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Commit a302c2d1a82dd6bc9090cf886be443cec4a84022

Authored by Paulo Henrique Junqueira Amorim
1 parent e5314ee9
Exists in master and in 68 other branches 3d_inter_style, MIPs, beta3, beta4, brush_pix, canvas_reeng, canvas_text, casmoothing_cython, clean, command-line, cython_threshold, debian_cython, editor_improvements, encoding, ff_mask, ff_mask_improv, ffill_gui, ffill_segmentation, fill_holes_auto, fixes_pre_beta5, floodfill, get_pixel, import_mesh, interactor_style, inv3.0.1, invesalius-libift, mactoolbar, mactoolbar_bkp, manual_v3.1, mask_boolean_op, mask_boolean_op_bkp, mask_copy, mask_greatest_component, measure, measure_canvas, measure_improvements, measure_placement_test, measure_spacing, orientation, phoenix, region_growing_confidence, remote, remove_local_wxpython, rmatsuda-fix_ref_MTC, rmatsuda-fix_remove_marker_bug, rmatsuda-trigger_bug_fix, rotvol, segmentation_menu, select_part, smoothing_bin, smoothing_bin_pll, surface_area, threshold_history, user_guide_en, usp-navegador, vti, vtk6, watershed, watershed_improvements, watershed_improvements_bkp, watershed_merge, workdir, wwwlgui, wx2.9_mac, wxgtk3, wxgtk3_b5, wxgtk3_bkp, xmartlabs-command-line

ENH: Replaced the way it reads some data, changed of vtkgdcm to gdcm reader DICOM tags.

Showing 1 changed file with 154 additions and 98 deletions   Show diff stats
invesalius/reader/dicom.py
  Diff comments   View file @a302c2d
... ... @@ -104,10 +104,12 @@ class Parser():
104 104 DICOM standard tag (0x0008,0x0022) was used.
105 105 """
106 106 # TODO: internationalize data
107   - date = self.vtkgdcm_reader.GetMedicalImageProperties()\
108   - .GetAcquisitionDate()
109   - if (date) and (date != ''):
110   - return self.__format_date(date)
  107 + tag = gdcm.Tag(0x0008, 0x0022)
  108 + ds = self.gdcm_reader.GetFile().GetDataSet()
  109 + if ds.FindDataElement(tag):
  110 + date = ds.GetDataElement(tag).GetValue()
  111 + if (date) and (date != ''):
  112 + return self.__format_date(str(date))
111 113 return ""
112 114  
113 115 def GetAcquisitionNumber(self):
... ... @@ -151,10 +153,12 @@ class Parser():
151 153  
152 154 DICOM standard tag (0x0008,0x0032) was used.
153 155 """
154   - time = self.vtkgdcm_reader.GetMedicalImageProperties()\
155   - .GetAcquisitionTime()
156   - if (time) and (time != 'None'):
157   - return self.__format_time(time)
  156 + tag = gdcm.Tag(0x0008, 0x0032)
  157 + ds = self.gdcm_reader.GetFile().GetDataSet()
  158 + if ds.FindDataElement(tag):
  159 + data = ds.GetDataElement(tag).GetValue()
  160 + if (data) and (data != ''):
  161 + return self.__format_time(str(data))
158 162 return ""
159 163  
160 164 def GetPatientAdmittingDiagnosis(self):
... ... @@ -164,7 +168,6 @@ class Parser():
164 168  
165 169 DICOM standard tag (0x0008,0x1080) was used.
166 170 """
167   -
168 171 tag = gdcm.Tag(0x0008, 0x1080)
169 172 sf = gdcm.StringFilter()
170 173 sf.SetFile(self.gdcm_reader.GetFile())
... ... @@ -1063,14 +1066,15 @@ class Parser():
1063 1066 DICOM standard tag (0x0010,0x0030) was used.
1064 1067 """
1065 1068 # TODO: internationalize data
1066   - date = self.vtkgdcm_reader.GetMedicalImageProperties()\
1067   - .GetPatientBirthDate()
1068   - if (date) and (date!='None'):
1069   - self.__format_date(date)
  1069 + tag = gdcm.Tag(0x0010, 0x0030)
  1070 + ds = self.gdcm_reader.GetFile().GetDataSet()
  1071 + if ds.FindDataElement(tag):
  1072 + data = ds.GetDataElement(tag).GetValue()
  1073 + if (data) and (data != 'None'):
  1074 + return self.__format_date(str(data))
1070 1075 return ""
1071 1076  
1072 1077  
1073   -
1074 1078 def GetStudyID(self):
1075 1079 """
1076 1080 Return string containing the Study ID.
... ... @@ -1078,13 +1082,14 @@ class Parser():
1078 1082  
1079 1083 DICOM standard tag (0x0020,0x0010) was used.
1080 1084 """
1081   -
1082   - data = self.vtkgdcm_reader.GetMedicalImageProperties()\
1083   - .GetStudyID()
1084   - if (data):
1085   - return data
  1085 + tag = gdcm.Tag(0x0020, 0x0010)
  1086 + ds = self.gdcm_reader.GetFile().GetDataSet()
  1087 + if ds.FindDataElement(tag):
  1088 + data = ds.GetDataElement(tag).GetValue()
  1089 + if (data):
  1090 + return str(data)
1086 1091 return ""
1087   -
  1092 +
1088 1093 def GetAcquisitionGantryTilt(self):
1089 1094 """
1090 1095 Return floating point containing nominal angle of
... ... @@ -1093,10 +1098,14 @@ class Parser():
1093 1098  
1094 1099 DICOM standard tag (0x0018,0x1120) was used.
1095 1100 """
1096   - data = self.vtkgdcm_reader.GetMedicalImageProperties()\
1097   - .GetGantryTilt()
1098   - if (data):
1099   - return float(data)
  1101 + tag = gdcm.Tag(0x0018, 0x1120)
  1102 + ds = self.gdcm_reader.GetFile().GetDataSet()
  1103 + if ds.FindDataElement(tag):
  1104 + data = ds.GetDataElement(tag).GetValue()
  1105 +
  1106 + if (data):
  1107 + return float(str(data))
  1108 +
1100 1109 return 0.0
1101 1110  
1102 1111 def GetPatientGender(self):
... ... @@ -1109,10 +1118,13 @@ class Parser():
1109 1118  
1110 1119 DICOM standard tag (0x0010,0x0040) was used.
1111 1120 """
1112   - data = self.vtkgdcm_reader.GetMedicalImageProperties()\
1113   - .GetPatientSex()
1114   - if (data):
1115   - return data
  1121 + tag = gdcm.Tag(0x0010, 0x0040)
  1122 + ds = self.gdcm_reader.GetFile().GetDataSet()
  1123 + if ds.FindDataElement(tag):
  1124 + data = ds.GetDataElement(tag).GetValue()
  1125 +
  1126 + if (data):
  1127 + return str(data)
1116 1128 return ""
1117 1129  
1118 1130 def GetPatientAge(self):
... ... @@ -1123,14 +1135,17 @@ class Parser():
1123 1135  
1124 1136 DICOM standard tag (0x0010, 0x1010) was used.
1125 1137 """
1126   - data = self.vtkgdcm_reader.GetMedicalImageProperties()\
1127   - .GetPatientAge()
1128   - if (data):
1129   - age = (data.split('Y')[0])
1130   - try:
1131   - return int(age)
1132   - except ValueError:
1133   - return age
  1138 + tag = gdcm.Tag(0x0010, 0x1010)
  1139 + ds = self.gdcm_reader.GetFile().GetDataSet()
  1140 + if ds.FindDataElement(tag):
  1141 + data = str(ds.GetDataElement(tag).GetValue())
  1142 +
  1143 + if (data):
  1144 + age = (data.split('Y')[0])
  1145 + try:
  1146 + return int(age)
  1147 + except ValueError:
  1148 + return age
1134 1149 return ""
1135 1150  
1136 1151 def GetPatientName(self):
... ... @@ -1140,14 +1155,16 @@ class Parser():
1140 1155  
1141 1156 DICOM standard tag (0x0010,0x0010) was used.
1142 1157 """
1143   - data = self.vtkgdcm_reader.GetMedicalImageProperties()\
1144   - .GetPatientName()
  1158 + tag = gdcm.Tag(0x0010, 0x0010)
  1159 + ds = self.gdcm_reader.GetFile().GetDataSet()
  1160 + if ds.FindDataElement(tag):
  1161 + data = str(ds.GetDataElement(tag).GetValue())
1145 1162  
1146   - if (data):
1147   - name = data.strip()
1148   - encoding = self.GetEncoding()
1149   - # Returns a unicode decoded in the own dicom encoding
1150   - return name.decode(encoding)
  1163 + if (data):
  1164 + name = data.strip()
  1165 + encoding = self.GetEncoding()
  1166 + # Returns a unicode decoded in the own dicom encoding
  1167 + return name.decode(encoding)
1151 1168 return ""
1152 1169  
1153 1170 def GetPatientID(self):
... ... @@ -1158,12 +1175,15 @@ class Parser():
1158 1175  
1159 1176 DICOM standard tag (0x0010,0x0020) was used.
1160 1177 """
1161   - data = self.vtkgdcm_reader.GetMedicalImageProperties()\
1162   - .GetPatientID()
1163   - if (data):
1164   - encoding = self.GetEncoding()
1165   - # Returns a unicode decoded in the own dicom encoding
1166   - return data.decode(encoding)
  1178 + tag = gdcm.Tag(0x0010, 0x0020)
  1179 + ds = self.gdcm_reader.GetFile().GetDataSet()
  1180 + if ds.FindDataElement(tag):
  1181 + data = str(ds.GetDataElement(tag).GetValue())
  1182 +
  1183 + if (data):
  1184 + encoding = self.GetEncoding()
  1185 + # Returns a unicode decoded in the own dicom encoding
  1186 + return data.decode(encoding)
1167 1187 return ""
1168 1188  
1169 1189  
... ... @@ -1212,10 +1232,13 @@ class Parser():
1212 1232  
1213 1233 DICOM standard tag (0x0018,0x1151) was used.
1214 1234 """
1215   - data = self.vtkgdcm_reader.GetMedicalImageProperties()\
1216   - .GetXRayTubeCurrent()
1217   - if (data):
1218   - return data
  1235 + tag = gdcm.Tag(0x0018, 0x1151)
  1236 + ds = self.gdcm_reader.GetFile().GetDataSet()
  1237 + if ds.FindDataElement(tag):
  1238 + data = str(ds.GetDataElement(tag).GetValue())
  1239 +
  1240 + if (data):
  1241 + return data
1219 1242 return ""
1220 1243  
1221 1244 def GetExposureTime(self):
... ... @@ -1226,10 +1249,13 @@ class Parser():
1226 1249  
1227 1250 DICOM standard tag (0x0018, 0x1152) was used.
1228 1251 """
1229   - data = self.vtkgdcm_reader.GetMedicalImageProperties()\
1230   - .GetExposureTime()
1231   - if (data):
1232   - return float(data)
  1252 + tag = gdcm.Tag(0x0018, 0x1152)
  1253 + ds = self.gdcm_reader.GetFile().GetDataSet()
  1254 + if ds.FindDataElement(tag):
  1255 + data = str(ds.GetDataElement(tag).GetValue())
  1256 +
  1257 + if (data):
  1258 + return float(data)
1233 1259 return ""
1234 1260  
1235 1261 def GetEquipmentKVP(self):
... ... @@ -1240,10 +1266,13 @@ class Parser():
1240 1266  
1241 1267 DICOM standard tag (0x0018,0x0060) was used.
1242 1268 """
1243   - data = self.vtkgdcm_reader.GetMedicalImageProperties()\
1244   - .GetKVP()
1245   - if (data):
1246   - return float(data)
  1269 + tag = gdcm.Tag(0x0018, 0x0060)
  1270 + ds = self.gdcm_reader.GetFile().GetDataSet()
  1271 + if ds.FindDataElement(tag):
  1272 + data = str(ds.GetDataElement(tag).GetValue())
  1273 +
  1274 + if (data):
  1275 + return float(data)
1247 1276 return ""
1248 1277  
1249 1278 def GetImageThickness(self):
... ... @@ -1254,10 +1283,13 @@ class Parser():
1254 1283  
1255 1284 DICOM standard tag (0x0018,0x0050) was used.
1256 1285 """
1257   - data = self.vtkgdcm_reader.GetMedicalImageProperties()\
1258   - .GetSliceThickness()
1259   - if (data):
1260   - return float(data)
  1286 + tag = gdcm.Tag(0x0018, 0x1050)
  1287 + ds = self.gdcm_reader.GetFile().GetDataSet()
  1288 + if ds.FindDataElement(tag):
  1289 + data = str(ds.GetDataElement(tag).GetValue())
  1290 +
  1291 + if (data):
  1292 + return float(data)
1261 1293 return 0
1262 1294  
1263 1295 def GetImageConvolutionKernel(self):
... ... @@ -1270,10 +1302,13 @@ class Parser():
1270 1302  
1271 1303 DICOM standard tag (0x0018,0x1210) was used.
1272 1304 """
1273   - data = self.vtkgdcm_reader.GetMedicalImageProperties()\
1274   - .GetConvolutionKernel()
1275   - if (data):
1276   - return data
  1305 + tag = gdcm.Tag(0x0018, 0x1210)
  1306 + ds = self.gdcm_reader.GetFile().GetDataSet()
  1307 + if ds.FindDataElement(tag):
  1308 + data = str(ds.GetDataElement(tag).GetValue())
  1309 +
  1310 + if (data):
  1311 + return data
1277 1312 return ""
1278 1313  
1279 1314 def GetEquipmentInstitutionName(self):
... ... @@ -1284,10 +1319,13 @@ class Parser():
1284 1319  
1285 1320 DICOM standard tag (0x0008,0x0080) was used.
1286 1321 """
1287   - data = self.vtkgdcm_reader.GetMedicalImageProperties()\
1288   - .GetInstitutionName()
1289   - if (data):
1290   - return data
  1322 + tag = gdcm.Tag(0x0008, 0x0080)
  1323 + ds = self.gdcm_reader.GetFile().GetDataSet()
  1324 + if ds.FindDataElement(tag):
  1325 + data = str(ds.GetDataElement(tag).GetValue())
  1326 +
  1327 + if (data):
  1328 + return data
1291 1329 return ""
1292 1330  
1293 1331 def GetStationName(self):
... ... @@ -1298,10 +1336,13 @@ class Parser():
1298 1336  
1299 1337 DICOM standard tag (0x0008, 0x1010) was used.
1300 1338 """
1301   - data = self.vtkgdcm_reader.GetMedicalImageProperties()\
1302   - .GetStationName()
1303   - if (data):
1304   - return data
  1339 + tag = gdcm.Tag(0x0008, 0x1010)
  1340 + ds = self.gdcm_reader.GetFile().GetDataSet()
  1341 + if ds.FindDataElement(tag):
  1342 + data = str(ds.GetDataElement(tag).GetValue())
  1343 +
  1344 + if (data):
  1345 + return data
1305 1346 return ""
1306 1347  
1307 1348 def GetManufacturerModelName(self):
... ... @@ -1312,10 +1353,13 @@ class Parser():
1312 1353  
1313 1354 DICOM standard tag (0x0008,0x1090) was used.
1314 1355 """
1315   - data = self.vtkgdcm_reader.GetMedicalImageProperties()\
1316   - .GetManufacturerModelName()
1317   - if (data):
1318   - return data
  1356 + tag = gdcm.Tag(0x0008, 0x1090)
  1357 + ds = self.gdcm_reader.GetFile().GetDataSet()
  1358 + if ds.FindDataElement(tag):
  1359 + data = str(ds.GetDataElement(tag).GetValue())
  1360 +
  1361 + if (data):
  1362 + return data
1319 1363 return ""
1320 1364  
1321 1365 def GetEquipmentManufacturer(self):
... ... @@ -1325,10 +1369,13 @@ class Parser():
1325 1369  
1326 1370 DICOM standard tag (0x0008, 0x1010) was used.
1327 1371 """
1328   - data = self.vtkgdcm_reader.GetMedicalImageProperties()\
1329   - .GetManufacturer()
1330   - if (data):
1331   - return data
  1372 + tag = gdcm.Tag(0x0008, 0x1010)
  1373 + ds = self.gdcm_reader.GetFile().GetDataSet()
  1374 + if ds.FindDataElement(tag):
  1375 + data = str(ds.GetDataElement(tag).GetValue())
  1376 +
  1377 + if (data):
  1378 + return data
1332 1379 return ""
1333 1380  
1334 1381 def GetAcquisitionModality(self):
... ... @@ -1340,10 +1387,13 @@ class Parser():
1340 1387  
1341 1388 DICOM standard tag (0x0008,0x0060) was used.
1342 1389 """
1343   - data = self.vtkgdcm_reader.GetMedicalImageProperties()\
1344   - .GetModality()
1345   - if (data):
1346   - return data
  1390 + tag = gdcm.Tag(0x0008, 0x0060)
  1391 + ds = self.gdcm_reader.GetFile().GetDataSet()
  1392 + if ds.FindDataElement(tag):
  1393 + data = str(ds.GetDataElement(tag).GetValue())
  1394 +
  1395 + if (data):
  1396 + return data
1347 1397 return ""
1348 1398  
1349 1399  
... ... @@ -1354,10 +1404,13 @@ class Parser():
1354 1404  
1355 1405 DICOM standard tag (0x0020,0x0013) was used.
1356 1406 """
1357   - data = self.vtkgdcm_reader.GetMedicalImageProperties()\
1358   - .GetImageNumber()
1359   - if (data):
1360   - return int(data)
  1407 + tag = gdcm.Tag(0x0020, 0x0013)
  1408 + ds = self.gdcm_reader.GetFile().GetDataSet()
  1409 + if ds.FindDataElement(tag):
  1410 + data = str(ds.GetDataElement(tag).GetValue())
  1411 +
  1412 + if (data):
  1413 + return int(data)
1361 1414 return ""
1362 1415  
1363 1416 def GetStudyDescription(self):
... ... @@ -1367,11 +1420,14 @@ class Parser():
1367 1420  
1368 1421 DICOM standard tag (0x0008,0x1030) was used.
1369 1422 """
1370   - data = self.vtkgdcm_reader.GetMedicalImageProperties()\
1371   - .GetStudyDescription()
1372   - if (data):
1373   - encoding = self.GetEncoding()
1374   - return data.decode(encoding)
  1423 + tag = gdcm.Tag(0x0008, 0x1030)
  1424 + ds = self.gdcm_reader.GetFile().GetDataSet()
  1425 + if ds.FindDataElement(tag):
  1426 + data = str(ds.GetDataElement(tag).GetValue())
  1427 +
  1428 + if (data):
  1429 + encoding = self.GetEncoding()
  1430 + return data.decode(encoding)
1375 1431 return ""
1376 1432  
1377 1433 def GetStudyAdmittingDiagnosis(self):
... ...