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19""" A SimpleITK example script demonstrating how to read a DICOM series,
20 modify it, and then write a new DICOM series. """
21
22import sys
23import time
24import os
25import SimpleITK as sitk
26
27if len(sys.argv) < 3:
28 print(
29 "Usage: python "
30 + __file__
31 + " <input_directory_with_DICOM_series> <output_directory>"
32 )
33 sys.exit(1)
34
35
36
37data_directory = sys.argv[1]
38series_IDs = sitk.ImageSeriesReader.GetGDCMSeriesIDs(data_directory)
39if not series_IDs:
40 print(
41 'ERROR: given directory "'
42 + data_directory
43 + '" does not contain a DICOM series.'
44 )
45 sys.exit(1)
46series_file_names = sitk.ImageSeriesReader.GetGDCMSeriesFileNames(
47 data_directory, series_IDs[0]
48)
49
51series_reader.SetFileNames(series_file_names)
52
53
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57
58series_reader.MetaDataDictionaryArrayUpdateOn()
59series_reader.LoadPrivateTagsOn()
60image3D = series_reader.Execute()
61
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74
75writer.KeepOriginalImageUIDOn()
76
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78
79tags_to_copy = [
80 "0010|0010",
81 "0010|0020",
82 "0010|0030",
83 "0020|000d",
84 "0020|0010",
85 "0008|0020",
86 "0008|0030",
87 "0008|0050",
88 "0008|0060",
89]
90
91modification_time = time.strftime("%H%M%S")
92modification_date = time.strftime("%Y%m%d")
93
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104
105direction = filtered_image.GetDirection()
106series_tag_values = [
107 (k, series_reader.GetMetaData(0, k))
108 for k in tags_to_copy
109 if series_reader.HasMetaDataKey(0, k)
110] + [
111 ("0008|0031", modification_time),
112 ("0008|0021", modification_date),
113 ("0008|0008", "DERIVED\\SECONDARY"),
114 (
115 "0020|000e",
116 "1.2.826.0.1.3680043.2.1125." + modification_date + ".1" + modification_time,
117 ),
118
119 (
120 "0020|0037",
121 "\\".join(
122 map(
123 str,
124 (
125 direction[0],
126 direction[3],
127 direction[6],
128 direction[1],
129 direction[4],
130 direction[7],
131 ),
132 )
133 ),
134 ),
135 (
136 "0008|103e",
137 (
138 series_reader.GetMetaData(0, "0008|103e")
139 if series_reader.HasMetaDataKey(0, "0008|103e")
140 else "" + " Processed-SimpleITK"
141 ),
142 ),
143]
144
145for i in range(filtered_image.GetDepth()):
146 image_slice = filtered_image[:, :, i]
147
148 for tag, value in series_tag_values:
149 image_slice.SetMetaData(tag, value)
150
151
152 image_slice.SetMetaData("0008|0012", time.strftime("%Y%m%d"))
153
154 image_slice.SetMetaData("0008|0013", time.strftime("%H%M%S"))
155
156 image_slice.SetMetaData(
157 "0020|0032",
158 "\\".join(map(str, filtered_image.TransformIndexToPhysicalPoint((0, 0, i)))),
159 )
160
161 image_slice.SetMetaData("0020|0013", str(i))
162
163
164
165 writer.SetFileName(os.path.join(sys.argv[2], str(i) + ".dcm"))
166 writer.Execute(image_slice)
167sys.exit(0)
Write out a SimpleITK image to the specified file location.
Read series of image files into a SimpleITK image.
SITKBasicFilters_EXPORT Image DiscreteGaussian(const Image &image1, double variance, unsigned int maximumKernelWidth=32u, double maximumError=0.01, bool useImageSpacing=true)
Blurs an image by separable convolution with discrete gaussian kernels. This filter performs Gaussian...