Fix and relax bboxes requirements

movement/io/load_bboxes.py

@@ -13,7 +13,11 @@
 
 from movement.utils.logging import log_error
 from movement.validators.datasets import ValidBboxesDataset
-from movement.validators.files import ValidFile, ValidVIATracksCSV
+from movement.validators.files import (
+    DEFAULT_FRAME_REGEXP,
+    ValidFile,
+    ValidVIATracksCSV,
+)
 
 logger = logging.getLogger(__name__)
 
@@ -58,7 +62,7 @@ def from_numpy(
         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.
+        these need to be integers sorted in increasing order.
     fps : float, optional
         The video sampling rate. If None (default), the ``time`` coordinates
         of the resulting ``movement`` dataset will be in frame numbers. If
@@ -151,6 +155,7 @@ def from_file(
     source_software: Literal["VIA-tracks"],
     fps: float | None = None,
     use_frame_numbers_from_file: bool = False,
+    frame_regexp: str = DEFAULT_FRAME_REGEXP,
 ) -> xr.Dataset:
     """Create a ``movement`` bounding boxes dataset from a supported file.
 
@@ -180,6 +185,12 @@ def from_file(
         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.
+    frame_regexp : str, optional
+        Regular expression pattern to extract the frame number from the frame
+        filename. By default, the frame number is expected to be encoded in
+        the filename as an integer number led by at least one zero, followed
+        by the file extension.
+
 
     Returns
     -------
@@ -214,6 +225,7 @@ def from_file(
             file_path,
             fps,
             use_frame_numbers_from_file=use_frame_numbers_from_file,
+            frame_regexp=frame_regexp,
         )
     else:
         raise log_error(
@@ -225,6 +237,7 @@ def from_via_tracks_file(
     file_path: Path | str,
     fps: float | None = None,
     use_frame_numbers_from_file: bool = False,
+    frame_regexp: str = DEFAULT_FRAME_REGEXP,
 ) -> xr.Dataset:
     """Create a ``movement`` dataset from a VIA tracks .csv file.
 
@@ -248,6 +261,11 @@ def from_via_tracks_file(
         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.
+    frame_regexp : str, optional
+        Regular expression pattern to extract the frame number from the frame
+        filename. By default, the frame number is expected to be encoded in
+        the filename as an integer number led by at least one zero, followed
+        by the file extension.
 
     Returns
     -------
@@ -316,17 +334,19 @@ def from_via_tracks_file(
     )
 
     # Specific VIA-tracks .csv file validation
-    via_file = ValidVIATracksCSV(file.path)
+    via_file = ValidVIATracksCSV(file.path, frame_regexp=frame_regexp)
     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)
+    bboxes_arrays = _numpy_arrays_from_via_tracks_file(
+        via_file.path, via_file.frame_regexp
+    )
     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()
+            f"id_{id.item()}" for id in bboxes_arrays["ID_array"]
         ],
         frame_array=(
             bboxes_arrays["frame_array"]
@@ -346,7 +366,9 @@ def from_via_tracks_file(
     return ds
 
 
-def _numpy_arrays_from_via_tracks_file(file_path: Path) -> dict:
+def _numpy_arrays_from_via_tracks_file(
+    file_path: Path, frame_regexp: str = DEFAULT_FRAME_REGEXP
+) -> dict:
     """Extract numpy arrays from the input VIA tracks .csv file.
 
     The extracted numpy arrays are returned in a dictionary with the following
@@ -369,6 +391,12 @@ def _numpy_arrays_from_via_tracks_file(file_path: Path) -> dict:
     file_path : pathlib.Path
         Path to the VIA tracks .csv file containing the bounding boxes' tracks.
 
+    frame_regexp : str
+        Regular expression pattern to extract the frame number from the frame
+        filename. By default, the frame number is expected to be encoded in
+        the filename as an integer number led by at least one zero, followed
+        by the file extension.
+
     Returns
     -------
     dict
@@ -378,7 +406,7 @@ def _numpy_arrays_from_via_tracks_file(file_path: Path) -> dict:
     # 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)
+    df = _df_from_via_tracks_file(file_path, frame_regexp)
 
     # Compute indices of the rows where the IDs switch
     bool_id_diff_from_prev = df["ID"].ne(df["ID"].shift())  # pandas series
@@ -398,8 +426,11 @@ def _numpy_arrays_from_via_tracks_file(file_path: Path) -> dict:
             df[map_key_to_columns[key]].to_numpy(),
             indices_id_switch,  # indices along axis=0
         )
+        array_dict[key] = np.stack(list_arrays, axis=1)
 
-        array_dict[key] = np.stack(list_arrays, axis=1).squeeze()
+        # squeeze only last dimension if it is 1
+        if array_dict[key].shape[-1] == 1:
+            array_dict[key] = array_dict[key].squeeze(axis=-1)
 
     # Transform position_array to represent centroid of bbox,
     # rather than top-left corner
@@ -413,7 +444,9 @@ def _numpy_arrays_from_via_tracks_file(file_path: Path) -> dict:
     return array_dict
 
 
-def _df_from_via_tracks_file(file_path: Path) -> pd.DataFrame:
+def _df_from_via_tracks_file(
+    file_path: Path, frame_regexp: str = DEFAULT_FRAME_REGEXP
+) -> pd.DataFrame:
     """Load VIA tracks .csv file as a dataframe.
 
     Read the VIA tracks .csv file as a pandas dataframe with columns:
@@ -429,6 +462,10 @@ def _df_from_via_tracks_file(file_path: Path) -> pd.DataFrame:
     empty frames are filled in with NaNs. The coordinates of the bboxes
     are assumed to be in the image coordinate system (i.e., the top-left
     corner of a bbox is its corner with minimum x and y coordinates).
+
+    The frame number is extracted from the filename using the provided
+    regexp if it is not defined as a 'file_attribute' in the VIA tracks .csv
+    file.
     """
     # Read VIA tracks .csv file as a pandas dataframe
     df_file = pd.read_csv(file_path, sep=",", header=0)
@@ -439,7 +476,9 @@ def _df_from_via_tracks_file(file_path: Path) -> 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),
+            "frame_number": _extract_frame_number_from_via_tracks_df(
+                df_file, frame_regexp
+            ),
             "x": _via_attribute_column_to_numpy(
                 df_file, "region_shape_attributes", ["x"], float
             ),
@@ -473,7 +512,7 @@ def _df_from_via_tracks_file(file_path: Path) -> pd.DataFrame:
     return df
 
 
-def _extract_confidence_from_via_tracks_df(df) -> np.ndarray:
+def _extract_confidence_from_via_tracks_df(df: pd.DataFrame) -> np.ndarray:
     """Extract confidence scores from the VIA tracks input dataframe.
 
     Parameters
@@ -504,7 +543,9 @@ def _extract_confidence_from_via_tracks_df(df) -> np.ndarray:
     return bbox_confidence
 
 
-def _extract_frame_number_from_via_tracks_df(df) -> np.ndarray:
+def _extract_frame_number_from_via_tracks_df(
+    df: pd.DataFrame, frame_regexp: str = DEFAULT_FRAME_REGEXP
+) -> np.ndarray:
     """Extract frame numbers from the VIA tracks input dataframe.
 
     Parameters
@@ -513,14 +554,20 @@ def _extract_frame_number_from_via_tracks_df(df) -> np.ndarray:
         The VIA tracks input dataframe is the one obtained from
         ``df = pd.read_csv(file_path, sep=",", header=0)``.
 
+    frame_regexp : str
+        Regular expression pattern to extract the frame number from the frame
+        filename. By default, the frame number is expected to be encoded in
+        the filename as an integer number led by at least one zero, followed by
+        the file extension.
+
     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.
+        integer number led by at least one zero, followed by the file
+        extension.
 
     """
     # Extract frame number from file_attributes if exists
@@ -534,10 +581,9 @@ def _extract_frame_number_from_via_tracks_df(df) -> np.ndarray:
         )
     # 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)
+            int(re.search(frame_regexp, f).group(1))  # type: ignore
+            if re.search(frame_regexp, f)
             else np.nan
             for f in df["filename"]
         ]

movement/validators/datasets.py

@@ -349,11 +349,12 @@ def _validate_frame_array(self, attribute, value):
                 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):
+            # check frames are monotonically increasing
+            if not np.all(np.diff(value, axis=0) >= 1):
                 raise log_error(
                     ValueError,
-                    f"Frame numbers in {attribute.name} are not continuous.",
+                    f"Frame numbers in {attribute.name} are not monotonically "
+                    "increasing.",
                 )
 
     # Define defaults

movement/validators/files.py

@@ -12,6 +12,8 @@
 
 from movement.utils.logging import log_error
 
+DEFAULT_FRAME_REGEXP = r"(0\d*)\.\w+$"
+
 
 @define
 class ValidFile:
@@ -234,6 +236,11 @@ class ValidVIATracksCSV:
     ----------
     path : pathlib.Path
         Path to the VIA tracks .csv file.
+    frame_regexp : str
+        Regular expression pattern to extract the frame number from the
+        filename. By default, the frame number is expected to be encoded in
+        the filename as an integer number led by at least one zero, followed
+        by the file extension.
 
     Raises
     ------
@@ -243,6 +250,7 @@ class ValidVIATracksCSV:
     """
 
     path: Path = field(validator=validators.instance_of(Path))
+    frame_regexp: str = DEFAULT_FRAME_REGEXP
 
     @path.validator
     def _file_contains_valid_header(self, attribute, value):
@@ -281,8 +289,10 @@ def _file_contains_valid_frame_numbers(self, attribute, value):
           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.
+        it is expected to be captured by the regular expression in the
+        `frame_regexp` attribute of the ValidVIATracksCSV object. The default
+        regexp matches an integer led by at least one zero, followed by the
+        file extension.
 
         """
         df = pd.read_csv(value, sep=",", header=0)
@@ -294,40 +304,15 @@ def _file_contains_valid_frame_numbers(self, attribute, value):
 
         # 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
-
+            list_frame_numbers = (
+                self._extract_frame_numbers_from_file_attributes(
+                    df, file_attributes_dicts
+                )
+            )
         # 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).",
-                    )
+            list_frame_numbers = self._extract_frame_numbers_using_regexp(df)
 
         # Check we have as many unique frame numbers as unique image files
         if len(set(list_frame_numbers)) != len(df.filename.unique()):
@@ -339,6 +324,62 @@ def _file_contains_valid_frame_numbers(self, attribute, value):
                 "file. ",
             )
 
+    def _extract_frame_numbers_from_file_attributes(
+        self, df, file_attributes_dicts
+    ):
+        """Get frame numbers from the 'frame' key under 'file_attributes'."""
+        list_frame_numbers = []
+        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
+        return list_frame_numbers
+
+    def _extract_frame_numbers_using_regexp(self, df):
+        """Get frame numbers from the file names using the provided regexp."""
+        list_frame_numbers = []
+        for f_i, f in enumerate(df["filename"]):
+            # try compiling the frame regexp
+            try:
+                regex_match = re.search(self.frame_regexp, f)
+            except re.error as e:
+                raise log_error(
+                    re.error,
+                    "The provided regular expression for the frame "
+                    f"numbers ({self.frame_regexp}) could not be compiled."
+                    " Please review its syntax.",
+                ) from e
+            # try extracting the frame number from the filename using the
+            # compiled regexp
+            try:
+                list_frame_numbers.append(int(regex_match.group(1)))  # type: ignore
+            except AttributeError as e:
+                raise log_error(
+                    AttributeError,
+                    f"{f} (row {f_i}): The frame regexp did not "
+                    "return any matches and 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 before the file extension "
+                    "(e.g. 00234.png).",
+                ) from e
+            except ValueError as e:
+                raise log_error(
+                    ValueError,
+                    f"{f} (row {f_i}): "
+                    "The frame number extracted from the filename using "
+                    f"the provided regexp ({self.frame_regexp}) could not "
+                    "be cast as an integer.",
+                ) from e
+
+        return list_frame_numbers
+
     @path.validator
     def _file_contains_tracked_bboxes(self, attribute, value):
         """Ensure that the VIA tracks .csv contains tracked bounding boxes.