diff --git a/genindex.html b/genindex.html index 7c6abf9..66c118f 100644 --- a/genindex.html +++ b/genindex.html @@ -562,6 +562,8 @@

P

  • @@ -657,12 +659,8 @@

    S

  • start_ts (pyneon.events.NeonEV property)
    • -
  • sync_gaze_to_video() (in module pyneon.video) - -
    • diff --git a/objects.inv b/objects.inv index c4f7cab..48a95ad 100644 Binary files a/objects.inv and b/objects.inv differ diff --git a/reference/index.html b/reference/index.html index 1b86c59..2b2638b 100644 --- a/reference/index.html +++ b/reference/index.html @@ -379,7 +379,6 @@
  • Scene video class
    • diff --git a/reference/recording.html b/reference/recording.html index 5657ce7..5ee3c23 100644 --- a/reference/recording.html +++ b/reference/recording.html @@ -602,39 +602,37 @@

    NeonRecording class
    -sync_gaze_to_video(window_size: int | None = None) → NeonGaze#
    +sync_gaze_to_video(window_size: int | None = None, inplace: bool = False) → NeonGaze | None#

    Synchronize gaze data to video frames by applying windowed averaging -around each video frame timestamp.

    -
    -

    Parameters:#

    -
    -
    recNeonRecording

    Recording object containing gaze and video data.

    -
    -
    window_sizeint, optional

    The size of the time window (in nanoseconds) +around timestamps of each video frame. +See pyneon.stream.NeonStream.window_average() for details.

    +
    +
    Parameters:
    +
      +

    • window_size (int, optional) – The size of the time window (in nanoseconds) over which to compute the average around each new timestamp. If None (default), the window size is set to the median interval between the new timestamps, i.e., np.median(np.diff(new_ts)). The window size must be larger than the median interval between the original data timestamps, -i.e., window_size > np.median(np.diff(data.index)).

      +i.e., window_size > np.median(np.diff(data.index)).

      • +

    • inplace (bool, optional) – Whether to replace the gaze data in the instance with the window averaged data.

      • +
    -
    -
    -
    returns:
    -

    Gaze object containing data synchronized to video frames.

    +
    Returns:
    +

    Gaze object containing data synchronized to video frames.

    -
    rtype:
    -

    NeonGaze

    +
    Return type:
    +

    NeonGaze

    -
    estimate_scanpath(sync_gaze: NeonGaze | None = None, lk_params: dict | None = None) → DataFrame#

    Map fixations to video frames.

    -
    -

    Parameters:#

    +
    +

    Parameters:#

    sync_gazeNeonGaze

    Gaze data synchronized to video frames. If None (default), a windowed average is applied to synchronize gaze data to video frames.

    @@ -647,7 +645,7 @@

    Parameters:#<
    -plot_scanpath_on_video(scanpath: DataFrame, circle_radius: int = 10, line_thickness: int | None = 2, max_fixations: int = 10, show_video: bool = False, video_output_path: Path | str | None = 'scanpath.mp4') → None#
    +plot_scanpath_on_video(scanpath: DataFrame | None = None, circle_radius: int = 10, line_thickness: int = 2, max_fixations: int = 10, show_video: bool = False, video_output_path: Path | str = 'scanpath.mp4') → None#

    Plot scanpath on top of the video frames. The resulting video can be displayed and/or saved.

    Parameters:
    @@ -685,13 +683,13 @@

    Parameters:#<

    Notes

    Motion-BIDS is an extension to the Brain Imaging Data Structure (BIDS) to -standardize the organization of motion data for reproducible research [1]. +standardize the organization of motion data for reproducible research [1]. For more information, see https://bids-specification.readthedocs.io/en/stable/modality-specific-files/motion.html.

    References

    -
    - -
    -
    -pyneon.video.sync_gaze_to_video(rec: NeonRecording, window_size: int | None = None) → DataFrame#
    -

    Synchronize gaze data to video frames by applying windowed averaging -around each video frame timestamp. See window_average() for details -on the averaging process.

    -
    -

    Parameters:#

    -
    -
    recNeonRecording

    Recording object containing gaze and video data.

    -
    -
    window_sizeint, optional

    The size of the time window (in nanoseconds) -over which to compute the average around each new timestamp. -If None (default), the window size is set to the median interval -between the new timestamps, i.e., np.median(np.diff(new_ts)). -The window size must be larger than the median interval between the original data timestamps, -i.e., window_size > np.median(np.diff(data.index)).

    -
    -
    -
    -
    -

    Returns:#

    -
    -
    pd.DataFrame

    DataFrame containing gaze data mapped to video timestamps.

    +
    +
    +plot_scanpath_on_video(scanpath: DataFrame, circle_radius: int = 10, line_thickness: int = 2, max_fixations: int = 10, show_video: bool = False, video_output_path: Path | str = 'scanpath.mp4') → None#
    +

    Plot scanpath on top of the video frames. The resulting video can be displayed and/or saved.

    +
    +
    Parameters:
    +
      +

    • scanpath (pandas.DataFrame) – DataFrame containing the fixations and gaze data.

      • +

    • circle_radius (int) – Radius of the fixation circles in pixels. Defaults to 10.

      • +

    • line_thickness (int or None) – Thickness of the lines connecting fixations. If None, no lines are drawn. +Defaults to 2.

      • +

    • max_fixations (int) – Maximum number of fixations to plot per frame. Defaults to 10.

      • +

    • show_video (bool) – Whether to display the video with fixations overlaid. Defaults to False.

      • +

    • video_output_path (pathlib.Path or str or None) – Path to save the video with fixations overlaid. If None, the video is not saved. +Defaults to ‘scanpath.mp4’.

      • +
    -
    +
    +
    @@ -568,9 +559,9 @@

    Returns:#
  • NeonVideo.width
  • NeonVideo.height
  • NeonVideo.plot_frame()
    • +
  • NeonVideo.plot_scanpath_on_video()
    • -
  • sync_gaze_to_video()
  • estimate_scanpath()
    • diff --git a/reference/vis.html b/reference/vis.html index 4f67260..697127c 100644 --- a/reference/vis.html +++ b/reference/vis.html @@ -418,7 +418,7 @@
    -pyneon.vis.plot_scanpath_on_video(video: NeonVideo, scanpath: DataFrame, circle_radius: int = 10, line_thickness: int | None = 2, max_fixations: int = 10, show_video: bool = False, video_output_path: Path | str | None = 'scanpath.mp4') → None#
    +pyneon.vis.plot_scanpath_on_video(video: NeonVideo, scanpath: DataFrame, circle_radius: int = 10, line_thickness: int = 2, max_fixations: int = 10, show_video: bool = False, video_output_path: Path | str | None = 'scanpath.mp4') → None#

    Plot scanpath on top of the video frames. The resulting video can be displayed and/or saved.

    Parameters:
    diff --git a/searchindex.js b/searchindex.js index e7d7a8b..784140d 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"alltitles": {"1. Setup: Loading a Neon Recording": [[15, "1.-Setup:-Loading-a-Neon-Recording"]], "2. Mapping Gaze Data to Video Frames": [[15, "2.-Mapping-Gaze-Data-to-Video-Frames"]], "3. Estimating the Scanpath": [[15, "3.-Estimating-the-Scanpath"]], "4. Understanding Fixation Status": [[15, "4.-Understanding-Fixation-Status"]], "5. Overlaying Fixations on the Video": [[15, "5.-Overlaying-Fixations-on-the-Video"]], "An example plot of cropped data": [[14, "An-example-plot-of-cropped-data"]], "Concatenating different streams": [[13, "Concatenating-different-streams"]], "Conclusion": [[10, "Conclusion"]], "Data and metadata of a NeonRecording": [[14, "Data-and-metadata-of-a-NeonRecording"]], "Data as DataFrames": [[14, "Data-as-DataFrames"]], "Data format": [[0, "data-format"]], "Data stream classes (gaze, eye states, IMU)": [[7, null]], "Event classes (blinks, fixations, saccades, events)": [[2, null]], "Export Neon data recording to BIDS formats": [[11, null]], "Exportation module": [[3, null]], "Installation": [[0, "installation"]], "Interpolate data and concatenate streams": [[13, null]], "Interpolating data streams": [[13, "Interpolating-data-streams"]], "Irregular sampling in data streams": [[13, "Irregular-sampling-in-data-streams"]], "License": [[0, "license"]], "NeonDataset class": [[1, null]], "NeonRecording class": [[6, null]], "Parameters:": [[6, "parameters"], [6, "id1"], [8, "parameters"]], "Preprocessing module": [[5, null]], "PyNeon API": [[4, null]], "PyNeon Tutorials": [[12, null]], "Reading a Neon dataset/recording": [[14, null]], "Reading sample data": [[14, "Reading-sample-data"]], "Returns:": [[8, "returns"]], "Scene video and scanpath mapping": [[15, null]], "Scene video class": [[8, null]], "Step 1: Loading Sample Data": [[10, "Step-1:-Loading-Sample-Data"]], "Step 2: Constructing Event Times": [[10, "Step-2:-Constructing-Event-Times"]], "Step 3: Verifying Event Intervals": [[10, "Step-3:-Verifying-Event-Intervals"]], "Step 4: Creating Epochs from the Data": [[10, "Step-4:-Creating-Epochs-from-the-Data"]], "Step 5: Initializing the Epoch Class": [[10, "Step-5:-Initializing-the-Epoch-Class"]], "Step 6: Converting Epochs to NumPy Array": [[10, "Step-6:-Converting-Epochs-to-NumPy-Array"]], "Step 7: Averaging Across Epochs": [[10, "Step-7:-Averaging-Across-Epochs"]], "Step 8: Averaging Over Time": [[10, "Step-8:-Averaging-Over-Time"]], "Summary": [[15, "Summary"]], "Tutorial: Processing Eye-Tracking Data with PyNeon": [[10, null]], "Useful attributes and methods for NeonStream and NeonEV": [[14, "Useful-attributes-and-methods-for-NeonStream-and-NeonEV"]], "Visualization module": [[9, null]], "Visualizing gaze heatmap": [[14, "Visualizing-gaze-heatmap"]], "Welcome to PyNeon documentation": [[0, null]]}, "docnames": ["index", "reference/dataset", "reference/events", "reference/export", "reference/index", "reference/preprocess", "reference/recording", "reference/stream", "reference/video", "reference/vis", "tutorials/epoching", "tutorials/export_to_bids", "tutorials/index", "tutorials/interpolate_and_concat", "tutorials/read_recording", "tutorials/video"], "envversion": {"nbsphinx": 4, "sphinx": 64, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, 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