Fix HDF5 and NWB get_frames behavior (#174)

* for HDF5:
* fix get_frames. It was previously assuming contiguous frames
* improve get_video. It was previously reading frame-by-frame, which is not optimal for HDF5

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Added integer handling to default get_frames method

* added squeeze logic to get_frames

* specify axis for squeeze

* inverted if so that squeeze occurs in the int section

* removed np.newaxis so that bruker tests expect squeezing behavior on single frame

* removed np.newaxis so that micromanager tests expect squeezing behavior on single frame

* added squeeze logic to multiimaging
 extractor

* reverted imagingextractor changes

* reverted multiimagingextractor and testing.py changes

* reverted test_brukertiffimagingextractor changes

* reverted test_micromanagertiffimagingextractor changes

* reverted test_brukertiffimagingextractor changes

* added get_frames to hdf5imagingextractor

* added test for non-cts frames

* fixed nwb get_frames

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Heberto Mayorquin <h.mayorquin@gmail.com>
Co-authored-by: Paul Adkisson <paul.wesley.adkisson@gmail.com>

src/roiextractors/extractors/hdf5imagingextractor/hdf5imagingextractor.py

@@ -122,25 +122,22 @@ def __del__(self):
         self._file.close()
 
     def get_frames(self, frame_idxs: ArrayType, channel: Optional[int] = 0):
-        # Fancy indexing is non performant for h5.py with long frame lists
-        if frame_idxs is not None:
-            slice_start = np.min(frame_idxs)
-            slice_stop = min(np.max(frame_idxs) + 1, self.get_num_frames())
-        else:
-            slice_start = 0
-            slice_stop = self.get_num_frames()
-
-        frames = self._video.lazy_slice[slice_start:slice_stop, :, :, channel].dsetread()
+        squeeze_data = False
         if isinstance(frame_idxs, int):
+            squeeze_data = True
+            frame_idxs = [frame_idxs]
+        elif isinstance(frame_idxs, np.ndarray):
+            frame_idxs = frame_idxs.tolist()
+        frames = self._video.lazy_slice[frame_idxs, :, :, channel].dsetread()
+        if squeeze_data:
             frames = frames.squeeze()
-
         return frames
 
     def get_video(self, start_frame=None, end_frame=None, channel: Optional[int] = 0) -> np.ndarray:
         return self._video.lazy_slice[start_frame:end_frame, :, :, channel].dsetread()
 
     def get_image_size(self) -> Tuple[int, int]:
-        return (self._num_rows, self._num_cols)
+        return self._num_rows, self._num_cols
 
     def get_num_frames(self):
         return self._num_frames

src/roiextractors/extractors/nwbextractors/nwbextractors.py

@@ -181,18 +181,14 @@ def make_nwb_metadata(
         )
 
     def get_frames(self, frame_idxs: ArrayType, channel: Optional[int] = 0):
-        # Fancy indexing is non performant for h5.py with long frame lists
-        if frame_idxs is not None:
-            slice_start = np.min(frame_idxs)
-            slice_stop = min(np.max(frame_idxs) + 1, self.get_num_frames())
-        else:
-            slice_start = 0
-            slice_stop = self.get_num_frames()
-
-        data = self.photon_series.data
-        frames = data[slice_start:slice_stop, ...].transpose([0, 2, 1])
-
+        squeeze_data = False
         if isinstance(frame_idxs, int):
+            squeeze_data = True
+            frame_idxs = [frame_idxs]
+        elif isinstance(frame_idxs, np.ndarray):
+            frame_idxs = frame_idxs.tolist()
+        frames = self.photon_series.data[frame_idxs].transpose([0, 2, 1])
+        if squeeze_data:
             frames = frames.squeeze()
         return frames
 

src/roiextractors/testing.py

@@ -406,6 +406,11 @@ def assert_get_frames_return_shape(imaging_extractor: ImagingExtractor):
     assert_msg = "get_frames does not work correctly with frame_idxs=np.arrray([0, 1])"
     assert frames_with_array.shape == (2, image_size[0], image_size[1]), assert_msg
 
+    frame_idxs = [0, 2]
+    frames_with_array = imaging_extractor.get_frames(frame_idxs=frame_idxs, channel=0)
+    assert_msg = "get_frames does not work correctly with frame_idxs=[0, 2]"
+    assert frames_with_array.shape == (2, image_size[0], image_size[1]), assert_msg
+
 
 def check_imaging_return_types(img_ex: ImagingExtractor):
     """Check that the return types of the imaging extractor are correct."""