Merge pull request #2 from gschramm/pydicom3

Pydicom3

examples/fileio/convert_kul_nifti_to_dicom.py

@@ -1,8 +1,10 @@
 import sys, os
-pymirc_path = os.path.join('..','..')
-if not pymirc_path in sys.path: sys.path.append(pymirc_path)
 
-import numpy   as np
+pymirc_path = os.path.join("..", "..")
+if not pymirc_path in sys.path:
+    sys.path.append(pymirc_path)
+
+import numpy as np
 import nibabel as nib
 import pydicom
 
@@ -11,52 +13,60 @@
 from argparse import ArgumentParser
 
 parser = ArgumentParser()
-parser.add_argument('nifti_file',   help = 'nifti file to be converted into dicom')
-parser.add_argument('ref_dcm_file', help = 'the reference dicom file')
-parser.add_argument('output_dir',   help = 'output directory')
-
-parser.add_argument('--dcm_tag_file',       help = 'txt file with dcm tags to copy', 
-                    default = 'dcm_tags_to_copy.txt')
-parser.add_argument('--series_desc_prefix', help = 'prefix for dcm series description', 
-                    default = '(KUL Segmentation)')
-parser.add_argument('--output_modality', help = 'dicom modality of output', 
-                    default = 'CT')
-
-args       = parser.parse_args()
+parser.add_argument("nifti_file", help="nifti file to be converted into dicom")
+parser.add_argument("ref_dcm_file", help="the reference dicom file")
+parser.add_argument("output_dir", help="output directory")
+
+parser.add_argument(
+    "--dcm_tag_file",
+    help="txt file with dcm tags to copy",
+    default="dcm_tags_to_copy.txt",
+)
+parser.add_argument(
+    "--series_desc_prefix",
+    help="prefix for dcm series description",
+    default="(KUL Segmentation)",
+)
+parser.add_argument("--output_modality", help="dicom modality of output", default="CT")
+
+args = parser.parse_args()
 output_dir = args.output_dir
 
-#-----------------------------------------------------------------------------------------
+# -----------------------------------------------------------------------------------------
 
 if os.path.isdir(output_dir):
-  raise FileExistsError('output directory ' + output_dir + ' already exists')
+    raise FileExistsError("output directory " + output_dir + " already exists")
 
 # load the nifti and the affine and convert to LPS orientation
-nii        = nib.load(args.nifti_file)
-nii        = nib.as_closest_canonical(nii)
-vol_ras    = nii.get_data()
+nii = nib.load(args.nifti_file)
+nii = nib.as_closest_canonical(nii)
+vol_ras = nii.get_data()
 
 affine_ras = nii.affine
-vol    = np.flip(np.flip(vol_ras, 0), 1)
+vol = np.flip(np.flip(vol_ras, 0), 1)
 affine = affine_ras.copy()
-affine[0,-1] = (-1 * nii.affine @ np.array([vol.shape[0]-1,0,0,1]))[0]
-affine[1,-1] = (-1 * nii.affine @ np.array([0,vol.shape[1]-1,0,1]))[1]
+affine[0, -1] = (-1 * nii.affine @ np.array([vol.shape[0] - 1, 0, 0, 1]))[0]
+affine[1, -1] = (-1 * nii.affine @ np.array([0, vol.shape[1] - 1, 0, 1]))[1]
 
 # load the list of dicom tags to copy from the reference header from an input text file
-with open(args.dcm_tag_file,'r') as f:
-  tags_to_copy = [x.strip() for x in f.read().splitlines()]
+with open(args.dcm_tag_file, "r") as f:
+    tags_to_copy = [x.strip() for x in f.read().splitlines()]
 
 # read the reference dicom volume
-ref_dcm = pydicom.read_file(args.ref_dcm_file)
+ref_dcm = pydicom.dcmread(args.ref_dcm_file)
 
 # create the dictionary of tags and values that are copied from the reference dicom header
 dcm_header_kwargs = {}
 for tag in tags_to_copy:
-  if tag in ref_dcm:
-    dcm_header_kwargs[tag] = ref_dcm.data_element(tag).value
+    if tag in ref_dcm:
+        dcm_header_kwargs[tag] = ref_dcm.data_element(tag).value
 
 # write the dicoms
-pymf.write_3d_static_dicom(vol, output_dir, 
-                           affine              = affine,
-                           SeriesDescription   = args.series_desc_prefix + ' ' + ref_dcm.SeriesDescription,
-                           modality            = args.output_modality,
-                           **dcm_header_kwargs)
+pymf.write_3d_static_dicom(
+    vol,
+    output_dir,
+    affine=affine,
+    SeriesDescription=args.series_desc_prefix + " " + ref_dcm.SeriesDescription,
+    modality=args.output_modality,
+    **dcm_header_kwargs
+)

pymirc/__init__.py

@@ -4,6 +4,7 @@
 from . import viewer
 
 from pkg_resources import get_distribution, DistributionNotFound
+
 try:
     __version__ = get_distribution(__name__).version
 except DistributionNotFound:

pymirc/fileio/__init__.py

@@ -1,6 +1,9 @@
-from .read_dicom    import DicomVolume, DicomSearch
-from .write_dicom   import write_3d_static_dicom, write_4d_dicom, write_dicom_slice
-from .read_rtstruct import read_rtstruct_contour_data, convert_contour_data_to_roi_indices
+from .read_dicom import DicomVolume, DicomSearch
+from .write_dicom import write_3d_static_dicom, write_4d_dicom, write_dicom_slice
+from .read_rtstruct import (
+    read_rtstruct_contour_data,
+    convert_contour_data_to_roi_indices,
+)
 
 from .labelvol_to_rtstruct import labelvol_to_rtstruct