19 import SimpleITK
as sitk
26 pixel_dtypes = {
"int16": np.int16,
"float64": np.float64}
29 def writeSlices(series_tag_values, new_img, out_dir, i):
30 image_slice = new_img[:, :, i]
35 lambda tag_value: image_slice.SetMetaData(tag_value[0], tag_value[1]),
42 image_slice.SetMetaData(
"0008|0012", time.strftime(
"%Y%m%d"))
44 image_slice.SetMetaData(
"0008|0013", time.strftime(
"%H%M%S"))
48 image_slice.SetMetaData(
"0008|0060",
"CT")
53 image_slice.SetMetaData(
55 "\\".join(map(str, new_img.TransformIndexToPhysicalPoint((0, 0, i)))),
58 image_slice.SetMetaData(
"0020|0013", str(i))
62 writer.SetFileName(os.path.join(out_dir, str(i) +
".dcm"))
63 writer.Execute(image_slice)
70 +
" <output_directory> ["
71 +
", ".join(pixel_dtypes)
78 pixel_dtype = pixel_dtypes[sys.argv[2]]
80 pixel_dtype = pixel_dtypes[
"int16"]
82 new_arr = np.random.uniform(-10, 10, size=(3, 4, 5)).astype(pixel_dtype)
83 new_img = sitk.GetImageFromArray(new_arr)
84 new_img.SetSpacing([2.5, 3.5, 4.5])
100 writer.KeepOriginalImageUIDOn()
102 modification_time = time.strftime(
"%H%M%S")
103 modification_date = time.strftime(
"%Y%m%d")
109 direction = new_img.GetDirection()
110 series_tag_values = [
111 (
"0008|0031", modification_time),
112 (
"0008|0021", modification_date),
113 (
"0008|0008",
"DERIVED\\SECONDARY"),
116 "1.2.826.0.1.3680043.2.1125." + modification_date +
".1" + modification_time,
135 (
"0008|103e",
"Created-SimpleITK"),
138 if pixel_dtype == np.float64:
143 rescale_slope = 0.001
144 series_tag_values = series_tag_values + [
145 (
"0028|1053", str(rescale_slope)),
156 lambda i: writeSlices(series_tag_values, new_img, sys.argv[1], i),
157 range(new_img.GetDepth()),
164 data_directory = sys.argv[1]
165 series_IDs = sitk.ImageSeriesReader.GetGDCMSeriesIDs(data_directory)
168 'ERROR: given directory "'
170 +
'" does not contain a DICOM series.'
173 series_file_names = sitk.ImageSeriesReader.GetGDCMSeriesFileNames(
174 data_directory, series_IDs[0]
178 series_reader.SetFileNames(series_file_names)
185 series_reader.LoadPrivateTagsOn()
186 image3D = series_reader.Execute()
187 print(image3D.GetSpacing(),
"vs", new_img.GetSpacing())