add scan_line_rate, grid_spacing and origin_coords from scanimage metadata

CHANGELOG.md

@@ -8,6 +8,7 @@
 
 * Add InscopixImagingExtractor: [#276](https://github.com/catalystneuro/roiextractors/pull/276)
 * Updated testing workflows to include python 3.12, m1/intel macos, and dev tests to check neuroconv: [PR #317](https://github.com/catalystneuro/roiextractors/pull/317)
+* Updated  `parse_metadata()` from `scaimagetiff_utils` to include `scan_line_rate`, `grid_spacing`, `grid_spacing_unit`,`origin_coords`, `origin_coords_unit`
 
 ### Fixes
 

src/roiextractors/extractors/tiffimagingextractors/scanimagetiff_utils.py

@@ -95,6 +95,12 @@ def parse_metadata(metadata: dict) -> dict:
     - frames_per_slice
     - channel_names
     - num_channels
+    - scan_line_rate,
+    - grid_spacing,
+    - grid_spacing_unit,
+    - origin_coords,
+    - origin_coords_unit,
+    - roi_metadata,
 
     Parameters
     ----------
@@ -119,18 +125,34 @@ def parse_metadata(metadata: dict) -> dict:
     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])
+    scan_line_rate = 1 / float(metadata["SI.hRoiManager.linePeriod"])
     channel_names = channel_names[channel_indices].tolist()
     num_channels = len(channel_names)
-    if "RoiGroups" in metadata.keys():
-        roi_metadata = metadata["RoiGroups"]
-    else:
-        roi_metadata = None
+    roi_metadata = metadata["RoiGroups"]
+    grid_spacing = None
+    grid_spacing_unit = "n.a"
+    origin_coords = None
+    origin_coords_unit = "n.a"
+    if roi_metadata["imagingRoiGroup"]["rois"].__contains__("scanfields"):
+        scanfields = roi_metadata["imagingRoiGroup"]["rois"]["scanfields"]
+        fov_size_in_um = np.array(scanfields["sizeXY"])
+        frame_dimension = np.array(scanfields["pixelResolutionXY"])
+        grid_spacing = fov_size_in_um / frame_dimension
+        grid_spacing_unit = "micrometers"
+        origin_coords = scanfields["centerXY"]
+        origin_coords_unit = "micrometers"
+
     metadata_parsed = dict(
         sampling_frequency=sampling_frequency,
         num_channels=num_channels,
         num_planes=num_planes,
         frames_per_slice=frames_per_slice,
         channel_names=channel_names,
+        scan_line_rate=scan_line_rate,
+        grid_spacing=grid_spacing,
+        grid_spacing_unit=grid_spacing_unit,
+        origin_coords=origin_coords,
+        origin_coords_unit=origin_coords_unit,
         roi_metadata=roi_metadata,
     )
     return metadata_parsed

tests/test_scanimage_utils.py

@@ -70,6 +70,11 @@ def test_parse_matlab_vector_invalid():
                 "num_planes": 20,
                 "frames_per_slice": 24,
                 "channel_names": ["Channel 1"],
+                "scan_line_rate": 15847.40847329236,
+                "grid_spacing": [0.01757812, 0.01757812],
+                "grid_spacing_unit": "micrometers",
+                "origin_coords": [0, 0],
+                "origin_coords_unit": "micrometers",
                 "roi_metadata": {
                     "imagingRoiGroup": {
                         "ver": 1,
@@ -147,6 +152,11 @@ def test_parse_matlab_vector_invalid():
                 "num_planes": 2,
                 "frames_per_slice": 2,
                 "channel_names": ["Channel 1", "Channel 4"],
+                "scan_line_rate": 15843.868185354244,
+                "grid_spacing": None,
+                "grid_spacing_unit": "n.a",
+                "origin_coords": None,
+                "origin_coords_unit": "n.a",
                 "roi_metadata": {
                     "imagingRoiGroup": {
                         "ver": 1,