Merge branch 'main' into add_seeds_to_generators

.github/workflows/dev-testing.yaml

@@ -47,4 +47,4 @@ jobs:
 
       - name: Run NeuroConv tests
         run: |
-            pytest -n auto --dist loadscope neuroconv/tests/test_ophys neuroconv/tests/test_on_data/test_imaging_interfaces.py neuroconv/tests/test_on_data/test_segmentation_interfaces.py
+            pytest -n auto --dist loadscope neuroconv/tests/test_ophys neuroconv/tests/test_on_data/ophys/test_imaging_interfaces.py neuroconv/tests/test_on_data/ophys/test_segmentation_interfaces.py

CHANGELOG.md

@@ -1,4 +1,15 @@
-# Upcoming (v0.5.9)
+# Upcoming (v0.5.10)
+
+### Features
+
+### Fixes
+* Added specific error message for single-frame scanimage data [PR #360](https://github.com/catalystneuro/roiextractors/pull/360)
+
+### Improvements
+
+### Testing
+
+# v0.5.9
 
 ### Deprecations
 
@@ -21,6 +32,7 @@
 * Change the criteria of determining if Bruker data is volumetric [#342](https://github.com/catalystneuro/roiextractors/pull/342)
 * Fixes a bug that assumes the channel name is is on the tiff file for `BrukerTiffSinglePlaneImagingExtractor` [#343](https://github.com/catalystneuro/roiextractors/pull/343)
 * Including `packaging` explicitly in minimal requirements [#347](https://github.com/catalystneuro/roiextractors/pull/347)
+* Updated requirements to include cv2 and update dev testing locations for neuroconv: [#357](https://github.com/catalystneuro/roiextractors/pull/357)
 
 ### Improvements
 

requirements-full.txt

@@ -1,5 +1,6 @@
 tifffile>=2018.10.18
 scanimage-tiff-reader>=1.4.1.4
 neuroconv[video]>=0.4.6  # Uses the VideoCaptureContext class
+opencv-python-headless>=4.8.1.78
 natsort>=8.3.1
 isx>=1.0.4

setup.py

@@ -22,7 +22,7 @@
 
 setup(
     name="roiextractors",
-    version="0.5.9",
+    version="0.5.10",
     author="Heberto Mayorquin, Szonja Weigl, Cody Baker, Ben Dichter, Alessio Buccino, Paul Adkisson",
     author_email="[email protected]",
     description="Python module for extracting optical physiology ROIs and traces for various file types and formats",

src/roiextractors/extractors/tiffimagingextractors/scanimagetiffimagingextractor.py

@@ -299,7 +299,12 @@ def __init__(
         ScanImageTiffReader = _get_scanimage_reader()
         with ScanImageTiffReader(str(self.file_path)) as io:
             shape = io.shape()  # [frames, rows, columns]
-        if len(shape) == 3:
+        if len(shape) == 2:  # [rows, columns]
+            raise NotImplementedError(
+                "Extractor cannot handle single-frame ScanImageTiff data. Please raise an issue to request this feature: "
+                "https://github.com/catalystneuro/roiextractors/issues "
+            )
+        elif len(shape) == 3:
             self._total_num_frames, self._num_rows, self._num_columns = shape
             if (
                 self._num_planes == 1

src/roiextractors/testing.py

@@ -122,23 +122,23 @@ def generate_dummy_segmentation_extractor(
     num_rois : int, optional
         number of regions of interest, by default 10.
     num_frames : int, optional
-        _description_, by default 30
-    num_rows : number of frames used in the hypotethical video from which the data was extracted, optional
-        number of rows in the hypotethical video from which the data was extracted, by default 25.
+       Number of frames in the recording, by default 30.
+    num_rows : int, optional
+        number of rows in the hypothetical video from which the data was extracted, by default 25.
     num_columns : int, optional
-        numbe rof columns in the hypotethical video from which the data was extracted, by default 25.
+        number of columns in the hypothetical video from which the data was extracted, by default 25.
     sampling_frequency : float, optional
-        sampling frequency of the hypotethical video form which the data was extracted, by default 30.0.
+        sampling frequency of the hypothetical video from which the data was extracted, by default 30.0.
     has_summary_images : bool, optional
-        whether the dummy segmentation extractor has summary images or not (mean and correlation)
+        whether the dummy segmentation extractor has summary images or not (mean and correlation).
     has_raw_signal : bool, optional
-        whether a raw fluoresence signal is desired in the object, by default True.
+        whether a raw fluorescence signal is desired in the object, by default True.
     has_dff_signal : bool, optional
-        whether a relative (df/f) fluoresence signal is desired in the object, by default True.
+        whether a relative (df/f) fluorescence signal is desired in the object, by default True.
     has_deconvolved_signal : bool, optional
         whether a deconvolved signal is desired in the object, by default True.
     has_neuropil_signal : bool, optional
-        whether a neuropil signal is desiredi n the object, by default True.
+        whether a neuropil signal is desired in the object, by default True.
     rejected_list: list, optional
         A list of rejected rois, None by default.
     seed : int, default 0