Merge branch 'main' into fix_extra_requirement_logic

Author: CodyCBakerPhD

CHANGELOG.md

@@ -47,6 +47,7 @@
 * Added direct imports for all base classes from the outer level; you may now call `from neuroconv import BaseDataInterface, BaseTemporalAlignmentInterface, BaseExtractorInterface`. [PR #442](https://github.com/catalystneuro/neuroconv/pull/442)
 * Added basic temporal alignment methods to the AudioInterface. `align_starting_time` is split into `align_starting_times` (list of times, one per audio file) and `align_global_starting_time` (shift all by a scalar amount). `align_by_interpolation` and other timestamp-based approaches is not yet implemented for this interface. [PR #402](https://github.com/catalystneuro/neuroconv/pull/402)
 * Changed the order of recording properties extraction in `NeuroscopeRecordingInterface` and `NeuroScopeLFPInterface` to make them consistent with each other [PR #466](https://github.com/catalystneuro/neuroconv/pull/466)
+* The `ScanImageImagingInterface` has been updated to read metadata from more recent versions of ScanImage [PR #457](https://github.com/catalystneuro/neuroconv/pull/457)
 
 ### Testing
 * The tests for `automatic_dandi_upload` now follow up-to-date DANDI validation rules for file name conventions. [PR #310](https://github.com/catalystneuro/neuroconv/pull/310)

src/neuroconv/datainterfaces/ophys/scanimage/scanimageimaginginterface.py

@@ -1,3 +1,4 @@
+import datetime
 import json
 from typing import Optional
 
@@ -12,10 +13,15 @@ def extract_extra_metadata(file_path) -> dict:
     ScanImageTiffReader = get_package(
         package_name="ScanImageTiffReader", installation_instructions="pip install scanimage-tiff-reader"
     )
-
-    description = ScanImageTiffReader.ScanImageTiffReader(str(file_path)).description(iframe=0)
-    extra_metadata = {x.split("=")[0]: x.split("=")[1] for x in description.split("\r") if "=" in x}
-
+    src_file = ScanImageTiffReader.ScanImageTiffReader(str(file_path))
+    extra_metadata = {}
+    for metadata_string in (src_file.description(iframe=0), src_file.metadata()):
+        metadata_dict = {
+            x.split("=")[0].strip(): x.split("=")[1].strip()
+            for x in metadata_string.replace("\n", "\r").split("\r")
+            if "=" in x
+        }
+        extra_metadata = dict(**extra_metadata, **metadata_dict)
     return extra_metadata
 
 
@@ -50,6 +56,8 @@ def __init__(
 
         if "state.acq.frameRate" in self.image_metadata:
             sampling_frequency = float(self.image_metadata["state.acq.frameRate"])
+        elif "SI.hRoiManager.scanFrameRate" in self.image_metadata:
+            sampling_frequency = float(self.image_metadata["SI.hRoiManager.scanFrameRate"])
         else:
             assert_msg = (
                 "sampling frequency not found in image metadata, "
@@ -68,6 +76,14 @@ def get_metadata(self) -> dict:
         if "state.internal.triggerTimeString" in self.image_metadata:
             extracted_session_start_time = dateparse(self.image_metadata["state.internal.triggerTimeString"])
             metadata["NWBFile"].update(session_start_time=extracted_session_start_time)
+        elif "epoch" in self.image_metadata:
+            # Versions of ScanImage at least as recent as 2020, and possibly earlier, store the start time under keyword
+            # `epoch`, as a string encoding of a Matlab array, example `'[2022  8  8 16 56 7.329]'`
+            # dateparse can't cope with this representation, so using strptime directly
+            extracted_session_start_time = datetime.datetime.strptime(
+                self.image_metadata["epoch"], "[%Y %m %d %H %M %S.%f]"
+            )
+            metadata["NWBFile"].update(session_start_time=extracted_session_start_time)
 
         # Extract many scan image properties and attach them as dic in the description
         ophys_metadata = metadata["Ophys"]