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Commit b09b522f3091ec4ebd338deda75b4fa821a5c022

Authored by Paulo Henrique Junqueira Amorim
1 parent 3a7f3445
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: Restructuring of the class group DICOM

Showing 3 changed files with 155 additions and 265 deletions   Show diff stats
invesalius/reader/dicom.py
  Diff comments   View file @b09b522
@@ -1620,3 +1620,79 @@ if __name__ == "__main__": @@ -1620,3 +1620,79 @@ if __name__ == "__main__":
1620 #print info 1620 #print info
1621 1621
1622 1622
  1623 +
  1624 +
  1625 +
  1626 +class Dicom(object):
  1627 + def __init__(self):
  1628 + pass
  1629 +
  1630 + def SetParser(self, parser):
  1631 + self.parser = parser
  1632 +
  1633 + self.LoadImageInfo()
  1634 + self.LoadPatientInfo()
  1635 + self.LoadAcquisitionInfo()
  1636 + #self.LoadStudyInfo()
  1637 +
  1638 + def LoadImageInfo(self):
  1639 + self.image = Image()
  1640 + self.image.SetParser(self.parser)
  1641 +
  1642 + def LoadPatientInfo(self):
  1643 + self.patient = Patient()
  1644 + self.patient.SetParser(self.parser)
  1645 +
  1646 + def LoadAcquisitionInfo(self):
  1647 + self.acquisition = Acquisition()
  1648 + self.acquisition.SetParser(self.parser)
  1649 +
  1650 +
  1651 +
  1652 +class Patient(object):
  1653 + def __init__(self):
  1654 + pass
  1655 +
  1656 + def SetParser(self, parser):
  1657 + self.name = parser.GetPatientName()
  1658 + self.physician = parser.GetPhysicianName()
  1659 +
  1660 +class Acquisition(object):
  1661 +
  1662 + def __init__(self):
  1663 + pass
  1664 +
  1665 + def SetParser(self, parser):
  1666 + self.patient_orientation = parser.GetImagePatientOrientation()
  1667 + self.series_description = parser.GetSeriesDescrition()
  1668 + self.tilt = parser.GetAcquisitionGantryTilt()
  1669 + self.serie_number = parser.GetImageSeriesNumber()
  1670 + self.id_study = parser.GetStudyID()
  1671 +
  1672 +class Image(object):
  1673 +
  1674 + def __init__(self):
  1675 + pass
  1676 +
  1677 + def SetParser(self, parser):
  1678 + self.level = parser.GetImageWindowLevel()
  1679 + self.window = parser.GetImageWindowWidth()
  1680 + self.position = parser.GetImagePosition()
  1681 + self.number = parser.GetImageNumber()
  1682 + self.spacing = spacing = parser.GetPixelSpacing()
  1683 + self.orientation_label = parser.GetImageOrientationLabel()
  1684 + self.file = parser.filename
  1685 +
  1686 + if (parser.GetImageThickness()):
  1687 + spacing.append(parser.GetImageThickness())
  1688 + else:
  1689 + spacing.append(1.5)
  1690 +
  1691 + spacing[0] = round(spacing[0],2)
  1692 + spacing[1] = round(spacing[1],2)
  1693 + spacing[2] = round(spacing[2],2)
  1694 +
  1695 + try:
  1696 + self.type = parser.GetImageType()[2]
  1697 + except(IndexError):
  1698 + self.type = None
invesalius/reader/dicom_grouper.py
  Diff comments   View file @b09b522
@@ -19,23 +19,23 @@ @@ -19,23 +19,23 @@
19 # detalhes. 19 # detalhes.
20 #--------------------------------------------------------------------- 20 #---------------------------------------------------------------------
21 21
22 -import dicom as ivDicom 22 +import dicom
23 23
24 -class ivDicomGroups: 24 +class DicomGroups:
25 """ 25 """
26 It is possible to separate sets of a set 26 It is possible to separate sets of a set
27 of files dicom. 27 of files dicom.
28 28
29 To use: 29 To use:
30 list_dicoms = [c:\a.dcm, c:\a1.gdcm] 30 list_dicoms = [c:\a.dcm, c:\a1.gdcm]
31 - dicom_splitter = ivDicomGroups() 31 + dicom_splitter = DicomGroups()
32 dicom_splitter.SetFileList(list_dicoms) 32 dicom_splitter.SetFileList(list_dicoms)
33 dicom_splitter.Update() 33 dicom_splitter.Update()
34 splitted = dicom_splitter.GetOutput() 34 splitted = dicom_splitter.GetOutput()
35 """ 35 """
36 36
37 def __init__(self): 37 def __init__(self):
38 - self.parser = ivDicom.Parser() 38 + self.parser = dicom.Parser()
39 #List of DICOM from Directory 39 #List of DICOM from Directory
40 self.filenamelist = [] 40 self.filenamelist = []
41 # List of DICOM with Informations 41 # List of DICOM with Informations
@@ -62,12 +62,13 @@ class ivDicomGroups: @@ -62,12 +62,13 @@ class ivDicomGroups:
62 self.__Split1() 62 self.__Split1()
63 63
64 if (len(self.GetOutput().keys()) == len(self.filenamelist)): 64 if (len(self.GetOutput().keys()) == len(self.filenamelist)):
  65 + print "Vai entrar na 2"
65 self.__Split2() 66 self.__Split2()
66 self.split_type = 1 67 self.split_type = 1
67 68
68 self.__Split3() 69 self.__Split3()
69 70
70 - self.__Info() 71 + self.__UpdateZSpacing()
71 72
72 73
73 def GetOutput(self): 74 def GetOutput(self):
@@ -103,45 +104,13 @@ class ivDicomGroups: @@ -103,45 +104,13 @@ class ivDicomGroups:
103 if not parser.SetFileName(filenamelist[x]): 104 if not parser.SetFileName(filenamelist[x]):
104 return None 105 return None
105 106
106 - file = filenamelist[x]  
107 - patient_name = parser.GetPatientName()  
108 - serie_number = parser.GetImageSeriesNumber()  
109 -  
110 - image_position = parser.GetImagePosition()  
111 - image_number = parser.GetImageNumber()  
112 -  
113 - try:  
114 - image_type = parser.GetImageType()[2]  
115 - except(IndexError):  
116 - image_type = None  
117 -  
118 - patient_position = parser.GetImagePatientOrientation()  
119 - image_orientation_label = parser.GetImageOrientationLabel()  
120 - series_description = parser.GetSeriesDescrition()  
121 - spacing = parser.GetPixelSpacing()  
122 - id_study = parser.GetStudyID()  
123 - tilt = parser.GetAcquisitionGantryTilt()  
124 - window = parser.GetImageWindowWidth()  
125 - level = parser.GetImageWindowLevel()  
126 -  
127 - if (parser.GetImageThickness()):  
128 - spacing.append(parser.GetImageThickness())  
129 - else:  
130 - spacing.append(1.5)  
131 -  
132 - spacing[0] = round(spacing[0],2)  
133 - spacing[1] = round(spacing[1],2)  
134 - spacing[2] = round(spacing[2],2)  
135 -  
136 - filelist.append([image_number, serie_number, spacing,  
137 - image_position, patient_position,  
138 - image_type,patient_name,  
139 - image_orientation_label, file,  
140 - series_description, id_study, tilt,  
141 - window, level]) 107 + information = dicom.Dicom()
  108 + information.SetParser(parser)
142 109
  110 + self.filelist.append(information)
143 self.filelist = filelist 111 self.filelist = filelist
144 - 112 +
  113 +
145 def __GetInformations(self, ind): 114 def __GetInformations(self, ind):
146 """ 115 """
147 Return a list referring to a specific DICOM 116 Return a list referring to a specific DICOM
@@ -149,32 +118,7 @@ class ivDicomGroups: @@ -149,32 +118,7 @@ class ivDicomGroups:
149 to pass only the index 118 to pass only the index
150 """ 119 """
151 filelist = self.filelist 120 filelist = self.filelist
152 -  
153 - self.filelist.sort()  
154 -  
155 - image_number = filelist[ind][0]  
156 - serie_number = filelist[ind][1]  
157 - spacing = filelist[ind][2]  
158 - image_position = filelist[ind][3]  
159 - patient_position = filelist[ind][4]  
160 - image_type = filelist[ind][5]  
161 - patient_name = filelist[ind][6]  
162 - image_orientation_label = filelist[ind][7]  
163 - file = filelist[ind][8]  
164 - series_description = filelist[ind][9]  
165 - id_study = filelist[ind][10]  
166 - tilt = filelist[ind][11]  
167 - window = filelist[ind][12]  
168 - level = filelist[ind][13]  
169 -  
170 - list = [image_number, serie_number, spacing,  
171 - image_position, patient_position,  
172 - image_type,patient_name,  
173 - image_orientation_label, file,  
174 - series_description, id_study, tilt,  
175 - window, level]  
176 -  
177 - return list 121 + return filelist[ind]
178 122
179 123
180 def __Split1(self): 124 def __Split1(self):
@@ -185,22 +129,16 @@ class ivDicomGroups: @@ -185,22 +129,16 @@ class ivDicomGroups:
185 """ 129 """
186 groups_dcm = self.groups_dcm 130 groups_dcm = self.groups_dcm
187 131
188 - for x in xrange(len(self.filelist)):  
189 -  
190 - list = self.__GetInformations(x) 132 + for x in xrange(len(self.filelist)):
  133 + information = self.__GetInformations(x)
191 134
192 - patient_name = list[6]  
193 - serie_number = list[1]  
194 - id_study = list[10]  
195 - image_orientation_label = list[7]  
196 -  
197 - key = (patient_name, id_study, serie_number,  
198 - image_orientation_label) 135 + key = (information.patient.name, information.acquisition.id_study,\
  136 + information.acquisition.serie_number, information.image.orientation_label)
199 137
200 if (key in groups_dcm.keys()): 138 if (key in groups_dcm.keys()):
201 - groups_dcm[key][0].append(list) 139 + groups_dcm[key][0].append(information)
202 else: 140 else:
203 - groups_dcm[key] = [[list]] 141 + groups_dcm[key] = [[information]]
204 142
205 self.groups_dcm = groups_dcm 143 self.groups_dcm = groups_dcm
206 144
@@ -219,17 +157,8 @@ class ivDicomGroups: @@ -219,17 +157,8 @@ class ivDicomGroups:
219 #Through in the series (index of the dictionary) 157 #Through in the series (index of the dictionary)
220 for x in xrange(len(self.filelist)): 158 for x in xrange(len(self.filelist)):
221 #Slices through in the serie 159 #Slices through in the serie
222 - list = self.__GetInformations(x)  
223 -  
224 - spacing = list[2]  
225 - image_position = list[3]  
226 - image_orientation_label = list[7]  
227 - patient_name = list[6]  
228 - serie_number = list[1]  
229 - id_study = list[10]  
230 - image_orientation_label = list[7]  
231 -  
232 - key = (patient_name, cont_series) 160 + information = self.__GetInformations(x)
  161 + key = (information.patient.name, cont_series)
233 162
234 #If there exists only one slice. 163 #If there exists only one slice.
235 if (len(self.filelist) > 1): 164 if (len(self.filelist) > 1):
@@ -262,19 +191,19 @@ class ivDicomGroups: @@ -262,19 +191,19 @@ class ivDicomGroups:
262 #only adds value. Otherwise this key create in the 191 #only adds value. Otherwise this key create in the
263 #dictionary and add value 192 #dictionary and add value
264 if (key in groups_dcm.keys()): 193 if (key in groups_dcm.keys()):
265 - groups_dcm[key][0].append(list) 194 + groups_dcm[key][0].append(information)
266 else: 195 else:
267 - groups_dcm[key] = [[list]] 196 + groups_dcm[key] = [[information]]
268 else: 197 else:
269 cont_series = cont_series + 1 198 cont_series = cont_series + 1
270 - groups_dcm[key] = [[list]] 199 + groups_dcm[key] = [[information]]
271 200
272 else: 201 else:
273 202
274 if (cont_series in groups_dcm.keys()): 203 if (cont_series in groups_dcm.keys()):
275 - groups_dcm[key].append(list) 204 + groups_dcm[key].append(information)
276 else: 205 else:
277 - groups_dcm[key] = [[list]] 206 + groups_dcm[key] = [[information]]
278 207
279 cont_series = cont_series + 1 208 cont_series = cont_series + 1
280 209
@@ -305,39 +234,21 @@ class ivDicomGroups: @@ -305,39 +234,21 @@ class ivDicomGroups:
305 for y in xrange(size_list): 234 for y in xrange(size_list):
306 235
307 #Slices walks in the series 236 #Slices walks in the series
308 - image_pos = groups_dcm[key][0][y][3]  
309 - image_number = groups_dcm[key][0][y][0]  
310 - serie_number = groups_dcm[key][0][y][1]  
311 - spacing = groups_dcm[key][0][y][2]  
312 - image_position = groups_dcm[key][0][y][3]  
313 - patient_position = groups_dcm[key][0][y][4]  
314 - image_type = groups_dcm[key][0][y][5]  
315 - patient_name = groups_dcm[key][0][y][6]  
316 - image_orientation_label = groups_dcm[key][0][y][7]  
317 - file = groups_dcm[key][0][y][8]  
318 - series_description = groups_dcm[key][0][y][9]  
319 - id_study = groups_dcm[key][0][y][10]  
320 - tilt = groups_dcm[key][0][y][11]  
321 - window = groups_dcm[key][0][y][12]  
322 - level = groups_dcm[key][0][y][13] 237 + information = groups_dcm[key][0][y]
323 238
324 #Generate new key to dictionary 239 #Generate new key to dictionary
  240 + image_pos = information.image.position
325 key_ = (image_pos[0], image_pos[1], image_pos[2]) 241 key_ = (image_pos[0], image_pos[1], image_pos[2])
326 242
327 #Add informations in the list 243 #Add informations in the list
328 - list = [image_number, serie_number, spacing,  
329 - image_position, patient_position,  
330 - image_type,patient_name,  
331 - image_orientation_label, file,  
332 - series_description, id_study, tilt,  
333 - window, level] 244 + list = [information]
334 245
335 #If list Null, create dictionary 246 #If list Null, create dictionary
336 #and add list with information 247 #and add list with information
337 #after add in a temporary list 248 #after add in a temporary list
338 if (tmp_list == []): 249 if (tmp_list == []):
339 tmp = {} 250 tmp = {}
340 - tmp[key_] = list 251 + tmp[key_] = information
341 tmp_list.append(tmp) 252 tmp_list.append(tmp)
342 253
343 else: 254 else:
@@ -353,13 +264,13 @@ class ivDicomGroups: @@ -353,13 +264,13 @@ class ivDicomGroups:
353 #dictionary 264 #dictionary
354 265
355 if not (key_ in (tmp_list[a]).keys()): 266 if not (key_ in (tmp_list[a]).keys()):
356 - (tmp_list[a])[key_] = list 267 + (tmp_list[a])[key_] = information
357 flag = 1 268 flag = 1
358 a = a + 1 269 a = a + 1
359 270
360 if (flag == 0): 271 if (flag == 0):
361 tmp = {} 272 tmp = {}
362 - tmp[key_] = list 273 + tmp[key_] = information
363 274
364 tmp_list.append(tmp) 275 tmp_list.append(tmp)
365 276
@@ -375,37 +286,16 @@ class ivDicomGroups: @@ -375,37 +286,16 @@ class ivDicomGroups:
375 for m in xrange(len(tmp1.keys())): 286 for m in xrange(len(tmp1.keys())):
376 287
377 key = tmp1.keys()[m] 288 key = tmp1.keys()[m]
  289 + information = tmp1[key]
  290 + new_key = (information.patient.name, None, x, information.image.orientation_label)
378 291
379 - image_pos = tmp1[key][3]  
380 - image_number = tmp1[key][0]  
381 - serie_number = tmp1[key][1]  
382 - spacing = tmp1[key][2]  
383 - image_position = tmp1[key][3]  
384 - patient_position = tmp1[key][4]  
385 - image_type = tmp1[key][5]  
386 - patient_name = tmp1[key][6]  
387 - image_orientation_label = tmp1[key][7]  
388 - file = tmp1[key][8]  
389 - series_description = tmp1[key][9]  
390 - id_study = tmp1[key][10]  
391 - tilt = tmp1[key][11]  
392 - window = tmp1[key][12]  
393 - level = tmp1[key][13]  
394 -  
395 - new_key = (patient_name, None, x, image_orientation_label)  
396 -  
397 -  
398 - list = [image_number, serie_number, spacing,  
399 - image_position, patient_position,  
400 - image_type,patient_name,  
401 - image_orientation_label, file,  
402 - series_description, id_study, tilt,  
403 - window, level] 292 +
  293 + list = [information]
404 294
405 if (new_key in groups_dcm_.keys()): 295 if (new_key in groups_dcm_.keys()):
406 - groups_dcm_[new_key][0].append(list) 296 + groups_dcm_[new_key][0].append(information)
407 else: 297 else:
408 - groups_dcm_[new_key] = [[list]] 298 + groups_dcm_[new_key] = [[information]]
409 299
410 for j in xrange(len(groups_dcm_.keys())): 300 for j in xrange(len(groups_dcm_.keys())):
411 key = groups_dcm_.keys()[j] 301 key = groups_dcm_.keys()[j]
@@ -417,97 +307,30 @@ class ivDicomGroups: @@ -417,97 +307,30 @@ class ivDicomGroups:
417 self.groups_dcm = groups_dcm_ 307 self.groups_dcm = groups_dcm_
418 308
419 309
420 - def __Info(self): 310 + def __UpdateZSpacing(self):
421 """ 311 """
422 - This INFO is used in InVesalius 2 to learn the  
423 - characteristics of the test. Add a list at the end  
424 - of each series. 312 + Calculate Z spacing from slices
425 """ 313 """
426 - INFO_KEYS = \  
427 - ['AcquisitionDate',  
428 - 'AcquisitionGantryTilt',  
429 - 'AcquisitionModality',  
430 - 'AcquisitionNumber',  
431 - 'AcquisionSequence',  
432 - 'AcquisitionTime',  
433 - 'EquipmentKVP',  
434 - 'EquipmentInstitutionName',  
435 - 'EquipmentManufacturer',  
436 - 'EquipmentXRayTubeCurrent',  
437 - 'ImageColumnOrientation',  
438 - 'ImageConvolutionKernel',  
439 - 'ImageDataType',  
440 - 'ImageLocation',  
441 - 'ImageNumber',  
442 - 'ImagePixelSpacingX',  
443 - 'ImagePixelSpacingY',  
444 - 'ImagePosition',  
445 - 'ImageRowOrientation',  
446 - 'ImageSamplesPerPixel',  
447 - 'ImageSeriesNumber',  
448 - 'ImageThickness',  
449 - 'ImageWindowLevel',  
450 - 'ImageWindowWidth',  
451 - 'PatientAge',  
452 - 'PatientBirthDate',  
453 - 'PatientGender',  
454 - 'PatientName',  
455 - 'PhysicianName',  
456 - 'StudyID',  
457 - 'StudyInstanceUID',  
458 - 'StudyAdmittingDiagnosis',  
459 - ]  
460 314
461 for x in xrange(len(self.groups_dcm.keys())): 315 for x in xrange(len(self.groups_dcm.keys())):
462 316
463 key = self.groups_dcm.keys()[x] 317 key = self.groups_dcm.keys()[x]
464 -  
465 - file = self.groups_dcm[key][0][0][8]  
466 -  
467 - self.parser.SetFileName(file)  
468 -  
469 - acquisition_date = self.parser.GetAcquisitionDate()  
470 - acquisition_gantry_tilt = self.parser.GetAcquisitionGantryTilt()  
471 - acquisition_number = self.parser.GetAcquisitionNumber()  
472 - acquision_sequence = self.parser.GetAcquisionSequence()  
473 - acquisition_time = self.parser.GetAcquisitionTime()  
474 - equipment_kvp = self.parser.GetEquipmentKVP()  
475 - equipment_institution_name = self.parser.GetEquipmentInstitutionName()  
476 - equipment_manufacturer = self.parser.GetEquipmentManufacturer()  
477 - equipmentxraytubecurrent = self.parser.GetEquipmentXRayTubeCurrent()  
478 - image_column_orientation = self.parser.GetImageColumnOrientation()  
479 - image_convolution_kernel = self.parser.GetImageConvolutionKernel()  
480 - image_data_type = self.parser.GetImageDataType()  
481 - image_location = self.parser.GetImageLocation()  
482 - image_number = self.parser.GetImageNumber()  
483 - image_pixel_spacing_x = self.parser.GetImagePixelSpacingX()  
484 - image_pixel_spacing_y = self.parser.GetImagePixelSpacingY()  
485 - image_position = self.parser.GetImagePosition()  
486 - image_row_orientation = self.parser.GetImageRowOrientation()  
487 - image_samples_perpixel = self.parser.GetImageSamplesPerPixel()  
488 - image_series_number = self.parser.GetImageSeriesNumber()  
489 - image_thickness = self.parser.GetImageThickness()  
490 - image_window_level = self.parser.GetImageWindowLevel()  
491 - image_windowWidth = self.parser.GetImageWindowWidth()  
492 - patient_age = self.parser.GetPatientAge()  
493 - patient_birth_date = self.parser.GetPatientBirthDate()  
494 - patient_gender = self.parser.GetPatientGender()  
495 - patient_name = self.parser.GetPatientName()  
496 - study_id = self.parser.GetStudyID()  
497 - study_instance_UID = self.parser.GetStudyInstanceUID()  
498 - study_admitting_diagnosis = self.parser.GetStudyAdmittingDiagnosis()  
499 - image_dimension = (self.parser.GetDimensionX(), self.parser.GetDimensionY())  
500 -  
501 - if (len(self.groups_dcm[key][0]) > 1 ): 318 + information = self.groups_dcm[key][0]
  319 +
  320 + if (len(self.groups_dcm[key][0]) > 1):
502 #Catch a slice of middle and the next to find the spacing. 321 #Catch a slice of middle and the next to find the spacing.
503 center = len(self.groups_dcm[key][0])/2 322 center = len(self.groups_dcm[key][0])/2
504 if (center == 1): 323 if (center == 1):
505 - center = 0  
506 - current_position = self.groups_dcm[key][0][center][3]  
507 - next_position = self.groups_dcm[key][0][center + 1][3] 324 + center = 0
  325 +
  326 + information = self.groups_dcm[key][0][center]
  327 + current_position = information.image.position
  328 +
  329 + information = self.groups_dcm[key][0][center + 1]
  330 + next_position = information.image.position
508 331
509 try: 332 try:
510 - image_orientation_label = self.groups_dcm.keys()[x][3] 333 + image_orientation_label = self.groups_dcm.keys()[3]
511 except(IndexError): 334 except(IndexError):
512 image_orientation_label = None 335 image_orientation_label = None
513 336
@@ -522,17 +345,6 @@ class ivDicomGroups: @@ -522,17 +345,6 @@ class ivDicomGroups:
522 345
523 else: 346 else:
524 spacing = None 347 spacing = None
525 -  
526 - info = [acquisition_date, acquisition_gantry_tilt, acquisition_number,  
527 - acquision_sequence, acquisition_time, equipment_kvp,  
528 - equipment_institution_name, equipment_manufacturer,  
529 - equipmentxraytubecurrent, image_column_orientation,  
530 - image_convolution_kernel, image_data_type, image_location,  
531 - image_number, image_pixel_spacing_x, image_pixel_spacing_y,  
532 - image_position, image_row_orientation, image_samples_perpixel,  
533 - image_series_number, image_thickness, image_window_level,  
534 - image_windowWidth,patient_age, patient_birth_date,patient_gender,  
535 - patient_name, study_id, study_instance_UID, study_admitting_diagnosis,  
536 - spacing, image_dimension]  
537 -  
538 - self.groups_dcm[key].append(info) 348 +
  349 + for information in self.groups_dcm[key][0]:
  350 + information.image.spacing[2] = spacing
invesalius/reader/dicom_reader.py
  Diff comments   View file @b09b522
@@ -39,7 +39,7 @@ def LoadImages(dir_): @@ -39,7 +39,7 @@ def LoadImages(dir_):
39 39
40 dcm_files, acquisition_modality = GetDicomFiles(dir_) 40 dcm_files, acquisition_modality = GetDicomFiles(dir_)
41 41
42 - dcm_series = dicom_grouper.ivDicomGroups() 42 + dcm_series = dicom_grouper.DicomGroups()
43 dcm_series.SetFileList(dcm_files) 43 dcm_series.SetFileList(dcm_files)
44 dcm_series.Update() 44 dcm_series.Update()
45 45
@@ -52,8 +52,8 @@ def LoadImages(dir_): @@ -52,8 +52,8 @@ def LoadImages(dir_):
52 key = groups.keys()[x] 52 key = groups.keys()[x]
53 53
54 for y in xrange(len(groups[key][0])): 54 for y in xrange(len(groups[key][0])):
55 -  
56 - file = groups[key][0][y][8] 55 + dicom = groups[key][0][y]
  56 + file = dicom.image.file
57 tmp_list.append(file) 57 tmp_list.append(file)
58 58
59 list_files.append([len(tmp_list), key]) 59 list_files.append([len(tmp_list), key])
@@ -66,19 +66,22 @@ def LoadImages(dir_): @@ -66,19 +66,22 @@ def LoadImages(dir_):
66 66
67 file_list = [] 67 file_list = []
68 for x in xrange(len(groups[key][0])): 68 for x in xrange(len(groups[key][0])):
69 - file_list.append(groups[key][0][x][8])  
70 -  
71 - tilt = groups[key][0][x][11]  
72 - spacing = groups[key][1][14]  
73 - spacing_z = groups[key][1][30]  
74 - orientation = groups[key][0][x][7]  
75 - window = groups[key][0][x][12]  
76 - level = groups[key][0][x][13]  
77 - 69 + dicom = groups[key][0][x]
  70 + file_list.append(dicom.image.file)
  71 +
  72 + information = groups[key][0][x]
  73 +
  74 + tilt = dicom.acquisition.tilt#groups[key][0][x][11]
  75 + spacing = dicom.image.spacing#groups[key][1][14]
  76 + #spacing_z = #groups[key][1][30]
  77 + orientation = dicom.image.orientation_label#groups[key][0][x][7]
  78 + window = dicom.image.window#groups[key][0][x][12]
  79 + level = dicom.image.level#groups[key][0][x][13]
78 80
79 files = file_list 81 files = file_list
  82 + print dicom.image.orientation_label
80 #Coronal Crash. necessary verify 83 #Coronal Crash. necessary verify
81 - if (orientation <> "CORONAL"): 84 + if (dicom.image.orientation_label <> "CORONAL"):
82 #Organize reversed image 85 #Organize reversed image
83 sorter = gdcm.IPPSorter() 86 sorter = gdcm.IPPSorter()
84 sorter.SetComputeZSpacing(True) 87 sorter.SetComputeZSpacing(True)
@@ -100,9 +103,9 @@ def LoadImages(dir_): @@ -100,9 +103,9 @@ def LoadImages(dir_):
100 read.SetFileNames(array) 103 read.SetFileNames(array)
101 read.Update() 104 read.Update()
102 105
103 - img_axial = vtk.vtkImageData()  
104 - img_axial.DeepCopy(read.GetOutput())  
105 - img_axial.SetSpacing(spacing, spacing, spacing_z) 106 + image_data = vtk.vtkImageData()
  107 + image_data.DeepCopy(read.GetOutput())
  108 + image_data.SetSpacing(spacing, spacing, spacing_z)
106 else: 109 else:
107 for x in xrange(len(files)): 110 for x in xrange(len(files)):
108 #SIf the resolution of the 111 #SIf the resolution of the
@@ -118,16 +121,15 @@ def LoadImages(dir_): @@ -118,16 +121,15 @@ def LoadImages(dir_):
118 img_app.AddInput(img) 121 img_app.AddInput(img)
119 img_app.Update() 122 img_app.Update()
120 123
121 - img_axial = vtk.vtkImageData()  
122 - img_axial.DeepCopy(img_app.GetOutput())  
123 - img_axial.SetSpacing(img_axial.GetSpacing()[0],\  
124 - img_axial.GetSpacing()[1],\  
125 - spacing_z)  
126 - 124 + image_data = vtk.vtkImageData()
  125 + image_data.DeepCopy(img_app.GetOutput())
  126 + image_data.SetSpacing(image_data.GetSpacing()[0],\
  127 + image_data.GetSpacing()[1],\
  128 + dicom.image.spacing[2])
127 129
128 - img_axial.Update() 130 + image_data.Update()
129 131
130 - return img_axial, acquisition_modality, tilt, orientation, window, level 132 + return image_data, acquisition_modality, tilt, orientation, window, level
131 133
132 def GetDicomFiles(path, recursive = False): 134 def GetDicomFiles(path, recursive = False):
133 # TODO!!! SUPER GAMBIARRA!!! DO THIS BETTER 135 # TODO!!! SUPER GAMBIARRA!!! DO THIS BETTER