SimaSegmentationExtractor#

class SimaSegmentationExtractor(file_path: str | Path, sima_segmentation_label: str = 'auto_ROIs')[source]#

Bases: SegmentationExtractor

A segmentation extractor for Sima.

This class inherits from the SegmentationExtractor class, having all its functionality specifically applied to the dataset output from the ‘SIMA’ ROI segmentation method.

Create a SegmentationExtractor instance from a sima file.

Parameters:

  • file_path (str or Path) – The location of the folder containing dataset.sima file and the raw image file(s) (tiff, h5, .zip)

  • sima_segmentation_label (str) – name of the ROIs in the dataset from which to extract all ROI info

get_frame_shape()[source]#

Get the frame shape (height, width) of the movie.

Returns:

The frame shape as (height, width).

Return type:

tuple

get_native_timestamps(start_sample: int | None = None, end_sample: int | None = None) → ndarray | None[source]#

Retrieve the original unaltered timestamps for the data in this interface.

Returns:

timestamps – The timestamps for the data stream, or None if native timestamps are not available.

Return type:

numpy.ndarray or None