move import utils locally

catalystneuro · May 30, 2024 · 3722f6d · 3722f6d
1 parent 894dfef
commit 3722f6d
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Showing 2 changed files with 7 additions and 2 deletions.
diff --git a/src/roiextractors/extractors/bioformatsimagingextractor/bioformats_utils.py b/src/roiextractors/extractors/bioformatsimagingextractor/bioformats_utils.py
@@ -64,7 +64,7 @@ def parse_ome_metadata(metadata: OME) -> dict:
     - channel_names
 
     """
-    images_metadata = metadata["images"][0]
+    images_metadata = metadata.images[0]
     pixels_metadata = images_metadata.pixels
 
     sampling_frequency = None

diff --git a/src/roiextractors/extractors/bioformatsimagingextractor/cxdimagingextractor.py b/src/roiextractors/extractors/bioformatsimagingextractor/cxdimagingextractor.py
@@ -14,7 +14,6 @@
 
 from ...extraction_tools import PathType
 from .bioformatsimagingextractor import BioFormatsImagingExtractor
-from .bioformats_utils import extract_ome_metadata, parse_ome_metadata
 
 
 class CxdImagingExtractor(BioFormatsImagingExtractor):
@@ -36,6 +35,8 @@ def get_available_channels(cls, file_path) -> List[str]:
         channel_names: list
             List of channel names.
         """
+        from .bioformats_utils import extract_ome_metadata, parse_ome_metadata
+
         ome_metadata = extract_ome_metadata(file_path=file_path)
         parsed_metadata = parse_ome_metadata(metadata=ome_metadata)
         channel_names = parsed_metadata["channel_names"]
@@ -55,6 +56,8 @@ def get_available_planes(cls, file_path):
         plane_names: list
             List of plane names.
         """
+        from .bioformats_utils import extract_ome_metadata, parse_ome_metadata
+
         ome_metadata = extract_ome_metadata(file_path=file_path)
         parsed_metadata = parse_ome_metadata(metadata=ome_metadata)
         num_planes = parsed_metadata["num_planes"]
@@ -87,6 +90,8 @@ def __init__(self, file_path: PathType, channel_name: str = None, plane_name: st
         plane_name : str
             The name of the plane for this extractor. (default=None)
         """
+        from .bioformats_utils import extract_ome_metadata, parse_ome_metadata
+
         if "JAVA_HOME" not in os.environ:
             conda_home = os.environ.get("CONDA_PREFIX")
             os.environ["JAVA_HOME"] = conda_home