Mercurial > hg > orthanc-tests
annotate Tests/Toolbox.py @ 391:227d9a932467
testing revisions in metadata
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Fri, 16 Apr 2021 17:13:53 +0200 |
| parents | 79ce0f7a9714 |
| children | 9528e2a03d3c |
| 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) 2017-2021 Osimis S.A., Belgium |
| 1 | 7 # |
| 8 # This program is free software: you can redistribute it and/or | |
| 9 # modify it under the terms of the GNU General Public License as | |
| 10 # published by the Free Software Foundation, either version 3 of the | |
| 11 # License, or (at your option) any later version. | |
| 12 # | |
| 13 # This program is distributed in the hope that it will be useful, but | |
| 14 # WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 15 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
| 16 # General Public License for more details. | |
| 17 # | |
| 18 # You should have received a copy of the GNU General Public License | |
| 19 # along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 0 | 20 |
| 21 | |
| 22 import hashlib | |
| 23 import httplib2 | |
| 24 import json | |
| 4 | 25 import os |
| 1 | 26 import re |
| 4 | 27 import signal |
| 1 | 28 import subprocess |
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29 import tempfile |
| 4 | 30 import threading |
| 83 | 31 import sys |
| 0 | 32 import time |
| 1 | 33 import zipfile |
| 0 | 34 |
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35 from xml.dom import minidom |
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36 |
| 304 | 37 from PIL import Image, ImageChops |
| 38 import math | |
| 39 import operator | |
| 40 | |
| 83 | 41 |
| 42 if (sys.version_info >= (3, 0)): | |
| 43 from urllib.parse import urlencode | |
| 44 from io import StringIO | |
| 45 from io import BytesIO | |
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46 from urllib.parse import unquote |
| 83 | 47 |
| 48 else: | |
| 49 from urllib import urlencode | |
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50 from urlparse import unquote |
| 83 | 51 |
| 52 # http://stackoverflow.com/a/1313868/881731 | |
| 53 try: | |
| 54 from cStringIO import StringIO | |
| 55 except: | |
| 56 from StringIO import StringIO | |
| 3 | 57 |
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58 |
| 83 | 59 def _DecodeJson(s): |
| 60 t = s | |
| 61 | |
| 62 if (sys.version_info >= (3, 0)): | |
| 63 try: | |
| 64 t = s.decode() | |
| 65 except: | |
| 66 pass | |
| 67 | |
| 68 try: | |
| 69 return json.loads(t) | |
| 70 except: | |
| 71 return t | |
| 0 | 72 |
| 73 | |
| 13 | 74 def DefineOrthanc(server = 'localhost', |
| 75 restPort = 8042, | |
| 1 | 76 username = None, |
| 77 password = None, | |
| 78 aet = 'ORTHANC', | |
| 79 dicomPort = 4242): | |
| 13 | 80 #m = re.match(r'(http|https)://([^:]+):([^@]+)@([^@]+)', url) |
| 81 #if m != None: | |
| 82 # url = m.groups()[0] + '://' + m.groups()[3] | |
| 83 # username = m.groups()[1] | |
| 84 # password = m.groups()[2] | |
| 0 | 85 |
| 13 | 86 #if not url.endswith('/'): |
| 87 # url += '/' | |
| 0 | 88 |
| 1 | 89 return { |
| 13 | 90 'Server' : server, |
| 91 'Url' : 'http://%s:%d/' % (server, restPort), | |
| 1 | 92 'Username' : username, |
| 93 'Password' : password, | |
| 94 'DicomAet' : aet, | |
| 95 'DicomPort' : dicomPort | |
| 96 } | |
| 0 | 97 |
| 98 | |
| 99 def _SetupCredentials(orthanc, http): | |
| 1 | 100 if (orthanc['Username'] != None and |
| 101 orthanc['Password'] != None): | |
| 102 http.add_credentials(orthanc['Username'], orthanc['Password']) | |
| 0 | 103 |
| 28 | 104 def DoGetRaw(orthanc, uri, data = {}, body = None, headers = {}): |
| 0 | 105 d = '' |
| 106 if len(data.keys()) > 0: | |
| 107 d = '?' + urlencode(data) | |
| 108 | |
| 109 http = httplib2.Http() | |
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110 http.follow_redirects = False |
| 0 | 111 _SetupCredentials(orthanc, http) |
| 112 | |
| 1 | 113 resp, content = http.request(orthanc['Url'] + uri + d, 'GET', body = body, |
| 0 | 114 headers = headers) |
| 28 | 115 return (resp, content) |
| 116 | |
| 117 | |
| 118 def DoGet(orthanc, uri, data = {}, body = None, headers = {}): | |
| 119 (resp, content) = DoGetRaw(orthanc, uri, data = data, body = body, headers = headers) | |
| 120 | |
| 0 | 121 if not (resp.status in [ 200 ]): |
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122 raise Exception(resp.status, resp) |
| 0 | 123 else: |
| 83 | 124 return _DecodeJson(content) |
| 0 | 125 |
| 126 def _DoPutOrPost(orthanc, uri, method, data, contentType, headers): | |
| 127 http = httplib2.Http() | |
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128 http.follow_redirects = False |
| 0 | 129 _SetupCredentials(orthanc, http) |
| 130 | |
| 83 | 131 if isinstance(data, (str, bytearray, bytes)): |
| 0 | 132 body = data |
| 133 if len(contentType) != 0: | |
| 134 headers['content-type'] = contentType | |
| 135 else: | |
| 136 body = json.dumps(data) | |
| 137 headers['content-type'] = 'application/json' | |
| 138 | |
| 139 headers['expect'] = '' | |
| 140 | |
| 1 | 141 resp, content = http.request(orthanc['Url'] + uri, method, |
| 0 | 142 body = body, |
| 143 headers = headers) | |
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144 return (resp, content) |
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145 |
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146 def DoDeleteRaw(orthanc, uri, headers = {}): |
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147 http = httplib2.Http() |
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148 http.follow_redirects = False |
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149 _SetupCredentials(orthanc, http) |
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150 |
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151 resp, content = http.request(orthanc['Url'] + uri, 'DELETE', headers = headers) |
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152 return (resp, content) |
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153 |
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154 def DoDelete(orthanc, uri, headers = {}): |
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155 (resp, content) = DoDeleteRaw(orthanc, uri, headers) |
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156 if not (resp.status in [ 200 ]): |
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157 raise Exception(resp.status, resp) |
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158 else: |
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159 return _DecodeJson(content) |
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160 |
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161 def DoPutRaw(orthanc, uri, data = {}, contentType = '', headers = {}): |
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162 return _DoPutOrPost(orthanc, uri, 'PUT', data, contentType, headers) |
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163 |
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164 def DoPut(orthanc, uri, data = {}, contentType = '', headers = {}): |
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165 (resp, content) = DoPutRaw(orthanc, uri, data, contentType, headers) |
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166 if not (resp.status in [ 200, 201, 302 ]): |
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167 raise Exception(resp.status, resp) |
| 0 | 168 else: |
| 83 | 169 return _DecodeJson(content) |
| 0 | 170 |
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171 def DoPostRaw(orthanc, uri, data = {}, contentType = '', headers = {}): |
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172 return _DoPutOrPost(orthanc, uri, 'POST', data, contentType, headers) |
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173 |
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174 def DoPost(orthanc, uri, data = {}, contentType = '', headers = {}): |
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175 (resp, content) = DoPostRaw(orthanc, uri, data, contentType, headers) |
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176 if not (resp.status in [ 200, 201, 302 ]): |
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177 raise Exception(resp.status, resp) |
| 0 | 178 else: |
| 83 | 179 return _DecodeJson(content) |
| 0 | 180 |
| 13 | 181 def GetDatabasePath(filename): |
| 182 return os.path.join(os.path.dirname(__file__), '..', 'Database', filename) | |
| 183 | |
| 0 | 184 def UploadInstance(orthanc, filename): |
| 83 | 185 with open(GetDatabasePath(filename), 'rb') as f: |
| 186 d = f.read() | |
| 187 | |
| 0 | 188 return DoPost(orthanc, '/instances', d, 'application/dicom') |
| 189 | |
| 190 def UploadFolder(orthanc, path): | |
| 13 | 191 for i in os.listdir(GetDatabasePath(path)): |
| 1 | 192 try: |
| 193 UploadInstance(orthanc, os.path.join(path, i)) | |
| 194 except: | |
| 195 pass | |
| 0 | 196 |
| 197 def DropOrthanc(orthanc): | |
| 198 # Reset the Lua callbacks | |
| 199 DoPost(orthanc, '/tools/execute-script', 'function OnStoredInstance(instanceId, tags, metadata) end', 'application/lua') | |
| 200 | |
| 201 DoDelete(orthanc, '/exports') | |
| 202 | |
| 203 for s in DoGet(orthanc, '/patients'): | |
| 204 DoDelete(orthanc, '/patients/%s' % s) | |
| 205 | |
| 174 | 206 def InstallLuaScriptFromPath(orthanc, path): |
| 207 with open(GetDatabasePath(path), 'r') as f: | |
| 208 InstallLuaScript(orthanc, f.read()) | |
| 209 | |
| 210 def InstallLuaScript(orthanc, script): | |
| 211 DoPost(orthanc, '/tools/execute-script', script, 'application/lua') | |
| 212 | |
| 213 def UninstallLuaCallbacks(orthanc): | |
| 214 DoPost(orthanc, '/tools/execute-script', 'function OnStoredInstance() end', 'application/lua') | |
| 215 InstallLuaScriptFromPath(orthanc, 'Lua/TransferSyntaxEnable.lua') | |
| 216 | |
| 217 | |
| 0 | 218 def ComputeMD5(data): |
| 219 m = hashlib.md5() | |
| 220 m.update(data) | |
| 221 return m.hexdigest() | |
| 222 | |
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223 def UncompressImage(data): |
| 83 | 224 if (sys.version_info >= (3, 0)): |
| 225 return Image.open(BytesIO(data)) | |
| 226 else: | |
| 227 return Image.open(StringIO(data)) | |
| 0 | 228 |
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229 def GetImage(orthanc, uri, headers = {}): |
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230 # http://www.pythonware.com/library/pil/handbook/introduction.htm |
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231 return UncompressImage(DoGet(orthanc, uri, headers = headers)) |
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232 |
| 0 | 233 def GetArchive(orthanc, uri): |
| 234 # http://stackoverflow.com/a/1313868/881731 | |
| 235 s = DoGet(orthanc, uri) | |
| 83 | 236 |
| 237 if (sys.version_info >= (3, 0)): | |
| 238 return zipfile.ZipFile(BytesIO(s), "r") | |
| 239 else: | |
| 240 return zipfile.ZipFile(StringIO(s), "r") | |
| 0 | 241 |
| 192 | 242 def PostArchive(orthanc, uri, body): |
| 243 # http://stackoverflow.com/a/1313868/881731 | |
| 244 s = DoPost(orthanc, uri, body) | |
| 245 | |
| 246 if (sys.version_info >= (3, 0)): | |
| 247 return zipfile.ZipFile(BytesIO(s), "r") | |
| 248 else: | |
| 249 return zipfile.ZipFile(StringIO(s), "r") | |
| 250 | |
| 1 | 251 def IsDefinedInLua(orthanc, name): |
| 0 | 252 s = DoPost(orthanc, '/tools/execute-script', 'print(type(%s))' % name, 'application/lua') |
| 253 return (s.strip() != 'nil') | |
| 254 | |
| 1 | 255 def WaitEmpty(orthanc): |
| 0 | 256 while True: |
| 1 | 257 if len(DoGet(orthanc, '/instances')) == 0: |
| 0 | 258 return |
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259 time.sleep(0.01) |
| 0 | 260 |
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261 def WaitJobDone(orthanc, job): |
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262 while True: |
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263 s = DoGet(orthanc, '/jobs/%s' % job) ['State'] |
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264 |
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265 if s == 'Success': |
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266 return True |
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267 elif s == 'Failure': |
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268 return False |
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269 |
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270 time.sleep(0.01) |
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271 |
| 138 | 272 def MonitorJob(orthanc, func): # "func" is a lambda |
| 273 a = set(DoGet(orthanc, '/jobs')) | |
| 274 func() | |
| 275 b = set(DoGet(orthanc, '/jobs')) | |
| 276 | |
| 277 diff = list(b - a) | |
| 278 if len(diff) != 1: | |
| 279 print('No job was created!') | |
| 280 return False | |
| 281 else: | |
| 282 return WaitJobDone(orthanc, diff[0]) | |
| 283 | |
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284 def MonitorJob2(orthanc, func): # "func" is a lambda |
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285 a = set(DoGet(orthanc, '/jobs')) |
| 181 | 286 job = func() |
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287 b = set(DoGet(orthanc, '/jobs')) |
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288 |
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289 diff = list(b - a) |
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290 if len(diff) != 1: |
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291 print('No job was created!') |
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292 return None |
| 181 | 293 elif (not 'ID' in job or |
| 294 diff[0] != job['ID']): | |
| 295 print('Mismatch in the job ID') | |
| 296 return None | |
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297 elif WaitJobDone(orthanc, diff[0]): |
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298 return diff[0] |
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299 else: |
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300 print('Error while executing the job') |
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301 return None |
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302 |
| 220 | 303 def WaitAllNewJobsDone(orthanc, func): # "func" is a lambda |
| 304 a = set(DoGet(orthanc, '/jobs')) | |
| 305 func() | |
| 306 | |
| 307 first = True | |
| 308 | |
| 309 while True: | |
| 310 b = set(DoGet(orthanc, '/jobs')) | |
| 311 | |
| 312 diff = list(b - a) | |
| 313 if len(diff) == 0: | |
| 314 if first: | |
| 315 raise Exception('No job was created') | |
| 316 else: | |
| 317 return # We're done | |
| 318 else: | |
| 319 first = False | |
| 320 | |
| 321 if WaitJobDone(orthanc, diff[0]): | |
| 322 a.add(diff[0]) | |
| 323 else: | |
| 324 raise Exception('Error while executing the job') | |
| 325 | |
| 326 | |
| 1 | 327 def GetDockerHostAddress(): |
| 328 route = subprocess.check_output([ '/sbin/ip', 'route' ]) | |
| 329 m = re.search(r'default via ([0-9.]+)', route) | |
| 330 if m == None: | |
| 331 return 'localhost' | |
| 332 else: | |
| 333 return m.groups()[0] | |
| 4 | 334 |
|
44
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335 def FindExecutable(name): |
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336 p = os.path.join('/usr/local/bin', name) |
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337 if os.path.isfile(p): |
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338 return p |
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339 |
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340 p = os.path.join('/usr/local/sbin', name) |
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341 if os.path.isfile(p): |
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342 return p |
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343 |
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344 return name |
| 4 | 345 |
| 173 | 346 def IsOrthancVersionAbove(orthanc, major, minor, revision): |
| 347 v = DoGet(orthanc, '/system')['Version'] | |
| 348 | |
| 349 if v == 'mainline': | |
| 350 return True | |
| 351 else: | |
| 352 tmp = v.split('.') | |
| 353 a = int(tmp[0]) | |
| 354 b = int(tmp[1]) | |
| 355 c = int(tmp[2]) | |
| 356 return (a > major or | |
| 357 (a == major and b > minor) or | |
| 358 (a == major and b == minor and c >= revision)) | |
| 4 | 359 |
| 360 | |
| 361 class ExternalCommandThread: | |
| 362 @staticmethod | |
| 363 def ExternalCommandFunction(arg, stop_event, command, env): | |
|
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364 with open(os.devnull, 'w') as devnull: |
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365 external = subprocess.Popen(command, env = env, stderr = devnull) |
| 4 | 366 |
|
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367 while (not stop_event.is_set()): |
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368 error = external.poll() |
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369 if error != None: |
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370 # http://stackoverflow.com/a/1489838/881731 |
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371 os._exit(-1) |
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372 stop_event.wait(0.1) |
| 4 | 373 |
| 83 | 374 print('Stopping the external command') |
| 4 | 375 external.terminate() |
| 9 | 376 external.communicate() # Wait for the command to stop |
| 4 | 377 |
| 378 def __init__(self, command, env = None): | |
| 379 self.thread_stop = threading.Event() | |
| 380 self.thread = threading.Thread(target = self.ExternalCommandFunction, | |
| 381 args = (10, self.thread_stop, command, env)) | |
| 9 | 382 #self.daemon = True |
| 4 | 383 self.thread.start() |
| 384 | |
| 385 def stop(self): | |
| 386 self.thread_stop.set() | |
| 387 self.thread.join() | |
| 220 | 388 |
| 389 | |
|
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390 def AssertAlmostEqualRecursive(self, a, b, places = 7, ignoreKeys = []): |
| 220 | 391 if type(a) is dict: |
| 392 self.assertTrue(type(b) is dict) | |
| 393 self.assertEqual(a.keys(), b.keys()) | |
| 394 for key, value in a.items(): | |
|
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395 if not key in ignoreKeys: |
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396 AssertAlmostEqualRecursive(self, a[key], b[key], places) |
| 220 | 397 |
| 398 elif type(a) is list: | |
| 399 self.assertTrue(type(b) is list) | |
| 400 self.assertEqual(len(a), len(b)) | |
| 401 for i in range(len(a)): | |
| 402 AssertAlmostEqualRecursive(self, a[i], b[i], places) | |
| 403 | |
| 404 else: | |
| 405 self.assertAlmostEqual(a, b, places = places) | |
|
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406 |
|
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407 |
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408 def GetTransferSyntax(dicom): |
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409 with tempfile.NamedTemporaryFile(delete = True) as f: |
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410 f.write(dicom) |
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411 f.flush() |
|
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412 |
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413 with open(os.devnull, 'w') as devnull: |
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414 data = subprocess.check_output([ FindExecutable('dcm2xml'), f.name ], |
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415 stderr = devnull) |
|
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416 |
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417 return re.search('<data-set xfer="(.*?)"', data).group(1) |
| 304 | 418 |
| 419 | |
| 420 def HasGdcmPlugin(orthanc): | |
| 421 plugins = DoGet(orthanc, '/plugins') | |
| 422 return ('gdcm' in plugins) | |
| 423 | |
| 424 | |
| 425 def _GetMaxImageDifference(im1, im2): | |
| 426 h = ImageChops.difference(im1, im2).histogram() | |
| 427 | |
| 428 if len(h) < 256: | |
| 429 raise Exception() | |
| 430 | |
| 431 i = len(h) - 1 | |
| 432 while h[i] == 0: | |
| 433 i -= 1 | |
| 434 | |
| 435 return i | |
| 436 | |
| 437 | |
| 438 def GetMaxImageDifference(im1, im2): | |
| 439 if im1.mode != im2.mode: | |
| 440 raise Exception('Incompatible image modes') | |
| 441 | |
| 442 if im1.mode == 'RGB': | |
| 443 red1, green1, blue1 = im1.split() | |
| 444 red2, green2, blue2 = im2.split() | |
| 445 return max([ _GetMaxImageDifference(red1, red2), | |
| 446 _GetMaxImageDifference(green1, green2), | |
| 447 _GetMaxImageDifference(blue1, blue2) ]) | |
| 448 else: | |
| 449 return _GetMaxImageDifference(im1, im2) | |
|
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450 |
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451 |
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452 def DoPropFind(orthanc, uri, depth): |
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453 http = httplib2.Http() |
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454 http.follow_redirects = False |
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455 _SetupCredentials(orthanc, http) |
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456 |
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457 resp, content = http.request(orthanc['Url'] + uri, 'PROPFIND', headers = { 'Depth' : str(depth) }) |
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458 |
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459 if not (resp.status in [ 207 ]): |
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460 raise Exception(resp.status, resp) |
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461 else: |
|
341
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462 xml = minidom.parseString(content) |
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463 |
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464 if (xml.documentElement.nodeName != 'D:multistatus' or |
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465 xml.documentElement.attributes['xmlns:D'].value != 'DAV:'): |
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466 raise Exception() |
|
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467 |
|
341
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468 result = {} |
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469 |
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470 for i in xml.documentElement.childNodes: |
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471 if i.nodeType == minidom.Node.ELEMENT_NODE: |
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472 if i.nodeName != 'D:response': |
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473 raise Exception() |
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474 href = None |
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475 prop = None |
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476 for j in i.childNodes: |
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477 if j.nodeType == minidom.Node.ELEMENT_NODE: |
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478 if j.nodeName == 'D:href': |
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479 if href == None: |
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480 href = unquote(j.firstChild.nodeValue) |
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481 else: |
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482 raise Exception() |
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483 elif j.nodeName == 'D:propstat': |
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484 for k in j.childNodes: |
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485 if k.nodeName == 'D:status': |
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486 if k.firstChild.nodeValue != 'HTTP/1.1 200 OK': |
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487 raise Exception() |
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488 elif k.nodeType == minidom.Node.ELEMENT_NODE: |
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489 if (k.nodeName != 'D:prop' or |
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490 prop != None): |
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491 raise Exception() |
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492 prop = k |
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493 else: |
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494 raise Exception() |
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495 if href == None or prop == None: |
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496 raise Exception() |
|
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497 |
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498 info = {} |
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499 |
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500 for j in prop.childNodes: |
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501 if j.nodeType == minidom.Node.ELEMENT_NODE: |
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502 if j.nodeName == 'D:displayname': |
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503 info['displayname'] = j.firstChild.nodeValue if j.firstChild != None else '' |
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504 elif j.nodeName == 'D:creationdate': |
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505 info['creationdate'] = j.firstChild.nodeValue |
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506 elif j.nodeName == 'D:getlastmodified': |
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507 info['lastmodified'] = j.firstChild.nodeValue |
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508 elif j.nodeName == 'D:resourcetype': |
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509 k = j.getElementsByTagName('D:collection') |
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510 info['folder'] = (len(k) == 1) |
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511 |
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512 result[href] = info |
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513 elif i.nodeType != minidom.Node.TEXT_NODE: |
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514 raise Exception() |
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515 |
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516 return result |