supervisely 6.73.334__py3-none-any.whl → 6.73.335__py3-none-any.whl

supervisely/convert/image/medical2d/medical2d_helper.py

@@ -135,6 +135,28 @@ def create_pixel_data_set(dcm: FileDataset, frame_axis: int) -> Tuple[List[np.nd
     list_of_images = np.split(pixel_array, int(dcm.NumberOfFrames), axis=frame_axis)
     return list_of_images, frame_axis
 
+def convert_to_monochrome2(dcm_path: str, dcm: FileDataset) -> FileDataset:
+    if getattr(dcm, "PhotometricInterpretation", None) == "YBR_FULL_422":
+        # * Convert dicom to monochrome
+        if len(dcm.pixel_array.shape) == 4 and dcm.pixel_array.shape[-1] == 3:
+            monochrome = dcm.pixel_array[..., 0].astype(np.uint8)
+        else:
+            logger.warn("Unexpected shape for YBR_FULL_422 data: " + str(dcm.pixel_array.shape))
+
+        try:
+            dcm.SamplesPerPixel = 1
+            dcm.PhotometricInterpretation = "MONOCHROME2"
+            dcm.PlanarConfiguration = 0
+            if len(monochrome.shape) == 3:
+                dcm.NumberOfFrames = str(monochrome.shape[0])
+                dcm.Rows, dcm.Columns = monochrome.shape[1:3]
+            dcm.PixelData = monochrome.tobytes()
+        except AttributeError as ae:
+            logger.error(f"Error occurred while converting dicom to monochrome: {ae}")
+
+        logger.info("Rewriting DICOM file with monochrome2 format")
+        dcm.save_as(dcm_path)
+    return dcm
 
 def convert_dcm_to_nrrd(
     image_path: str, converted_dir: str, group_tag_name: Optional[list] = None
@@ -147,6 +169,13 @@ def convert_dcm_to_nrrd(
     mkdir(curr_convert_dir)
 
     dcm = pydicom.read_file(image_path)
+    try:
+        if dcm.file_meta.TransferSyntaxUID.is_compressed:
+            dcm.decompress()
+    except AttributeError:
+        logger.warn("Couldn't find key 'TransferSyntaxUID' in dicom's metadata.")
+    dcm = convert_to_monochrome2(image_path, dcm)
+
     dcm_meta = get_dcm_meta(dcm)
 
     if group_tag_name is None:

{supervisely-6.73.334.dist-info → supervisely-6.73.335.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: supervisely
-Version: 6.73.334
+Version: 6.73.335
 Summary: Supervisely Python SDK.
 Home-page: https://github.com/supervisely/supervisely
 Author: Supervisely

{supervisely-6.73.334.dist-info → supervisely-6.73.335.dist-info}/RECORD

@@ -594,7 +594,7 @@ supervisely/convert/image/masks/image_with_masks_helper.py,sha256=TSHiAIH3qlYdjR
 supervisely/convert/image/masks/images_with_masks_converter.py,sha256=Won5LihYXZZmimgaJHmK0_rVmOadWYk21OHKri21R08,6866
 supervisely/convert/image/medical2d/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 supervisely/convert/image/medical2d/medical2d_converter.py,sha256=cYEaRfr8YFxEG_Pv-_SVMxrqZudi3kWbGQ3aArL2mds,8156
-supervisely/convert/image/medical2d/medical2d_helper.py,sha256=pfLRCSFbFa5EIhmbB7kdmdWRu01OwIEDPXeNHzAeagg,12329
+supervisely/convert/image/medical2d/medical2d_helper.py,sha256=UzZRJHtbTC7Tw-BIXaGrk3FhwPR-gglvHyVv2wio0Uw,13633
 supervisely/convert/image/multi_view/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 supervisely/convert/image/multi_view/multi_view.py,sha256=V-6oFN6oDre7UhejfyDkGKAg4rbM3C9JCQ8pHhuUBb8,4436
 supervisely/convert/image/multispectral/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -1082,9 +1082,9 @@ supervisely/worker_proto/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZ
 supervisely/worker_proto/worker_api_pb2.py,sha256=VQfi5JRBHs2pFCK1snec3JECgGnua3Xjqw_-b3aFxuM,59142
 supervisely/worker_proto/worker_api_pb2_grpc.py,sha256=3BwQXOaP9qpdi0Dt9EKG--Lm8KGN0C5AgmUfRv77_Jk,28940
 supervisely_lib/__init__.py,sha256=7-3QnN8Zf0wj8NCr2oJmqoQWMKKPKTECvjH9pd2S5vY,159
-supervisely-6.73.334.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-supervisely-6.73.334.dist-info/METADATA,sha256=jD55cUT6bmdvsvTMuPD3Jt61Aus-DzBZciz5C5VO2HA,33596
-supervisely-6.73.334.dist-info/WHEEL,sha256=iAkIy5fosb7FzIOwONchHf19Qu7_1wCWyFNR5gu9nU0,91
-supervisely-6.73.334.dist-info/entry_points.txt,sha256=U96-5Hxrp2ApRjnCoUiUhWMqijqh8zLR03sEhWtAcms,102
-supervisely-6.73.334.dist-info/top_level.txt,sha256=kcFVwb7SXtfqZifrZaSE3owHExX4gcNYe7Q2uoby084,28
-supervisely-6.73.334.dist-info/RECORD,,
+supervisely-6.73.335.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+supervisely-6.73.335.dist-info/METADATA,sha256=-Xv7Subzo7aabPOrXvxNbLXl9oIF6HIKstyMecAGzV0,33596
+supervisely-6.73.335.dist-info/WHEEL,sha256=iAkIy5fosb7FzIOwONchHf19Qu7_1wCWyFNR5gu9nU0,91
+supervisely-6.73.335.dist-info/entry_points.txt,sha256=U96-5Hxrp2ApRjnCoUiUhWMqijqh8zLR03sEhWtAcms,102
+supervisely-6.73.335.dist-info/top_level.txt,sha256=kcFVwb7SXtfqZifrZaSE3owHExX4gcNYe7Q2uoby084,28
+supervisely-6.73.335.dist-info/RECORD,,