refactoring of dicom module

mu_map/file/dicom.py

@@ -6,7 +6,11 @@ from typing import Tuple
 import numpy as np
 import pydicom
 
-dcm_type = pydicom.dataset.FileDataset
+
+"""
+Alias for the main dicom datatype.
+"""
+DICOM = pydicom.dataset.FileDataset
 
 """
 Since DICOM images only allow images stored in short integer format,
@@ -58,7 +62,7 @@ class DICOMTime(Enum):
         """
         return f"{self.name}Time"
 
-    def to_datetime(self, dicom: dcm_type) -> datetime:
+    def to_datetime(self, dicom: DICOM) -> datetime:
         """
         Get the datetime according to this DICOMTime type.
         """
@@ -94,7 +98,7 @@ def parse_age(patient_age: str) -> int:
     return int(_num)
 
 
-def load_dcm(filename: str) -> Tuple[pydicom.dataset.FileDataset, np.ndarray]:
+def load_dcm(filename: str) -> Tuple[DICOM, np.ndarray]:
     """
     Load a DICOM image, the data as a numpy array and apply normalization of the Siemens SPECT/CT
     Scanner.
@@ -144,9 +148,7 @@ def scale_image(image: np.ndarray, initial_scale=10000000) -> Tuple[np.ndarray,
     return image, scale
 
 
-def update_dcm(
-    dcm: pydicom.dataset.FileDataset, image: np.ndarray
-) -> pydicom.dataset.FileDataset:
+def update_dcm(dcm: DICOM, image: np.ndarray) -> DICOM:
     """
     Update the image data in a DICOM file. This function scales the image, converts
     it to unsigned integers with 16 bits and updates the pixel data in the DICOM file.
@@ -176,7 +178,7 @@ def update_dcm(
     return dcm
 
 
-def change_uid(dcm: pydicom.dataset.FileDataset) -> pydicom.dataset.FileDataset:
+def change_uid(dcm: DICOM) -> DICOM:
     """
     Change the UIDs (SeriesInstance and SOPInstance) in a DICOM header so that
     it becomes its own unique file. Note that this method does not guarantee

mu_map/file/interfile_to_dicom.py

@@ -8,22 +8,22 @@ from mu_map.file.dicom import update_dcm, change_uid
 from mu_map.file.interfile import load_interfile_img
 
 parser = argparse.ArgumentParser(
-    description="convert an INTERFILE image to a DICOM image",
+    description="convert an Interfile image to a DICOM image",
     formatter_class=argparse.ArgumentDefaultsHelpFormatter,
 )
 parser.add_argument(
-    "--inter", type=str, required=True, help="the INTERFILE image to be converted"
+    "--inter", type=str, required=True, help="the Interfile image to be converted"
 )
 parser.add_argument(
     "--dcm",
     type=str,
     required=True,
-    help="a DICOM reference image - data and according fields are exchanged from the INTERFILE image",
+    help="a DICOM reference image - data and according fields are exchanged from the Interfile image",
 )
 parser.add_argument(
     "--out",
     type=str,
-    help="the output file - defaults to the INTERFILE input with a dcm extension",
+    help="the output file - defaults to the Interfile input with a dcm extension",
 )
 parser.add_argument(
     "--description",