Mercurial > hg > orthanc

annotate OrthancServer/Resources/Samples/Python/MicroCTDicomization.py @ 5640:f7adfb22e20e

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
updated copyright, as Orthanc Team now replaces Osimis
author Sebastien Jodogne <s.jodogne@gmail.com>
date Thu, 30 May 2024 21:19:57 +0200
parents 48b8dae6dc77
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5240
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1 #!/usr/bin/python3
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
2 # -*- coding: utf-8 -*-
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
3
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
4 # Orthanc - A Lightweight, RESTful DICOM Store
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
5 # Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
6 # Department, University Hospital of Liege, Belgium
5640
f7adfb22e20e updated copyright, as Orthanc Team now replaces Osimis
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5485
diff changeset
7 # Copyright (C) 2017-2023 Osimis S.A., Belgium
f7adfb22e20e updated copyright, as Orthanc Team now replaces Osimis
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5485
diff changeset
8 # Copyright (C) 2024-2024 Orthanc Team SRL, Belgium
5485
48b8dae6dc77 upgrade to year 2024
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5240
diff changeset
9 # Copyright (C) 2021-2024 Sebastien Jodogne, ICTEAM UCLouvain, Belgium
5240
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
10 #
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
11 # This program is free software: you can redistribute it and/or
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
12 # modify it under the terms of the GNU General Public License as
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
13 # published by the Free Software Foundation, either version 3 of the
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
14 # License, or (at your option) any later version.
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
15 #
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
16 # This program is distributed in the hope that it will be useful, but
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
17 # WITHOUT ANY WARRANTY; without even the implied warranty of
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
18 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
19 # General Public License for more details.
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
20 #
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
21 # You should have received a copy of the GNU General Public License
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
22 # along with this program. If not, see <http://www.gnu.org/licenses/>.
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
23
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
24
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
25 #
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
26 # This sample Python script illustrates how to DICOM-ize a micro-CT
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
27 # acquisition, then to upload it to Orthanc.
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
28 #
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
29 # This sample assumes that the slices of the micro-CT are encoded as
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
30 # TIFF files, that are all stored inside the same ZIP archive. Make
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
31 # sure to adapt the parameters of the DICOM-ization below.
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
32 #
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
33 # The following command-line will install the required libraries:
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
34 #
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
35 # $ sudo pip3 install libtiff numpy pydicom requests
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
36 #
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
37
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
38 import datetime
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
39 import io
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
40 import os
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
41 import tempfile
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
42 import zipfile
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
43
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
44 import libtiff
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
45 import numpy
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
46 import pydicom
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
47 import pydicom._storage_sopclass_uids
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
48 import pydicom.datadict
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
49 import pydicom.tag
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
50 import requests
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
51 import requests.auth
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
52
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
53
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
54 ########################################
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
55 ## Parameters for the DICOM-ization ##
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
56 ########################################
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
57
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
58 ZIP = os.path.join(os.getenv('HOME'), 'Downloads', 'SpyII_mb.zip')
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
59
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
60 URL = 'http://localhost:8042/'
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
61 USERNAME = 'orthanc'
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
62 PASSWORD = 'orthanc'
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
63
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
64 VOXEL_WIDTH = 1
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
65 VOXEL_HEIGHT = 1
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
66 VOXEL_DEPTH = 1
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
67
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
68 TAGS = {
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
69 'PatientID' : 'Test',
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
70 'PatientName' : 'Hello^World',
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
71 'StudyDate' : datetime.datetime.now().strftime('%Y%m%d'),
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
72 'StudyTime' : datetime.datetime.now().strftime('%H%M%S'),
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
73
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
74 'AccessionNumber' : None,
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
75 'AcquisitionNumber' : None,
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
76 'KVP' : None,
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
77 'Laterality' : None,
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
78 'Manufacturer' : None,
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
79 'PatientBirthDate' : '',
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
80 'PatientPosition' : None,
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
81 'PatientSex' : 'O',
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
82 'PositionReferenceIndicator' : None,
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
83 'ReferringPhysicianName' : None,
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
84 'SeriesNumber' : 1,
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
85 'StudyID' : 'Test',
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
86 }
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
87
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
88
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
89
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
90 ########################################
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
91 ## Application of the DICOM-ization ##
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
92 ########################################
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
93
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
94 # Add the DICOM unique identifiers
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
95 for tag in [ 'StudyInstanceUID',
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
96 'SeriesInstanceUID',
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
97 'FrameOfReferenceUID' ]:
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
98 if not tag in TAGS:
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
99 TAGS[tag] = pydicom.uid.generate_uid()
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
100
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
101
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
102 def CreateDicomDataset(tif, sliceIndex):
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
103 image = tif.read_image().astype(numpy.uint16)
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
104
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
105 meta = pydicom.Dataset()
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
106 meta.MediaStorageSOPClassUID = pydicom._storage_sopclass_uids.CTImageStorage
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
107 meta.MediaStorageSOPInstanceUID = pydicom.uid.generate_uid()
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
108 meta.TransferSyntaxUID = pydicom.uid.ImplicitVRLittleEndian
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
109
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
110 dataset = pydicom.Dataset()
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
111 dataset.file_meta = meta
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
112
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
113 dataset.is_little_endian = True
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
114 dataset.is_implicit_VR = True
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
115 dataset.SOPClassUID = meta.MediaStorageSOPClassUID
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
116 dataset.SOPInstanceUID = meta.MediaStorageSOPInstanceUID
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
117 dataset.Modality = 'CT'
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
118
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
119 for (key, value) in TAGS.items():
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
120 tag = pydicom.tag.Tag(key)
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
121 vr = pydicom.datadict.dictionary_VR(tag)
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
122 dataset.add_new(tag, vr, value)
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
123
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
124 assert(image.dtype == numpy.uint16)
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
125 dataset.BitsStored = 16
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
126 dataset.BitsAllocated = 16
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
127 dataset.SamplesPerPixel = 1
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
128 dataset.HighBit = 15
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
129
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
130 dataset.Rows = image.shape[0]
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
131 dataset.Columns = image.shape[1]
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
132 dataset.InstanceNumber = (sliceIndex + 1)
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
133 dataset.ImagePositionPatient = r'0\0\%f' % (-float(sliceIndex) * VOXEL_DEPTH)
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
134 dataset.ImageOrientationPatient = r'1\0\0\0\-1\0'
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
135 dataset.SliceThickness = VOXEL_DEPTH
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
136 dataset.ImageType = r'ORIGINAL\PRIMARY\AXIAL'
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
137 dataset.RescaleIntercept = '0'
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
138 dataset.RescaleSlope = '1'
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
139 dataset.PixelSpacing = r'%f\%f' % (VOXEL_HEIGHT, VOXEL_WIDTH)
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
140 dataset.PhotometricInterpretation = 'MONOCHROME2'
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
141 dataset.PixelRepresentation = 1
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
142
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
143 minValue = numpy.min(image)
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
144 maxValue = numpy.max(image)
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
145 dataset.WindowWidth = maxValue - minValue
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
146 dataset.WindowCenter = (minValue + maxValue) / 2.0
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
147
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
148 pydicom.dataset.validate_file_meta(dataset.file_meta, enforce_standard=True)
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
149 dataset.PixelData = image.tobytes()
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
150
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
151 return dataset
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
152
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
153
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
154 # Create a temporary file, as libtiff is not able to read from BytesIO()
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
155 with tempfile.NamedTemporaryFile() as tmp:
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
156 sliceIndex = 0
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
157
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
158 # Loop over the files in the ZIP archive, after having sorted them
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
159 with zipfile.ZipFile(ZIP, 'r') as z:
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
160 for path in sorted(z.namelist()):
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
161
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
162 # Ignore folders in the ZIP archive
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
163 info = z.getinfo(path)
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
164 if info.is_dir():
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
165 continue
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
166
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
167 # Extract the current file from the ZIP archive, into the temporary file
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
168 print('DICOM-izing: %s' % path)
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
169 data = z.read(path)
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
170
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
171 with open(tmp.name, 'wb') as f:
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
172 f.write(data)
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
173
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
174 # Try and decode the TIFF file
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
175 try:
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
176 tif = libtiff.TIFF.open(tmp.name)
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
177 except:
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
178 # Not a TIFF file, ignore
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
179 continue
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
180
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
181 # Create a DICOM dataset from the TIFF
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
182 dataset = CreateDicomDataset(tif, sliceIndex)
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
183 b = io.BytesIO()
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
184 dataset.save_as(b, False)
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
185
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
186 # Upload the DICOM dataset to Orthanc
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
187 r = requests.post('%s/instances' % URL, b.getvalue(),
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
188 auth = requests.auth.HTTPBasicAuth(USERNAME, PASSWORD))
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
189 r.raise_for_status()
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
190
c9e2c6d1cd62 added two Python samples: DicomizeImage.py and MicroCTDicomization.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
191 sliceIndex += 1