hu api

VERSION

@@ -1 +1 @@
-1.1.6
+1.1.7

api/preprocessing/hu.py

@@ -0,0 +1,5 @@
+import medviz as viz
+
+image = "/storage/sync/git/mohsen/medviz/test_local/dataset/Patient 1/CT/I1000000.dcm"
+
+viz.get_hu(image, save_path="/path/to/save")

medviz/preprocess/__init__.py

@@ -2,3 +2,4 @@
 from .match_image_mask import match_image_masks
 from .resampling import resample
 from .metadata import metadata
+from .hu import get_hu

medviz/preprocess/hu.py

@@ -0,0 +1,74 @@
+import numpy as np
+import pydicom
+
+from ..utils import path2loader, path_in, save_path_file
+
+
+#     return pydicom.tag.Tag(int(group, 16), int(element, 16))
+def convert_tag(tag_str):
+    if "|" in tag_str:
+        group, element = tag_str.split("|")
+        return pydicom.tag.Tag(int(group, 16), int(element, 16))
+    else:
+        return None  # Return None for strings that don't contain "|"
+
+
+def get_hu(file_path, save_path=None):
+    file_path = path_in(file_path)
+
+    dicom_file = pydicom.dcmread(file_path)
+    pixel_array = dicom_file.pixel_array
+
+    rescale_slope = dicom_file.RescaleSlope
+    rescale_intercept = dicom_file.RescaleIntercept
+
+    hu_pixel_array = pixel_array * rescale_slope + rescale_intercept
+    hu_pixel_array = hu_pixel_array.astype(np.int16)
+    dicom_file.PixelData = hu_pixel_array.tobytes()
+    if save_path is not None:
+        name = f"{file_path.stem}_hu"
+        save_path = save_path + "/" + name
+
+        save_path = save_path_file(save_path, suffix=".dcm")
+        dicom_file.save_as(save_path)
+
+
+# def get_hu(path):
+#     image = path2loader(path)
+#     image_and_properties, reader, image_and_properties_itk = image
+
+#     if reader == "pydicom":
+#         ds = image_and_properties
+
+
+#     else:
+#         image = image_and_properties_itk
+
+#         metadata_keys = image.GetMetaDataKeys()
+
+#         metadata = {
+#         pydicom.datadict.keyword_for_tag(convert_tag(key)): image.GetMetaData(key)
+#         for key in metadata_keys
+#         if convert_tag(key) is not None
+#         and pydicom.datadict.keyword_for_tag(
+#             convert_tag(key)
+#         )  # Only include known tags with "|"
+#     }
+
+
+#         rescale_intercept = (
+#             float(image.GetMetaData("0028|1052"))
+#             if "0028|1052" in metadata_keys
+#             else metadata.get("scl_inter", None)
+#         )
+
+#         rescale_slope = (
+#             float(image.GetMetaData("0028|1053"))
+#             if "0028|1053" in metadata_keys
+#             else metadata.get("scl_slope", None)
+#         )
+
+
+#         metadata["itk_HU"] = rescale_intercept == -1024 and rescale_slope == 1
+
+#         return metadata["itk_HU"]

medviz/utils/helper_reader.py

@@ -24,7 +24,7 @@ def path2loader(path: PathMedicalImage) -> PathMedicalImage:
     if isinstance(path, MedicalImage):
         return path
 
-    path_obj = Path(path)
+    path_obj = path_in(path)
     suffixes = path_obj.suffixes
 
     try: