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annotate OrthancServer/Resources/Samples/Python/MicroCTDicomization.py @ 5240:c9e2c6d1cd62

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added two Python samples: DicomizeImage.py and MicroCTDicomization.py
author Sebastien Jodogne <s.jodogne@gmail.com>
date Wed, 05 Apr 2023 17:54:21 +0200
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children 48b8dae6dc77
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5240
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
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1 #!/usr/bin/python3
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2 # -*- coding: utf-8 -*-
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3
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4 # Orthanc - A Lightweight, RESTful DICOM Store
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5 # Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
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6 # Department, University Hospital of Liege, Belgium
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7 # Copyright (C) 2017-2023 Osimis S.A., Belgium
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8 # Copyright (C) 2021-2023 Sebastien Jodogne, ICTEAM UCLouvain, Belgium
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9 #
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10 # This program is free software: you can redistribute it and/or
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11 # modify it under the terms of the GNU General Public License as
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12 # published by the Free Software Foundation, either version 3 of the
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13 # License, or (at your option) any later version.
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14 #
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15 # This program is distributed in the hope that it will be useful, but
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16 # WITHOUT ANY WARRANTY; without even the implied warranty of
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17 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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18 # General Public License for more details.
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19 #
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20 # You should have received a copy of the GNU General Public License
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21 # along with this program. If not, see <http://www.gnu.org/licenses/>.
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22
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23
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24 #
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25 # This sample Python script illustrates how to DICOM-ize a micro-CT
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26 # acquisition, then to upload it to Orthanc.
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27 #
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28 # This sample assumes that the slices of the micro-CT are encoded as
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29 # TIFF files, that are all stored inside the same ZIP archive. Make
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30 # sure to adapt the parameters of the DICOM-ization below.
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31 #
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32 # The following command-line will install the required libraries:
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33 #
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34 # $ sudo pip3 install libtiff numpy pydicom requests
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35 #
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36
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37 import datetime
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38 import io
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39 import os
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40 import tempfile
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41 import zipfile
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42
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43 import libtiff
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44 import numpy
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45 import pydicom
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46 import pydicom._storage_sopclass_uids
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47 import pydicom.datadict
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48 import pydicom.tag
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49 import requests
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50 import requests.auth
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51
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52
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53 ########################################
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54 ## Parameters for the DICOM-ization ##
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55 ########################################
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56
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57 ZIP = os.path.join(os.getenv('HOME'), 'Downloads', 'SpyII_mb.zip')
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58
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59 URL = 'http://localhost:8042/'
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60 USERNAME = 'orthanc'
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61 PASSWORD = 'orthanc'
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62
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63 VOXEL_WIDTH = 1
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64 VOXEL_HEIGHT = 1
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65 VOXEL_DEPTH = 1
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66
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67 TAGS = {
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68 'PatientID' : 'Test',
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69 'PatientName' : 'Hello^World',
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70 'StudyDate' : datetime.datetime.now().strftime('%Y%m%d'),
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71 'StudyTime' : datetime.datetime.now().strftime('%H%M%S'),
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72
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73 'AccessionNumber' : None,
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74 'AcquisitionNumber' : None,
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75 'KVP' : None,
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76 'Laterality' : None,
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77 'Manufacturer' : None,
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78 'PatientBirthDate' : '',
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79 'PatientPosition' : None,
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80 'PatientSex' : 'O',
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81 'PositionReferenceIndicator' : None,
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82 'ReferringPhysicianName' : None,
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83 'SeriesNumber' : 1,
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84 'StudyID' : 'Test',
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85 }
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86
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87
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88
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89 ########################################
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90 ## Application of the DICOM-ization ##
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91 ########################################
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92
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93 # Add the DICOM unique identifiers
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94 for tag in [ 'StudyInstanceUID',
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95 'SeriesInstanceUID',
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96 'FrameOfReferenceUID' ]:
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97 if not tag in TAGS:
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98 TAGS[tag] = pydicom.uid.generate_uid()
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99
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100
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101 def CreateDicomDataset(tif, sliceIndex):
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102 image = tif.read_image().astype(numpy.uint16)
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103
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104 meta = pydicom.Dataset()
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105 meta.MediaStorageSOPClassUID = pydicom._storage_sopclass_uids.CTImageStorage
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106 meta.MediaStorageSOPInstanceUID = pydicom.uid.generate_uid()
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107 meta.TransferSyntaxUID = pydicom.uid.ImplicitVRLittleEndian
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108
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109 dataset = pydicom.Dataset()
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110 dataset.file_meta = meta
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111
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112 dataset.is_little_endian = True
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113 dataset.is_implicit_VR = True
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114 dataset.SOPClassUID = meta.MediaStorageSOPClassUID
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115 dataset.SOPInstanceUID = meta.MediaStorageSOPInstanceUID
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116 dataset.Modality = 'CT'
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117
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118 for (key, value) in TAGS.items():
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119 tag = pydicom.tag.Tag(key)
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120 vr = pydicom.datadict.dictionary_VR(tag)
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121 dataset.add_new(tag, vr, value)
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122
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123 assert(image.dtype == numpy.uint16)
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124 dataset.BitsStored = 16
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125 dataset.BitsAllocated = 16
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126 dataset.SamplesPerPixel = 1
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127 dataset.HighBit = 15
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128
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129 dataset.Rows = image.shape[0]
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130 dataset.Columns = image.shape[1]
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131 dataset.InstanceNumber = (sliceIndex + 1)
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132 dataset.ImagePositionPatient = r'0\0\%f' % (-float(sliceIndex) * VOXEL_DEPTH)
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133 dataset.ImageOrientationPatient = r'1\0\0\0\-1\0'
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134 dataset.SliceThickness = VOXEL_DEPTH
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135 dataset.ImageType = r'ORIGINAL\PRIMARY\AXIAL'
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136 dataset.RescaleIntercept = '0'
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137 dataset.RescaleSlope = '1'
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138 dataset.PixelSpacing = r'%f\%f' % (VOXEL_HEIGHT, VOXEL_WIDTH)
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139 dataset.PhotometricInterpretation = 'MONOCHROME2'
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140 dataset.PixelRepresentation = 1
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141
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142 minValue = numpy.min(image)
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143 maxValue = numpy.max(image)
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144 dataset.WindowWidth = maxValue - minValue
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145 dataset.WindowCenter = (minValue + maxValue) / 2.0
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146
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147 pydicom.dataset.validate_file_meta(dataset.file_meta, enforce_standard=True)
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148 dataset.PixelData = image.tobytes()
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149
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150 return dataset
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151
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152
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153 # Create a temporary file, as libtiff is not able to read from BytesIO()
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154 with tempfile.NamedTemporaryFile() as tmp:
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155 sliceIndex = 0
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156
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157 # Loop over the files in the ZIP archive, after having sorted them
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158 with zipfile.ZipFile(ZIP, 'r') as z:
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159 for path in sorted(z.namelist()):
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160
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161 # Ignore folders in the ZIP archive
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162 info = z.getinfo(path)
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163 if info.is_dir():
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164 continue
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165
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166 # Extract the current file from the ZIP archive, into the temporary file
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167 print('DICOM-izing: %s' % path)
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168 data = z.read(path)
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169
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170 with open(tmp.name, 'wb') as f:
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171 f.write(data)
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172
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173 # Try and decode the TIFF file
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174 try:
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175 tif = libtiff.TIFF.open(tmp.name)
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176 except:
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177 # Not a TIFF file, ignore
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178 continue
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179
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180 # Create a DICOM dataset from the TIFF
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181 dataset = CreateDicomDataset(tif, sliceIndex)
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182 b = io.BytesIO()
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183 dataset.save_as(b, False)
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184
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185 # Upload the DICOM dataset to Orthanc
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186 r = requests.post('%s/instances' % URL, b.getvalue(),
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187 auth = requests.auth.HTTPBasicAuth(USERNAME, PASSWORD))
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188 r.raise_for_status()
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189
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190 sliceIndex += 1