supervisely 6.73.334__py3-none-any.whl → 6.73.336__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/convert/volume/dicom/dicom_converter.py

@@ -4,9 +4,9 @@ from supervisely.api.api import Api
 from supervisely import generate_free_name, logger, ProjectMeta
 from supervisely.convert.base_converter import AvailableVolumeConverters
 from supervisely.convert.volume.volume_converter import VolumeConverter
+from supervisely.convert.volume.dicom import dicom_helper as h
 from supervisely.volume.volume import inspect_dicom_series, get_extension, read_dicom_serie_volume
 
-
 class DICOMConverter(VolumeConverter):
     class Item(VolumeConverter.Item):
         """Item class for DICOM series."""
@@ -60,6 +60,9 @@ class DICOMConverter(VolumeConverter):
                     f"Can not recognize file extension {item_path}, serie will be skipped"
                 )
                 continue
+
+            for dicom_path in dicom_paths:
+                h.convert_to_monochrome2(dicom_path)
             _, meta = read_dicom_serie_volume(dicom_paths, anonymize=True)
             item = self.Item(serie_id=dicom_id, item_paths=dicom_paths, volume_meta=meta)
             self._items.append(item)

supervisely/convert/volume/dicom/dicom_helper.py

@@ -37,3 +37,49 @@ def dcm_to_nrrd(id: str, paths: List[str]) -> str:
     nrrd.write(nrrd_path, volume_np, nrrd_header)
 
     return nrrd_path, volume_meta
+
+def convert_to_monochrome2(dcm_path: str):
+    import pydicom
+
+    is_modified = False
+
+    try:
+        dcm = pydicom.dcmread(dcm_path)
+    except Exception as e:
+        logger.warn("Failed to read DICOM file: " + str(e))
+        return
+
+    try:
+        if dcm.file_meta.TransferSyntaxUID.is_compressed:
+            dcm.decompress()
+            is_modified = True
+    except Exception as e:
+        logger.warn("Failed to decompress DICOM file: " + str(e))
+        return
+
+    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 photometric interpretation.")
+        is_modified = True
+
+    try:
+        if is_modified:
+            dcm.save_as(dcm_path)
+    except Exception as e:
+        logger.warn("Failed to save DICOM file: " + str(e))

{supervisely-6.73.334.dist-info → supervisely-6.73.336.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: supervisely
-Version: 6.73.334
+Version: 6.73.336
 Summary: Supervisely Python SDK.
 Home-page: https://github.com/supervisely/supervisely
 Author: Supervisely

{supervisely-6.73.334.dist-info → supervisely-6.73.336.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
@@ -661,8 +661,8 @@ supervisely/convert/video/sly/sly_video_helper.py,sha256=D8PgoXpi0y3z-VEqvBLDf_g
 supervisely/convert/volume/__init__.py,sha256=RpSYjufciJT6AdhI9Oqp70b3XoFTtSkxFNexoqeOPW4,353
 supervisely/convert/volume/volume_converter.py,sha256=3jpt2Yn_G4FSP_vHFsJHQfYNQpT7q6ar_sRyr_xrPnA,5335
 supervisely/convert/volume/dicom/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-supervisely/convert/volume/dicom/dicom_converter.py,sha256=__QP8fMAaq_BdWFYh1_nAYT2gpY1WwZzdlDj39YwHhw,3195
-supervisely/convert/volume/dicom/dicom_helper.py,sha256=1EXmxl5Z8Xi3ZkZnfJ4EbiPCVyITSXUc0Cn_oo02pPE,1284
+supervisely/convert/volume/dicom/dicom_converter.py,sha256=Hw4RxU_qvllk6M26udZE6G-m1RWR8-VVPcEPwFlqrVg,3354
+supervisely/convert/volume/dicom/dicom_helper.py,sha256=OrKlyt1hA5BOXKhE1LF1WxBIv3b6t96xRras4OSAuNM,2891
 supervisely/convert/volume/nii/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 supervisely/convert/volume/nii/nii_planes_volume_converter.py,sha256=9TtN_AgCQgv16Olip6inFanCA5JlEEJ7JQf-0XjIw_Q,7091
 supervisely/convert/volume/nii/nii_volume_converter.py,sha256=IZ6DJeLLbLAW-kifOJ_9ddV3h7gL3AswM2TTbXB9Os0,8476
@@ -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-6.73.336.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+supervisely-6.73.336.dist-info/METADATA,sha256=xBFjKa2mZUNV7BqRSbxj_Bvws6FYn1DsuvDP4M4myUQ,33596
+supervisely-6.73.336.dist-info/WHEEL,sha256=iAkIy5fosb7FzIOwONchHf19Qu7_1wCWyFNR5gu9nU0,91
+supervisely-6.73.336.dist-info/entry_points.txt,sha256=U96-5Hxrp2ApRjnCoUiUhWMqijqh8zLR03sEhWtAcms,102
+supervisely-6.73.336.dist-info/top_level.txt,sha256=kcFVwb7SXtfqZifrZaSE3owHExX4gcNYe7Q2uoby084,28
+supervisely-6.73.336.dist-info/RECORD,,