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Commit c020e9044bc39e052bad3910a09fd2ad783ec787

Authored by tatiana
1 parent f3bf4279
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: Import modularization and implementation, working both command line and int… 

…erface (still working on slices preview)
Showing 7 changed files with 268 additions and 104 deletions   Show diff stats
invesalius/control.py
  Diff comments   View file @c020e90
@@ -9,6 +9,7 @@ import project as prj @@ -9,6 +9,7 @@ import project as prj
9 import data.imagedata_utils as utils 9 import data.imagedata_utils as utils
10 import data.surface as surface 10 import data.surface as surface
11 import data.volume as volume 11 import data.volume as volume
  12 +import reader.dicom_grouper
12 import gui.dialogs as dialog 13 import gui.dialogs as dialog
13 import reader.dicom_reader as dcm 14 import reader.dicom_reader as dcm
14 import reader.analyze_reader as analyze 15 import reader.analyze_reader as analyze
@@ -23,23 +24,125 @@ class Controller(): @@ -23,23 +24,125 @@ class Controller():
23 self.__bind_events() 24 self.__bind_events()
24 25
25 def __bind_events(self): 26 def __bind_events(self):
26 - ps.Publisher().subscribe(self.ImportDirectory, 'Import directory') 27 + ps.Publisher().subscribe(self.OnImportMedicalImages, 'Import directory')
27 ps.Publisher().subscribe(self.StartImportPanel, "Load data to import panel") 28 ps.Publisher().subscribe(self.StartImportPanel, "Load data to import panel")
28 ps.Publisher().subscribe(self.LoadRaycastingPreset, 29 ps.Publisher().subscribe(self.LoadRaycastingPreset,
29 'Load raycasting preset') 30 'Load raycasting preset')
30 ps.Publisher().subscribe(self.SaveRaycastingPreset, 31 ps.Publisher().subscribe(self.SaveRaycastingPreset,
31 'Save raycasting preset') 32 'Save raycasting preset')
  33 + ps.Publisher().subscribe(self.OnOpenDicomGroup,
  34 + 'Open DICOM group')
32 35
33 def StartImportPanel(self, pubsub_evt): 36 def StartImportPanel(self, pubsub_evt):
34 # path to directory 37 # path to directory
35 path = pubsub_evt.data 38 path = pubsub_evt.data
36 39
37 # retrieve DICOM files splited into groups 40 # retrieve DICOM files splited into groups
38 - dicom_series = dcm.GetDicomGroups(path)  
39 - ps.Publisher().sendMessage("Load import panel", dicom_series) 41 + patient_series = dcm.GetDicomGroups(path)
  42 + ps.Publisher().sendMessage("Load import panel", patient_series)
  43 + first_patient = patient_series[0]
  44 + #ps.Publisher().sendMessage("Load dicom preview", first_patient)
  45 +
  46 + def OnImportMedicalImages(self, pubsub_evt):
  47 + directory = pubsub_evt.data
  48 + self.ImportMedicalImages(directory)
  49 +
  50 + def ImportMedicalImages(self, directory):
  51 + # OPTION 1: DICOM?
  52 + patients_groups = dcm.GetDicomGroups(directory)
  53 + if len(patients_groups):
  54 + group = dcm.SelectLargerDicomGroup(patients_groups)
  55 + imagedata, dicom = self.OpenDicomGroup(group, gui=False)
  56 + self.CreateDicomProject(imagedata, dicom)
  57 + # OPTION 2: ANALYZE?
  58 + else:
  59 + imagedata = analyze.ReadDirectory(directory)
  60 + if imagedata:
  61 + self.CreateAnalyzeProject(imagedata)
  62 + # OPTION 3: Nothing...
  63 + else:
  64 + print "No medical images found on given directory"
  65 + return
  66 + self.LoadProject()
  67 +
  68 + def LoadProject(self):
  69 + proj = prj.Project()
  70 + ps.Publisher().sendMessage('Set project name', proj.name)
  71 + ps.Publisher().sendMessage('Load slice to viewer', (proj.imagedata))
  72 + self.LoadImagedataInfo() # TODO: where do we insert this <<<?
  73 + ps.Publisher().sendMessage('Bright and contrast adjustment image',\
  74 + (proj.window, proj.level))
  75 + ps.Publisher().sendMessage('Update window level value',\
  76 + (proj.window, proj.level))
  77 + ps.Publisher().sendMessage('Show content panel')
  78 + ps.Publisher().sendMessage('Update AUI')
  79 +
  80 + def CreateAnalyzeProject(self, imagedata):
  81 + proj = prj.Project()
  82 + proj.name = "Untitled"
  83 + proj.SetAcquisitionModality("MRI")
  84 + proj.imagedata = imagedata
  85 + #TODO: Verify if all Analyse are in AXIAL orientation
  86 + proj.original_orientation = const.AXIAL
  87 + proj.threshold_range = imagedata.GetScalarRange()
  88 + proj.window = proj.threshold_range[1] - proj.threshold_range[0]
  89 + proj.level (0.5 * (proj.threshold_range[1] + proj.threshold_range[0]))
  90 +
  91 + const.THRESHOLD_OUTVALUE = proj.threshold_range[0]
  92 + const.THRESHOLD_INVALUE = proj.threshold_range[1]
  93 + const.WINDOW_LEVEL['Default'] = (proj.window, proj.level)
  94 + const.WINDOW_LEVEL['Manual'] = (proj.window, proj.level)
40 95
41 - #ps.Publisher().sendMessage("Load dicom preview", series_preview)  
42 96
  97 + def CreateDicomProject(self, imagedata, dicom):
  98 + name_to_const = {"AXIAL":const.AXIAL,
  99 + "CORONAL":const.CORONAL,
  100 + "SAGITTAL":const.SAGITAL}
  101 +
  102 + proj = prj.Project()
  103 + proj.name = dicom.patient.name
  104 + proj.SetAcquisitionModality(dicom.acquisition.modality)
  105 + proj.imagedata = imagedata
  106 + proj.original_orientation =\
  107 + name_to_const[dicom.image.orientation_label]
  108 + proj.window = float(dicom.image.window)
  109 + proj.level = float(dicom.image.level)
  110 + proj.threshold_range = imagedata.GetScalarRange()
  111 +
  112 + const.THRESHOLD_OUTVALUE = proj.threshold_range[0]
  113 + const.THRESHOLD_INVALUE = proj.threshold_range[1]
  114 + const.WINDOW_LEVEL['Default'] = (proj.window, proj.level)
  115 + const.WINDOW_LEVEL['Manual'] = (proj.window, proj.level)
  116 +
  117 + def OnOpenDicomGroup(self, pubsub_evt):
  118 + group = pubsub_evt.data
  119 + imagedata, dicom = self.OpenDicomGroup(group, gui=False)
  120 + self.CreateDicomProject(imagedata, dicom)
  121 + self.LoadProject()
  122 +
  123 + def OpenDicomGroup(self, dicom_group, gui=True):
  124 +
  125 + # Retrieve general DICOM headers
  126 + dicom = dicom_group.GetDicomSample()
  127 +
  128 + # Create imagedata
  129 + filelist = dicom_group.GetFilenameList()
  130 + zspacing = dicom_group.zspacing
  131 + imagedata = utils.CreateImageData(filelist, zspacing)
  132 +
  133 + # 1(a): Fix gantry tilt, if any
  134 + tilt_value = dicom.acquisition.tilt
  135 + if (tilt_value) and (gui):
  136 + # Tell user gantry tilt and fix, according to answer
  137 + message = "Fix gantry tilt applying the degrees bellow"
  138 + value = -1*tilt_value
  139 + tilt_value = dialog.ShowNumberDialog(message, value)
  140 + imagedata = utils.FixGantryTilt(imagedata, tilt_value)
  141 + elif (tilt_value) and not (gui):
  142 + tilt_value = -1*tilt_value
  143 + imagedata = utils.FixGantryTilt(imagedata, tilt_value)
  144 +
  145 + return imagedata, dicom
43 146
44 def ImportDirectory(self, pubsub_evt=None, dir_=None): 147 def ImportDirectory(self, pubsub_evt=None, dir_=None):
45 """ 148 """
@@ -84,19 +187,20 @@ class Controller(): @@ -84,19 +187,20 @@ class Controller():
84 else: 187 else:
85 "No DICOM files were found. Trying to read with ITK..." 188 "No DICOM files were found. Trying to read with ITK..."
86 imagedata = analyze.ReadDirectory(dir_) 189 imagedata = analyze.ReadDirectory(dir_)
87 - acquisition_modality = "MRI" 190 + if imagedata:
  191 + acquisition_modality = "MRI"
88 192
89 - #TODO: Verify if all Analyse is AXIAL orientation  
90 - orientation = const.AXIAL 193 + #TODO: Verify if all Analyse is AXIAL orientation
  194 + orientation = const.AXIAL
91 195
92 - proj.SetAcquisitionModality(acquisition_modality)  
93 - proj.imagedata = imagedata  
94 - proj.original_orientation = orientation  
95 - threshold_range = proj.imagedata.GetScalarRange()  
96 - proj.window = window = threshold_range[1] - threshold_range[0]  
97 - proj.level = level = (0.5 * (threshold_range[1] + threshold_range[0])) 196 + proj.SetAcquisitionModality(acquisition_modality)
  197 + proj.imagedata = imagedata
  198 + proj.original_orientation = orientation
  199 + threshold_range = proj.imagedata.GetScalarRange()
  200 + proj.window = window = threshold_range[1] - threshold_range[0]
  201 + proj.level = level = (0.5 * (threshold_range[1] + threshold_range[0]))
98 202
99 - ps.Publisher().sendMessage('Update window level value',\ 203 + ps.Publisher().sendMessage('Update window level value',\
100 (proj.window, proj.level)) 204 (proj.window, proj.level))
101 205
102 if not imagedata: 206 if not imagedata:
invesalius/data/imagedata_utils.py
  Diff comments   View file @c020e90
1 import math 1 import math
2 import vtk 2 import vtk
  3 +import vtkgdcm
  4 +
  5 +import constants as const
3 6
4 # TODO: Test cases which are originally in sagittal/coronal orientation 7 # TODO: Test cases which are originally in sagittal/coronal orientation
5 # and have gantry 8 # and have gantry
@@ -162,3 +165,52 @@ def ExtractVOI(imagedata,xi,xf,yi,yf,zi,zf): @@ -162,3 +165,52 @@ def ExtractVOI(imagedata,xi,xf,yi,yf,zi,zf):
162 voi.SetSampleRate(1, 1, 1) 165 voi.SetSampleRate(1, 1, 1)
163 voi.Update() 166 voi.Update()
164 return voi.GetOutput() 167 return voi.GetOutput()
  168 +
  169 +def CreateImageData(filelist, zspacing):
  170 +
  171 + if not(const.REDUCE_IMAGEDATA_QUALITY):
  172 + array = vtk.vtkStringArray()
  173 + for x in xrange(len(filelist)):
  174 + array.InsertValue(x,filelist[x])
  175 +
  176 + reader = vtkgdcm.vtkGDCMImageReader()
  177 + reader.SetFileNames(array)
  178 + reader.Update()
  179 +
  180 + # The zpacing is a DicomGroup property, so we need to set it
  181 + imagedata = vtk.vtkImageData()
  182 + imagedata.DeepCopy(reader.GetOutput())
  183 + spacing = imagedata.GetSpacing()
  184 + imagedata.SetSpacing(spacing[0], spacing[1], zspacing)
  185 + else:
  186 + # Reformat each slice and future append them
  187 + appender = vtk.vtkImageAppend()
  188 + appender.SetAppendAxis(2) #Define Stack in Z
  189 +
  190 + # Reformat each slice
  191 + for x in xrange(len(filelist)):
  192 + # TODO: We need to check this automatically according
  193 + # to each computer's architecture
  194 + # If the resolution of the matrix is too large
  195 + reader = vtkgdcm.vtkGDCMImageReader()
  196 + reader.SetFileName(filelist[x])
  197 + reader.Update()
  198 +
  199 + #Resample image in x,y dimension
  200 + slice_imagedata = ResampleImage2D(reader.GetOutput(), 256)
  201 +
  202 + #Stack images in Z axes
  203 + appender.AddInput(slice_imagedata)
  204 + appender.Update()
  205 +
  206 + # The zpacing is a DicomGroup property, so we need to set it
  207 + imagedata = vtk.vtkImageData()
  208 + imagedata.DeepCopy(appender.GetOutput())
  209 + spacing = imagedata.GetSpacing()
  210 +
  211 + imagedata.SetSpacing(spacing[0], spacing[1], zspacing)
  212 +
  213 + imagedata.Update()
  214 + return imagedata
  215 +
  216 +
invesalius/gui/dicom_preview_panel.py
  Diff comments   View file @c020e90
@@ -31,6 +31,27 @@ class SerieEvent(PreviewEvent): @@ -31,6 +31,27 @@ class SerieEvent(PreviewEvent):
31 def __init__(self , evtType, id): 31 def __init__(self , evtType, id):
32 super(SerieEvent, self).__init__(evtType, id) 32 super(SerieEvent, self).__init__(evtType, id)
33 33
  34 +class DicomImageData(object):
  35 + def __init__(self):
  36 + pass
  37 +
  38 + def SetInput(self, dicom):
  39 + reader = vtkgdcm.vtkGDCMImageReader()
  40 + reader.SetFileName(dicom.image.file)
  41 + imagedata = reader.GetOutput()
  42 +
  43 + scale = imagedata.GetScalarRange()
  44 +
  45 + cast = vtk.vtkImageMapToWindowLevelColors()
  46 + cast.SetInput(imagedata)
  47 + cast.SetWindow(float(dicom.image.window))
  48 + cast.SetLevel(float(dicom.image.level))
  49 +
  50 + self.imagedata = cast.GetOutput()
  51 +
  52 + def GetOutput(self):
  53 + return self.imagedata
  54 +
34 55
35 class DicomLoader(object): 56 class DicomLoader(object):
36 """ 57 """
@@ -119,6 +140,15 @@ class Preview(wx.Panel): @@ -119,6 +140,15 @@ class Preview(wx.Panel):
119 def SetSubtitle(self, subtitle): 140 def SetSubtitle(self, subtitle):
120 self.subtitle.SetLabel(subtitle) 141 self.subtitle.SetLabel(subtitle)
121 142
  143 + def SetGroup(self, group):
  144 + self.SetTitle(group.title)
  145 + self.SetSubtitle("%d images"%(group.nslices))
  146 + d = DicomImageData()
  147 + d.SetInput(group.dicom)
  148 + imagedata = d.GetOutput()
  149 + self.actor.SetInput(imagedata)
  150 + self.render.ResetCamera()
  151 +
122 def SetImage(self, image_data): 152 def SetImage(self, image_data):
123 """ 153 """
124 Set a Image to preview. 154 Set a Image to preview.
@@ -198,23 +228,23 @@ class DicomPreviewSeries(wx.Panel): @@ -198,23 +228,23 @@ class DicomPreviewSeries(wx.Panel):
198 "%d Images" % len(self.series[i][0]), # Subtitle 228 "%d Images" % len(self.series[i][0]), # Subtitle
199 i) for n, i in enumerate(self.series)] 229 i) for n, i in enumerate(self.series)]
200 230
201 - def SetDicomSeries(self, files):  
202 - self.files = files  
203 - scroll_range = len(files)/5  
204 - if scroll_range * 5 < len(files): 231 + def SetDicomSeries(self, patient):
  232 + #self.files = files
  233 + ngroups = patient.ngroups
  234 + self.groups = patient.GetGroups()
  235 +
  236 + scroll_range = ngroups/5
  237 + if scroll_range * 5 < ngroups:
205 scroll_range +=1 238 scroll_range +=1
206 self.scroll.SetScrollbar(0, 3, scroll_range, 5) 239 self.scroll.SetScrollbar(0, 3, scroll_range, 5)
207 self._display_previews() 240 self._display_previews()
208 241
209 def _display_previews(self): 242 def _display_previews(self):
210 - initial = self.displayed_position * 5  
211 - final = initial + 15  
212 - for f, p in zip(self.files[initial:final], self.previews):  
213 - print "--------"  
214 - print "f:", f  
215 - print "p: ", p  
216 - p.SetImage(f)  
217 - p.Show() 243 + begin = self.displayed_position * 5
  244 + end = begin + 15
  245 + for group, preview in zip(self.groups[begin:end], self.previews):
  246 + preview.SetGroup(group)
  247 + preview.Show()
218 248
219 def OnScroll(self, evt): 249 def OnScroll(self, evt):
220 self.displayed_position = evt.GetPosition() 250 self.displayed_position = evt.GetPosition()
invesalius/gui/frame.py
  Diff comments   View file @c020e90
@@ -80,6 +80,11 @@ class Frame(wx.Frame): @@ -80,6 +80,11 @@ class Frame(wx.Frame):
80 ps.Publisher().subscribe(self.UpdateAui, "Update AUI") 80 ps.Publisher().subscribe(self.UpdateAui, "Update AUI")
81 ps.Publisher().subscribe(self.ShowTask, 'Show task panel') 81 ps.Publisher().subscribe(self.ShowTask, 'Show task panel')
82 ps.Publisher().subscribe(self.HideTask, 'Hide task panel') 82 ps.Publisher().subscribe(self.HideTask, 'Hide task panel')
  83 + ps.Publisher().subscribe(self.SetProjectName, 'Set project name')
  84 +
  85 + def SetProjectName(self, pubsub_evt):
  86 + proj_name = pubsub_evt.data
  87 + self.SetTitle("InVesalius 3 - %s"%(proj_name))
83 88
84 def UpdateAui(self, pubsub_evt): 89 def UpdateAui(self, pubsub_evt):
85 self.aui_manager.Update() 90 self.aui_manager.Update()
@@ -169,7 +174,9 @@ class Frame(wx.Frame): @@ -169,7 +174,9 @@ class Frame(wx.Frame):
169 174
170 def ShowContentPanel(self, evt_pubsub): 175 def ShowContentPanel(self, evt_pubsub):
171 aui_manager = self.aui_manager 176 aui_manager = self.aui_manager
  177 + aui_manager.GetPane("Import").Show(0)
172 aui_manager.GetPane("Data").Show(1) 178 aui_manager.GetPane("Data").Show(1)
  179 + aui_manager.GetPane("Tasks").Show(1)
173 aui_manager.Update() 180 aui_manager.Update()
174 181
175 def OnSize(self, evt): 182 def OnSize(self, evt):
invesalius/gui/import_panel.py
  Diff comments   View file @c020e90
@@ -130,21 +130,22 @@ class TextPanel(wx.Panel): @@ -130,21 +130,22 @@ class TextPanel(wx.Panel):
130 130
131 tree.Expand(self.root) 131 tree.Expand(self.root)
132 132
133 - tree.GetMainWindow().Bind(wx.EVT_RIGHT_UP, self.OnRightUp)  
134 tree.Bind(wx.EVT_TREE_ITEM_ACTIVATED, self.OnActivate) 133 tree.Bind(wx.EVT_TREE_ITEM_ACTIVATED, self.OnActivate)
135 134
136 def OnActivate(self, evt): 135 def OnActivate(self, evt):
137 print "OnActivate" 136 print "OnActivate"
138 item = evt.GetItem() 137 item = evt.GetItem()
139 - print self.tree.GetItemPyData(item)  
140 -  
141 -  
142 - def OnRightUp(self, evt):  
143 - pos = evt.GetPosition()  
144 - item, flags, col = self.tree.HitTest(pos)  
145 - if item:  
146 - print 'Flags: %s, Col:%s, Text: %s' %\  
147 - (flags, col, self.tree.GetItemText(item, col)) 138 + group = self.tree.GetItemPyData(item)
  139 + if group:
  140 + print "send"
  141 + ps.Publisher().sendMessage('Open DICOM group',
  142 + group)
  143 +
  144 + else:
  145 + if self.tree.IsExpanded(item):
  146 + self.tree.Collapse(item)
  147 + else:
  148 + self.tree.Expand(item)
148 149
149 def OnSize(self, evt): 150 def OnSize(self, evt):
150 self.tree.SetSize(self.GetSize()) 151 self.tree.SetSize(self.GetSize())
invesalius/reader/dicom_grouper.py
  Diff comments   View file @c020e90
@@ -51,6 +51,8 @@ @@ -51,6 +51,8 @@
51 # <dicom.image.number> and <dicom.acquisition.series_number> 51 # <dicom.image.number> and <dicom.acquisition.series_number>
52 # were swapped 52 # were swapped
53 53
  54 +import gdcm
  55 +
54 ORIENT_MAP = {"SAGITTAL":0, "CORONAL":1, "AXIAL":2, "OBLIQUE":2} 56 ORIENT_MAP = {"SAGITTAL":0, "CORONAL":1, "AXIAL":2, "OBLIQUE":2}
55 57
56 58
@@ -96,7 +98,28 @@ class DicomGroup: @@ -96,7 +98,28 @@ class DicomGroup:
96 # (interpolated) 98 # (interpolated)
97 return self.slices_dict.values() 99 return self.slices_dict.values()
98 100
99 - def GetSortedList(self): 101 + def GetFilenameList(self):
  102 + # Should be called when user selects this group
  103 + # This list will be used to create the vtkImageData
  104 + # (interpolated)
  105 +
  106 + filelist = [dicom.image.file for dicom in
  107 + self.slices_dict.values()]
  108 +
  109 + # Sort slices using GDCM
  110 + if (self.dicom.image.orientation_label <> "CORONAL"):
  111 + #Organize reversed image
  112 + sorter = gdcm.IPPSorter()
  113 + sorter.SetComputeZSpacing(True)
  114 + sorter.SetZSpacingTolerance(1e-10)
  115 + sorter.Sort(filelist)
  116 + filelist = sorter.GetFilenames()
  117 +
  118 + #Getting organized image
  119 + return filelist
  120 +
  121 +
  122 + def GetHandSortedList(self):
100 # This will be used to fix problem 1, after merging 123 # This will be used to fix problem 1, after merging
101 # single DicomGroups of same study_id and orientation 124 # single DicomGroups of same study_id and orientation
102 list_ = self.slices_dict.values() 125 list_ = self.slices_dict.values()
@@ -106,7 +129,7 @@ class DicomGroup: @@ -106,7 +129,7 @@ class DicomGroup:
106 return list_ 129 return list_
107 130
108 def UpdateZSpacing(self): 131 def UpdateZSpacing(self):
109 - list_ = self.GetSortedList() 132 + list_ = self.GetHandSortedList()
110 133
111 if (len(list_) > 1): 134 if (len(list_) > 1):
112 dicom = list_[0] 135 dicom = list_[0]
@@ -246,7 +269,7 @@ class PatientGroup: @@ -246,7 +269,7 @@ class PatientGroup:
246 group_counter = 0 269 group_counter = 0
247 for group_key in dict_to_change: 270 for group_key in dict_to_change:
248 # 2nd STEP: SORT 271 # 2nd STEP: SORT
249 - sorted_list = dict_to_change[group_key].GetSortedList() 272 + sorted_list = dict_to_change[group_key].GetHandSortedList()
250 273
251 # 3rd STEP: CHECK DIFFERENCES 274 # 3rd STEP: CHECK DIFFERENCES
252 axis = ORIENT_MAP[group_key[0]] # based on orientation 275 axis = ORIENT_MAP[group_key[0]] # based on orientation
invesalius/reader/dicom_reader.py
  Diff comments   View file @c020e90
@@ -28,32 +28,26 @@ import dicom @@ -28,32 +28,26 @@ import dicom
28 import dicom_grouper 28 import dicom_grouper
29 import data.imagedata_utils as iu 29 import data.imagedata_utils as iu
30 30
31 -def LoadImages(dir_): 31 +def ReadDicomGroup(dir_):
32 32
33 patient_group = GetDicomGroups(dir_) 33 patient_group = GetDicomGroups(dir_)
34 - filelist, dicom, zspacing = SelectLargerDicomGroup(patient_group)  
35 - filelist = SortFiles(filelist, dicom)  
36 - imagedata = CreateImageData(filelist, zspacing)  
37 -  
38 - return imagedata, dicom 34 + if len(patient_group) > 0:
  35 + filelist, dicom, zspacing = SelectLargerDicomGroup(patient_group)
  36 + filelist = SortFiles(filelist, dicom)
  37 + imagedata = CreateImageData(filelist, zspacing)
  38 + return imagedata, dicom
  39 + else:
  40 + return False
39 41
40 42
41 def SelectLargerDicomGroup(patient_group): 43 def SelectLargerDicomGroup(patient_group):
42 - nslices_old = 0 44 + maxslices = 0
43 for patient in patient_group: 45 for patient in patient_group:
44 group_list = patient.GetGroups() 46 group_list = patient.GetGroups()
45 for group in group_list: 47 for group in group_list:
46 - nslices = group.nslices  
47 - print "nslices:", nslices  
48 - if (nslices >= nslices_old):  
49 - dicoms = group.GetList()  
50 - zspacing = group.zspacing  
51 - nslices_old = nslices  
52 -  
53 - filelist = []  
54 - for dicom in dicoms:  
55 - filelist.append(dicom.image.file)  
56 - return filelist, dicom, zspacing 48 + if group.nslices > maxslices:
  49 + larger_group = group
  50 + return larger_group
57 51
58 def SortFiles(filelist, dicom): 52 def SortFiles(filelist, dicom):
59 # Sort slices 53 # Sort slices
@@ -71,53 +65,6 @@ def SortFiles(filelist, dicom): @@ -71,53 +65,6 @@ def SortFiles(filelist, dicom):
71 return filelist 65 return filelist
72 66
73 67
74 -def CreateImageData(filelist, zspacing):  
75 -  
76 - if not(const.REDUCE_IMAGEDATA_QUALITY):  
77 - array = vtk.vtkStringArray()  
78 - for x in xrange(len(filelist)):  
79 - array.InsertValue(x,filelist[x])  
80 -  
81 - reader = vtkgdcm.vtkGDCMImageReader()  
82 - reader.SetFileNames(array)  
83 - reader.Update()  
84 -  
85 - # The zpacing is a DicomGroup property, so we need to set it  
86 - imagedata = vtk.vtkImageData()  
87 - imagedata.DeepCopy(reader.GetOutput())  
88 - spacing = imagedata.GetSpacing()  
89 - imagedata.SetSpacing(spacing[0], spacing[1], zspacing)  
90 - else:  
91 - # Reformat each slice and future append them  
92 - appender = vtk.vtkImageAppend()  
93 - appender.SetAppendAxis(2) #Define Stack in Z  
94 -  
95 - # Reformat each slice  
96 - for x in xrange(len(filelist)):  
97 - # TODO: We need to check this automatically according  
98 - # to each computer's architecture  
99 - # If the resolution of the matrix is too large  
100 - reader = vtkgdcm.vtkGDCMImageReader()  
101 - reader.SetFileName(filelist[x])  
102 - reader.Update()  
103 -  
104 - #Resample image in x,y dimension  
105 - slice_imagedata = iu.ResampleImage2D(reader.GetOutput(), 256)  
106 -  
107 - #Stack images in Z axes  
108 - appender.AddInput(slice_imagedata)  
109 - appender.Update()  
110 -  
111 - # The zpacing is a DicomGroup property, so we need to set it  
112 - imagedata = vtk.vtkImageData()  
113 - imagedata.DeepCopy(appender.GetOutput())  
114 - spacing = imagedata.GetSpacing()  
115 -  
116 - imagedata.SetSpacing(spacing[0], spacing[1], zspacing)  
117 -  
118 - imagedata.Update()  
119 - return imagedata  
120 -  
121 68
122 def GetDicomGroups(directory, recursive=True): 69 def GetDicomGroups(directory, recursive=True):
123 """ 70 """