Fixed bug with ScanImage's parse_metadata so that it works properly w…

…hen hStackManager is disabled (#373) fixed bug with parse_metadata so that it works properly when hStackManager is disabled
catalystneuro · Oct 11, 2024 · 2cf9235 · 2cf9235
1 parent 9a5f0c9
commit 2cf9235
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Showing 3 changed files with 9 additions and 4 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -6,6 +6,7 @@
 
 ### Fixes
 * Added specific error message for single-frame scanimage data [PR #360](https://github.com/catalystneuro/roiextractors/pull/360)
+* Fixed bug with ScanImage's parse_metadata so that it works properly when hStackManager is disabled [PR #373](https://github.com/catalystneuro/roiextractors/pull/373)
 
 ### Improvements
 * Removed unnecessary import checks for scipy, h5py, and zarr [PR #364](https://github.com/catalystneuro/roiextractors/pull/364)

diff --git a/src/roiextractors/extractors/tiffimagingextractors/scanimagetiff_utils.py b/src/roiextractors/extractors/tiffimagingextractors/scanimagetiff_utils.py
@@ -114,8 +114,12 @@ def parse_metadata(metadata: dict) -> dict:
         where M is the number of channels (active or not).
     """
     sampling_frequency = float(metadata["SI.hRoiManager.scanFrameRate"])
-    num_planes = int(metadata["SI.hStackManager.numSlices"])
-    frames_per_slice = int(metadata["SI.hStackManager.framesPerSlice"])
+    if metadata["SI.hStackManager.enable"] == "true":
+        num_planes = int(metadata["SI.hStackManager.numSlices"])
+        frames_per_slice = int(metadata["SI.hStackManager.framesPerSlice"])
+    else:
+        num_planes = 1
+        frames_per_slice = 1
     active_channels = parse_matlab_vector(metadata["SI.hChannels.channelsActive"])
     channel_indices = np.array(active_channels) - 1  # Account for MATLAB indexing
     channel_names = np.array(metadata["SI.hChannels.channelName"].split("'")[1::2])

diff --git a/tests/test_scanimage_utils.py b/tests/test_scanimage_utils.py
@@ -67,8 +67,8 @@ def test_parse_matlab_vector_invalid():
             {
                 "sampling_frequency": 15.2379,
                 "num_channels": 1,
-                "num_planes": 20,
-                "frames_per_slice": 24,
+                "num_planes": 1,
+                "frames_per_slice": 1,
                 "channel_names": ["Channel 1"],
                 "roi_metadata": {
                     "imagingRoiGroup": {