner/.movement/data/frames/single-mouse_EPM_frame-20sec.png
    video_path :
    None


    • @@ -3963,6 +3979,7 @@ Next, let's linearly interpolate over gaps smaller than 1 second (30 frames). } html[theme=dark], + html[data-theme=dark], body[data-theme=dark], body.vscode-dark { --xr-font-color0: rgba(255, 255, 255, 1); @@ -4310,10 +4327,11 @@ Next, let's linearly interpolate over gaps smaller than 1 second (30 frames). time_unit: seconds source_software: SLEAP source_file: /home/runner/.movement/data/poses/SLEAP_single-mouse_EP... + ds_type: poses frame_path: /home/runner/.movement/data/frames/single-mouse_EPM_fra... - video_path: None
  • fps :
    30.0
    time_unit :
    seconds
    source_software :
    SLEAP
    source_file :
    /home/runner/.movement/data/poses/SLEAP_single-mouse_EPM.analysis.h5
    ds_type :
    poses
    frame_path :
    /home/runner/.movement/data/frames/single-mouse_EPM_frame-20sec.png
    video_path :
    None


    • @@ -4462,6 +4480,7 @@ Finally, let's apply the Savitzky-Golay filter over a 0.4-second window } html[theme=dark], + html[data-theme=dark], body[data-theme=dark], body.vscode-dark { --xr-font-color0: rgba(255, 255, 255, 1); @@ -4809,10 +4828,11 @@ Finally, let's apply the Savitzky-Golay filter over a 0.4-second window time_unit: seconds source_software: SLEAP source_file: /home/runner/.movement/data/poses/SLEAP_single-mouse_EP... + ds_type: poses frame_path: /home/runner/.movement/data/frames/single-mouse_EPM_fra... - video_path: None
  • fps :
    30.0
    time_unit :
    seconds
    source_software :
    SLEAP
    source_file :
    /home/runner/.movement/data/poses/SLEAP_single-mouse_EPM.analysis.h5
    ds_type :
    poses
    frame_path :
    /home/runner/.movement/data/frames/single-mouse_EPM_frame-20sec.png
    video_path :
    None


    • @@ -4906,9 +4926,9 @@ what we've done. .. code-block:: none - {'operation': 'median_filter', 'datetime': '2024-07-17 10:15:53.447567', 'arg_1': 3, 'min_periods': 2} - {'operation': 'interpolate_over_time', 'datetime': '2024-07-17 10:15:53.492524', 'max_gap': 30} - {'operation': 'savgol_filter', 'datetime': '2024-07-17 10:15:53.515244', 'arg_1': 12} + {'operation': 'median_filter', 'datetime': '2024-09-06 12:30:59.785008', 'arg_1': 3, 'min_periods': 2} + {'operation': 'interpolate_over_time', 'datetime': '2024-09-06 12:30:59.828414', 'max_gap': 30} + {'operation': 'savgol_filter', 'datetime': '2024-09-06 12:30:59.850284', 'arg_1': 12} @@ -4957,7 +4977,7 @@ also look at other keypoints and time ranges. .. rst-class:: sphx-glr-timing - **Total running time of the script:** (0 minutes 1.601 seconds) + **Total running time of the script:** (0 minutes 1.767 seconds) .. _sphx_glr_download_examples_smooth.py: @@ -4981,6 +5001,10 @@ also look at other keypoints and time ranges. :download:`Download Python source code: smooth.py ` + .. container:: sphx-glr-download sphx-glr-download-zip + + :download:`Download zipped: smooth.zip ` + .. only:: html diff --git a/_sources/getting_started/index.md.txt b/_sources/getting_started/index.md.txt index b98a529c..4795a9cd 100644 --- a/_sources/getting_started/index.md.txt +++ b/_sources/getting_started/index.md.txt @@ -2,7 +2,7 @@ Start by [installing the package](installation.md). -After that try [loading some of your own predicted poses](target-loading), +After that, try [loading some of your own tracked poses](target-loading-pose-tracks) or [bounding boxes' trajectories](target-loading-bbox-tracks), from one of the [supported formats](target-formats). Alternatively, you can use the [sample data](target-sample-data) provided with the package. diff --git a/_sources/getting_started/input_output.md.txt b/_sources/getting_started/input_output.md.txt index b4ad43f9..ccb16a7b 100644 --- a/_sources/getting_started/input_output.md.txt +++ b/_sources/getting_started/input_output.md.txt @@ -4,35 +4,40 @@ (target-formats)= ## Supported formats (target-supported-formats)= -`movement` can load pose tracks from various pose estimation frameworks. -Currently, these include: +`movement` supports the analysis of trajectories of keypoints (_pose tracks_) and of bounding boxes' centroids (_bounding boxes' tracks_). + +To analyse pose tracks, `movement` supports loading data from various frameworks: - [DeepLabCut](dlc:) (DLC) - [SLEAP](sleap:) (SLEAP) - [LightingPose](lp:) (LP) -:::{warning} -`movement` only deals with the predicted pose tracks output by these -software packages. It does not support the training or labelling of the data. +To analyse bounding boxes' tracks, `movement` currently supports the [VGG Image Annotator](via:) (VIA) format for [tracks annotation](via:docs/face_track_annotation.html). + +:::{note} +At the moment `movement` only deals with tracked data: either keypoints or bounding boxes whose identities are known from one frame to the next, for a consecutive set of frames. For the pose estimation case, this means it only deals with the predictions output by the software packages above. It currently does not support loading manually labelled data (since this is most often defined over a non-continuous set of frames). ::: -(target-loading)= +Below we explain how you can load pose tracks and bounding boxes' tracks into `movement`, and how you can export a `movement` poses dataset to different file formats. You can also try `movement` out on some [sample data](target-sample-data) +included with the package. + + +(target-loading-pose-tracks)= ## Loading pose tracks -The loading functionalities are provided by the +The pose tracks loading functionalities are provided by the {mod}`movement.io.load_poses` module, which can be imported as follows: ```python from movement.io import load_poses ``` -Depending on the source sofrware, one of the following functions can be used. +To read a pose tracks file into a [movement poses dataset](target-poses-and-bboxes-dataset), we provide specific functions for each of the supported formats. We additionally provide a more general `from_numpy()` method, with which we can build a [movement poses dataset](target-poses-and-bboxes-dataset) from a set of NumPy arrays. ::::{tab-set} :::{tab-item} SLEAP -Load from [SLEAP analysis files](sleap:tutorials/analysis) (.h5, recommended), -or from .slp files (experimental): +To load [SLEAP analysis files](sleap:tutorials/analysis) in .h5 format (recommended): ```python ds = load_poses.from_sleap_file("/path/to/file.analysis.h5", fps=30) @@ -41,9 +46,7 @@ ds = load_poses.from_file( "/path/to/file.analysis.h5", source_software="SLEAP", fps=30 ) ``` - -You can also load from SLEAP .slp files in the same way, but there are caveats -to that approach (see notes in {func}`movement.io.load_poses.from_sleap_file`). +To load [SLEAP analysis files](sleap:tutorials/analysis) in .slp format (experimental, see notes in {func}`movement.io.load_poses.from_sleap_file`): ```python ds = load_poses.from_sleap_file("/path/to/file.predictions.slp", fps=30) @@ -52,7 +55,7 @@ ds = load_poses.from_sleap_file("/path/to/file.predictions.slp", fps=30) :::{tab-item} DeepLabCut -Load from DeepLabCut files (.h5): +To load DeepLabCut files in .h5 format: ```python ds = load_poses.from_dlc_file("/path/to/file.h5", fps=30) @@ -62,8 +65,7 @@ ds = load_poses.from_file( ) ``` -You may also load .csv files -(assuming they are formatted as DeepLabCut expects them): +To load DeepLabCut files in .csv format: ```python ds = load_poses.from_dlc_file("/path/to/file.csv", fps=30) ``` @@ -71,7 +73,7 @@ ds = load_poses.from_dlc_file("/path/to/file.csv", fps=30) :::{tab-item} LightningPose -Load from LightningPose files (.csv): +To load LightningPose files in .csv format: ```python ds = load_poses.from_lp_file("/path/to/file.analysis.csv", fps=30) @@ -82,23 +84,91 @@ ds = load_poses.from_file( ``` ::: +:::{tab-item} From NumPy + +In the example below, we create random position data for two individuals, ``Alice`` and ``Bob``, +with three keypoints each: ``snout``, ``centre``, and ``tail_base``. These keypoints are tracked in 2D space for 100 frames, at 30 fps. The confidence scores are set to 1 for all points. + +```python +import numpy as np + +ds = load_poses.from_numpy( + position_array=np.random.rand((100, 2, 3, 2)), + confidence_array=np.ones((100, 2, 3)), + individual_names=["Alice", "Bob"], + keypoint_names=["snout", "centre", "tail_base"], + fps=30, +) +``` +::: + :::: -The loaded data include the predicted positions for each individual and -keypoint as well as the associated point-wise confidence values, as reported by -the pose estimation software. See the [movement dataset](target-dataset) page -for more information on data structure. +The resulting poses data structure `ds` will include the predicted trajectories for each individual and +keypoint, as well as the associated point-wise confidence values reported by +the pose estimation software. -You can also try `movement` out on some [sample data](target-sample-data) -included with the package. +For more information on the poses data structure, see the [movement poses dataset](target-poses-and-bboxes-dataset) page. + + +(target-loading-bbox-tracks)= +## Loading bounding boxes' tracks +To load bounding boxes' tracks into a [movement bounding boxes dataset](target-poses-and-bboxes-dataset), we need the functions from the +{mod}`movement.io.load_bboxes` module. This module can be imported as: + +```python +from movement.io import load_bboxes +``` + +We currently support loading bounding boxes' tracks in the VGG Image Annotator (VIA) format only. However, like in the poses datasets, we additionally provide a `from_numpy()` method, with which we can build a [movement bounding boxes dataset](target-poses-and-bboxes-dataset) from a set of NumPy arrays. + +::::{tab-set} +:::{tab-item} VGG Image Annotator + +To load a VIA tracks .csv file: +```python +ds = load_bboxes.from_via_tracks_file("path/to/file.csv", fps=30) + +# or equivalently +ds = load_bboxes.from_file( + "path/to/file.csv", + source_software="VIA-tracks", + fps=30, +) +``` +::: + +:::{tab-item} From NumPy + +In the example below, we create random position data for two bounding boxes, ``id_0`` and ``id_1``, +both with the same width (40 pixels) and height (30 pixels). These are tracked in 2D space for 100 frames, which will be numbered in the resulting dataset from 0 to 99. The confidence score for all bounding boxes is set to 0.5. + +```python +import numpy as np + +ds = load_bboxes.from_numpy( + position_array=np.random.rand(100, 2, 2), + shape_array=np.ones((100, 2, 2)) * [40, 30], + confidence_array=np.ones((100, 2)) * 0.5, + individual_names=["id_0", "id_1"] +) +``` +::: + +:::: + +The resulting data structure `ds` will include the centroid trajectories for each tracked bounding box, the boxes' widths and heights, and their associated confidence values if provided. -(target-saving)= +For more information on the bounding boxes data structure, see the [movement bounding boxes dataset](target-poses-and-bboxes-dataset) page. + + +(target-saving-pose-tracks)= ## Saving pose tracks -[movement datasets](target-dataset) can be saved as a variety of +[movement poses datasets](target-poses-and-bboxes-dataset) can be saved in a variety of formats, including DeepLabCut-style files (.h5 or .csv) and [SLEAP-style analysis files](sleap:tutorials/analysis) (.h5). -First import the {mod}`movement.io.save_poses` module: +To export pose tracks from `movement`, first import the {mod}`movement.io.save_poses` module: ```python from movement.io import save_poses @@ -110,7 +180,7 @@ Then, depending on the desired format, use one of the following functions: ::::{tab-item} SLEAP -Save to SLEAP-style analysis files (.h5): +To save as a SLEAP analysis file in .h5 format: ```python save_poses.to_sleap_analysis_file(ds, "/path/to/file.h5") ``` @@ -129,7 +199,7 @@ each attribute and data variable represents, see the ::::{tab-item} DeepLabCut -Save to DeepLabCut-style files (.h5 or .csv): +To save as a DeepLabCut file, in .h5 or .csv format: ```python save_poses.to_dlc_file(ds, "/path/to/file.h5") # preferred format save_poses.to_dlc_file(ds, "/path/to/file.csv") @@ -143,13 +213,13 @@ save the data as separate single-animal DeepLabCut-style files. ::::{tab-item} LightningPose -Save to LightningPose files (.csv). +To save as a LightningPose file in .csv format: ```python save_poses.to_lp_file(ds, "/path/to/file.csv") ``` :::{note} -Because LightningPose saves pose estimation outputs in the same format as single-animal -DeepLabCut projects, the above command is equivalent to: +Because LightningPose follows the single-animal +DeepLabCut .csv format, the above command is equivalent to: ```python save_poses.to_dlc_file(ds, "/path/to/file.csv", split_individuals=True) ``` @@ -157,3 +227,33 @@ save_poses.to_dlc_file(ds, "/path/to/file.csv", split_individuals=True) :::: ::::: + + +(target-saving-bboxes-tracks)= +## Saving bounding boxes' tracks + +We currently do not provide explicit methods to export a movement bounding boxes dataset in a specific format. However, you can easily save the bounding boxes' trajectories to a .csv file using the standard Python library `csv`. + +Here is an example of how you can save a bounding boxes dataset to a .csv file: + +```python +# define name for output csv file +file = 'tracking_output.csv" + +# open the csv file in write mode +with open(filepath, mode="w", newline="") as file: + writer = csv.writer(file) + + # write the header + writer.writerow(["frame_idx", "bbox_ID", "x", "y", "width", "height", "confidence"]) + + # write the data + for individual in ds.individuals.data: + for frame in ds.time.data: + x, y = ds.position.sel(time=frame, individuals=individual).data + width, height = ds.shape.sel(time=frame, individuals=individual).data + confidence = ds.confidence.sel(time=frame, individuals=individual).data + writer.writerow([frame, individual, x, y, width, height, confidence]) + +``` +Alternatively, we can convert the `movement` bounding boxes' dataset to a pandas DataFrame with the {func}`.xarray.DataArray.to_dataframe()` method, wrangle the dataframe as required, and then apply the {func}`.pandas.DataFrame.to_csv()` method to save the data as a .csv file. diff --git a/_sources/getting_started/installation.md.txt b/_sources/getting_started/installation.md.txt index d1937944..404acceb 100644 --- a/_sources/getting_started/installation.md.txt +++ b/_sources/getting_started/installation.md.txt @@ -1,68 +1,62 @@ (target-installation)= # Installation -## Create a conda environment - +## Install the package :::{admonition} Use a conda environment :class: note -We recommend you install movement inside a [conda](conda:) -or [mamba](mamba:) environment, to avoid dependency conflicts with other packages. -In the following we assume you have `conda` installed, -but the same commands will also work with `mamba`/`micromamba`. +To avoid dependency conflicts with other packages, it is best practice to install Python packages within a virtual environment. +We recommend using [conda](conda:) or [mamba](mamba:) to create and manage this environment, as they simplify the installation process. +The following instructions assume that you have conda installed, but the same commands will also work with `mamba`/`micromamba`. ::: -First, create and activate an environment with some prerequisites. -You can call your environment whatever you like, we've used `movement-env`. +### Users +To install movement in a new environment, follow one of the options below. +We will use `movement-env` as the environment name, but you can choose any name you prefer. +::::{tab-set} +:::{tab-item} Conda +Create and activate an environment with movement installed: ```sh -conda create -n movement-env -c conda-forge python=3.11 pytables +conda create -n movement-env -c conda-forge movement conda activate movement-env ``` - -## Install the package - -Then install the `movement` package as described below. - -::::{tab-set} - -:::{tab-item} Users -To get the latest release from PyPI: - +::: +:::{tab-item} Pip +Create and activate an environment with some prerequisites: ```sh -pip install movement +conda create -n movement-env -c conda-forge python=3.11 pytables +conda activate movement-env ``` -If you have an older version of `movement` installed in the same environment, -you can update to the latest version with: - +Install the latest movement release from PyPI: ```sh -pip install --upgrade movement +pip install movement ``` ::: +:::: -:::{tab-item} Developers -To get the latest development version, clone the -[GitHub repository](movement-github:) -and then run from inside the repository: +### Developers +If you are a developer looking to contribute to movement, please refer to our [contributing guide](target-contributing) for detailed setup instructions and guidelines. +## Check the installation +To verify that the installation was successful, run (with `movement-env` activated): ```sh -pip install -e .[dev] # works on most shells -pip install -e '.[dev]' # works on zsh (the default shell on macOS) +movement info ``` +You should see a printout including the version numbers of movement +and some of its dependencies. -This will install the package in editable mode, including all `dev` dependencies. -Please see the [contributing guide](target-contributing) for more information. -::: - -:::: - -## Check the installation - -To verify that the installation was successful, you can run the following -command (with the `movement-env` activated): +## Update the package +To update movement to the latest version, we recommend installing it in a new environment, +as this prevents potential compatibility issues caused by changes in dependency versions. +To uninstall an existing environment named `movement-env`: ```sh -movement info +conda env remove -n movement-env ``` - -You should see a printout including the version numbers of `movement` -and some of its dependencies. +:::{tip} +If you are unsure about the environment name, you can get a list of the environments on your system with: +```sh +conda env list +``` +::: +Once the environment has been removed, you can create a new one following the [installation instructions](#install-the-package) above. diff --git a/_sources/getting_started/movement_dataset.md.txt b/_sources/getting_started/movement_dataset.md.txt index 9c85adc6..6b2ef5e9 100644 --- a/_sources/getting_started/movement_dataset.md.txt +++ b/_sources/getting_started/movement_dataset.md.txt @@ -1,92 +1,199 @@ -(target-dataset)= -# The movement dataset +(target-poses-and-bboxes-dataset)= +# The movement datasets -When you load predicted pose tracks into `movement`, they are represented -as an {class}`xarray.Dataset` object, which is a container for multiple data -arrays. Each array is in turn represented as an {class}`xarray.DataArray` -object, which you can think of as a multi-dimensional {class}`numpy.ndarray` +In `movement`, poses or bounding boxes' tracks are represented +as an {class}`xarray.Dataset` object. + +An {class}`xarray.Dataset` object is a container for multiple arrays. Each array is an {class}`xarray.DataArray` object holding different aspects of the collected data (position, time, confidence scores...). You can think of a {class}`xarray.DataArray` object as a multi-dimensional {class}`numpy.ndarray` with pandas-style indexing and labelling. -So, a `movement` dataset is simply an {class}`xarray.Dataset` with a specific -structure to represent pose tracks, associated confidence scores and relevant -metadata. Each dataset consists of **data variables**, **dimensions**, -**coordinates** and **attributes**. +So a `movement` dataset is simply an {class}`xarray.Dataset` with a specific +structure to represent pose tracks or bounding boxes' tracks. Because pose data and bounding boxes data are somewhat different, `movement` provides two types of datasets: `poses` datasets and `bboxes` datasets. + +To discuss the specifics of both types of `movement` datasets, it is useful to clarify some concepts such as **data variables**, **dimensions**, +**coordinates** and **attributes**. In the next section, we will describe these concepts and the `movement` datasets' structure in some detail. -In the next section, we will describe the -structure of a `movement` dataset in some detail. To learn more about `xarray` data structures in general, see the relevant [documentation](xarray:user-guide/data-structures.html). ## Dataset structure -![](../_static/dataset_structure.png) +```{figure} ../_static/dataset_structure.png +:alt: movement dataset structure + +An {class}`xarray.Dataset` is a collection of several data arrays that share some dimensions. The schematic shows the data arrays that make up the `poses` and `bboxes` datasets in `movement`. +``` + +The structure of a `movement` dataset `ds` can be easily inspected by simply +printing it. -You can always inspect the structure of a `movement` dataset `ds` by simply -printing it: +::::{tab-set} + +:::{tab-item} Poses dataset +To inspect a sample poses dataset, we can run: ```python -ds = load_poses.from_dlc_file("/path/to/file.h5", fps=30) +from movement import sample_data + +ds = sample_data.fetch_dataset( + "SLEAP_three-mice_Aeon_proofread.analysis.h5", +) print(ds) ``` -If you are working in a Jupyter notebook, you can also view an interactive -representation of the dataset by typing its name - e.g. `ds` - in a cell. + +and we would obtain an output such as: +``` + Size: 27kB +Dimensions: (time: 601, individuals: 3, keypoints: 1, space: 2) +Coordinates: + * time (time) float64 5kB 0.0 0.02 0.04 0.06 ... 11.96 11.98 12.0 + * individuals (individuals) Size: 19kB +Dimensions: 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justify-content: space-between; } + +/* Disable decoration for all but movement backrefs */ +a[class^="sphx-glr-backref-module-"], +a[class^="sphx-glr-backref-type-"] { + text-decoration: none; +} +a[class^="sphx-glr-backref-module-movement"] { + text-decoration: underline; +} diff --git a/_static/dataset_structure.png b/_static/dataset_structure.png index 4e6a17d9..13506196 100644 Binary files a/_static/dataset_structure.png and b/_static/dataset_structure.png differ diff --git a/_static/documentation_options.js b/_static/documentation_options.js index 07da1489..c65c0345 100644 --- a/_static/documentation_options.js +++ b/_static/documentation_options.js @@ -1,5 +1,5 @@ const DOCUMENTATION_OPTIONS = { - VERSION: '0.0.19', + VERSION: '0.0.20', LANGUAGE: 'en', COLLAPSE_INDEX: false, BUILDER: 'html', diff --git a/_static/movement_overview.png b/_static/movement_overview.png index 8af12daa..33c5927a 100644 Binary files a/_static/movement_overview.png and b/_static/movement_overview.png differ diff --git a/_static/sg_gallery.css b/_static/sg_gallery.css index 72227837..9bcd33c8 100644 --- a/_static/sg_gallery.css +++ b/_static/sg_gallery.css @@ -178,23 +178,44 @@ thumbnail with its default link Background color */ max-height: 112px; max-width: 160px; } -.sphx-glr-thumbcontainer[tooltip]:hover:after { - background: var(--sg-tooltip-background); + +.sphx-glr-thumbcontainer[tooltip]::before { + content: ""; + position: absolute; + pointer-events: none; + top: 0; + left: 0; + width: 100%; + height: 100%; + z-index: 97; + background-color: var(--sg-tooltip-background); + backdrop-filter: blur(3px); + opacity: 0; + transition: opacity 0.3s; +} + +.sphx-glr-thumbcontainer[tooltip]:hover::before { + opacity: 1; +} + +.sphx-glr-thumbcontainer[tooltip]:hover::after { -webkit-border-radius: 4px; -moz-border-radius: 4px; border-radius: 4px; color: var(--sg-tooltip-foreground); content: attr(tooltip); - padding: 10px; + padding: 10px 10px 5px; z-index: 98; width: 100%; - height: 100%; + max-height: 100%; position: absolute; pointer-events: none; top: 0; box-sizing: border-box; overflow: hidden; - backdrop-filter: blur(3px); + display: -webkit-box; + -webkit-box-orient: vertical; + -webkit-line-clamp: 6; } .sphx-glr-script-out { @@ -283,6 +304,10 @@ div.sphx-glr-download a:hover { background-color: var(--sg-download-a-hover-background-color); } +div.sphx-glr-sidebar-item img { + max-height: 20px; +} + .sphx-glr-example-title:target::before { display: block; content: ""; diff --git a/_static/sphinx-design.min.css b/_static/sphinx-design.min.css index a325746f..860c36da 100644 --- a/_static/sphinx-design.min.css +++ b/_static/sphinx-design.min.css @@ -1 +1 @@ -.sd-bg-primary{background-color:var(--sd-color-primary) !important}.sd-bg-text-primary{color:var(--sd-color-primary-text) !important}button.sd-bg-primary:focus,button.sd-bg-primary:hover{background-color:var(--sd-color-primary-highlight) 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a/api/movement.analysis.kinematics.compute_acceleration.html +++ b/api/movement.analysis.kinematics.compute_acceleration.html @@ -28,20 +28,20 @@ - + - + - + - + @@ -128,7 +128,7 @@ -

    movement v0.0.19

    +

    movement v0.0.20

    @@ -368,26 +368,6 @@ aria-label="Section Navigation">

    Section Navigation

      -
    • movement.move_accessor
      -
      • -
    • movement.io.load_poses
      -
      • -
    • movement.io.save_poses
      -
    • movement.filtering
      • -
    • movement.analysis.kinematics
        -
      • compute_acceleration
        • -
      • compute_displacement
        • -
      • compute_velocity
        • +
      • movement.move_accessor
        • -
      • movement.utils.vector
          -
        • cart2pol
          • -
        • pol2cart
          • +
        • movement.sample_data
        • movement.utils.logging
          • -
        • movement.sample_data
            -
          • fetch_dataset
            • -
          • fetch_dataset_paths
            • -
          • list_datasets
            • +
          • movement.utils.vector
            +
            • +
          • movement.analysis.kinematics
            +
            • +
          • movement.validators.datasets
          • movement.validators.files
            • -
          • movement.validators.datasets
            @@ -500,21 +509,37 @@

            compute_acceleration
            movement.analysis.kinematics.compute_acceleration(data)[source]#
            -

            Compute acceleration in cartesian (x,y) coordinates.

            -

            Acceleration represents the second derivative of position for each keypoint -and individual across time. It’s computed using numerical differentiation -and assumes equidistant time spacing.

            +

            Compute acceleration array in cartesian coordinates.

            +

            The acceleration array is the second time-derivative of the +position array. It is computed by applying the second-order accurate +central differences method on the velocity array.

            Parameters:
            -

            data (xarray.DataArray) – The input data containing time as a dimension.

            +

            data (xarray.DataArray) – The input data array containing position vectors in cartesian +coordinates, with``time`` as a dimension.

            Returns:
            -

            An xarray DataArray containing the computed acceleration.

            +

            An xarray DataArray containing acceleration vectors in cartesian +coordinates.

            Return type:
            -

            xarray.DataArray

            +

            xarray.DataArray

            +
            +
            +

            Notes

            +

            For the position array of a poses dataset, the acceleration +array will hold the acceleration vectors for every keypoint and every +individual.

            +

            For the position array of a bboxes dataset, the acceleration +array will hold the acceleration vectors for the centroid of every +individual bounding box.

            +
            +

            See also

            +
            +
            xarray.DataArray.differentiate()

            The underlying method used.

            +
            @@ -600,7 +625,7 @@

            compute_acceleration

            - Created using Sphinx 7.4.5. + Created using Sphinx 8.0.2.

            diff --git a/api/movement.analysis.kinematics.compute_displacement.html b/api/movement.analysis.kinematics.compute_displacement.html index dde2111b..0a81035b 100644 --- a/api/movement.analysis.kinematics.compute_displacement.html +++ b/api/movement.analysis.kinematics.compute_displacement.html @@ -28,20 +28,20 @@ - + - + - + - + @@ -128,7 +128,7 @@ -

            movement v0.0.19

            +

            movement v0.0.20

            @@ -368,26 +368,6 @@ aria-label="Section Navigation">

            Section Navigation

            @@ -368,26 +368,6 @@ aria-label="Section Navigation">

            Section Navigation

              -
            • movement.move_accessor
              -
              • -
            • movement.io.load_poses
              -
              • -
            • movement.io.save_poses
              -
            • movement.filtering
              • -
            • movement.analysis.kinematics
                -
              • compute_acceleration
                • -
              • compute_displacement
                • -
              • compute_velocity
                • +
              • movement.move_accessor
                • -
              • movement.utils.vector
                  -
                • cart2pol
                  • -
                • pol2cart
                  • +
                • movement.sample_data
                • movement.utils.logging
                  • -
                • movement.sample_data
                    -
                  • fetch_dataset
                    • -
                  • fetch_dataset_paths
                    • -
                  • list_datasets
                    • +
                  • movement.utils.vector
                    +
                    • +
                  • movement.analysis.kinematics
                    +
                    • +
                  • movement.validators.datasets
                  • movement.validators.files
                    • -
                  • movement.validators.datasets
                    @@ -500,7 +509,7 @@

                    from_dlc_file
                    movement.io.load_poses.from_dlc_file(file_path, fps=None)[source]#
                    -

                    Create a movement dataset from a DeepLabCut file.

                    +

                    Create a movement poses dataset from a DeepLabCut file.

                    Parameters:
                    @@ -612,7 +621,7 @@

                    from_dlc_file

                    - Created using Sphinx 7.4.5. + Created using Sphinx 8.0.2.

                    diff --git a/api/movement.io.load_poses.from_dlc_style_df.html b/api/movement.io.load_poses.from_dlc_style_df.html index 1c8d83ac..6bc9b561 100644 --- a/api/movement.io.load_poses.from_dlc_style_df.html +++ b/api/movement.io.load_poses.from_dlc_style_df.html @@ -28,20 +28,20 @@ - + - + - + - + @@ -128,7 +128,7 @@ -

                    movement v0.0.19

                    +

                    movement v0.0.20

                    @@ -368,26 +368,6 @@ aria-label="Section Navigation">

                    Section Navigation

                      -
                    • movement.move_accessor
                      -
                      • -
                    • movement.io.load_poses
                      -
                      • -
                    • movement.io.save_poses
                      -
                    • movement.filtering
                      • -
                    • movement.analysis.kinematics
                        -
                      • compute_acceleration
                        • -
                      • compute_displacement
                        • -
                      • compute_velocity
                        • +
                      • movement.move_accessor
                        • -
                      • movement.utils.vector
                          -
                        • cart2pol
                          • -
                        • pol2cart
                          • +
                        • movement.sample_data
                        • movement.utils.logging
                          • -
                        • movement.sample_data
                            -
                          • fetch_dataset
                            • -
                          • fetch_dataset_paths
                            • -
                          • list_datasets
                            • +
                          • movement.utils.vector
                            +
                            • +
                          • movement.analysis.kinematics
                            +
                            • +
                          • movement.validators.datasets
                          • movement.validators.files
                            • -
                          • movement.validators.datasets
                            @@ -500,7 +509,7 @@

                            from_dlc_style_df
                            movement.io.load_poses.from_dlc_style_df(df, fps=None, source_software='DeepLabCut')[source]#
                            -

                            Create a movement dataset from a DeepLabCut-style DataFrame.

                            +

                            Create a movement poses dataset from a DeepLabCut-style DataFrame.

                            Parameters:

                            Notes

                            @@ -617,7 +626,7 @@

                            from_dlc_style_df

                            - Created using Sphinx 7.4.5. + Created using Sphinx 8.0.2.

                            diff --git a/api/movement.io.load_poses.from_file.html b/api/movement.io.load_poses.from_file.html index 02aafbcf..2ce531c6 100644 --- a/api/movement.io.load_poses.from_file.html +++ b/api/movement.io.load_poses.from_file.html @@ -28,20 +28,20 @@ - + - + - + - + @@ -128,7 +128,7 @@ -

                            movement v0.0.19

                            +

                            movement v0.0.20

                            @@ -368,26 +368,6 @@ aria-label="Section Navigation">

                            Section Navigation

                              -
                            • movement.move_accessor
                              -
                              • -
                            • movement.io.load_poses
                              -
                              • -
                            • movement.io.save_poses
                              -
                            • movement.filtering
                              • -
                            • movement.analysis.kinematics
                                -
                              • compute_acceleration
                                • -
                              • compute_displacement
                                • -
                              • compute_velocity
                                • +
                              • movement.move_accessor
                                • -
                              • movement.utils.vector
                                  -
                                • cart2pol
                                  • -
                                • pol2cart
                                  • +
                                • movement.sample_data
                                • movement.utils.logging
                                  • -
                                • movement.sample_data
                                    -
                                  • fetch_dataset
                                    • -
                                  • fetch_dataset_paths
                                    • -
                                  • list_datasets
                                    • +
                                  • movement.utils.vector
                                    +
                                    • +
                                  • movement.analysis.kinematics
                                    +
                                    • +
                                  • movement.validators.datasets
                                  • movement.validators.files
                                    • -
                                  • movement.validators.datasets
                                    @@ -500,7 +509,7 @@

                                    from_file
                                    movement.io.load_poses.from_file(file_path, source_software, fps=None)[source]#
                                    -

                                    Create a movement dataset from any supported file.

                                    +

                                    Create a movement poses dataset from any supported file.

                                    Parameters:
                                    @@ -618,7 +627,7 @@

                                    from_file

                                    - Created using Sphinx 7.4.5. + Created using Sphinx 8.0.2.

                                    diff --git a/api/movement.io.load_poses.from_lp_file.html b/api/movement.io.load_poses.from_lp_file.html index f8099057..67db7fba 100644 --- a/api/movement.io.load_poses.from_lp_file.html +++ b/api/movement.io.load_poses.from_lp_file.html @@ -28,20 +28,20 @@ - + - + - + - + @@ -128,7 +128,7 @@ -

                                    movement v0.0.19

                                    +

                                    movement v0.0.20

                                    @@ -368,26 +368,6 @@ aria-label="Section Navigation">

                                    Section Navigation

                                      -
                                    • movement.move_accessor
                                      -
                                      • -
                                    • movement.io.load_poses
                                      -
                                      • -
                                    • movement.io.save_poses
                                      -
                                    • movement.filtering
                                      • -
                                    • movement.analysis.kinematics
                                        -
                                      • compute_acceleration
                                        • -
                                      • compute_displacement
                                        • -
                                      • compute_velocity
                                        • +
                                      • movement.move_accessor
                                        • -
                                      • movement.utils.vector
                                          -
                                        • cart2pol
                                          • -
                                        • pol2cart
                                          • +
                                        • movement.sample_data
                                        • movement.utils.logging
                                          • -
                                        • movement.sample_data
                                            -
                                          • fetch_dataset
                                            • -
                                          • fetch_dataset_paths
                                            • -
                                          • list_datasets
                                            • +
                                          • movement.utils.vector
                                            +
                                            • +
                                          • movement.analysis.kinematics
                                            +
                                            • +
                                          • movement.validators.datasets
                                          • movement.validators.files
                                            • -
                                          • movement.validators.datasets
                                            @@ -500,7 +509,7 @@

                                            from_lp_file
                                            movement.io.load_poses.from_lp_file(file_path, fps=None)[source]#
                                            -

                                            Create a movement dataset from a LightningPose file.

                                            +

                                            Create a movement poses dataset from a LightningPose file.

                                            Parameters:

                                            Examples

                                            @@ -607,7 +616,7 @@

                                            from_lp_file

                                            - Created using Sphinx 7.4.5. + Created using Sphinx 8.0.2.

                                            diff --git a/api/movement.io.load_poses.from_numpy.html b/api/movement.io.load_poses.from_numpy.html index cab9fbe2..0fb70e9e 100644 --- a/api/movement.io.load_poses.from_numpy.html +++ b/api/movement.io.load_poses.from_numpy.html @@ -28,20 +28,20 @@ - + - + - + - + @@ -128,7 +128,7 @@ -

                                            movement v0.0.19

                                            +

                                            movement v0.0.20

                                            @@ -368,26 +368,6 @@ aria-label="Section Navigation">

                                            Section Navigation

                                              -
                                            • movement.move_accessor
                                              -
                                              • -
                                            • movement.io.load_poses
                                              -
                                              • -
                                            • movement.io.save_poses
                                              -
                                            • movement.filtering
                                              • -
                                            • movement.analysis.kinematics
                                                -
                                              • compute_acceleration
                                                • -
                                              • compute_displacement
                                                • -
                                              • compute_velocity
                                                • +
                                              • movement.move_accessor
                                                • -
                                              • movement.utils.vector
                                                  -
                                                • cart2pol
                                                  • -
                                                • pol2cart
                                                  • +
                                                • movement.sample_data
                                                • movement.utils.logging
                                                  • -
                                                • movement.sample_data
                                                    -
                                                  • fetch_dataset
                                                    • -
                                                  • fetch_dataset_paths
                                                    • -
                                                  • list_datasets
                                                    • +
                                                  • movement.utils.vector
                                                    +
                                                    • +
                                                  • movement.analysis.kinematics
                                                    +
                                                    • +
                                                  • movement.validators.datasets
                                                  • movement.validators.files
                                                    • -
                                                  • movement.validators.datasets
                                                    @@ -500,16 +509,16 @@

                                                    from_numpy
                                                    movement.io.load_poses.from_numpy(position_array, confidence_array=None, individual_names=None, keypoint_names=None, fps=None, source_software=None)[source]#
                                                    -

                                                    Create a movement dataset from NumPy arrays.

                                                    +

                                                    Create a movement poses dataset from NumPy arrays.

                                                    Parameters:

                                                    • position_array (np.ndarray) – Array of shape (n_frames, n_individuals, n_keypoints, n_space) containing the poses. It will be converted to a -xarray.DataArray object named “position”.

                                                      • +xarray.DataArray object named “position”.

                                                    • confidence_array (np.ndarray, optional) – Array of shape (n_frames, n_individuals, n_keypoints) containing the point-wise confidence scores. It will be converted to a -xarray.DataArray object named “confidence”. +xarray.DataArray object named “confidence”. If None (default), the scores will be set to an array of NaNs.

                                                    • individual_names (list of str, optional) – List of unique names for the individuals in the video. If None (default), the individuals will be named “individual_0”, @@ -528,7 +537,7 @@

                                                      from_numpyReturn type: -

                                                      xarray.Dataset

                                                      +

                                                      xarray.Dataset

                                                    Examples

                                                    @@ -632,7 +641,7 @@

                                                    from_numpy

                                                    - Created using Sphinx 7.4.5. + Created using Sphinx 8.0.2.

                                                    diff --git a/api/movement.io.load_poses.from_sleap_file.html b/api/movement.io.load_poses.from_sleap_file.html index d2a62611..a1b2ea3b 100644 --- a/api/movement.io.load_poses.from_sleap_file.html +++ b/api/movement.io.load_poses.from_sleap_file.html @@ -28,20 +28,20 @@ - + - + - + - + @@ -128,7 +128,7 @@ -

                                                    movement v0.0.19

                                                    +

                                                    movement v0.0.20

                                                    @@ -368,26 +368,6 @@ aria-label="Section Navigation">

                                                    Section Navigation

                                                      -
                                                    • movement.move_accessor
                                                      -
                                                      • -
                                                    • movement.io.load_poses
                                                      -
                                                      • -
                                                    • movement.io.save_poses
                                                      -
                                                    • movement.filtering
                                                      • -
                                                    • movement.analysis.kinematics
                                                        -
                                                      • compute_acceleration
                                                        • -
                                                      • compute_displacement
                                                        • -
                                                      • compute_velocity
                                                        • +
                                                      • movement.move_accessor
                                                        • -
                                                      • movement.utils.vector
                                                          -
                                                        • cart2pol
                                                          • -
                                                        • pol2cart
                                                          • +
                                                        • movement.sample_data
                                                        • movement.utils.logging
                                                          • -
                                                        • movement.sample_data
                                                            -
                                                          • fetch_dataset
                                                            • -
                                                          • fetch_dataset_paths
                                                            • -
                                                          • list_datasets
                                                            • +
                                                          • movement.utils.vector
                                                            +
                                                            • +
                                                          • movement.analysis.kinematics
                                                            +
                                                            • +
                                                          • movement.validators.datasets
                                                          • movement.validators.files
                                                            • -
                                                          • movement.validators.datasets
                                                            @@ -500,7 +509,7 @@

                                                            from_sleap_file
                                                            movement.io.load_poses.from_sleap_file(file_path, fps=None)[source]#
                                                            -

                                                            Create a movement dataset from a SLEAP file.

                                                            +

                                                            Create a movement poses dataset from a SLEAP file.

                                                            Parameters:

                                                            Notes

                                                            @@ -644,7 +653,7 @@

                                                            from_sleap_file

                                                            - Created using Sphinx 7.4.5. + Created using Sphinx 8.0.2.

                                                            diff --git a/api/movement.io.load_poses.html b/api/movement.io.load_poses.html index e69273cf..69586634 100644 --- a/api/movement.io.load_poses.html +++ b/api/movement.io.load_poses.html @@ -28,20 +28,20 @@ - + - + - + - + @@ -52,7 +52,7 @@ - + @@ -128,7 +128,7 @@ -

                                                            movement v0.0.19

                                                            +

                                                            movement v0.0.20

                                                            @@ -368,26 +368,6 @@ aria-label="Section Navigation">

                                                            Section Navigation

                                                              -
                                                            • movement.move_accessor
                                                              -
                                                              • -
                                                            • movement.io.load_poses
                                                              -
                                                              • -
                                                            • movement.io.save_poses
                                                              -
                                                            • movement.filtering
                                                              • -
                                                            • movement.analysis.kinematics
                                                                -
                                                              • compute_acceleration
                                                                • -
                                                              • compute_displacement
                                                                • -
                                                              • compute_velocity
                                                                • +
                                                              • movement.move_accessor
                                                                • -
                                                              • movement.utils.vector
                                                                  -
                                                                • cart2pol
                                                                  • -
                                                                • pol2cart
                                                                  • +
                                                                • movement.sample_data
                                                                • movement.utils.logging
                                                                  • -
                                                                • movement.sample_data
                                                                    -
                                                                  • fetch_dataset
                                                                    • -
                                                                  • fetch_dataset_paths
                                                                    • -
                                                                  • list_datasets
                                                                    • +
                                                                  • movement.utils.vector
                                                                    +
                                                                    • +
                                                                  • movement.analysis.kinematics
                                                                    +
                                                                    • +
                                                                  • movement.validators.datasets
                                                                  • movement.validators.files
                                                                    • -
                                                                  • movement.validators.datasets
                                                                    @@ -500,22 +509,22 @@

                                                                    movement.io.load_poses - + - + - + - + - + - +

                                                                    from_dlc_file

                                                                    Create a movement dataset from a DeepLabCut file.

                                                                    Create a movement poses dataset from a DeepLabCut file.

                                                                    from_dlc_style_df

                                                                    Create a movement dataset from a DeepLabCut-style DataFrame.

                                                                    Create a movement poses dataset from a DeepLabCut-style DataFrame.

                                                                    from_file

                                                                    Create a movement dataset from any supported file.

                                                                    Create a movement poses dataset from any supported file.

                                                                    from_lp_file

                                                                    Create a movement dataset from a LightningPose file.

                                                                    Create a movement poses dataset from a LightningPose file.

                                                                    from_numpy

                                                                    Create a movement dataset from NumPy arrays.

                                                                    Create a movement poses dataset from NumPy arrays.

                                                                    from_sleap_file

                                                                    Create a movement dataset from a SLEAP file.

                                                                    Create a movement poses dataset from a SLEAP file.
                                                                    @@ -533,12 +542,12 @@

                                                                    movement.io.load_poses

                                                                    previous

                                                                    -

                                                                    MovementDataset

                                                                    +

                                                                    from_via_tracks_file

                                                                     movement.io.load_poses

                                                                    - Created using Sphinx 7.4.5. + Created using Sphinx 8.0.2.

                                                                    diff --git a/api/movement.io.save_poses.html b/api/movement.io.save_poses.html index a9b4f806..90ded1b5 100644 --- a/api/movement.io.save_poses.html +++ b/api/movement.io.save_poses.html @@ -28,20 +28,20 @@ - + - + - + - + @@ -128,7 +128,7 @@ -

                                                                    movement v0.0.19

                                                                    +

                                                                    movement v0.0.20

                                                                    @@ -368,26 +368,6 @@ aria-label="Section Navigation">

                                                                    Section Navigation

                                                                      -
                                                                    • movement.move_accessor
                                                                      -
                                                                      • -
                                                                    • movement.io.load_poses
                                                                      -
                                                                      • -
                                                                    • movement.io.save_poses
                                                                      -
                                                                    • movement.filtering
                                                                      • -
                                                                    • movement.analysis.kinematics
                                                                        -
                                                                      • compute_acceleration
                                                                        • -
                                                                      • compute_displacement
                                                                        • -
                                                                      • compute_velocity
                                                                        • +
                                                                      • movement.move_accessor
                                                                        • -
                                                                      • movement.utils.vector
                                                                          -
                                                                        • cart2pol
                                                                          • -
                                                                        • pol2cart
                                                                          • +
                                                                        • movement.sample_data
                                                                        • movement.utils.logging
                                                                          • -
                                                                        • movement.sample_data
                                                                            -
                                                                          • fetch_dataset
                                                                            • -
                                                                          • fetch_dataset_paths
                                                                            • -
                                                                          • list_datasets
                                                                            • +
                                                                          • movement.utils.vector
                                                                            +
                                                                            • +
                                                                          • movement.analysis.kinematics
                                                                            +
                                                                            • +
                                                                          • movement.validators.datasets
                                                                          • movement.validators.files
                                                                            • -
                                                                          • movement.validators.datasets
                                                                            @@ -585,7 +594,7 @@

                                                                            movement.io.save_poses

                                                                            - Created using Sphinx 7.4.5. + Created using Sphinx 8.0.2.

                                                                            diff --git a/api/movement.io.save_poses.to_dlc_file.html b/api/movement.io.save_poses.to_dlc_file.html index 27e00586..10d3c3d4 100644 --- a/api/movement.io.save_poses.to_dlc_file.html +++ b/api/movement.io.save_poses.to_dlc_file.html @@ -28,20 +28,20 @@ - + - + - + - + @@ -128,7 +128,7 @@ -

                                                                            movement v0.0.19

                                                                            +

                                                                            movement v0.0.20

                                                                            @@ -368,26 +368,6 @@ aria-label="Section Navigation">

                                                                            Section Navigation

                                                                              -
                                                                            • movement.move_accessor
                                                                              -
                                                                              • -
                                                                            • movement.io.load_poses
                                                                              -
                                                                              • -
                                                                            • movement.io.save_poses
                                                                              -
                                                                            • movement.filtering
                                                                              • -
                                                                            • movement.analysis.kinematics
                                                                                -
                                                                              • compute_acceleration
                                                                                • -
                                                                              • compute_displacement
                                                                                • -
                                                                              • compute_velocity
                                                                                • +
                                                                              • movement.move_accessor
                                                                                • -
                                                                              • movement.utils.vector
                                                                                  -
                                                                                • cart2pol
                                                                                  • -
                                                                                • pol2cart
                                                                                  • +
                                                                                • movement.sample_data
                                                                                • movement.utils.logging
                                                                                  • -
                                                                                • movement.sample_data
                                                                                    -
                                                                                  • fetch_dataset
                                                                                    • -
                                                                                  • fetch_dataset_paths
                                                                                    • -
                                                                                  • list_datasets
                                                                                    • +
                                                                                  • movement.utils.vector
                                                                                    +
                                                                                    • +
                                                                                  • movement.analysis.kinematics
                                                                                    +
                                                                                    • +
                                                                                  • movement.validators.datasets
                                                                                  • movement.validators.files
                                                                                    • -
                                                                                  • movement.validators.datasets
                                                                                    @@ -504,7 +513,7 @@

                                                                                    to_dlc_file
                                                                                    Parameters:
                                                                                      -

                                                                                    • ds (xarray.Dataset) – movement dataset containing pose tracks, confidence scores, +

                                                                                    • ds (xarray.Dataset) – movement dataset containing pose tracks, confidence scores, and associated metadata.

                                                                                    • file_path (pathlib.Path or str) – Path to the file to save the poses to. The file extension must be either .h5 (recommended) or .csv.

                                                                                      • @@ -624,7 +633,7 @@

                                                                                      to_dlc_file

                                                                                      - Created using Sphinx 7.4.5. + Created using Sphinx 8.0.2.

                                                                                      diff --git a/api/movement.io.save_poses.to_dlc_style_df.html b/api/movement.io.save_poses.to_dlc_style_df.html index 50e5dc0b..836bc55d 100644 --- a/api/movement.io.save_poses.to_dlc_style_df.html +++ b/api/movement.io.save_poses.to_dlc_style_df.html @@ -28,20 +28,20 @@ - + - + - + - + @@ -128,7 +128,7 @@ -

                                                                                      movement v0.0.19

                                                                                      +

                                                                                      movement v0.0.20

                                                                                      @@ -368,26 +368,6 @@ aria-label="Section Navigation">

                                                                                      Section Navigation

                                                                                        -
                                                                                      • movement.move_accessor
                                                                                        -
                                                                                        • -
                                                                                      • movement.io.load_poses
                                                                                        -
                                                                                        • -
                                                                                      • movement.io.save_poses
                                                                                        -
                                                                                      • movement.filtering
                                                                                        • -
                                                                                      • movement.analysis.kinematics
                                                                                          -
                                                                                        • compute_acceleration
                                                                                          • -
                                                                                        • compute_displacement
                                                                                          • -
                                                                                        • compute_velocity
                                                                                          • +
                                                                                        • movement.move_accessor
                                                                                          • -
                                                                                        • movement.utils.vector
                                                                                            -
                                                                                          • cart2pol
                                                                                            • -
                                                                                          • pol2cart
                                                                                            • +
                                                                                          • movement.sample_data
                                                                                          • movement.utils.logging
                                                                                            • -
                                                                                          • movement.sample_data
                                                                                              -
                                                                                            • fetch_dataset
                                                                                              • -
                                                                                            • fetch_dataset_paths
                                                                                              • -
                                                                                            • list_datasets
                                                                                              • +
                                                                                            • movement.utils.vector
                                                                                              +
                                                                                              • +
                                                                                            • movement.analysis.kinematics
                                                                                              +
                                                                                              • +
                                                                                            • movement.validators.datasets
                                                                                            • movement.validators.files
                                                                                              • -
                                                                                            • movement.validators.datasets
                                                                                              @@ -504,7 +513,7 @@

                                                                                              to_dlc_style_df
                                                                                              Parameters:
                                                                                                -

                                                                                              • ds (xarray.Dataset) – movement dataset containing pose tracks, confidence scores, +

                                                                                              • ds (xarray.Dataset) – movement dataset containing pose tracks, confidence scores, and associated metadata.

                                                                                              • split_individuals (bool, optional) – If True, return a dictionary of DataFrames per individual, with individual names as keys. If False (default), return a single @@ -618,7 +627,7 @@

                                                                                                to_dlc_style_df

                                                                                                - Created using Sphinx 7.4.5. + Created using Sphinx 8.0.2.

                                                                                                diff --git a/api/movement.io.save_poses.to_lp_file.html b/api/movement.io.save_poses.to_lp_file.html index 808ea4fc..167441e1 100644 --- a/api/movement.io.save_poses.to_lp_file.html +++ b/api/movement.io.save_poses.to_lp_file.html @@ -28,20 +28,20 @@ - + - + - + - + @@ -128,7 +128,7 @@ -

                                                                                                movement v0.0.19

                                                                                                +

                                                                                                movement v0.0.20

                                                                                                @@ -368,26 +368,6 @@ aria-label="Section Navigation">

                                                                                                Section Navigation

                                                                                                @@ -626,7 +625,7 @@

                                                                                                to_sleap_analysis_file

                                                                                                - Created using Sphinx 7.4.5. + Created using Sphinx 8.0.2.

                                                                                                diff --git a/api/movement.move_accessor.MovementDataset.html b/api/movement.move_accessor.MovementDataset.html index 3287b0d6..816658e9 100644 --- a/api/movement.move_accessor.MovementDataset.html +++ b/api/movement.move_accessor.MovementDataset.html @@ -28,20 +28,20 @@ - + - + - + - + @@ -51,7 +51,7 @@ - + @@ -128,7 +128,7 @@ -

                                                                                                movement v0.0.19

                                                                                                +

                                                                                                movement v0.0.20

                                                                                                @@ -368,26 +368,6 @@ aria-label="Section Navigation">

                                                                                                Section Navigation

                                                                                                  -
                                                                                                • movement.move_accessor
                                                                                                  -
                                                                                                  • -
                                                                                                • movement.io.load_poses
                                                                                                  -
                                                                                                  • -
                                                                                                • movement.io.save_poses
                                                                                                  -
                                                                                                • movement.filtering
                                                                                                  • -
                                                                                                • movement.analysis.kinematics
                                                                                                    -
                                                                                                  • compute_acceleration
                                                                                                    • -
                                                                                                  • compute_displacement
                                                                                                    • -
                                                                                                  • compute_velocity
                                                                                                    • +
                                                                                                  • movement.move_accessor
                                                                                                    • -
                                                                                                  • movement.utils.vector
                                                                                                      -
                                                                                                    • cart2pol
                                                                                                      • -
                                                                                                    • pol2cart
                                                                                                      • +
                                                                                                    • movement.sample_data
                                                                                                    • movement.utils.logging
                                                                                                      • -
                                                                                                    • movement.sample_data
                                                                                                        -
                                                                                                      • fetch_dataset
                                                                                                        • -
                                                                                                      • fetch_dataset_paths
                                                                                                        • -
                                                                                                      • list_datasets
                                                                                                        • +
                                                                                                      • movement.utils.vector
                                                                                                        +
                                                                                                        • +
                                                                                                      • movement.analysis.kinematics
                                                                                                        +
                                                                                                        • +
                                                                                                      • movement.validators.datasets
                                                                                                      • movement.validators.files
                                                                                                        • -
                                                                                                      • movement.validators.datasets
                                                                                                        @@ -501,10 +510,10 @@

                                                                                                        MovementDataset class movement.move_accessor.MovementDataset(ds)[source]#

                                                                                                        Bases: object

                                                                                                        -

                                                                                                        An xarray.Dataset accessor for pose tracking data.

                                                                                                        -

                                                                                                        A movement dataset is an xarray.Dataset with a specific -structure to represent pose tracks, associated confidence scores and -relevant metadata.

                                                                                                        +

                                                                                                        An xarray.Dataset accessor for movement data.

                                                                                                        +

                                                                                                        A movement dataset is an xarray.Dataset with a specific +structure to represent pose tracks or bounding boxes data, +associated confidence scores and relevant metadata.

                                                                                                        Methods/properties that extend the standard xarray functionality are defined in this class. To avoid conflicts with xarray’s namespace, movement-specific methods are accessed using the move keyword, @@ -512,10 +521,11 @@

                                                                                                        MovementDataset
                                                                                                        dim_names#
                                                                                                        -

                                                                                                        Names of the expected dimensions in the dataset.

                                                                                                        +

                                                                                                        A dictionary with the names of the expected dimensions in the dataset, +for each dataset type ("poses" or "bboxes").

                                                                                                        Type:
                                                                                                        -

                                                                                                        tuple

                                                                                                        +

                                                                                                        dict

                                                                                                        @@ -523,10 +533,11 @@

                                                                                                        MovementDataset
                                                                                                        var_names#
                                                                                                        -

                                                                                                        Names of the expected data variables in the dataset.

                                                                                                        +

                                                                                                        A dictionary with the expected data variables in the dataset, for each +dataset type ("poses" or "bboxes").

                                                                                                        Type:
                                                                                                        -

                                                                                                        tuple

                                                                                                        +

                                                                                                        dict

                                                                                                        @@ -576,7 +587,7 @@

                                                                                                        MovementDatasetReturn type: -

                                                                                                        xarray.DataArray | dict[str, xarray.DataArray]

                                                                                                        +

                                                                                                        xarray.DataArray | dict[str, xarray.DataArray]

                                                                                                        Raises:

                                                                                                        RuntimeError – If the requested function fails to execute.

                                                                                                        @@ -627,7 +638,7 @@

                                                                                                        MovementDataset

                                                                                                        The computed kinematics attribute value.

                                                                                                        Return type:
                                                                                                        -

                                                                                                        xarray.DataArray

                                                                                                        +

                                                                                                        xarray.DataArray

                                                                                                        Raises:

                                                                                                        RuntimeError – If the requested function fails to execute.

                                                                                                        @@ -657,10 +668,14 @@

                                                                                                        MovementDataset -
                                                                                                        Return type:
                                                                                                        -

                                                                                                        None

                                                                                                        +
                                                                                                        Raises:
                                                                                                        +

                                                                                                        ValueError – If the dataset is missing required dimensions, data variables, + or contains invalid poses or bounding boxes data.

                                                                                                        +
                                                                                                        +
                                                                                                        Return type:
                                                                                                        +

                                                                                                        None

                                                                                                        @@ -689,11 +704,11 @@

                                                                                                        MovementDataset

                                                                                                        next

                                                                                                        -

                                                                                                        movement.io.load_poses

                                                                                                        +

                                                                                                        movement.sample_data

                                                                                                         @@ -757,7 +772,7 @@

                                                                                                        MovementDataset

                                                                                                        - Created using Sphinx 7.4.5. + Created using Sphinx 8.0.2.

                                                                                                        diff --git a/api/movement.move_accessor.html b/api/movement.move_accessor.html index 8c6a0b8f..6ab5dcc5 100644 --- a/api/movement.move_accessor.html +++ b/api/movement.move_accessor.html @@ -28,20 +28,20 @@ - + - + - + - + @@ -52,7 +52,7 @@ - + @@ -128,7 +128,7 @@ -

                                                                                                        movement v0.0.19

                                                                                                        +

                                                                                                        movement v0.0.20

                                                                                                        @@ -368,26 +368,6 @@ aria-label="Section Navigation">

                                                                                                        Section Navigation

                                                                                                        Return type:
                                                                                                        -

                                                                                                        xarray.Dataset

                                                                                                        +

                                                                                                        xarray.Dataset

                                                                                                        Examples

                                                                                                        @@ -622,7 +631,7 @@

                                                                                                        fetch_dataset

                                                                                                        - Created using Sphinx 7.4.5. + Created using Sphinx 8.0.2.

                                                                                                        diff --git a/api/movement.sample_data.fetch_dataset_paths.html b/api/movement.sample_data.fetch_dataset_paths.html index 0c9070de..0cffe196 100644 --- a/api/movement.sample_data.fetch_dataset_paths.html +++ b/api/movement.sample_data.fetch_dataset_paths.html @@ -28,20 +28,20 @@ - + - + - + - + @@ -128,7 +128,7 @@ -

                                                                                                        movement v0.0.19

                                                                                                        +

                                                                                                        movement v0.0.20

                                                                                                        @@ -368,26 +368,6 @@ aria-label="Section Navigation">

                                                                                                        Section Navigation

                                                                                                          -
                                                                                                        • movement.move_accessor
                                                                                                          -
                                                                                                          • -
                                                                                                        • movement.io.load_poses
                                                                                                          -
                                                                                                          • -
                                                                                                        • movement.io.save_poses
                                                                                                          -
                                                                                                        • movement.filtering
                                                                                                          • -
                                                                                                        • movement.analysis.kinematics
                                                                                                            -
                                                                                                          • compute_acceleration
                                                                                                            • -
                                                                                                          • compute_displacement
                                                                                                            • -
                                                                                                          • compute_velocity
                                                                                                            • +
                                                                                                          • movement.move_accessor
                                                                                                            • -
                                                                                                          • movement.utils.vector
                                                                                                              -
                                                                                                            • cart2pol
                                                                                                              • -
                                                                                                            • pol2cart
                                                                                                              • +
                                                                                                            • movement.sample_data
                                                                                                            • movement.utils.logging
                                                                                                              • -
                                                                                                            • movement.sample_data
                                                                                                                -
                                                                                                              • fetch_dataset
                                                                                                                • -
                                                                                                              • fetch_dataset_paths
                                                                                                                • -
                                                                                                              • list_datasets
                                                                                                                • +
                                                                                                              • movement.utils.vector
                                                                                                                +
                                                                                                                • +
                                                                                                              • movement.analysis.kinematics
                                                                                                                +
                                                                                                                • +
                                                                                                              • movement.validators.datasets
                                                                                                              • movement.validators.files
                                                                                                                • -
                                                                                                              • movement.validators.datasets
                                                                                                                @@ -631,7 +640,7 @@

                                                                                                                fetch_dataset_paths

                                                                                                                - Created using Sphinx 7.4.5. + Created using Sphinx 8.0.2.

                                                                                                                diff --git a/api/movement.sample_data.html b/api/movement.sample_data.html index bc89d5fb..eaaf09a5 100644 --- a/api/movement.sample_data.html +++ b/api/movement.sample_data.html @@ -28,20 +28,20 @@ - + - + - + - + @@ -52,7 +52,7 @@ - + @@ -128,7 +128,7 @@ -

                                                                                                                movement v0.0.19

                                                                                                                +

                                                                                                                movement v0.0.20

                                                                                                                @@ -368,26 +368,6 @@ aria-label="Section Navigation">

                                                                                                                Section Navigation

                                                                                                                  -
                                                                                                                • movement.move_accessor
                                                                                                                  -
                                                                                                                  • -
                                                                                                                • movement.io.load_poses
                                                                                                                  -
                                                                                                                  • -
                                                                                                                • movement.io.save_poses
                                                                                                                  -
                                                                                                                • movement.filtering
                                                                                                                  • -
                                                                                                                • movement.analysis.kinematics
                                                                                                                    -
                                                                                                                  • compute_acceleration
                                                                                                                    • -
                                                                                                                  • compute_displacement
                                                                                                                    • -
                                                                                                                  • compute_velocity
                                                                                                                    • +
                                                                                                                  • movement.move_accessor
                                                                                                                    • -
                                                                                                                  • movement.utils.vector
                                                                                                                      -
                                                                                                                    • cart2pol
                                                                                                                      • -
                                                                                                                    • pol2cart
                                                                                                                      • +
                                                                                                                    • movement.sample_data
                                                                                                                    • movement.utils.logging
                                                                                                                      • -
                                                                                                                    • movement.sample_data
                                                                                                                        -
                                                                                                                      • fetch_dataset
                                                                                                                        • -
                                                                                                                      • fetch_dataset_paths
                                                                                                                        • -
                                                                                                                      • list_datasets
                                                                                                                        • +
                                                                                                                      • movement.utils.vector
                                                                                                                        +
                                                                                                                        • +
                                                                                                                      • movement.analysis.kinematics
                                                                                                                        +
                                                                                                                        • +
                                                                                                                      • movement.validators.datasets
                                                                                                                      • movement.validators.files
                                                                                                                        • -
                                                                                                                      • movement.validators.datasets
                                                                                                                        @@ -528,12 +537,12 @@

                                                                                                                        movement.sample_data

                                                                                                                        previous

                                                                                                                        -

                                                                                                                        report_nan_values

                                                                                                                        +

                                                                                                                        MovementDataset

                                                                                                                         movement.sample_data

                                                                                                                        - Created using Sphinx 7.4.5. + Created using Sphinx 8.0.2.

                                                                                                                        diff --git a/api/movement.sample_data.list_datasets.html b/api/movement.sample_data.list_datasets.html index c688e8ed..c4decbdd 100644 --- a/api/movement.sample_data.list_datasets.html +++ b/api/movement.sample_data.list_datasets.html @@ -28,20 +28,20 @@ - + - + - + - + @@ -51,7 +51,7 @@ - + @@ -128,7 +128,7 @@ -

                                                                                                                        movement v0.0.19

                                                                                                                        +

                                                                                                                        movement v0.0.20

                                                                                                                        @@ -368,26 +368,6 @@ aria-label="Section Navigation">

                                                                                                                        Section Navigation

                                                                                                                          -
                                                                                                                        • movement.move_accessor
                                                                                                                          -
                                                                                                                          • -
                                                                                                                        • movement.io.load_poses
                                                                                                                          -
                                                                                                                          • -
                                                                                                                        • movement.io.save_poses
                                                                                                                          -
                                                                                                                        • movement.filtering
                                                                                                                          • -
                                                                                                                        • movement.analysis.kinematics
                                                                                                                            -
                                                                                                                          • compute_acceleration
                                                                                                                            • -
                                                                                                                          • compute_displacement
                                                                                                                            • -
                                                                                                                          • compute_velocity
                                                                                                                            • +
                                                                                                                          • movement.move_accessor
                                                                                                                            • -
                                                                                                                          • movement.utils.vector
                                                                                                                              -
                                                                                                                            • cart2pol
                                                                                                                              • -
                                                                                                                            • pol2cart
                                                                                                                              • +
                                                                                                                            • movement.sample_data
                                                                                                                            • movement.utils.logging
                                                                                                                              • -
                                                                                                                            • movement.sample_data
                                                                                                                                -
                                                                                                                              • fetch_dataset
                                                                                                                                • -
                                                                                                                              • fetch_dataset_paths
                                                                                                                                • -
                                                                                                                              • list_datasets
                                                                                                                                • +
                                                                                                                              • movement.utils.vector
                                                                                                                                +
                                                                                                                                • +
                                                                                                                              • movement.analysis.kinematics
                                                                                                                                +
                                                                                                                                • +
                                                                                                                              • movement.validators.datasets
                                                                                                                              • movement.validators.files
                                                                                                                                • -
                                                                                                                              • movement.validators.datasets
                                                                                                                                @@ -533,11 +542,11 @@

                                                                                                                                list_datasets

                                                                                                                                next

                                                                                                                                -

                                                                                                                                movement.validators.files

                                                                                                                                +

                                                                                                                                movement.utils.logging

                                                                                                                                 @@ -594,7 +603,7 @@

                                                                                                                                list_datasets

                                                                                                                                - Created using Sphinx 7.4.5. + Created using Sphinx 8.0.2.

                                                                                                                                diff --git a/api/movement.utils.logging.configure_logging.html b/api/movement.utils.logging.configure_logging.html index fcb8b426..2fe6820c 100644 --- a/api/movement.utils.logging.configure_logging.html +++ b/api/movement.utils.logging.configure_logging.html @@ -28,20 +28,20 @@ - + - + - + - + @@ -128,7 +128,7 @@ -

                                                                                                                                movement v0.0.19

                                                                                                                                +

                                                                                                                                movement v0.0.20

                                                                                                                                @@ -368,26 +368,6 @@ aria-label="Section Navigation">

                                                                                                                                Section Navigation

                                                                                                                                  -
                                                                                                                                • movement.move_accessor
                                                                                                                                  -
                                                                                                                                  • -
                                                                                                                                • movement.io.load_poses
                                                                                                                                  -
                                                                                                                                  • -
                                                                                                                                • movement.io.save_poses
                                                                                                                                  -
                                                                                                                                • movement.filtering
                                                                                                                                  • -
                                                                                                                                • movement.analysis.kinematics
                                                                                                                                    -
                                                                                                                                  • compute_acceleration
                                                                                                                                    • -
                                                                                                                                  • compute_displacement
                                                                                                                                    • -
                                                                                                                                  • compute_velocity
                                                                                                                                    • +
                                                                                                                                  • movement.move_accessor
                                                                                                                                    • -
                                                                                                                                  • movement.utils.vector
                                                                                                                                      -
                                                                                                                                    • cart2pol
                                                                                                                                      • -
                                                                                                                                    • pol2cart
                                                                                                                                      • +
                                                                                                                                    • movement.sample_data
                                                                                                                                    • movement.utils.logging
                                                                                                                                      • -
                                                                                                                                    • movement.sample_data
                                                                                                                                        -
                                                                                                                                      • fetch_dataset
                                                                                                                                        • -
                                                                                                                                      • fetch_dataset_paths
                                                                                                                                        • -
                                                                                                                                      • list_datasets
                                                                                                                                        • +
                                                                                                                                      • movement.utils.vector
                                                                                                                                        +
                                                                                                                                        • +
                                                                                                                                      • movement.analysis.kinematics
                                                                                                                                        +
                                                                                                                                        • +
                                                                                                                                      • movement.validators.datasets
                                                                                                                                      • movement.validators.files
                                                                                                                                        • -
                                                                                                                                      • movement.validators.datasets
                                                                                                                                        @@ -599,7 +608,7 @@

                                                                                                                                        configure_logging

                                                                                                                                        - Created using Sphinx 7.4.5. + Created using Sphinx 8.0.2.

                                                                                                                                        diff --git a/api/movement.utils.logging.html b/api/movement.utils.logging.html index 2e6198c0..1283329a 100644 --- a/api/movement.utils.logging.html +++ b/api/movement.utils.logging.html @@ -28,20 +28,20 @@ - + - + - + - + @@ -52,7 +52,7 @@ - + @@ -128,7 +128,7 @@ -

                                                                                                                                        movement v0.0.19

                                                                                                                                        +

                                                                                                                                        movement v0.0.20

                                                                                                                                        @@ -368,26 +368,6 @@ aria-label="Section Navigation">

                                                                                                                                        Section Navigation

                                                                                                                                          -
                                                                                                                                        • movement.move_accessor
                                                                                                                                          -
                                                                                                                                          • -
                                                                                                                                        • movement.io.load_poses
                                                                                                                                          -
                                                                                                                                          • -
                                                                                                                                        • movement.io.save_poses
                                                                                                                                          -
                                                                                                                                        • movement.filtering
                                                                                                                                          • -
                                                                                                                                        • movement.analysis.kinematics
                                                                                                                                            -
                                                                                                                                          • compute_acceleration
                                                                                                                                            • -
                                                                                                                                          • compute_displacement
                                                                                                                                            • -
                                                                                                                                          • compute_velocity
                                                                                                                                            • +
                                                                                                                                          • movement.move_accessor
                                                                                                                                            • -
                                                                                                                                          • movement.utils.vector
                                                                                                                                              -
                                                                                                                                            • cart2pol
                                                                                                                                              • -
                                                                                                                                            • pol2cart
                                                                                                                                              • +
                                                                                                                                            • movement.sample_data
                                                                                                                                            • movement.utils.logging
                                                                                                                                              • -
                                                                                                                                            • movement.sample_data
                                                                                                                                                -
                                                                                                                                              • fetch_dataset
                                                                                                                                                • -
                                                                                                                                              • fetch_dataset_paths
                                                                                                                                                • -
                                                                                                                                              • list_datasets
                                                                                                                                                • +
                                                                                                                                              • movement.utils.vector
                                                                                                                                                +
                                                                                                                                                • +
                                                                                                                                              • movement.analysis.kinematics
                                                                                                                                                +
                                                                                                                                                • +
                                                                                                                                              • movement.validators.datasets
                                                                                                                                              • movement.validators.files
                                                                                                                                                • -
                                                                                                                                              • movement.validators.datasets
                                                                                                                                                @@ -527,12 +536,12 @@

                                                                                                                                                movement.utils.logging

                                                                                                                                                previous

                                                                                                                                                -

                                                                                                                                                pol2cart

                                                                                                                                                +

                                                                                                                                                list_datasets

                                                                                                                                                 movement.utils.logging

                                                                                                                                                - Created using Sphinx 7.4.5. + Created using Sphinx 8.0.2.

                                                                                                                                                diff --git a/api/movement.utils.logging.log_error.html b/api/movement.utils.logging.log_error.html index f9cb6841..9ebcc658 100644 --- a/api/movement.utils.logging.log_error.html +++ b/api/movement.utils.logging.log_error.html @@ -28,20 +28,20 @@ - + - + - + - + @@ -128,7 +128,7 @@ -

                                                                                                                                                movement v0.0.19

                                                                                                                                                +

                                                                                                                                                movement v0.0.20

                                                                                                                                                @@ -368,26 +368,6 @@ aria-label="Section Navigation">

                                                                                                                                                Section Navigation

                                                                                                                                                  -
                                                                                                                                                • movement.move_accessor
                                                                                                                                                  -
                                                                                                                                                  • -
                                                                                                                                                • movement.io.load_poses
                                                                                                                                                  -
                                                                                                                                                  • -
                                                                                                                                                • movement.io.save_poses
                                                                                                                                                  -
                                                                                                                                                • movement.filtering
                                                                                                                                                  • -
                                                                                                                                                • movement.analysis.kinematics
                                                                                                                                                    -
                                                                                                                                                  • compute_acceleration
                                                                                                                                                    • -
                                                                                                                                                  • compute_displacement
                                                                                                                                                    • -
                                                                                                                                                  • compute_velocity
                                                                                                                                                    • +
                                                                                                                                                  • movement.move_accessor
                                                                                                                                                    • -
                                                                                                                                                  • movement.utils.vector
                                                                                                                                                      -
                                                                                                                                                    • cart2pol
                                                                                                                                                      • -
                                                                                                                                                    • pol2cart
                                                                                                                                                      • +
                                                                                                                                                    • movement.sample_data
                                                                                                                                                    • movement.utils.logging
                                                                                                                                                      • -
                                                                                                                                                    • movement.sample_data
                                                                                                                                                        -
                                                                                                                                                      • fetch_dataset
                                                                                                                                                        • -
                                                                                                                                                      • fetch_dataset_paths
                                                                                                                                                        • -
                                                                                                                                                      • list_datasets
                                                                                                                                                        • +
                                                                                                                                                      • movement.utils.vector
                                                                                                                                                        +
                                                                                                                                                        • +
                                                                                                                                                      • movement.analysis.kinematics
                                                                                                                                                        +
                                                                                                                                                        • +
                                                                                                                                                      • movement.validators.datasets
                                                                                                                                                      • movement.validators.files
                                                                                                                                                        • -
                                                                                                                                                      • movement.validators.datasets
                                                                                                                                                        @@ -601,7 +610,7 @@

                                                                                                                                                        log_error

                                                                                                                                                        - Created using Sphinx 7.4.5. + Created using Sphinx 8.0.2.

                                                                                                                                                        diff --git a/api/movement.utils.logging.log_to_attrs.html b/api/movement.utils.logging.log_to_attrs.html index e94c5cd5..2f9f39bf 100644 --- a/api/movement.utils.logging.log_to_attrs.html +++ b/api/movement.utils.logging.log_to_attrs.html @@ -28,20 +28,20 @@ - + - + - + - + @@ -128,7 +128,7 @@ -

                                                                                                                                                        movement v0.0.19

                                                                                                                                                        +

                                                                                                                                                        movement v0.0.20

                                                                                                                                                        @@ -368,26 +368,6 @@ aria-label="Section Navigation">

                                                                                                                                                        Section Navigation

                                                                                                                                                          -
                                                                                                                                                        • movement.move_accessor
                                                                                                                                                          -
                                                                                                                                                          • -
                                                                                                                                                        • movement.io.load_poses
                                                                                                                                                          -
                                                                                                                                                          • -
                                                                                                                                                        • movement.io.save_poses
                                                                                                                                                          -
                                                                                                                                                        • movement.filtering
                                                                                                                                                          • -
                                                                                                                                                        • movement.analysis.kinematics
                                                                                                                                                            -
                                                                                                                                                          • compute_acceleration
                                                                                                                                                            • -
                                                                                                                                                          • compute_displacement
                                                                                                                                                            • -
                                                                                                                                                          • compute_velocity
                                                                                                                                                            • +
                                                                                                                                                          • movement.move_accessor
                                                                                                                                                            • -
                                                                                                                                                          • movement.utils.vector
                                                                                                                                                              -
                                                                                                                                                            • cart2pol
                                                                                                                                                              • -
                                                                                                                                                            • pol2cart
                                                                                                                                                              • +
                                                                                                                                                            • movement.sample_data
                                                                                                                                                            • movement.utils.logging
                                                                                                                                                              • -
                                                                                                                                                            • movement.sample_data
                                                                                                                                                                -
                                                                                                                                                              • fetch_dataset
                                                                                                                                                                • -
                                                                                                                                                              • fetch_dataset_paths
                                                                                                                                                                • -
                                                                                                                                                              • list_datasets
                                                                                                                                                                • +
                                                                                                                                                              • movement.utils.vector
                                                                                                                                                                +
                                                                                                                                                                • +
                                                                                                                                                              • movement.analysis.kinematics
                                                                                                                                                                +
                                                                                                                                                                • +
                                                                                                                                                              • movement.validators.datasets
                                                                                                                                                              • movement.validators.files
                                                                                                                                                                • -
                                                                                                                                                              • movement.validators.datasets
                                                                                                                                                                @@ -502,8 +511,8 @@

                                                                                                                                                                log_to_attrsmovement.utils.logging.log_to_attrs(func)[source]#

                                                                                                                                                                Log the operation performed by the wrapped function.

                                                                                                                                                                This decorator appends log entries to the data’s log -attribute. The wrapped function must accept an xarray.Dataset -or xarray.DataArray as its first argument and return an +attribute. The wrapped function must accept an xarray.Dataset +or xarray.DataArray as its first argument and return an object of the same type.

                                                                                                                                                                @@ -590,7 +599,7 @@

                                                                                                                                                                log_to_attrs

                                                                                                                                                                - Created using Sphinx 7.4.5. + Created using Sphinx 8.0.2.

                                                                                                                                                                diff --git a/api/movement.utils.logging.log_warning.html b/api/movement.utils.logging.log_warning.html index 551e8170..dab6e430 100644 --- a/api/movement.utils.logging.log_warning.html +++ b/api/movement.utils.logging.log_warning.html @@ -28,20 +28,20 @@ - + - + - + - + @@ -128,7 +128,7 @@ -

                                                                                                                                                                movement v0.0.19

                                                                                                                                                                +

                                                                                                                                                                movement v0.0.20

                                                                                                                                                                @@ -368,26 +368,6 @@ aria-label="Section Navigation">

                                                                                                                                                                Section Navigation

                                                                                                                                                                  -
                                                                                                                                                                • movement.move_accessor
                                                                                                                                                                  -
                                                                                                                                                                  • -
                                                                                                                                                                • movement.io.load_poses
                                                                                                                                                                  -
                                                                                                                                                                  • -
                                                                                                                                                                • movement.io.save_poses
                                                                                                                                                                  -
                                                                                                                                                                • movement.filtering
                                                                                                                                                                  • -
                                                                                                                                                                • movement.analysis.kinematics
                                                                                                                                                                    -
                                                                                                                                                                  • compute_acceleration
                                                                                                                                                                    • -
                                                                                                                                                                  • compute_displacement
                                                                                                                                                                    • -
                                                                                                                                                                  • compute_velocity
                                                                                                                                                                    • +
                                                                                                                                                                  • movement.move_accessor
                                                                                                                                                                    • -
                                                                                                                                                                  • movement.utils.vector
                                                                                                                                                                      -
                                                                                                                                                                    • cart2pol
                                                                                                                                                                      • -
                                                                                                                                                                    • pol2cart
                                                                                                                                                                      • +
                                                                                                                                                                    • movement.sample_data
                                                                                                                                                                    • movement.utils.logging
                                                                                                                                                                      • -
                                                                                                                                                                    • movement.sample_data
                                                                                                                                                                        -
                                                                                                                                                                      • fetch_dataset
                                                                                                                                                                        • -
                                                                                                                                                                      • fetch_dataset_paths
                                                                                                                                                                        • -
                                                                                                                                                                      • list_datasets
                                                                                                                                                                        • +
                                                                                                                                                                      • movement.utils.vector
                                                                                                                                                                        +
                                                                                                                                                                        • +
                                                                                                                                                                      • movement.analysis.kinematics
                                                                                                                                                                        +
                                                                                                                                                                        • +
                                                                                                                                                                      • movement.validators.datasets
                                                                                                                                                                      • movement.validators.files
                                                                                                                                                                        • -
                                                                                                                                                                      • movement.validators.datasets
                                                                                                                                                                        @@ -594,7 +603,7 @@

                                                                                                                                                                        log_warning

                                                                                                                                                                        - Created using Sphinx 7.4.5. + Created using Sphinx 8.0.2.

                                                                                                                                                                        diff --git a/api/movement.utils.reports.calculate_nan_stats.html b/api/movement.utils.reports.calculate_nan_stats.html index cdd64d4a..b9b40e96 100644 --- a/api/movement.utils.reports.calculate_nan_stats.html +++ b/api/movement.utils.reports.calculate_nan_stats.html @@ -28,20 +28,20 @@ - + - + - + - + @@ -128,7 +128,7 @@ -

                                                                                                                                                                        movement v0.0.19

                                                                                                                                                                        +

                                                                                                                                                                        movement v0.0.20

                                                                                                                                                                        @@ -368,26 +368,6 @@ aria-label="Section Navigation">

                                                                                                                                                                        Section Navigation

                                                                                                                                                                          -
                                                                                                                                                                        • movement.move_accessor
                                                                                                                                                                          -
                                                                                                                                                                          • -
                                                                                                                                                                        • movement.io.load_poses
                                                                                                                                                                          -
                                                                                                                                                                          • -
                                                                                                                                                                        • movement.io.save_poses
                                                                                                                                                                          -
                                                                                                                                                                        • movement.filtering
                                                                                                                                                                          • -
                                                                                                                                                                        • movement.analysis.kinematics
                                                                                                                                                                            -
                                                                                                                                                                          • compute_acceleration
                                                                                                                                                                            • -
                                                                                                                                                                          • compute_displacement
                                                                                                                                                                            • -
                                                                                                                                                                          • compute_velocity
                                                                                                                                                                            • +
                                                                                                                                                                          • movement.move_accessor
                                                                                                                                                                            • -
                                                                                                                                                                          • movement.utils.vector
                                                                                                                                                                              -
                                                                                                                                                                            • cart2pol
                                                                                                                                                                              • -
                                                                                                                                                                            • pol2cart
                                                                                                                                                                              • +
                                                                                                                                                                            • movement.sample_data
                                                                                                                                                                            • movement.utils.logging
                                                                                                                                                                              • -
                                                                                                                                                                            • movement.sample_data
                                                                                                                                                                                -
                                                                                                                                                                              • fetch_dataset
                                                                                                                                                                                • -
                                                                                                                                                                              • fetch_dataset_paths
                                                                                                                                                                                • -
                                                                                                                                                                              • list_datasets
                                                                                                                                                                                • +
                                                                                                                                                                              • movement.utils.vector
                                                                                                                                                                                +
                                                                                                                                                                                • +
                                                                                                                                                                              • movement.analysis.kinematics
                                                                                                                                                                                +
                                                                                                                                                                                • +
                                                                                                                                                                              • movement.validators.datasets
                                                                                                                                                                              • movement.validators.files
                                                                                                                                                                                • -
                                                                                                                                                                              • movement.validators.datasets
                                                                                                                                                                                @@ -507,7 +516,7 @@

                                                                                                                                                                                calculate_nan_stats
                                                                                                                                                                                Parameters:
                                                                                                                                                                                @@ -530,20 +539,20 @@

                                                                                                                                                                                pol2cart

                                                                                                                                                                                previous

                                                                                                                                                                                -

                                                                                                                                                                                cart2pol

                                                                                                                                                                                +

                                                                                                                                                                                convert_to_unit

                                                                                                                                                                                next

                                                                                                                                                                                -

                                                                                                                                                                                movement.utils.logging

                                                                                                                                                                                +

                                                                                                                                                                                movement.analysis.kinematics

                                                                                                                                                                                 @@ -600,7 +609,7 @@

                                                                                                                                                                                pol2cart

                                                                                                                                                                                - Created using Sphinx 7.4.5. + Created using Sphinx 8.0.2.

                                                                                                                                                                                diff --git a/api/movement.validators.datasets.ValidBboxesDataset.html b/api/movement.validators.datasets.ValidBboxesDataset.html index 8cae21f7..79cb6ccb 100644 --- a/api/movement.validators.datasets.ValidBboxesDataset.html +++ b/api/movement.validators.datasets.ValidBboxesDataset.html @@ -28,20 +28,20 @@ - + - + - + - + @@ -128,7 +128,7 @@ -

                                                                                                                                                                                movement v0.0.19

                                                                                                                                                                                +

                                                                                                                                                                                movement v0.0.20

                                                                                                                                                                                @@ -368,26 +368,6 @@ aria-label="Section Navigation">

                                                                                                                                                                                Section Navigation

                                                                                                                                                                                @@ -659,7 +698,7 @@

                                                                                                                                                                                ValidPosesDataset

                                                                                                                                                                                - Created using Sphinx 7.4.5. + Created using Sphinx 8.0.2.

                                                                                                                                                                                diff --git a/api/movement.validators.datasets.html b/api/movement.validators.datasets.html index e670c365..cddfc1ff 100644 --- a/api/movement.validators.datasets.html +++ b/api/movement.validators.datasets.html @@ -28,20 +28,20 @@ - + - + - + - + @@ -52,7 +52,7 @@ - + @@ -128,7 +128,7 @@ -

                                                                                                                                                                                movement v0.0.19

                                                                                                                                                                                +

                                                                                                                                                                                movement v0.0.20

                                                                                                                                                                                @@ -368,26 +368,6 @@ aria-label="Section Navigation">

                                                                                                                                                                                Section Navigation

                                                                                                                                                                                  -
                                                                                                                                                                                • movement.move_accessor
                                                                                                                                                                                  -
                                                                                                                                                                                  • -
                                                                                                                                                                                • movement.io.load_poses
                                                                                                                                                                                  -
                                                                                                                                                                                  • -
                                                                                                                                                                                • movement.io.save_poses
                                                                                                                                                                                  -
                                                                                                                                                                                • movement.filtering
                                                                                                                                                                                  • -
                                                                                                                                                                                • movement.analysis.kinematics
                                                                                                                                                                                    -
                                                                                                                                                                                  • compute_acceleration
                                                                                                                                                                                    • -
                                                                                                                                                                                  • compute_displacement
                                                                                                                                                                                    • -
                                                                                                                                                                                  • compute_velocity
                                                                                                                                                                                    • +
                                                                                                                                                                                  • movement.move_accessor
                                                                                                                                                                                    • -
                                                                                                                                                                                  • movement.utils.vector
                                                                                                                                                                                      -
                                                                                                                                                                                    • cart2pol
                                                                                                                                                                                      • -
                                                                                                                                                                                    • pol2cart
                                                                                                                                                                                      • +
                                                                                                                                                                                    • movement.sample_data
                                                                                                                                                                                    • movement.utils.logging
                                                                                                                                                                                      • -
                                                                                                                                                                                    • movement.sample_data
                                                                                                                                                                                        -
                                                                                                                                                                                      • fetch_dataset
                                                                                                                                                                                        • -
                                                                                                                                                                                      • fetch_dataset_paths
                                                                                                                                                                                        • -
                                                                                                                                                                                      • list_datasets
                                                                                                                                                                                        • +
                                                                                                                                                                                      • movement.utils.vector
                                                                                                                                                                                        +
                                                                                                                                                                                        • +
                                                                                                                                                                                      • movement.analysis.kinematics
                                                                                                                                                                                        +
                                                                                                                                                                                        • +
                                                                                                                                                                                      • movement.validators.datasets
                                                                                                                                                                                      • movement.validators.files
                                                                                                                                                                                        • -
                                                                                                                                                                                      • movement.validators.datasets
                                                                                                                                                                                        @@ -503,7 +512,7 @@

                                                                                                                                                                                        movement.validators.datasetsmovement dataset.

                                                                                                                                                                                        ValidPosesDataset

                                                                                                                                                                                        -

                                                                                                                                                                                        Class for validating data intended for a movement dataset.

                                                                                                                                                                                        +

                                                                                                                                                                                        Class for validating poses data intended for a movement dataset.

                                                                                                                                                                                        @@ -521,12 +530,12 @@

                                                                                                                                                                                        movement.validators.datasets

                                                                                                                                                                                        previous

                                                                                                                                                                                        -

                                                                                                                                                                                        ValidHDF5

                                                                                                                                                                                        +

                                                                                                                                                                                        compute_velocity

                                                                                                                                                                                         movement.validators.datasets

                                                                                                                                                                                        - Created using Sphinx 7.4.5. + Created using Sphinx 8.0.2.

                                                                                                                                                                                        diff --git a/api/movement.validators.files.ValidDeepLabCutCSV.html b/api/movement.validators.files.ValidDeepLabCutCSV.html index 8c0849ab..0b4d479e 100644 --- a/api/movement.validators.files.ValidDeepLabCutCSV.html +++ b/api/movement.validators.files.ValidDeepLabCutCSV.html @@ -28,20 +28,20 @@ - + - + - + - + @@ -128,7 +128,7 @@ -

                                                                                                                                                                                        movement v0.0.19

                                                                                                                                                                                        +

                                                                                                                                                                                        movement v0.0.20

                                                                                                                                                                                        @@ -368,26 +368,6 @@ aria-label="Section Navigation">

                                                                                                                                                                                        Section Navigation

                                                                                                                                                                                          -
                                                                                                                                                                                        • movement.move_accessor
                                                                                                                                                                                          -
                                                                                                                                                                                          • -
                                                                                                                                                                                        • movement.io.load_poses
                                                                                                                                                                                          -
                                                                                                                                                                                          • -
                                                                                                                                                                                        • movement.io.save_poses
                                                                                                                                                                                          -
                                                                                                                                                                                        • movement.filtering
                                                                                                                                                                                          • -
                                                                                                                                                                                        • movement.analysis.kinematics
                                                                                                                                                                                            -
                                                                                                                                                                                          • compute_acceleration
                                                                                                                                                                                            • -
                                                                                                                                                                                          • compute_displacement
                                                                                                                                                                                            • -
                                                                                                                                                                                          • compute_velocity
                                                                                                                                                                                            • +
                                                                                                                                                                                          • movement.move_accessor
                                                                                                                                                                                            • -
                                                                                                                                                                                          • movement.utils.vector
                                                                                                                                                                                              -
                                                                                                                                                                                            • cart2pol
                                                                                                                                                                                              • -
                                                                                                                                                                                            • pol2cart
                                                                                                                                                                                              • +
                                                                                                                                                                                            • movement.sample_data
                                                                                                                                                                                            • movement.utils.logging
                                                                                                                                                                                              • -
                                                                                                                                                                                            • movement.sample_data
                                                                                                                                                                                                -
                                                                                                                                                                                              • fetch_dataset
                                                                                                                                                                                                • -
                                                                                                                                                                                              • fetch_dataset_paths
                                                                                                                                                                                                • -
                                                                                                                                                                                              • list_datasets
                                                                                                                                                                                                • +
                                                                                                                                                                                              • movement.utils.vector
                                                                                                                                                                                                +
                                                                                                                                                                                                • +
                                                                                                                                                                                              • movement.analysis.kinematics
                                                                                                                                                                                                +
                                                                                                                                                                                                • +
                                                                                                                                                                                              • movement.validators.datasets
                                                                                                                                                                                              • movement.validators.files
                                                                                                                                                                                                • -
                                                                                                                                                                                              • movement.validators.datasets
                                                                                                                                                                                                @@ -502,6 +511,8 @@

                                                                                                                                                                                                ValidDeepLabCutCSVclass movement.validators.files.ValidDeepLabCutCSV(path)[source]#

                                                                                                                                                                                                Bases: object

                                                                                                                                                                                                Class for validating DeepLabCut-style .csv files.

                                                                                                                                                                                                +

                                                                                                                                                                                                The validator ensures that the file contains the +expected index column levels.

                                                                                                                                                                                                path#
                                                                                                                                                                                                @@ -607,7 +618,7 @@

                                                                                                                                                                                                ValidDeepLabCutCSV

                                                                                                                                                                                                - Created using Sphinx 7.4.5. + Created using Sphinx 8.0.2.

                                                                                                                                                                                                diff --git a/api/movement.validators.files.ValidFile.html b/api/movement.validators.files.ValidFile.html index 139e19fb..7ffab5ec 100644 --- a/api/movement.validators.files.ValidFile.html +++ b/api/movement.validators.files.ValidFile.html @@ -28,20 +28,20 @@ - + - + - + - + @@ -128,7 +128,7 @@ -

                                                                                                                                                                                                movement v0.0.19

                                                                                                                                                                                                +

                                                                                                                                                                                                movement v0.0.20

                                                                                                                                                                                                @@ -368,26 +368,6 @@ aria-label="Section Navigation">

                                                                                                                                                                                                Section Navigation

                                                                                                                                                                                                  -
                                                                                                                                                                                                • movement.move_accessor
                                                                                                                                                                                                  -
                                                                                                                                                                                                  • -
                                                                                                                                                                                                • movement.io.load_poses
                                                                                                                                                                                                  -
                                                                                                                                                                                                  • -
                                                                                                                                                                                                • movement.io.save_poses
                                                                                                                                                                                                  -
                                                                                                                                                                                                • movement.filtering
                                                                                                                                                                                                  • -
                                                                                                                                                                                                • movement.analysis.kinematics
                                                                                                                                                                                                    -
                                                                                                                                                                                                  • compute_acceleration
                                                                                                                                                                                                    • -
                                                                                                                                                                                                  • compute_displacement
                                                                                                                                                                                                    • -
                                                                                                                                                                                                  • compute_velocity
                                                                                                                                                                                                    • +
                                                                                                                                                                                                  • movement.move_accessor
                                                                                                                                                                                                    • -
                                                                                                                                                                                                  • movement.utils.vector
                                                                                                                                                                                                      -
                                                                                                                                                                                                    • cart2pol
                                                                                                                                                                                                      • -
                                                                                                                                                                                                    • pol2cart
                                                                                                                                                                                                      • +
                                                                                                                                                                                                    • movement.sample_data
                                                                                                                                                                                                    • movement.utils.logging
                                                                                                                                                                                                      • -
                                                                                                                                                                                                    • movement.sample_data
                                                                                                                                                                                                        -
                                                                                                                                                                                                      • fetch_dataset
                                                                                                                                                                                                        • -
                                                                                                                                                                                                      • fetch_dataset_paths
                                                                                                                                                                                                        • -
                                                                                                                                                                                                      • list_datasets
                                                                                                                                                                                                        • +
                                                                                                                                                                                                      • movement.utils.vector
                                                                                                                                                                                                        +
                                                                                                                                                                                                        • +
                                                                                                                                                                                                      • movement.analysis.kinematics
                                                                                                                                                                                                        +
                                                                                                                                                                                                        • +
                                                                                                                                                                                                      • movement.validators.datasets
                                                                                                                                                                                                      • movement.validators.files
                                                                                                                                                                                                        • -
                                                                                                                                                                                                      • movement.validators.datasets
                                                                                                                                                                                                        @@ -502,6 +511,14 @@

                                                                                                                                                                                                        ValidFileclass movement.validators.files.ValidFile(path, *, expected_permission='r', expected_suffix=NOTHING)[source]#

                                                                                                                                                                                                        Bases: object

                                                                                                                                                                                                        Class for validating file paths.

                                                                                                                                                                                                        +

                                                                                                                                                                                                        The validator ensures that the file:

                                                                                                                                                                                                        +
                                                                                                                                                                                                          +

                                                                                                                                                                                                        • is not a directory,

                                                                                                                                                                                                          • +

                                                                                                                                                                                                        • exists if it is meant to be read,

                                                                                                                                                                                                          • +

                                                                                                                                                                                                        • does not exist if it is meant to be written,

                                                                                                                                                                                                          • +

                                                                                                                                                                                                        • has the expected access permission(s), and

                                                                                                                                                                                                          • +

                                                                                                                                                                                                        • has one of the expected suffix(es).

                                                                                                                                                                                                          • +
                                                                                                                                                                                                        path#
                                                                                                                                                                                                        @@ -544,8 +561,8 @@

                                                                                                                                                                                                        ValidFile

                                                                                                                                                                                                        • IsADirectoryError – If the path points to a directory.

                                                                                                                                                                                                        • PermissionError – If the file does not have the expected access permission(s).

                                                                                                                                                                                                          • -

                                                                                                                                                                                                        • FileNotFoundError – If the file does not exist when expected_permission is “r” or “rw”.

                                                                                                                                                                                                          • -

                                                                                                                                                                                                        • FileExistsError – If the file exists when expected_permission is “w”.

                                                                                                                                                                                                          • +

                                                                                                                                                                                                        • FileNotFoundError – If the file does not exist when expected_permission is “r” or “rw”.

                                                                                                                                                                                                          • +

                                                                                                                                                                                                        • FileExistsError – If the file exists when expected_permission is “w”.

                                                                                                                                                                                                        • ValueError – If the file does not have one of the expected suffix(es).

                                                                                                                                                                                                        @@ -640,7 +657,7 @@

                                                                                                                                                                                                        ValidFile

                                                                                                                                                                                                        - Created using Sphinx 7.4.5. + Created using Sphinx 8.0.2.

                                                                                                                                                                                                        diff --git a/api/movement.validators.files.ValidHDF5.html b/api/movement.validators.files.ValidHDF5.html index 094fcccf..6d41cf44 100644 --- a/api/movement.validators.files.ValidHDF5.html +++ b/api/movement.validators.files.ValidHDF5.html @@ -28,20 +28,20 @@ - + - + - + - + @@ -51,7 +51,7 @@ - + @@ -128,7 +128,7 @@ -

                                                                                                                                                                                                        movement v0.0.19

                                                                                                                                                                                                        +

                                                                                                                                                                                                        movement v0.0.20

                                                                                                                                                                                                        @@ -368,26 +368,6 @@ aria-label="Section Navigation">

                                                                                                                                                                                                        Section Navigation

                                                                                                                                                                                                          -
                                                                                                                                                                                                        • movement.move_accessor
                                                                                                                                                                                                          -
                                                                                                                                                                                                          • -
                                                                                                                                                                                                        • movement.io.load_poses
                                                                                                                                                                                                          -
                                                                                                                                                                                                          • -
                                                                                                                                                                                                        • movement.io.save_poses
                                                                                                                                                                                                          -
                                                                                                                                                                                                        • movement.filtering
                                                                                                                                                                                                          • -
                                                                                                                                                                                                        • movement.analysis.kinematics
                                                                                                                                                                                                            -
                                                                                                                                                                                                          • compute_acceleration
                                                                                                                                                                                                            • -
                                                                                                                                                                                                          • compute_displacement
                                                                                                                                                                                                            • -
                                                                                                                                                                                                          • compute_velocity
                                                                                                                                                                                                            • +
                                                                                                                                                                                                          • movement.move_accessor
                                                                                                                                                                                                            • -
                                                                                                                                                                                                          • movement.utils.vector
                                                                                                                                                                                                              -
                                                                                                                                                                                                            • cart2pol
                                                                                                                                                                                                              • -
                                                                                                                                                                                                            • pol2cart
                                                                                                                                                                                                              • +
                                                                                                                                                                                                            • movement.sample_data
                                                                                                                                                                                                            • movement.utils.logging
                                                                                                                                                                                                              • -
                                                                                                                                                                                                            • movement.sample_data
                                                                                                                                                                                                                -
                                                                                                                                                                                                              • fetch_dataset
                                                                                                                                                                                                                • -
                                                                                                                                                                                                              • fetch_dataset_paths
                                                                                                                                                                                                                • -
                                                                                                                                                                                                              • list_datasets
                                                                                                                                                                                                                • +
                                                                                                                                                                                                              • movement.utils.vector
                                                                                                                                                                                                                +
                                                                                                                                                                                                                • +
                                                                                                                                                                                                              • movement.analysis.kinematics
                                                                                                                                                                                                                +
                                                                                                                                                                                                                • +
                                                                                                                                                                                                              • movement.validators.datasets
                                                                                                                                                                                                              • movement.validators.files
                                                                                                                                                                                                                • -
                                                                                                                                                                                                              • movement.validators.datasets
                                                                                                                                                                                                                @@ -502,6 +511,11 @@

                                                                                                                                                                                                                ValidHDF5class movement.validators.files.ValidHDF5(path, *, expected_datasets=NOTHING)[source]#

                                                                                                                                                                                                                Bases: object

                                                                                                                                                                                                                Class for validating HDF5 files.

                                                                                                                                                                                                                +

                                                                                                                                                                                                                The validator ensures that the file:

                                                                                                                                                                                                                +
                                                                                                                                                                                                                  +

                                                                                                                                                                                                                • is in HDF5 format, and

                                                                                                                                                                                                                  • +

                                                                                                                                                                                                                • contains the expected datasets.

                                                                                                                                                                                                                  • +
                                                                                                                                                                                                                path#
                                                                                                                                                                                                                @@ -555,11 +569,11 @@

                                                                                                                                                                                                                ValidHDF5

                                                                                                                                                                                                                next

                                                                                                                                                                                                                -

                                                                                                                                                                                                                movement.validators.datasets

                                                                                                                                                                                                                +

                                                                                                                                                                                                                ValidVIATracksCSV

                                                                                                                                                                                                                 @@ -620,7 +634,7 @@

                                                                                                                                                                                                                ValidHDF5

                                                                                                                                                                                                                - Created using Sphinx 7.4.5. + Created using Sphinx 8.0.2.

                                                                                                                                                                                                                diff --git a/api/movement.validators.files.ValidVIATracksCSV.html b/api/movement.validators.files.ValidVIATracksCSV.html new file mode 100644 index 00000000..dffb1f47 --- /dev/null +++ b/api/movement.validators.files.ValidVIATracksCSV.html @@ -0,0 +1,665 @@ + + + + + + + + + + + ValidVIATracksCSV — movement + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

                                                                                                                                                                                                                + +
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                                                                                                                                                                                                                +
                                                                                                                                                                                                                +
                                                                                                                                                                                                                +
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                                                                                                                                                                                                                ValidVIATracksCSV#

                                                                                                                                                                                                                +
                                                                                                                                                                                                                +
                                                                                                                                                                                                                +class movement.validators.files.ValidVIATracksCSV(path)[source]#
                                                                                                                                                                                                                +

                                                                                                                                                                                                                Bases: object

                                                                                                                                                                                                                +

                                                                                                                                                                                                                Class for validating VIA tracks .csv files.

                                                                                                                                                                                                                +

                                                                                                                                                                                                                The validator ensures that the file:

                                                                                                                                                                                                                +
                                                                                                                                                                                                                  +

                                                                                                                                                                                                                • contains the expected header,

                                                                                                                                                                                                                  • +

                                                                                                                                                                                                                • contains valid frame numbers,

                                                                                                                                                                                                                  • +

                                                                                                                                                                                                                • contains tracked bounding boxes, and

                                                                                                                                                                                                                  • +

                                                                                                                                                                                                                • defines bounding boxes whose IDs are unique per image file.

                                                                                                                                                                                                                  • +
                                                                                                                                                                                                                +
                                                                                                                                                                                                                +
                                                                                                                                                                                                                +path#
                                                                                                                                                                                                                +

                                                                                                                                                                                                                Path to the VIA tracks .csv file.

                                                                                                                                                                                                                +
                                                                                                                                                                                                                +
                                                                                                                                                                                                                Type:
                                                                                                                                                                                                                +

                                                                                                                                                                                                                pathlib.Path

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                                                                                                                                                                                                                + +
                                                                                                                                                                                                                +
                                                                                                                                                                                                                Raises:
                                                                                                                                                                                                                +

                                                                                                                                                                                                                ValueError – If the file does not match the VIA tracks .csv file requirements.

                                                                                                                                                                                                                +
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                                                                                                                                                                                                                + On this page +
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                                                                                                                                                                                                                + + + + + + + + \ No newline at end of file diff --git a/api/movement.validators.files.html b/api/movement.validators.files.html index a293dd16..061a5d9a 100644 --- a/api/movement.validators.files.html +++ b/api/movement.validators.files.html @@ -28,20 +28,20 @@ - + - + - + - + @@ -52,7 +52,7 @@ - + @@ -128,7 +128,7 @@ -

                                                                                                                                                                                                                movement v0.0.19

                                                                                                                                                                                                                +

                                                                                                                                                                                                                movement v0.0.20

                                                                                                                                                                                                                @@ -368,26 +368,6 @@ aria-label="Section Navigation">

                                                                                                                                                                                                                Section Navigation

                                                                                                                                                                                                                @@ -524,12 +536,12 @@

                                                                                                                                                                                                                movement.validators.files

                                                                                                                                                                                                                previous

                                                                                                                                                                                                                -

                                                                                                                                                                                                                list_datasets

                                                                                                                                                                                                                +

                                                                                                                                                                                                                ValidPosesDataset

                                                                                                                                                                                                                 movement.validators.files

                                                                                                                                                                                                                - Created using Sphinx 7.4.5. + Created using Sphinx 8.0.2.

                                                                                                                                                                                                                diff --git a/api_index.html b/api_index.html index 96b127a5..3dbb627a 100644 --- a/api_index.html +++ b/api_index.html @@ -28,20 +28,20 @@ - + - + - + - + @@ -51,7 +51,7 @@ - + @@ -128,7 +128,7 @@ -

                                                                                                                                                                                                                movement v0.0.19

                                                                                                                                                                                                                +

                                                                                                                                                                                                                movement v0.0.20

                                                                                                                                                                                                                @@ -368,26 +368,6 @@ aria-label="Section Navigation">

                                                                                                                                                                                                                Section Navigation

                                                                                                                                                                                                                  -
                                                                                                                                                                                                                • movement.move_accessor
                                                                                                                                                                                                                  -
                                                                                                                                                                                                                  • -
                                                                                                                                                                                                                • movement.io.load_poses
                                                                                                                                                                                                                  -
                                                                                                                                                                                                                  • -
                                                                                                                                                                                                                • movement.io.save_poses
                                                                                                                                                                                                                  -
                                                                                                                                                                                                                • movement.filtering
                                                                                                                                                                                                                  • -
                                                                                                                                                                                                                • movement.analysis.kinematics
                                                                                                                                                                                                                    -
                                                                                                                                                                                                                  • compute_acceleration
                                                                                                                                                                                                                    • -
                                                                                                                                                                                                                  • compute_displacement
                                                                                                                                                                                                                    • -
                                                                                                                                                                                                                  • compute_velocity
                                                                                                                                                                                                                    • +
                                                                                                                                                                                                                  • movement.move_accessor
                                                                                                                                                                                                                    • -
                                                                                                                                                                                                                  • movement.utils.vector
                                                                                                                                                                                                                      -
                                                                                                                                                                                                                    • cart2pol
                                                                                                                                                                                                                      • -
                                                                                                                                                                                                                    • pol2cart
                                                                                                                                                                                                                      • +
                                                                                                                                                                                                                    • movement.sample_data
                                                                                                                                                                                                                    • movement.utils.logging
                                                                                                                                                                                                                      • -
                                                                                                                                                                                                                    • movement.sample_data
                                                                                                                                                                                                                      @@ -544,7 +544,7 @@

                                                                                                                                                                                                                      Short-term milestone -

                                                                                                                                                                                                                      - Created using Sphinx 7.4.5. + Created using Sphinx 8.0.2.

                                                                                                                                                                                                                      diff --git a/examples/compute_kinematics.html b/examples/compute_kinematics.html index d590dac7..72cf1dd1 100644 --- a/examples/compute_kinematics.html +++ b/examples/compute_kinematics.html @@ -28,20 +28,20 @@ - + - + - + - + @@ -128,7 +128,7 @@ -

                                                                                                                                                                                                                      movement v0.0.19

                                                                                                                                                                                                                      +

                                                                                                                                                                                                                      movement v0.0.20

                                                                                                                                                                                                                      @@ -441,14 +441,13 @@ visualise the results.

                                                                                                                                                                                                                      Imports#

                                                                                                                                                                                                                      -
                                                                                                                                                                                                                      import numpy as np
-
-# For interactive plots: install ipympl with `pip install ipympl` and uncomment
+
                                                                                                                                                                                                                      # For interactive plots: install ipympl with `pip install ipympl` and uncomment
 # the following line in your notebook
 # %matplotlib widget
 from matplotlib import pyplot as plt
 
 from movement import sample_data
+from movement.utils.vector import compute_norm
                                                                                                                                                                                                                      @@ -456,11 +455,11 @@

                                                                                                                                                                                                                      Imports#<

                                                                                                                                                                                                                      Load sample dataset#

                                                                                                                                                                                                                      First, we load an example dataset. In this case, we select the SLEAP_three-mice_Aeon_proofread sample data.

                                                                                                                                                                                                                      -
                                                                                                                                                                                                                      ds = sample_data.fetch_dataset(
+
                                                                                                                                                                                                                      ds = sample_data.fetch_dataset(
     "SLEAP_three-mice_Aeon_proofread.analysis.h5",
 )
 
-print(ds)
+print(ds)
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      <xarray.Dataset> Size: 27kB
@@ -478,6 +477,7 @@ 
                                                                                                                                                                                                                      Load sample datasetposition and confidence.
 To compute displacement, velocity and acceleration, we will need the
 position one:
                                                                                                                                                                                                                      
-
                                                                                                                                                                                                                      position = ds.position
+
                                                                                                                                                                                                                      position = ds.position
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      
 
@@ -501,11 +501,11 @@ 
                                                                                                                                                                                                                      Visualise the data
                                                                                                                                                                                                                      fig, ax = plt.subplots(1, 1)
 for mouse_name, col in zip(
-    position.individuals.values, ["r", "g", "b"], strict=False
+    position.individuals.values, ["r", "g", "b"], strict=False
 ):
     ax.plot(
-        position.sel(individuals=mouse_name, space="x"),
-        position.sel(individuals=mouse_name, space="y"),
+        position.sel(individuals=mouse_name, space="x"),
+        position.sel(individuals=mouse_name, space="y"),
         linestyle="-",
         marker=".",
         markersize=2,
@@ -526,12 +526,12 @@ 
                                                                                                                                                                                                                      Visualise the data
                                                                                                                                                                                                                      fig, axes = plt.subplots(3, 1, sharey=True)
-for mouse_name, ax in zip(position.individuals.values, axes, strict=False):
+for mouse_name, ax in zip(position.individuals.values, axes, strict=False):
     sc = ax.scatter(
-        position.sel(individuals=mouse_name, space="x"),
-        position.sel(individuals=mouse_name, space="y"),
+        position.sel(individuals=mouse_name, space="x"),
+        position.sel(individuals=mouse_name, space="y"),
         s=2,
-        c=position.time,
+        c=position.time,
         cmap="viridis",
     )
     ax.invert_yaxis()
@@ -549,9 +549,9 @@ 
                                                                                                                                                                                                                      Visualise the dataAEON3B_TP2) followed an anti-clockwise direction.
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      We can also easily plot the components of the position vector against time
 using xarray’s built-in plotting methods. We use
-xarray.DataArray.squeeze() to
+xarray.DataArray.squeeze() to
 remove the dimension of length 1 from the data (the keypoints dimension).
                                                                                                                                                                                                                      
-
                                                                                                                                                                                                                      position.squeeze().plot.line(x="time", row="individuals", aspect=2, size=2.5)
+
                                                                                                                                                                                                                      position.squeeze().plot.line(x="time", row="individuals", aspect=2, size=2.5)
 plt.gcf().show()
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      
@@ -565,7 +565,7 @@ 
                                                                                                                                                                                                                      Compute displacementcompute_displacement method of the
 move accessor.
                                                                                                                                                                                                                      
-
                                                                                                                                                                                                                      displacement = ds.move.compute_displacement()
+
                                                                                                                                                                                                                      displacement = ds.move.compute_displacement()
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      This method will return a data array equivalent to the position one,
@@ -575,7 +575,7 @@ 
                                                                                                                                                                                                                      Compute displacementmovement.analysis.kinematics module:
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      import movement.analysis.kinematics as kin
 
-displacement_kin = kin.compute_displacement(position)
+displacement_kin = kin.compute_displacement(position)
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      The displacement data array holds, for a given individual and keypoint
@@ -585,8 +585,8 @@ 
                                                                                                                                                                                                                      Compute displacementt=0 to be the zero vector.
 This way the shape of the displacement data array is the
 same as the  position array:
                                                                                                                                                                                                                      
-
                                                                                                                                                                                                                      print(f"Shape of position: {position.shape}")
-print(f"Shape of displacement: {displacement.shape}")
+
                                                                                                                                                                                                                      print(f"Shape of position: {position.shape}")
+print(f"Shape of displacement: {displacement.shape}")
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      Shape of position: (601, 3, 1, 2)
@@ -602,19 +602,19 @@ 
                                                                                                                                                                                                                      Compute displacement# plot position data
 sc = ax.scatter(
-    position.sel(individuals=mouse_name, space="x"),
-    position.sel(individuals=mouse_name, space="y"),
+    position.sel(individuals=mouse_name, space="x"),
+    position.sel(individuals=mouse_name, space="y"),
     s=15,
-    c=position.time,
+    c=position.time,
     cmap="viridis",
 )
 
 # plot displacement vectors: at t, vector from t-1 to t
 ax.quiver(
-    position.sel(individuals=mouse_name, space="x"),
-    position.sel(individuals=mouse_name, space="y"),
-    displacement.sel(individuals=mouse_name, space="x"),
-    displacement.sel(individuals=mouse_name, space="y"),
+    position.sel(individuals=mouse_name, space="x"),
+    position.sel(individuals=mouse_name, space="y"),
+    displacement.sel(individuals=mouse_name, space="x"),
+    displacement.sel(individuals=mouse_name, space="y"),
     angles="xy",
     scale=1,
     scale_units="xy",
@@ -633,7 +633,7 @@ 
                                                                                                                                                                                                                      Compute displacementfig.colorbar(sc, ax=ax, label="time (s)")
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      
-Zoomed in trajectory of AEON3B_TP2
                                                                                                                                                                                                                      <matplotlib.colorbar.Colorbar object at 0x7fae95733350>
+Zoomed in trajectory of AEON3B_TP2
                                                                                                                                                                                                                      <matplotlib.colorbar.Colorbar object at 0x7fbbf8eaa250>
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      Notice that this figure is not very useful as a visual check:
@@ -656,19 +656,19 @@ 
                                                                                                                                                                                                                      Compute displacement# plot position data
 sc = ax.scatter(
-    position.sel(individuals=mouse_name, space="x"),
-    position.sel(individuals=mouse_name, space="y"),
+    position.sel(individuals=mouse_name, space="x"),
+    position.sel(individuals=mouse_name, space="y"),
     s=15,
-    c=position.time,
+    c=position.time,
     cmap="viridis",
 )
 
 # plot displacement vectors: at t, vector from t-1 to t
 ax.quiver(
-    position.sel(individuals=mouse_name, space="x"),
-    position.sel(individuals=mouse_name, space="y"),
-    -displacement.sel(individuals=mouse_name, space="x"),  # flipped sign
-    -displacement.sel(individuals=mouse_name, space="y"),  # flipped sign
+    position.sel(individuals=mouse_name, space="x"),
+    position.sel(individuals=mouse_name, space="y"),
+    -displacement.sel(individuals=mouse_name, space="x"),  # flipped sign
+    -displacement.sel(individuals=mouse_name, space="y"),  # flipped sign
     angles="xy",
     scale=1,
     scale_units="xy",
@@ -686,7 +686,7 @@ 
                                                                                                                                                                                                                      Compute displacementfig.colorbar(sc, ax=ax, label="time (s)")
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      
-Zoomed in trajectory of AEON3B_TP2
                                                                                                                                                                                                                      <matplotlib.colorbar.Colorbar object at 0x7fae957a64d0>
+Zoomed in trajectory of AEON3B_TP2
                                                                                                                                                                                                                      <matplotlib.colorbar.Colorbar object at 0x7fbbf8d34090>
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      Now we can visually verify that indeed the displacement vector
@@ -694,13 +694,12 @@ 
                                                                                                                                                                                                                      Compute displacementWith the displacement data we can compute the distance travelled by the
 mouse along its trajectory.
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      # length of each displacement vector
-displacement_vectors_lengths = np.linalg.norm(
-    displacement.sel(individuals=mouse_name, space=["x", "y"]).squeeze(),
-    axis=1,
+displacement_vectors_lengths = compute_norm(
+    displacement.sel(individuals=mouse_name)
 )
 
-# sum of all displacement vectors
-total_displacement = np.sum(displacement_vectors_lengths, axis=0)  # in pixels
+# sum the lengths of all displacement vectors (in pixels)
+total_displacement = displacement_vectors_lengths.sum(dim="time").values[0]
 
 print(
     f"The mouse {mouse_name}'s trajectory is {total_displacement:.2f} "
@@ -716,7 +715,7 @@ 
                                                                                                                                                                                                                      Compute displacementCompute velocity#
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      We can easily compute the velocity vectors for all individuals in our data
 array:
                                                                                                                                                                                                                      
-
                                                                                                                                                                                                                      velocity = ds.move.compute_velocity()
+
                                                                                                                                                                                                                      velocity = ds.move.compute_velocity()
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      The velocity method will return a data array equivalent to the
@@ -725,9 +724,9 @@ 
                                                                                                                                                                                                                      Compute velocityxarray’s built-in plotting methods. We use
-xarray.DataArray.squeeze() to
+xarray.DataArray.squeeze() to
 remove the dimension of length 1 from the data (the keypoints dimension).
                                                                                                                                                                                                                      
-
                                                                                                                                                                                                                      velocity.squeeze().plot.line(x="time", row="individuals", aspect=2, size=2.5)
+
                                                                                                                                                                                                                      velocity.squeeze().plot.line(x="time", row="individuals", aspect=2, size=2.5)
 plt.gcf().show()
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      
@@ -737,16 +736,14 @@ 
                                                                                                                                                                                                                      Compute velocity
                                                                                                                                                                                                                      fig, axes = plt.subplots(3, 1, sharex=True, sharey=True)
-for mouse_name, ax in zip(velocity.individuals.values, axes, strict=False):
-    # compute the norm of the velocity vector for one mouse
-    speed_one_mouse = np.linalg.norm(
-        velocity.sel(individuals=mouse_name, space=["x", "y"]).squeeze(),
-        axis=1,
-    )
+for mouse_name, ax in zip(velocity.individuals.values, axes, strict=False):
+    # compute the magnitude of the velocity vector for one mouse
+    speed_one_mouse = compute_norm(velocity.sel(individuals=mouse_name))
     # plot speed against time
-    ax.plot(speed_one_mouse)
+    ax.plot(speed_one_mouse)
     ax.set_title(mouse_name)
     ax.set_xlabel("time (s)")
     ax.set_ylabel("speed (px/s)")
@@ -760,18 +757,18 @@ 
                                                                                                                                                                                                                      Compute velocityax = fig.add_subplot()
 # plot trajectory (position data)
 sc = ax.scatter(
-    position.sel(individuals=mouse_name, space="x"),
-    position.sel(individuals=mouse_name, space="y"),
+    position.sel(individuals=mouse_name, space="x"),
+    position.sel(individuals=mouse_name, space="y"),
     s=15,
-    c=position.time,
+    c=position.time,
     cmap="viridis",
 )
 # plot velocity vectors
 ax.quiver(
-    position.sel(individuals=mouse_name, space="x"),
-    position.sel(individuals=mouse_name, space="y"),
-    velocity.sel(individuals=mouse_name, space="x"),
-    velocity.sel(individuals=mouse_name, space="y"),
+    position.sel(individuals=mouse_name, space="x"),
+    position.sel(individuals=mouse_name, space="y"),
+    velocity.sel(individuals=mouse_name, space="x"),
+    velocity.sel(individuals=mouse_name, space="y"),
     angles="xy",
     scale=2,
     scale_units="xy",
@@ -792,21 +789,21 @@ 
                                                                                                                                                                                                                      Compute velocity
 
                                                                                                                                                                                                                      Compute acceleration#
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      We can compute the acceleration of the data with an equivalent method:
                                                                                                                                                                                                                      
-
                                                                                                                                                                                                                      accel = ds.move.compute_acceleration()
+
                                                                                                                                                                                                                      accel = ds.move.compute_acceleration()
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      and plot of the components of the acceleration vector ax, ay per
 individual:
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      fig, axes = plt.subplots(3, 1, sharex=True, sharey=True)
-for mouse_name, ax in zip(accel.individuals.values, axes, strict=False):
+for mouse_name, ax in zip(accel.individuals.values, axes, strict=False):
     # plot x-component of acceleration vector
     ax.plot(
-        accel.sel(individuals=mouse_name, space=["x"]).squeeze(),
+        accel.sel(individuals=mouse_name, space=["x"]).squeeze(),
         label="ax",
     )
     # plot y-component of acceleration vector
     ax.plot(
-        accel.sel(individuals=mouse_name, space=["y"]).squeeze(),
+        accel.sel(individuals=mouse_name, space=["y"]).squeeze(),
         label="ay",
     )
     ax.set_title(mouse_name)
@@ -816,26 +813,22 @@ 
                                                                                                                                                                                                                      Compute accelerationfig.tight_layout()
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      
-AEON3B_NTP, AEON3B_TP1, AEON3B_TP2
                                                                                                                                                                                                                      The norm of the acceleration vector is the magnitude of the
-acceleration.
-We can also represent this for each individual.
                                                                                                                                                                                                                      
+AEON3B_NTP, AEON3B_TP1, AEON3B_TP2
                                                                                                                                                                                                                      The can also represent the magnitude (norm) of the acceleration vector
+for each individual:
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      fig, axes = plt.subplots(3, 1, sharex=True, sharey=True)
-for mouse_name, ax in zip(accel.individuals.values, axes, strict=False):
-    # compute norm of the acceleration vector for one mouse
-    accel_one_mouse = np.linalg.norm(
-        accel.sel(individuals=mouse_name, space=["x", "y"]).squeeze(),
-        axis=1,
-    )
+for mouse_name, ax in zip(accel.individuals.values, axes, strict=False):
+    # compute magnitude of the acceleration vector for one mouse
+    accel_one_mouse = compute_norm(accel.sel(individuals=mouse_name))
 
     # plot acceleration against time
-    ax.plot(accel_one_mouse)
+    ax.plot(accel_one_mouse)
     ax.set_title(mouse_name)
     ax.set_xlabel("time (s)")
     ax.set_ylabel("accel (px/s**2)")
 fig.tight_layout()
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      
-AEON3B_NTP, AEON3B_TP1, AEON3B_TP2
                                                                                                                                                                                                                      Total running time of the script: (0 minutes 2.105 seconds)
                                                                                                                                                                                                                      
+AEON3B_NTP, AEON3B_TP1, AEON3B_TP2
                                                                                                                                                                                                                      Total running time of the script: (0 minutes 2.379 seconds)
                                                                                                                                                                                                                      
 
 
                                                                                                                                                                                                                      Gallery generated by Sphinx-Gallery
                                                                                                                                                                                                                      
 
@@ -938,7 +934,7 @@ 
                                                                                                                                                                                                                      Compute acceleration
       
         
                                                                                                                                                                                                                      
-    Created using Sphinx 7.4.5.
+    Created using Sphinx 8.0.2.
     
                                                                                                                                                                                                                      
     
                                                                                                                                                                                                                      
     
                                                                                                                                                                                                                      
diff --git a/examples/compute_polar_coordinates.html b/examples/compute_polar_coordinates.html
index 36d33931..3013b597 100644
--- a/examples/compute_polar_coordinates.html
+++ b/examples/compute_polar_coordinates.html
@@ -28,20 +28,20 @@
 
 
 
-    
+    
     
-    
+    
     
     
     
-    
+    
   
   
   
 
   
 
-    
+    
     
     
     
@@ -128,7 +128,7 @@
   
   
   
-    
                                                                                                                                                                                                                      movement v0.0.19
                                                                                                                                                                                                                      
+    
                                                                                                                                                                                                                      movement v0.0.20
                                                                                                                                                                                                                      
   
 
                                                                                                                                                                                                                      
     
@@ -449,7 +449,7 @@ 
                                                                                                                                                                                                                      Imports#<
 
 from movement import sample_data
 from movement.io import load_poses
-from movement.utils.vector import cart2pol, pol2cart
+from movement.utils.vector import cart2pol, pol2cart
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      
 
@@ -457,15 +457,15 @@ 
                                                                                                                                                                                                                      Imports#<
 
                                                                                                                                                                                                                      Load sample dataset#
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      In this tutorial, we will use a sample dataset with a single individual
 (a mouse) and six keypoints.
                                                                                                                                                                                                                      
-
                                                                                                                                                                                                                      ds_path = sample_data.fetch_dataset_paths(
+
                                                                                                                                                                                                                      ds_path = sample_data.fetch_dataset_paths(
     "SLEAP_single-mouse_EPM.analysis.h5"
 )["poses"]
-ds = load_poses.from_sleap_file(ds_path, fps=None)  # force time_unit = frames
+ds = load_poses.from_sleap_file(ds_path, fps=None)  # force time_unit = frames
 
-print(ds)
+print(ds)
 print("-----------------------------")
-print(f"Individuals: {ds.individuals.values}")
-print(f"Keypoints: {ds.keypoints.values}")
+print(f"Individuals: {ds.individuals.values}")
+print(f"Keypoints: {ds.keypoints.values}")
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      <xarray.Dataset> Size: 1MB
@@ -483,6 +483,7 @@ 
                                                                                                                                                                                                                      Load sample datasetds contains two data variables:position and
 confidence. Both are stored as data arrays. In this tutorial, we will
 use only position:
                                                                                                                                                                                                                      
-
                                                                                                                                                                                                                      position = ds.position
+
                                                                                                                                                                                                                      position = ds.position
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      
 
@@ -501,17 +502,17 @@ 
                                                                                                                                                                                                                      Compute head vector
                                                                                                                                                                                                                      # compute the midpoint between the ears
-midpoint_ears = position.sel(keypoints=["left_ear", "right_ear"]).mean(
+midpoint_ears = position.sel(keypoints=["left_ear", "right_ear"]).mean(
     dim="keypoints"
 )
 
 # compute the head vector
-head_vector = position.sel(keypoints="snout") - midpoint_ears
+head_vector = position.sel(keypoints="snout") - midpoint_ears
 
 # drop the keypoints dimension
 # (otherwise the `head_vector` data array retains a `snout` keypoint from the
 # operation above)
-head_vector = head_vector.drop_vars("keypoints")
+head_vector = head_vector.drop_vars("keypoints")
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      
 
@@ -522,13 +523,13 @@ 
                                                                                                                                                                                                                      Visualise the head trajectory
                                                                                                                                                                                                                      fig, ax = plt.subplots(1, 1)
-mouse_name = ds.individuals.values[0]
+mouse_name = ds.individuals.values[0]
 
 sc = ax.scatter(
-    midpoint_ears.sel(individuals=mouse_name, space="x"),
-    midpoint_ears.sel(individuals=mouse_name, space="y"),
+    midpoint_ears.sel(individuals=mouse_name, space="x"),
+    midpoint_ears.sel(individuals=mouse_name, space="y"),
     s=15,
-    c=midpoint_ears.time,
+    c=midpoint_ears.time,
     cmap="viridis",
     marker="o",
 )
@@ -538,7 +539,7 @@ 
                                                                                                                                                                                                                      Visualise the head trajectoryax.set_ylabel("y (pixels)")
 ax.invert_yaxis()
 ax.set_title(f"Head trajectory ({mouse_name})")
-fig.colorbar(sc, ax=ax, label=f"time ({ds.attrs['time_unit']})")
+fig.colorbar(sc, ax=ax, label=f"time ({ds.attrs['time_unit']})")
 fig.show()
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      
@@ -548,7 +549,7 @@ 
                                                                                                                                                                                                                      Visualise the head trajectory
                                                                                                                                                                                                                      # read sample frame
-frame_path = sample_data.fetch_dataset_paths(
+frame_path = sample_data.fetch_dataset_paths(
     "SLEAP_single-mouse_EPM.analysis.h5"
 )["frame"]
 im = plt.imread(frame_path)
@@ -560,10 +561,10 @@ 
                                                                                                                                                                                                                      Visualise the head trajectory# plot head trajectory with semi-transparent markers
 sc = ax.scatter(
-    midpoint_ears.sel(individuals=mouse_name, space="x"),
-    midpoint_ears.sel(individuals=mouse_name, space="y"),
+    midpoint_ears.sel(individuals=mouse_name, space="x"),
+    midpoint_ears.sel(individuals=mouse_name, space="y"),
     s=15,
-    c=midpoint_ears.time,
+    c=midpoint_ears.time,
     cmap="viridis",
     marker="o",
     alpha=0.05,  # transparency
@@ -597,38 +598,38 @@ 
                                                                                                                                                                                                                      Visualise the head vector
                                                                                                                                                                                                                      fig, ax = plt.subplots(1, 1)
-mouse_name = ds.individuals.values[0]
+mouse_name = ds.individuals.values[0]
 
 # plot midpoint between the ears, and color based on time
 sc = ax.scatter(
-    midpoint_ears.sel(individuals=mouse_name, space="x", time=time_window),
-    midpoint_ears.sel(individuals=mouse_name, space="y", time=time_window),
+    midpoint_ears.sel(individuals=mouse_name, space="x", time=time_window),
+    midpoint_ears.sel(individuals=mouse_name, space="y", time=time_window),
     s=50,
-    c=midpoint_ears.time[time_window],
+    c=midpoint_ears.time[time_window],
     cmap="viridis",
     marker="*",
 )
 
 # plot snout, and color based on time
 sc = ax.scatter(
-    position.sel(
+    position.sel(
         individuals=mouse_name, space="x", time=time_window, keypoints="snout"
     ),
-    position.sel(
+    position.sel(
         individuals=mouse_name, space="y", time=time_window, keypoints="snout"
     ),
     s=50,
-    c=position.time[time_window],
+    c=position.time[time_window],
     cmap="viridis",
     marker="o",
 )
 
 # plot the computed head vector
 ax.quiver(
-    midpoint_ears.sel(individuals=mouse_name, space="x", time=time_window),
-    midpoint_ears.sel(individuals=mouse_name, space="y", time=time_window),
-    head_vector.sel(individuals=mouse_name, space="x", time=time_window),
-    head_vector.sel(individuals=mouse_name, space="y", time=time_window),
+    midpoint_ears.sel(individuals=mouse_name, space="x", time=time_window),
+    midpoint_ears.sel(individuals=mouse_name, space="y", time=time_window),
+    head_vector.sel(individuals=mouse_name, space="x", time=time_window),
+    head_vector.sel(individuals=mouse_name, space="y", time=time_window),
     angles="xy",
     scale=1,
     scale_units="xy",
@@ -648,7 +649,7 @@ 
                                                                                                                                                                                                                      Visualise the head vectorfig.colorbar(
     sc,
     ax=ax,
-    label=f"time ({ds.attrs['time_unit']})",
+    label=f"time ({ds.attrs['time_unit']})",
     ticks=list(time_window)[0::2],
 )
 
@@ -672,9 +673,9 @@ 
                                                                                                                                                                                                                      Express the head vector in polar coordinatescart2pol:
                                                                                                                                                                                                                      
-
                                                                                                                                                                                                                      head_vector_polar = cart2pol(head_vector)
+
                                                                                                                                                                                                                      head_vector_polar = cart2pol(head_vector)
 
-print(head_vector_polar)
+print(head_vector_polar)
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      <xarray.DataArray 'position' (time: 18485, individuals: 1, space_pol: 2)> Size: 148kB
@@ -706,12 +707,12 @@ 
                                                                                                                                                                                                                      Histogram of rh
 
                                                                                                                                                                                                                      fig, ax = plt.subplots(1, 1)
 
 # plot histogram using xarray's built-in histogram function
-rho_data = head_vector_polar.sel(individuals=mouse_name, space_pol="rho")
-rho_data.plot.hist(bins=50, ax=ax, edgecolor="lightgray", linewidth=0.5)
+rho_data = head_vector_polar.sel(individuals=mouse_name, space_pol="rho")
+rho_data.plot.hist(bins=50, ax=ax, edgecolor="lightgray", linewidth=0.5)
 
 # add mean
 ax.axvline(
-    x=rho_data.mean().values,
+    x=rho_data.mean().values,
     c="b",
     linestyle="--",
 )
@@ -719,7 +720,7 @@ 
                                                                                                                                                                                                                      Histogram of rh
 
 # add median
 ax.axvline(
-    x=rho_data.median().values,
+    x=rho_data.median().values,
     c="r",
     linestyle="-",
 )
@@ -727,8 +728,8 @@ 
                                                                                                                                                                                                                      Histogram of rh
 # add legend
 ax.legend(
     [
-        f"mean = {np.nanmean(rho_data):.2f} pixels",
-        f"median = {np.nanmedian(rho_data):.2f} pixels",
+        f"mean = {np.nanmean(rho_data):.2f} pixels",
+        f"median = {np.nanmedian(rho_data):.2f} pixels",
     ],
     loc="best",
 )
@@ -754,7 +755,7 @@ 
                                                                                                                                                                                                                      Histogram of ph
 ax = fig.add_subplot(projection="polar")
 
 # plot histogram using xarray's built-in histogram function
-head_vector_polar.sel(individuals=mouse_name, space_pol="phi").plot.hist(
+head_vector_polar.sel(individuals=mouse_name, space_pol="phi").plot.hist(
     bins=np.linspace(-np.pi, np.pi, n_bins + 1), ax=ax
 )
 
@@ -786,7 +787,7 @@ 
                                                                                                                                                                                                                      Polar plot of the head vector within a time window
 
                                                                                                                                                                                                                      # select phi values within a time window
-phi = head_vector_polar.sel(
+phi = head_vector_polar.sel(
     individuals=mouse_name,
     space_pol="phi",
     time=time_window,
@@ -809,7 +810,7 @@ 
                                                                                                                                                                                                                      Polar plot of the head vector within a time windowcax = fig.colorbar(
     sc,
     ax=ax,
-    label=f"time ({ds.attrs['time_unit']})",
+    label=f"time ({ds.attrs['time_unit']})",
     ticks=list(time_window)[0::2],
 )
 
@@ -834,9 +835,9 @@ 
                                                                                                                                                                                                                      Polar plot of the head vector within a time windowConvert polar coordinates to cartesian#
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      movement also provides a pol2cart convenience function to transform
 a vector in polar coordinates back to cartesian.
                                                                                                                                                                                                                      
-
                                                                                                                                                                                                                      head_vector_cart = pol2cart(head_vector_polar)
+
                                                                                                                                                                                                                      head_vector_cart = pol2cart(head_vector_polar)
 
-print(head_vector_cart)
+print(head_vector_cart)
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      <xarray.DataArray 'position' (time: 18485, individuals: 1, space: 2)> Size: 148kB
@@ -849,7 +850,7 @@ 
                                                                                                                                                                                                                      Convert polar coordinates to cartesianspace dimension
 with two coordinates: x and y.
                                                                                                                                                                                                                      
-
                                                                                                                                                                                                                      Total running time of the script: (0 minutes 16.520 seconds)
                                                                                                                                                                                                                      
+
                                                                                                                                                                                                                      Total running time of the script: (0 minutes 16.565 seconds)
                                                                                                                                                                                                                      
                                                                                                                                                                                                                       
 
                                                                                                                                                                                                                      Gallery generated by Sphinx-Gallery
                                                                                                                                                                                                                      
 
@@ -956,7 +960,7 @@ 
                                                                                                                                                                                                                      Convert polar coordinates to cartesian
       
         
                                                                                                                                                                                                                      
-    Created using Sphinx 7.4.5.
+    Created using Sphinx 8.0.2.
     
                                                                                                                                                                                                                      
     
                                                                                                                                                                                                                      
     
                                                                                                                                                                                                                      
diff --git a/examples/filter_and_interpolate.html b/examples/filter_and_interpolate.html
index fd6f8f16..d55b532c 100644
--- a/examples/filter_and_interpolate.html
+++ b/examples/filter_and_interpolate.html
@@ -28,20 +28,20 @@
 
 
 
-    
+    
     
-    
+    
     
     
     
-    
+    
   
   
   
 
   
 
-    
+    
     
     
     
@@ -128,7 +128,7 @@
   
   
   
-    
                                                                                                                                                                                                                      movement v0.0.19
                                                                                                                                                                                                                      
+    
                                                                                                                                                                                                                      movement v0.0.20
                                                                                                                                                                                                                      
   
 
                                                                                                                                                                                                                      
     
@@ -447,8 +447,8 @@ 
                                                                                                                                                                                                                      Imports#<
 
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      Load a sample dataset#
                                                                                                                                                                                                                      
-
                                                                                                                                                                                                                      ds = sample_data.fetch_dataset("DLC_single-wasp.predictions.h5")
-print(ds)
+
                                                                                                                                                                                                                      ds = sample_data.fetch_dataset("DLC_single-wasp.predictions.h5")
+print(ds)
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      <xarray.Dataset> Size: 61kB
@@ -466,6 +466,7 @@ 
                                                                                                                                                                                                                      Load a sample dataset
                                                                                                                                                                                                                      
@@ -478,14 +479,14 @@ 
                                                                                                                                                                                                                      Load a sample dataset
 
                                                                                                                                                                                                                      Visualise the pose tracks#
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      Since the data contains only a single wasp, we use
-xarray.DataArray.squeeze() to remove
+xarray.DataArray.squeeze() to remove
 the dimension of length 1 from the data (the individuals dimension).
                                                                                                                                                                                                                      
-
                                                                                                                                                                                                                      ds.position.squeeze().plot.line(
+
                                                                                                                                                                                                                      ds.position.squeeze().plot.line(
     x="time", row="keypoints", hue="space", aspect=2, size=2.5
 )
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      
-keypoints = head, keypoints = stinger
                                                                                                                                                                                                                      <xarray.plot.facetgrid.FacetGrid object at 0x7faeaf004090>
+keypoints = head, keypoints = stinger
                                                                                                                                                                                                                      <xarray.plot.facetgrid.FacetGrid object at 0x7fbc07fa3550>
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      We can see that the pose tracks contain some implausible “jumps”, such
@@ -502,9 +503,9 @@ 
                                                                                                                                                                                                                      Visualise confidence scoresxarray.DataArray.squeeze() to remove the individuals dimension
+xarray.DataArray.squeeze() to remove the individuals dimension
 from the data.
                                                                                                                                                                                                                      
-
                                                                                                                                                                                                                      ds.confidence.squeeze().plot.hist(bins=20)
+
                                                                                                                                                                                                                      ds.confidence.squeeze().plot.hist(bins=20)
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      
 individuals = individual_0
                                                                                                                                                                                                                      (array([  61.,   13.,   16.,   10.,   10.,    8.,   21.,   11.,   14.,
@@ -519,12 +520,12 @@ 
                                                                                                                                                                                                                      Visualise confidence scores
                                                                                                                                                                                                                      ds.confidence.squeeze().plot.line(
+
                                                                                                                                                                                                                      ds.confidence.squeeze().plot.line(
     x="time", row="keypoints", aspect=2, size=2.5
 )
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      
-keypoints = head, keypoints = stinger
                                                                                                                                                                                                                      <xarray.plot.facetgrid.FacetGrid object at 0x7faea0dad290>
+keypoints = head, keypoints = stinger
                                                                                                                                                                                                                      <xarray.plot.facetgrid.FacetGrid object at 0x7fbc07614150>
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      Encouragingly, some of the drops in confidence scores do seem to correspond
@@ -541,9 +542,9 @@ 
                                                                                                                                                                                                                      Filter out points with low confidenceprint_report=True).
-We will use xarray.Dataset.update() to update ds in-place
+We will use xarray.Dataset.update() to update ds in-place
 with the filtered position.
                                                                                                                                                                                                                      
-
                                                                                                                                                                                                                      ds.update({"position": ds.move.filter_by_confidence()})
+
                                                                                                                                                                                                                      ds.update({"position": ds.move.filter_by_confidence()})
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      Missing points (marked as NaN) in input
@@ -589,6 +590,7 @@ 
                                                                                                                                                                                                                      Filter out points with low confidence
@@ -997,18 +1000,18 @@ 
                                                                                                                                                                                                                      Filter out points with low confidencemovement.filtering module would be:
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      from movement.filtering import filter_by_confidence
 
-ds.update({"position": filter_by_confidence(position, confidence)})
+ds.update({"position": filter_by_confidence(position, confidence)})
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      We can see that the filtering operation has introduced NaN values in the
 position data variable. Let’s visualise the filtered data.
                                                                                                                                                                                                                      
-
                                                                                                                                                                                                                      ds.position.squeeze().plot.line(
+
                                                                                                                                                                                                                      ds.position.squeeze().plot.line(
     x="time", row="keypoints", hue="space", aspect=2, size=2.5
 )
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      
-keypoints = head, keypoints = stinger
                                                                                                                                                                                                                      <xarray.plot.facetgrid.FacetGrid object at 0x7faea0db7a10>
+keypoints = head, keypoints = stinger
                                                                                                                                                                                                                      <xarray.plot.facetgrid.FacetGrid object at 0x7fbc0539c110>
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      Here we can see that gaps (consecutive NaNs) have appeared in the
@@ -1027,7 +1030,7 @@ 
                                                                                                                                                                                                                      Interpolate over missing valuesmax_gap=None would interpolate over all gaps, regardless of
 their length, but this should be used with caution as it can introduce
 spurious data. The print_report argument acts as described above.
                                                                                                                                                                                                                      
-
                                                                                                                                                                                                                      ds.update({"position": ds.move.interpolate_over_time(max_gap=40)})
+
                                                                                                                                                                                                                      ds.update({"position": ds.move.interpolate_over_time(max_gap=40)})
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      Missing points (marked as NaN) in input
@@ -1073,6 +1076,7 @@ 
                                                                                                                                                                                                                      Interpolate over missing values
@@ -1481,7 +1486,7 @@ 
                                                                                                                                                                                                                      Interpolate over missing valuesmovement.filtering module would be:
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      from movement.filtering import interpolate_over_time
 
-ds.update({"position": interpolate_over_time(
+ds.update({"position": interpolate_over_time(
     position_filtered, max_gap=40
 )})
 
                                                                                                                                                                                                                      
@@ -1490,12 +1495,12 @@ 
                                                                                                                                                                                                                      Interpolate over missing values
                                                                                                                                                                                                                      ds.position.squeeze().plot.line(
+
                                                                                                                                                                                                                      ds.position.squeeze().plot.line(
     x="time", row="keypoints", hue="space", aspect=2, size=2.5
 )
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      
-keypoints = head, keypoints = stinger
                                                                                                                                                                                                                      <xarray.plot.facetgrid.FacetGrid object at 0x7fae992e22d0>
+keypoints = head, keypoints = stinger
                                                                                                                                                                                                                      <xarray.plot.facetgrid.FacetGrid object at 0x7fbc053fad50>
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      
@@ -1507,17 +1512,17 @@ 
                                                                                                                                                                                                                      Log of processing stepslog attribute of the position data array.
 This is useful for keeping track of the processing steps that have been
 applied to the data. Let’s inspect the log entries.
                                                                                                                                                                                                                      
-
                                                                                                                                                                                                                      for log_entry in ds.position.log:
+
                                                                                                                                                                                                                      for log_entry in ds.position.log:
     print(log_entry)
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      
-
                                                                                                                                                                                                                      {'operation': 'filter_by_confidence', 'datetime': '2024-07-17 10:15:49.445284', 'confidence': <xarray.DataArray 'confidence' (time: 1085, individuals: 1, keypoints: 2)> Size: 17kB
+
                                                                                                                                                                                                                      {'operation': 'filter_by_confidence', 'datetime': '2024-09-06 12:30:55.519032', 'confidence': <xarray.DataArray 'confidence' (time: 1085, individuals: 1, keypoints: 2)> Size: 17kB
 0.05305 0.07366 0.03532 0.03293 0.01707 0.01022 ... 0.0 0.0 0.0 0.0 0.0 0.0
 Coordinates:
   * time         (time) float64 9kB 0.0 0.025 0.05 0.075 ... 27.05 27.07 27.1
   * individuals  (individuals) <U12 48B 'individual_0'
   * keypoints    (keypoints) <U7 56B 'head' 'stinger'}
-{'operation': 'interpolate_over_time', 'datetime': '2024-07-17 10:15:50.903194', 'max_gap': 40}
+{'operation': 'interpolate_over_time', 'datetime': '2024-09-06 12:30:56.977758', 'max_gap': 40}
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      
 
@@ -1538,13 +1543,13 @@ 
                                                                                                                                                                                                                      Filtering multiple data variablesds, based on the confidence scores, we can specify
 data_vars=["position", "velocity"] in the method call.
 As the filtered data variables are returned as a dictionary, we can once
-again use xarray.Dataset.update() to update ds in-place
+again use xarray.Dataset.update() to update ds in-place
 with the filtered data variables.
                                                                                                                                                                                                                      
-
                                                                                                                                                                                                                      ds["velocity"] = ds.move.compute_velocity()
-filtered_data_dict = ds.move.filter_by_confidence(
+
                                                                                                                                                                                                                      ds["velocity"] = ds.move.compute_velocity()
+filtered_data_dict = ds.move.filter_by_confidence(
     data_vars=["position", "velocity"]
 )
-ds.update(filtered_data_dict)
+ds.update(filtered_data_dict)
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      Missing points (marked as NaN) in input
@@ -1600,6 +1605,7 @@ 
                                                                                                                                                                                                                      Filtering multiple data variablesTotal running time of the script: (0 minutes 3.496 seconds)
                                                                                                                                                                                                                      
+
                                                                                                                                                                                                                      Total running time of the script: (0 minutes 2.401 seconds)
                                                                                                                                                                                                                      
                                                                                                                                                                                                                       
 
                                                                                                                                                                                                                      Gallery generated by Sphinx-Gallery
                                                                                                                                                                                                                      
 
@@ -2143,7 +2148,7 @@ 
                                                                                                                                                                                                                      Filtering multiple data variables
       
         
                                                                                                                                                                                                                      
-    Created using Sphinx 7.4.5.
+    Created using Sphinx 8.0.2.
     
                                                                                                                                                                                                                      
     
                                                                                                                                                                                                                      
     
                                                                                                                                                                                                                      
diff --git a/examples/index.html b/examples/index.html
index da1df7de..65bbb78b 100644
--- a/examples/index.html
+++ b/examples/index.html
@@ -28,20 +28,20 @@
 
 
 
-    
+    
     
-    
+    
     
     
     
-    
+    
   
   
   
 
   
 
-    
+    
     
     
     
@@ -52,7 +52,7 @@
     
     
     
-    
+    
   
   
   
@@ -128,7 +128,7 @@
   
   
   
-    
                                                                                                                                                                                                                      movement v0.0.19
                                                                                                                                                                                                                      
+    
                                                                                                                                                                                                                      movement v0.0.20
                                                                                                                                                                                                                      
   
 
                                                                                                                                                                                                                      
     
@@ -474,7 +474,7 @@
       
       
                                                                                                                                                                                                                      
         
                                                                                                                                                                                                                      previous
                                                                                                                                                                                                                      
-        
                                                                                                                                                                                                                      The movement dataset
                                                                                                                                                                                                                      
+        
                                                                                                                                                                                                                      The movement datasets
                                                                                                                                                                                                                      
       
                                                                                                                                                                                                                      
     
     
       
         
                                                                                                                                                                                                                      
-    Created using Sphinx 7.4.5.
+    Created using Sphinx 8.0.2.
     
                                                                                                                                                                                                                      
     
                                                                                                                                                                                                                      
     
                                                                                                                                                                                                                      
diff --git a/examples/load_and_explore_poses.html b/examples/load_and_explore_poses.html
index 61c7a747..ac937f35 100644
--- a/examples/load_and_explore_poses.html
+++ b/examples/load_and_explore_poses.html
@@ -28,20 +28,20 @@
 
 
 
-    
+    
     
-    
+    
     
     
     
-    
+    
   
   
   
 
   
 
-    
+    
     
     
     
@@ -128,7 +128,7 @@
   
   
   
-    
                                                                                                                                                                                                                      movement v0.0.19
                                                                                                                                                                                                                      
+    
                                                                                                                                                                                                                      movement v0.0.20
                                                                                                                                                                                                                      
   
 
                                                                                                                                                                                                                      
     
@@ -458,7 +458,7 @@ 
                                                                                                                                                                                                                      Define the file path
 
                                                                                                                                                                                                                      For the sake of this example, we will use the path to one of
 the sample datasets provided with movement.
                                                                                                                                                                                                                      
-
                                                                                                                                                                                                                      file_path = sample_data.fetch_dataset_paths(
+
                                                                                                                                                                                                                      file_path = sample_data.fetch_dataset_paths(
     "SLEAP_three-mice_Aeon_proofread.analysis.h5"
 )["poses"]
 print(file_path)
@@ -470,8 +470,8 @@ 
                                                                                                                                                                                                                      Define the file path
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      Load the data into movement#
                                                                                                                                                                                                                      
-
                                                                                                                                                                                                                      ds = load_poses.from_sleap_file(file_path, fps=50)
-print(ds)
+
                                                                                                                                                                                                                      ds = load_poses.from_sleap_file(file_path, fps=50)
+print(ds)
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      <xarray.Dataset> Size: 27kB
@@ -489,12 +489,13 @@ 
                                                                                                                                                                                                                      Load the data into movementposition and confidence.
 To get the position data:
                                                                                                                                                                                                                      
-
                                                                                                                                                                                                                      position = ds.position
+
                                                                                                                                                                                                                      position = ds.position
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      
@@ -503,8 +504,8 @@ 
                                                                                                                                                                                                                      Select and plot data with xarraysel method to index into xarray objects.
 For example, we can get a DataArray containing only data
 for a single keypoint of the first individual:
                                                                                                                                                                                                                      
-
                                                                                                                                                                                                                      da = position.sel(individuals="AEON3B_NTP", keypoints="centroid")
-print(da)
+
                                                                                                                                                                                                                      da = position.sel(individuals="AEON3B_NTP", keypoints="centroid")
+print(da)
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      <xarray.DataArray 'position' (time: 601, space: 2)> Size: 5kB
@@ -518,19 +519,19 @@ 
                                                                                                                                                                                                                      Select and plot data with xarrayxarray’s built-in plotting methods:
                                                                                                                                                                                                                      
-
                                                                                                                                                                                                                      da.plot.line(x="time", row="space", aspect=2, size=2.5)
+
                                                                                                                                                                                                                      da.plot.line(x="time", row="space", aspect=2, size=2.5)
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      
-space = x, space = y
                                                                                                                                                                                                                      <xarray.plot.facetgrid.FacetGrid object at 0x7fae95f69f50>
+space = x, space = y
                                                                                                                                                                                                                      <xarray.plot.facetgrid.FacetGrid object at 0x7fbbfd7e4790>
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      Similarly we could plot the same keypoint’s x, y coordinates
 for all individuals:
                                                                                                                                                                                                                      
-
                                                                                                                                                                                                                      da = position.sel(keypoints="centroid")
-da.plot.line(x="time", row="individuals", aspect=2, size=2.5)
+
                                                                                                                                                                                                                      da = position.sel(keypoints="centroid")
+da.plot.line(x="time", row="individuals", aspect=2, size=2.5)
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      
-individuals = AEON3B_NTP, individuals = AEON3B_TP1, individuals = AEON3B_TP2
                                                                                                                                                                                                                      <xarray.plot.facetgrid.FacetGrid object at 0x7fae95f64b50>
+individuals = AEON3B_NTP, individuals = AEON3B_TP1, individuals = AEON3B_TP2
                                                                                                                                                                                                                      <xarray.plot.facetgrid.FacetGrid object at 0x7fbbfd7a13d0>
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      
 
@@ -542,10 +543,10 @@ 
                                                                                                                                                                                                                      Trajectory plots
                                                                                                                                                                                                                      mouse_name = "AEON3B_TP1"
 
 plt.scatter(
-    da.sel(individuals=mouse_name, space="x"),
-    da.sel(individuals=mouse_name, space="y"),
+    da.sel(individuals=mouse_name, space="x"),
+    da.sel(individuals=mouse_name, space="y"),
     s=2,
-    c=da.time,
+    c=da.time,
     cmap="viridis",
 )
 plt.title(f"Trajectory of {mouse_name}")
@@ -554,10 +555,10 @@ 
                                                                                                                                                                                                                      Trajectory plotsplt.colorbar(label="time (sec)")
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      
-Trajectory of AEON3B_TP1
                                                                                                                                                                                                                      <matplotlib.colorbar.Colorbar object at 0x7faea0bf2250>
+Trajectory of AEON3B_TP1
                                                                                                                                                                                                                      <matplotlib.colorbar.Colorbar object at 0x7fbc0556f290>
 
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      
-
                                                                                                                                                                                                                      Total running time of the script: (0 minutes 0.637 seconds)
                                                                                                                                                                                                                      
+
                                                                                                                                                                                                                      Total running time of the script: (0 minutes 0.713 seconds)
                                                                                                                                                                                                                      
                                                                                                                                                                                                                       
 
                                                                                                                                                                                                                      Gallery generated by Sphinx-Gallery
                                                                                                                                                                                                                      
 
@@ -659,7 +663,7 @@ 
                                                                                                                                                                                                                      Trajectory plots
       
         
                                                                                                                                                                                                                      
-    Created using Sphinx 7.4.5.
+    Created using Sphinx 8.0.2.
     
                                                                                                                                                                                                                      
     
                                                                                                                                                                                                                      
     
                                                                                                                                                                                                                      
diff --git a/examples/sg_execution_times.html b/examples/sg_execution_times.html
index 1e6e972d..765803df 100644
--- a/examples/sg_execution_times.html
+++ b/examples/sg_execution_times.html
@@ -28,20 +28,20 @@
 
 
 
-    
+    
     
-    
+    
     
     
     
-    
+    
   
   
   
 
   
 
-    
+    
     
     
     
@@ -126,7 +126,7 @@
   
   
   
-    
                                                                                                                                                                                                                      movement v0.0.19
                                                                                                                                                                                                                      
+    
                                                                                                                                                                                                                      movement v0.0.20
                                                                                                                                                                                                                      
   
 
                                                                                                                                                                                                                      
     
@@ -413,7 +413,7 @@
                   
   
                                                                                                                                                                                                                      
 
                                                                                                                                                                                                                      Computation times#
                                                                                                                                                                                                                      
-
                                                                                                                                                                                                                      00:24.360 total execution time for 5 files from examples:
                                                                                                                                                                                                                      
+
                                                                                                                                                                                                                      00:23.826 total execution time for 5 files from examples: