Mercurial > hg > orthanc-tests
annotate Tests/Toolbox.py @ 610:ec657d1a62a6 Orthanc-1.12.3
fix compatibility with python3
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Wed, 31 Jan 2024 12:18:20 +0100 |
| parents | 8722f7f95a38 |
| children | 9f8276ac1cdd |
| rev | line source |
|---|---|
| 0 | 1 #!/usr/bin/python |
| 2 | |
| 1 | 3 # Orthanc - A Lightweight, RESTful DICOM Store |
| 73 | 4 # Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics |
| 1 | 5 # Department, University Hospital of Liege, Belgium |
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6 # Copyright (C) 2017-2023 Osimis S.A., Belgium |
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7 # Copyright (C) 2021-2023 Sebastien Jodogne, ICTEAM UCLouvain, Belgium |
| 1 | 8 # |
| 9 # This program is free software: you can redistribute it and/or | |
| 10 # modify it under the terms of the GNU General Public License as | |
| 11 # published by the Free Software Foundation, either version 3 of the | |
| 12 # License, or (at your option) any later version. | |
| 13 # | |
| 14 # This program is distributed in the hope that it will be useful, but | |
| 15 # WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 16 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
| 17 # General Public License for more details. | |
| 18 # | |
| 19 # You should have received a copy of the GNU General Public License | |
| 20 # along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 0 | 21 |
| 22 | |
| 23 import hashlib | |
| 24 import httplib2 | |
| 25 import json | |
| 4 | 26 import os |
| 1 | 27 import re |
| 4 | 28 import signal |
| 1 | 29 import subprocess |
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30 import tempfile |
| 4 | 31 import threading |
| 83 | 32 import sys |
| 0 | 33 import time |
| 1 | 34 import zipfile |
| 0 | 35 |
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36 from xml.dom import minidom |
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37 |
| 304 | 38 from PIL import Image, ImageChops |
| 39 import math | |
| 40 import operator | |
| 41 | |
| 83 | 42 |
| 43 if (sys.version_info >= (3, 0)): | |
| 44 from urllib.parse import urlencode | |
| 45 from io import StringIO | |
| 46 from io import BytesIO | |
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47 from urllib.parse import unquote |
| 83 | 48 |
| 49 else: | |
| 50 from urllib import urlencode | |
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51 from urlparse import unquote |
| 83 | 52 |
| 53 # http://stackoverflow.com/a/1313868/881731 | |
| 54 try: | |
| 55 from cStringIO import StringIO | |
| 56 except: | |
| 57 from StringIO import StringIO | |
| 3 | 58 |
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59 |
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60 def DecodeJson(s): |
| 83 | 61 t = s |
| 62 | |
| 63 if (sys.version_info >= (3, 0)): | |
| 64 try: | |
| 65 t = s.decode() | |
| 66 except: | |
| 67 pass | |
| 68 | |
| 69 try: | |
| 70 return json.loads(t) | |
| 71 except: | |
| 72 return t | |
| 0 | 73 |
| 74 | |
| 13 | 75 def DefineOrthanc(server = 'localhost', |
| 76 restPort = 8042, | |
| 1 | 77 username = None, |
| 78 password = None, | |
| 79 aet = 'ORTHANC', | |
| 80 dicomPort = 4242): | |
| 13 | 81 #m = re.match(r'(http|https)://([^:]+):([^@]+)@([^@]+)', url) |
| 82 #if m != None: | |
| 83 # url = m.groups()[0] + '://' + m.groups()[3] | |
| 84 # username = m.groups()[1] | |
| 85 # password = m.groups()[2] | |
| 0 | 86 |
| 13 | 87 #if not url.endswith('/'): |
| 88 # url += '/' | |
| 0 | 89 |
| 1 | 90 return { |
| 13 | 91 'Server' : server, |
| 92 'Url' : 'http://%s:%d/' % (server, restPort), | |
| 1 | 93 'Username' : username, |
| 94 'Password' : password, | |
| 95 'DicomAet' : aet, | |
| 96 'DicomPort' : dicomPort | |
| 97 } | |
| 0 | 98 |
| 99 | |
| 100 def _SetupCredentials(orthanc, http): | |
| 1 | 101 if (orthanc['Username'] != None and |
| 102 orthanc['Password'] != None): | |
| 103 http.add_credentials(orthanc['Username'], orthanc['Password']) | |
| 0 | 104 |
| 28 | 105 def DoGetRaw(orthanc, uri, data = {}, body = None, headers = {}): |
| 0 | 106 d = '' |
| 107 if len(data.keys()) > 0: | |
| 108 d = '?' + urlencode(data) | |
| 109 | |
| 110 http = httplib2.Http() | |
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111 http.follow_redirects = False |
| 0 | 112 _SetupCredentials(orthanc, http) |
| 113 | |
| 1 | 114 resp, content = http.request(orthanc['Url'] + uri + d, 'GET', body = body, |
| 0 | 115 headers = headers) |
| 28 | 116 return (resp, content) |
| 117 | |
| 118 | |
| 119 def DoGet(orthanc, uri, data = {}, body = None, headers = {}): | |
| 120 (resp, content) = DoGetRaw(orthanc, uri, data = data, body = body, headers = headers) | |
| 121 | |
| 0 | 122 if not (resp.status in [ 200 ]): |
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123 raise Exception(resp.status, resp) |
| 0 | 124 else: |
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125 return DecodeJson(content) |
| 0 | 126 |
| 127 def _DoPutOrPost(orthanc, uri, method, data, contentType, headers): | |
| 128 http = httplib2.Http() | |
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129 http.follow_redirects = False |
| 0 | 130 _SetupCredentials(orthanc, http) |
| 131 | |
| 83 | 132 if isinstance(data, (str, bytearray, bytes)): |
| 0 | 133 body = data |
| 134 if len(contentType) != 0: | |
| 135 headers['content-type'] = contentType | |
| 136 else: | |
| 137 body = json.dumps(data) | |
| 138 headers['content-type'] = 'application/json' | |
| 139 | |
| 140 headers['expect'] = '' | |
| 141 | |
| 1 | 142 resp, content = http.request(orthanc['Url'] + uri, method, |
| 0 | 143 body = body, |
| 144 headers = headers) | |
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145 return (resp, content) |
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146 |
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147 def DoDeleteRaw(orthanc, uri, headers = {}): |
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148 http = httplib2.Http() |
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149 http.follow_redirects = False |
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150 _SetupCredentials(orthanc, http) |
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151 |
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152 resp, content = http.request(orthanc['Url'] + uri, 'DELETE', headers = headers) |
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153 return (resp, content) |
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154 |
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155 def DoDelete(orthanc, uri, headers = {}): |
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156 (resp, content) = DoDeleteRaw(orthanc, uri, headers) |
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157 if not (resp.status in [ 200 ]): |
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158 raise Exception(resp.status, resp) |
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159 else: |
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160 return DecodeJson(content) |
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161 |
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162 def DoPutRaw(orthanc, uri, data = {}, contentType = '', headers = {}): |
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163 return _DoPutOrPost(orthanc, uri, 'PUT', data, contentType, headers) |
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164 |
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165 def DoPut(orthanc, uri, data = {}, contentType = '', headers = {}): |
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166 (resp, content) = DoPutRaw(orthanc, uri, data, contentType, headers) |
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167 if not (resp.status in [ 200, 201, 302 ]): |
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168 raise Exception(resp.status, resp) |
| 0 | 169 else: |
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170 return DecodeJson(content) |
| 0 | 171 |
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172 def DoPostRaw(orthanc, uri, data = {}, contentType = '', headers = {}): |
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173 return _DoPutOrPost(orthanc, uri, 'POST', data, contentType, headers) |
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174 |
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175 def DoPost(orthanc, uri, data = {}, contentType = '', headers = {}): |
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176 (resp, content) = DoPostRaw(orthanc, uri, data, contentType, headers) |
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177 if not (resp.status in [ 200, 201, 302 ]): |
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178 raise Exception(resp.status, resp) |
| 0 | 179 else: |
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180 return DecodeJson(content) |
| 0 | 181 |
| 13 | 182 def GetDatabasePath(filename): |
| 183 return os.path.join(os.path.dirname(__file__), '..', 'Database', filename) | |
| 184 | |
| 0 | 185 def UploadInstance(orthanc, filename): |
| 83 | 186 with open(GetDatabasePath(filename), 'rb') as f: |
| 187 d = f.read() | |
| 188 | |
| 0 | 189 return DoPost(orthanc, '/instances', d, 'application/dicom') |
| 190 | |
| 191 def UploadFolder(orthanc, path): | |
| 13 | 192 for i in os.listdir(GetDatabasePath(path)): |
| 1 | 193 try: |
| 194 UploadInstance(orthanc, os.path.join(path, i)) | |
| 195 except: | |
| 196 pass | |
| 0 | 197 |
| 198 def DropOrthanc(orthanc): | |
| 199 # Reset the Lua callbacks | |
| 200 DoPost(orthanc, '/tools/execute-script', 'function OnStoredInstance(instanceId, tags, metadata) end', 'application/lua') | |
| 201 | |
| 202 DoDelete(orthanc, '/exports') | |
| 203 | |
| 204 for s in DoGet(orthanc, '/patients'): | |
| 205 DoDelete(orthanc, '/patients/%s' % s) | |
| 206 | |
| 174 | 207 def InstallLuaScriptFromPath(orthanc, path): |
| 208 with open(GetDatabasePath(path), 'r') as f: | |
| 209 InstallLuaScript(orthanc, f.read()) | |
| 210 | |
| 211 def InstallLuaScript(orthanc, script): | |
| 212 DoPost(orthanc, '/tools/execute-script', script, 'application/lua') | |
| 213 | |
| 214 def UninstallLuaCallbacks(orthanc): | |
| 215 DoPost(orthanc, '/tools/execute-script', 'function OnStoredInstance() end', 'application/lua') | |
| 216 InstallLuaScriptFromPath(orthanc, 'Lua/TransferSyntaxEnable.lua') | |
| 217 | |
| 218 | |
| 0 | 219 def ComputeMD5(data): |
| 220 m = hashlib.md5() | |
| 221 m.update(data) | |
| 222 return m.hexdigest() | |
| 223 | |
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224 def UncompressImage(data): |
| 83 | 225 if (sys.version_info >= (3, 0)): |
| 226 return Image.open(BytesIO(data)) | |
| 227 else: | |
| 228 return Image.open(StringIO(data)) | |
| 0 | 229 |
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230 def GetImage(orthanc, uri, headers = {}): |
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231 # http://www.pythonware.com/library/pil/handbook/introduction.htm |
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232 return UncompressImage(DoGet(orthanc, uri, headers = headers)) |
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233 |
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234 def ParseArchive(s): |
| 0 | 235 # http://stackoverflow.com/a/1313868/881731 |
| 83 | 236 if (sys.version_info >= (3, 0)): |
| 237 return zipfile.ZipFile(BytesIO(s), "r") | |
| 238 else: | |
| 239 return zipfile.ZipFile(StringIO(s), "r") | |
| 0 | 240 |
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241 def GetArchive(orthanc, uri): |
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242 return ParseArchive(DoGet(orthanc, uri)) |
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243 |
| 192 | 244 def PostArchive(orthanc, uri, body): |
| 245 # http://stackoverflow.com/a/1313868/881731 | |
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246 return ParseArchive(DoPost(orthanc, uri, body)) |
| 192 | 247 |
| 1 | 248 def IsDefinedInLua(orthanc, name): |
| 0 | 249 s = DoPost(orthanc, '/tools/execute-script', 'print(type(%s))' % name, 'application/lua') |
| 250 return (s.strip() != 'nil') | |
| 251 | |
| 1 | 252 def WaitEmpty(orthanc): |
| 0 | 253 while True: |
| 1 | 254 if len(DoGet(orthanc, '/instances')) == 0: |
| 0 | 255 return |
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256 time.sleep(0.01) |
| 0 | 257 |
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258 def WaitJobDone(orthanc, job): |
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259 while True: |
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260 s = DoGet(orthanc, '/jobs/%s' % job) ['State'] |
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261 |
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262 if s == 'Success': |
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263 return True |
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264 elif s == 'Failure': |
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265 return False |
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266 |
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267 time.sleep(0.01) |
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268 |
| 138 | 269 def MonitorJob(orthanc, func): # "func" is a lambda |
| 270 a = set(DoGet(orthanc, '/jobs')) | |
| 271 func() | |
| 272 b = set(DoGet(orthanc, '/jobs')) | |
| 273 | |
| 274 diff = list(b - a) | |
| 275 if len(diff) != 1: | |
| 276 print('No job was created!') | |
| 277 return False | |
| 278 else: | |
| 279 return WaitJobDone(orthanc, diff[0]) | |
| 280 | |
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281 def MonitorJob2(orthanc, func): # "func" is a lambda |
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282 a = set(DoGet(orthanc, '/jobs')) |
| 181 | 283 job = func() |
|
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284 b = set(DoGet(orthanc, '/jobs')) |
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285 |
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286 diff = list(b - a) |
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287 if len(diff) != 1: |
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288 print('No job was created!') |
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289 return None |
| 181 | 290 elif (not 'ID' in job or |
| 291 diff[0] != job['ID']): | |
| 292 print('Mismatch in the job ID') | |
| 293 return None | |
|
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294 elif WaitJobDone(orthanc, diff[0]): |
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295 return diff[0] |
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296 else: |
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297 print('Error while executing the job') |
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298 return None |
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299 |
| 220 | 300 def WaitAllNewJobsDone(orthanc, func): # "func" is a lambda |
| 301 a = set(DoGet(orthanc, '/jobs')) | |
| 302 func() | |
| 303 | |
| 304 first = True | |
| 305 | |
| 306 while True: | |
| 307 b = set(DoGet(orthanc, '/jobs')) | |
| 308 | |
| 309 diff = list(b - a) | |
| 310 if len(diff) == 0: | |
| 311 if first: | |
| 312 raise Exception('No job was created') | |
| 313 else: | |
| 314 return # We're done | |
| 315 else: | |
| 316 first = False | |
| 317 | |
| 318 if WaitJobDone(orthanc, diff[0]): | |
| 319 a.add(diff[0]) | |
| 320 else: | |
| 321 raise Exception('Error while executing the job') | |
| 322 | |
| 323 | |
| 1 | 324 def GetDockerHostAddress(): |
| 325 route = subprocess.check_output([ '/sbin/ip', 'route' ]) | |
| 326 m = re.search(r'default via ([0-9.]+)', route) | |
| 327 if m == None: | |
| 328 return 'localhost' | |
| 329 else: | |
| 330 return m.groups()[0] | |
| 4 | 331 |
|
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332 def FindExecutable(name): |
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333 p = os.path.join('/usr/local/bin', name) |
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334 if os.path.isfile(p): |
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335 return p |
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336 |
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337 p = os.path.join('/usr/local/sbin', name) |
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338 if os.path.isfile(p): |
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339 return p |
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340 |
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341 return name |
| 4 | 342 |
| 173 | 343 def IsOrthancVersionAbove(orthanc, major, minor, revision): |
| 344 v = DoGet(orthanc, '/system')['Version'] | |
| 345 | |
| 346 if v == 'mainline': | |
| 347 return True | |
| 348 else: | |
| 349 tmp = v.split('.') | |
| 350 a = int(tmp[0]) | |
| 351 b = int(tmp[1]) | |
| 352 c = int(tmp[2]) | |
| 353 return (a > major or | |
| 354 (a == major and b > minor) or | |
| 355 (a == major and b == minor and c >= revision)) | |
| 4 | 356 |
| 532 | 357 def IsPluginVersionAbove(orthanc, plugin, major, minor, revision): |
| 358 v = DoGet(orthanc, '/plugins/%s' % plugin)['Version'] | |
| 359 | |
| 360 if v == 'mainline': | |
| 361 return True | |
| 362 else: | |
| 363 tmp = v.split('.') | |
| 364 if len(tmp) >= 3: | |
| 365 a = int(tmp[0]) | |
| 366 b = int(tmp[1]) | |
| 367 c = int(tmp[2]) | |
| 368 return (a > major or | |
| 369 (a == major and b > minor) or | |
| 370 (a == major and b == minor and c >= revision)) | |
| 371 elif len(tmp) >= 2: | |
| 372 a = int(tmp[0]) | |
| 373 b = int(tmp[1]) | |
| 374 return (a > major or | |
| 375 (a == major and b > minor)) | |
| 376 else: | |
| 377 return False | |
| 4 | 378 |
| 379 class ExternalCommandThread: | |
| 380 @staticmethod | |
| 381 def ExternalCommandFunction(arg, stop_event, command, env): | |
|
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382 with open(os.devnull, 'w') as devnull: |
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383 external = subprocess.Popen(command, env = env, stderr = devnull) |
| 4 | 384 |
|
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385 while (not stop_event.is_set()): |
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386 error = external.poll() |
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387 if error != None: |
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388 # http://stackoverflow.com/a/1489838/881731 |
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389 os._exit(-1) |
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390 stop_event.wait(0.1) |
| 4 | 391 |
| 83 | 392 print('Stopping the external command') |
| 4 | 393 external.terminate() |
| 9 | 394 external.communicate() # Wait for the command to stop |
| 4 | 395 |
| 396 def __init__(self, command, env = None): | |
| 397 self.thread_stop = threading.Event() | |
| 398 self.thread = threading.Thread(target = self.ExternalCommandFunction, | |
| 399 args = (10, self.thread_stop, command, env)) | |
| 9 | 400 #self.daemon = True |
| 4 | 401 self.thread.start() |
| 402 | |
| 403 def stop(self): | |
| 404 self.thread_stop.set() | |
| 405 self.thread.join() | |
| 220 | 406 |
| 407 | |
|
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408 def AssertAlmostEqualRecursive(self, a, b, places = 7, ignoreKeys = []): |
| 220 | 409 if type(a) is dict: |
| 410 self.assertTrue(type(b) is dict) | |
| 411 self.assertEqual(a.keys(), b.keys()) | |
| 412 for key, value in a.items(): | |
|
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413 if not key in ignoreKeys: |
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414 AssertAlmostEqualRecursive(self, a[key], b[key], places) |
| 220 | 415 |
| 416 elif type(a) is list: | |
| 417 self.assertTrue(type(b) is list) | |
| 418 self.assertEqual(len(a), len(b)) | |
| 419 for i in range(len(a)): | |
| 420 AssertAlmostEqualRecursive(self, a[i], b[i], places) | |
| 421 | |
| 422 else: | |
| 423 self.assertAlmostEqual(a, b, places = places) | |
|
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424 |
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425 |
| 543 | 426 def GetTransferSyntax(dicom, encoding='utf-8'): |
|
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427 with tempfile.NamedTemporaryFile(delete = True) as f: |
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428 f.write(dicom) |
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429 f.flush() |
|
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430 |
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431 with open(os.devnull, 'w') as devnull: |
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432 data = subprocess.check_output([ FindExecutable('dcm2xml'), f.name ], |
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433 stderr = devnull) |
| 543 | 434 return re.search('<data-set xfer="(.*?)"', data.decode(encoding)).group(1) |
| 304 | 435 |
| 436 | |
| 437 def HasGdcmPlugin(orthanc): | |
| 438 plugins = DoGet(orthanc, '/plugins') | |
| 439 return ('gdcm' in plugins) | |
| 440 | |
| 441 | |
| 442 def _GetMaxImageDifference(im1, im2): | |
| 443 h = ImageChops.difference(im1, im2).histogram() | |
| 444 | |
| 445 if len(h) < 256: | |
| 446 raise Exception() | |
| 447 | |
| 448 i = len(h) - 1 | |
| 449 while h[i] == 0: | |
| 450 i -= 1 | |
| 451 | |
| 452 return i | |
| 453 | |
| 454 | |
| 455 def GetMaxImageDifference(im1, im2): | |
| 456 if im1.mode != im2.mode: | |
| 457 raise Exception('Incompatible image modes') | |
| 458 | |
| 459 if im1.mode == 'RGB': | |
| 460 red1, green1, blue1 = im1.split() | |
| 461 red2, green2, blue2 = im2.split() | |
| 462 return max([ _GetMaxImageDifference(red1, red2), | |
| 463 _GetMaxImageDifference(green1, green2), | |
| 464 _GetMaxImageDifference(blue1, blue2) ]) | |
| 465 else: | |
| 466 return _GetMaxImageDifference(im1, im2) | |
|
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467 |
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468 |
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469 def DoPropFind(orthanc, uri, depth): |
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470 http = httplib2.Http() |
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471 http.follow_redirects = False |
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472 _SetupCredentials(orthanc, http) |
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473 |
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474 resp, content = http.request(orthanc['Url'] + uri, 'PROPFIND', headers = { 'Depth' : str(depth) }) |
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475 |
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476 if not (resp.status in [ 207 ]): |
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477 raise Exception(resp.status, resp) |
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478 else: |
|
341
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479 xml = minidom.parseString(content) |
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480 |
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481 if (xml.documentElement.nodeName != 'D:multistatus' or |
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482 xml.documentElement.attributes['xmlns:D'].value != 'DAV:'): |
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483 raise Exception() |
|
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484 |
|
341
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485 result = {} |
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486 |
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487 for i in xml.documentElement.childNodes: |
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488 if i.nodeType == minidom.Node.ELEMENT_NODE: |
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489 if i.nodeName != 'D:response': |
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490 raise Exception() |
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491 href = None |
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492 prop = None |
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493 for j in i.childNodes: |
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494 if j.nodeType == minidom.Node.ELEMENT_NODE: |
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495 if j.nodeName == 'D:href': |
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496 if href == None: |
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497 href = unquote(j.firstChild.nodeValue) |
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498 else: |
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499 raise Exception() |
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500 elif j.nodeName == 'D:propstat': |
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501 for k in j.childNodes: |
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502 if k.nodeName == 'D:status': |
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503 if k.firstChild.nodeValue != 'HTTP/1.1 200 OK': |
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504 raise Exception() |
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505 elif k.nodeType == minidom.Node.ELEMENT_NODE: |
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506 if (k.nodeName != 'D:prop' or |
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507 prop != None): |
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508 raise Exception() |
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509 prop = k |
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510 else: |
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511 raise Exception() |
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512 if href == None or prop == None: |
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513 raise Exception() |
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514 |
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515 info = {} |
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516 |
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517 for j in prop.childNodes: |
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518 if j.nodeType == minidom.Node.ELEMENT_NODE: |
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519 if j.nodeName == 'D:displayname': |
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520 info['displayname'] = j.firstChild.nodeValue if j.firstChild != None else '' |
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521 elif j.nodeName == 'D:creationdate': |
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522 info['creationdate'] = j.firstChild.nodeValue |
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523 elif j.nodeName == 'D:getlastmodified': |
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524 info['lastmodified'] = j.firstChild.nodeValue |
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525 elif j.nodeName == 'D:resourcetype': |
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526 k = j.getElementsByTagName('D:collection') |
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527 info['folder'] = (len(k) == 1) |
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528 |
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529 result[href] = info |
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530 elif i.nodeType != minidom.Node.TEXT_NODE: |
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531 raise Exception() |
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532 |
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533 return result |