diff --git a/src/roiextractors/extractors/bioformatsimagingextractor/bioformats_utils.py b/src/roiextractors/extractors/bioformatsimagingextractor/bioformats_utils.py index 6ce85e87..db8cd053 100644 --- 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 index bb840067..7d7d798f 100644 --- 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