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Commit 2239286d0ac93fe47a469d09cc4c505c23b583d6

Authored by Paulo Henrique Junqueira Amorim
1 parent 3b5cb43a
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

ADD:Window & Level default from DICOM

Showing 2 changed files with 26 additions and 11 deletions   Show diff stats
invesalius/reader/dicom_grouper.py
  Diff comments   View file @2239286
@@ -121,6 +121,8 @@ class ivDicomGroups: @@ -121,6 +121,8 @@ class ivDicomGroups:
121 spacing = parser.GetPixelSpacing() 121 spacing = parser.GetPixelSpacing()
122 id_study = parser.GetStudyID() 122 id_study = parser.GetStudyID()
123 tilt = parser.GetAcquisitionGantryTilt() 123 tilt = parser.GetAcquisitionGantryTilt()
  124 + window = parser.GetImageWindowWidth()
  125 + level = parser.GetImageWindowLevel()
124 126
125 if (parser.GetImageThickness()): 127 if (parser.GetImageThickness()):
126 spacing.append(parser.GetImageThickness()) 128 spacing.append(parser.GetImageThickness())
@@ -135,7 +137,9 @@ class ivDicomGroups: @@ -135,7 +137,9 @@ class ivDicomGroups:
135 image_position, patient_position, 137 image_position, patient_position,
136 image_type,patient_name, 138 image_type,patient_name,
137 image_orientation_label, file, 139 image_orientation_label, file,
138 - series_description, id_study, tilt]) 140 + series_description, id_study, tilt,
  141 + window, level])
  142 +
139 self.filelist = filelist 143 self.filelist = filelist
140 144
141 def __GetInformations(self, ind): 145 def __GetInformations(self, ind):
@@ -160,12 +164,15 @@ class ivDicomGroups: @@ -160,12 +164,15 @@ class ivDicomGroups:
160 series_description = filelist[ind][9] 164 series_description = filelist[ind][9]
161 id_study = filelist[ind][10] 165 id_study = filelist[ind][10]
162 tilt = filelist[ind][11] 166 tilt = filelist[ind][11]
  167 + window = filelist[ind][12]
  168 + level = filelist[ind][13]
163 169
164 list = [image_number, serie_number, spacing, 170 list = [image_number, serie_number, spacing,
165 image_position, patient_position, 171 image_position, patient_position,
166 image_type,patient_name, 172 image_type,patient_name,
167 image_orientation_label, file, 173 image_orientation_label, file,
168 - series_description, id_study, tilt] 174 + series_description, id_study, tilt,
  175 + window, level]
169 176
170 return list 177 return list
171 178
@@ -311,6 +318,8 @@ class ivDicomGroups: @@ -311,6 +318,8 @@ class ivDicomGroups:
311 series_description = groups_dcm[key][0][y][9] 318 series_description = groups_dcm[key][0][y][9]
312 id_study = groups_dcm[key][0][y][10] 319 id_study = groups_dcm[key][0][y][10]
313 tilt = groups_dcm[key][0][y][11] 320 tilt = groups_dcm[key][0][y][11]
  321 + window = groups_dcm[key][0][y][12]
  322 + level = groups_dcm[key][0][y][13]
314 323
315 #Generate new key to dictionary 324 #Generate new key to dictionary
316 key_ = (image_pos[0], image_pos[1], image_pos[2]) 325 key_ = (image_pos[0], image_pos[1], image_pos[2])
@@ -320,7 +329,8 @@ class ivDicomGroups: @@ -320,7 +329,8 @@ class ivDicomGroups:
320 image_position, patient_position, 329 image_position, patient_position,
321 image_type,patient_name, 330 image_type,patient_name,
322 image_orientation_label, file, 331 image_orientation_label, file,
323 - series_description, id_study, tilt] 332 + series_description, id_study, tilt,
  333 + window, level]
324 334
325 #If list Null, create dictionary 335 #If list Null, create dictionary
326 #and add list with information 336 #and add list with information
@@ -379,6 +389,8 @@ class ivDicomGroups: @@ -379,6 +389,8 @@ class ivDicomGroups:
379 series_description = tmp1[key][9] 389 series_description = tmp1[key][9]
380 id_study = tmp1[key][10] 390 id_study = tmp1[key][10]
381 tilt = tmp1[key][11] 391 tilt = tmp1[key][11]
  392 + window = tmp1[key][12]
  393 + level = tmp1[key][13]
382 394
383 new_key = (patient_name, None, x, image_orientation_label) 395 new_key = (patient_name, None, x, image_orientation_label)
384 396
@@ -387,8 +399,8 @@ class ivDicomGroups: @@ -387,8 +399,8 @@ class ivDicomGroups:
387 image_position, patient_position, 399 image_position, patient_position,
388 image_type,patient_name, 400 image_type,patient_name,
389 image_orientation_label, file, 401 image_orientation_label, file,
390 - series_description, id_study, tilt]  
391 - 402 + series_description, id_study, tilt,
  403 + window, level]
392 404
393 if (new_key in groups_dcm_.keys()): 405 if (new_key in groups_dcm_.keys()):
394 groups_dcm_[new_key][0].append(list) 406 groups_dcm_[new_key][0].append(list)
invesalius/reader/dicom_reader.py
  Diff comments   View file @2239286
@@ -72,10 +72,13 @@ def LoadImages(dir_): @@ -72,10 +72,13 @@ def LoadImages(dir_):
72 spacing = groups[key][1][14] 72 spacing = groups[key][1][14]
73 spacing_z = groups[key][1][30] 73 spacing_z = groups[key][1][30]
74 orientation = groups[key][0][x][7] 74 orientation = groups[key][0][x][7]
  75 + window = groups[key][0][x][12]
  76 + level = groups[key][0][x][13]
75 77
76 - files = file_list 78 +
  79 + files = file_list
77 #Coronal Crash. necessary verify 80 #Coronal Crash. necessary verify
78 - if (orientation <> "CORONAL"): 81 + if (orientation <> "CORONAL"):
79 #Organize reversed image 82 #Organize reversed image
80 sorter = gdcm.IPPSorter() 83 sorter = gdcm.IPPSorter()
81 sorter.SetComputeZSpacing(True) 84 sorter.SetComputeZSpacing(True)
@@ -83,7 +86,7 @@ def LoadImages(dir_): @@ -83,7 +86,7 @@ def LoadImages(dir_):
83 sorter.Sort(file_list) 86 sorter.Sort(file_list)
84 #Getting organized image 87 #Getting organized image
85 files = sorter.GetFilenames() 88 files = sorter.GetFilenames()
86 - 89 +
87 array = vtk.vtkStringArray() 90 array = vtk.vtkStringArray()
88 91
89 img_app = vtk.vtkImageAppend() 92 img_app = vtk.vtkImageAppend()
@@ -96,7 +99,7 @@ def LoadImages(dir_): @@ -96,7 +99,7 @@ def LoadImages(dir_):
96 read = vtkgdcm.vtkGDCMImageReader() 99 read = vtkgdcm.vtkGDCMImageReader()
97 read.SetFileNames(array) 100 read.SetFileNames(array)
98 read.Update() 101 read.Update()
99 - 102 +
100 img_axial = vtk.vtkImageData() 103 img_axial = vtk.vtkImageData()
101 img_axial.DeepCopy(read.GetOutput()) 104 img_axial.DeepCopy(read.GetOutput())
102 img_axial.SetSpacing(spacing, spacing, spacing_z) 105 img_axial.SetSpacing(spacing, spacing, spacing_z)
@@ -123,8 +126,8 @@ def LoadImages(dir_): @@ -123,8 +126,8 @@ def LoadImages(dir_):
123 126
124 127
125 img_axial.Update() 128 img_axial.Update()
126 -  
127 - return img_axial, acquisition_modality, tilt, orientation 129 +
  130 + return img_axial, acquisition_modality, tilt, orientation, window, level
128 131
129 def GetDicomFiles(path, recursive = False): 132 def GetDicomFiles(path, recursive = False):
130 # TODO!!! SUPER GAMBIARRA!!! DO THIS BETTER 133 # TODO!!! SUPER GAMBIARRA!!! DO THIS BETTER