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Commit 0317ac288355fd17282735cbe273c753c0bd9f25

Authored by Thiago Franco de Moraes
1 parent c06ff6da
Exists in master and in 32 other branches canvas_reeng, canvas_text, casmoothing_cython, command-line, debian_cython, ff_mask, ff_mask_improv, ffill_gui, ffill_segmentation, fill_holes_auto, get_pixel, import_mesh, inv3.0.1, manual_v3.1, measure_canvas, measure_improvements, measure_placement_test, phoenix, region_growing_confidence, 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, user_guide_en, vti, xmartlabs-command-line

Adapts InVesalius to run with VTK6 (#35) 

* Showing the slices

* cursor was not displayed correctly

* Watershed using vtk6

* generating surface with vtk6

* generating preview in vtk6

* Showing raycasting with vtk6

* Showing measures with vtk6

* saving project

* Saving screenshots with vtk6

* Saving meshes with vtk6

* It was not showing surfaces created with greatest region, selected region and all regions filters
Showing 16 changed files with 190 additions and 173 deletions   Show diff stats
@@ -20,3 +20,7 @@ invesalius/reader/*.pyc @@ -20,3 +20,7 @@ invesalius/reader/*.pyc
20 *.so 20 *.so
21 tags 21 tags
22 *.c 22 *.c
  23 +
  24 +build
  25 +*.patch
  26 +*.tgz
invesalius/data/converters.py
  Diff comments   View file @0317ac2
@@ -43,16 +43,16 @@ def to_vtk(n_array, spacing, slice_number, orientation): @@ -43,16 +43,16 @@ def to_vtk(n_array, spacing, slice_number, orientation):
43 image = vtk.vtkImageData() 43 image = vtk.vtkImageData()
44 image.SetOrigin(0, 0, 0) 44 image.SetOrigin(0, 0, 0)
45 image.SetSpacing(spacing) 45 image.SetSpacing(spacing)
46 - image.SetNumberOfScalarComponents(1)  
47 image.SetDimensions(dx, dy, dz) 46 image.SetDimensions(dx, dy, dz)
  47 + # SetNumberOfScalarComponents and SetScalrType were replaced by
  48 + # AllocateScalars
  49 + # image.SetNumberOfScalarComponents(1)
  50 + # image.SetScalarType(numpy_support.get_vtk_array_type(n_array.dtype))
  51 + image.AllocateScalars(numpy_support.get_vtk_array_type(n_array.dtype), 1)
48 image.SetExtent(extent) 52 image.SetExtent(extent)
49 - image.SetScalarType(numpy_support.get_vtk_array_type(n_array.dtype))  
50 - image.AllocateScalars()  
51 image.GetPointData().SetScalars(v_image) 53 image.GetPointData().SetScalars(v_image)
52 - image.Update()  
53 54
54 image_copy = vtk.vtkImageData() 55 image_copy = vtk.vtkImageData()
55 image_copy.DeepCopy(image) 56 image_copy.DeepCopy(image)
56 - image_copy.Update()  
57 57
58 return image_copy 58 return image_copy
invesalius/data/cursor_actors.py
  Diff comments   View file @0317ac2
@@ -55,19 +55,19 @@ def to_vtk(n_array, spacing, slice_number, orientation): @@ -55,19 +55,19 @@ def to_vtk(n_array, spacing, slice_number, orientation):
55 image = vtk.vtkImageData() 55 image = vtk.vtkImageData()
56 image.SetOrigin(0, 0, 0) 56 image.SetOrigin(0, 0, 0)
57 image.SetSpacing(spacing) 57 image.SetSpacing(spacing)
58 - image.SetNumberOfScalarComponents(1)  
59 image.SetDimensions(dx, dy, dz) 58 image.SetDimensions(dx, dy, dz)
60 image.SetExtent(extent) 59 image.SetExtent(extent)
61 - image.SetScalarType(numpy_support.get_vtk_array_type(n_array.dtype))  
62 - image.AllocateScalars()  
63 - image.Update() 60 + # image.SetNumberOfScalarComponents(1)
  61 + # image.SetScalarType(numpy_support.get_vtk_array_type(n_array.dtype))
  62 + image.AllocateScalars(numpy_support.get_vtk_array_type(n_array.dtype), 1)
  63 + # image.Update()
64 image.GetCellData().SetScalars(v_image) 64 image.GetCellData().SetScalars(v_image)
65 image.GetPointData().SetScalars(v_image) 65 image.GetPointData().SetScalars(v_image)
66 - image.Update() 66 + # image.Update()
67 67
68 image_copy = vtk.vtkImageData() 68 image_copy = vtk.vtkImageData()
69 image_copy.DeepCopy(image) 69 image_copy.DeepCopy(image)
70 - image_copy.Update() 70 + # image_copy.Update()
71 71
72 return image_copy 72 return image_copy
73 73
@@ -224,7 +224,7 @@ class CursorBase(object): @@ -224,7 +224,7 @@ class CursorBase(object):
224 img_colours_mask = vtk.vtkImageMapToColors() 224 img_colours_mask = vtk.vtkImageMapToColors()
225 img_colours_mask.SetLookupTable(lut_mask) 225 img_colours_mask.SetLookupTable(lut_mask)
226 img_colours_mask.SetOutputFormatToRGBA() 226 img_colours_mask.SetOutputFormatToRGBA()
227 - img_colours_mask.SetInput(imagedata) 227 + img_colours_mask.SetInputData(imagedata)
228 img_colours_mask.Update() 228 img_colours_mask.Update()
229 229
230 return img_colours_mask.GetOutput() 230 return img_colours_mask.GetOutput()
@@ -274,12 +274,12 @@ class CursorCircle(CursorBase): @@ -274,12 +274,12 @@ class CursorCircle(CursorBase):
274 circle_ci = self._set_colour(circle_i, self.colour) 274 circle_ci = self._set_colour(circle_i, self.colour)
275 275
276 if self.mapper is None: 276 if self.mapper is None:
277 - self.actor.SetInput(circle_ci) 277 + self.actor.SetInputData(circle_ci)
278 self.actor.InterpolateOff() 278 self.actor.InterpolateOff()
279 self.actor.PickableOff() 279 self.actor.PickableOff()
280 self.actor.SetDisplayExtent(circle_ci.GetExtent()) 280 self.actor.SetDisplayExtent(circle_ci.GetExtent())
281 else: 281 else:
282 - self.mapper.SetInput(circle_ci) 282 + self.mapper.SetInputData(circle_ci)
283 self.mapper.BorderOn() 283 self.mapper.BorderOn()
284 284
285 self.mapper.SetOrientation(ORIENTATION[self.orientation]) 285 self.mapper.SetOrientation(ORIENTATION[self.orientation])
@@ -347,12 +347,12 @@ class CursorRectangle(CursorBase): @@ -347,12 +347,12 @@ class CursorRectangle(CursorBase):
347 rectangle_ci = self._set_colour(rectangle_i, self.colour) 347 rectangle_ci = self._set_colour(rectangle_i, self.colour)
348 348
349 if self.mapper is None: 349 if self.mapper is None:
350 - self.actor.SetInput(rectangle_ci) 350 + self.actor.SetInputData(rectangle_ci)
351 self.actor.InterpolateOff() 351 self.actor.InterpolateOff()
352 self.actor.PickableOff() 352 self.actor.PickableOff()
353 self.actor.SetDisplayExtent(rectangle_ci.GetExtent()) 353 self.actor.SetDisplayExtent(rectangle_ci.GetExtent())
354 else: 354 else:
355 - self.mapper.SetInput(rectangle_ci) 355 + self.mapper.SetInputData(rectangle_ci)
356 self.mapper.BorderOn() 356 self.mapper.BorderOn()
357 self.mapper.SetOrientation(ORIENTATION[self.orientation]) 357 self.mapper.SetOrientation(ORIENTATION[self.orientation])
358 358
invesalius/data/measures.py
  Diff comments   View file @0317ac2
@@ -341,8 +341,8 @@ class CrossPointRepresentation(object): @@ -341,8 +341,8 @@ class CrossPointRepresentation(object):
341 sv.SetPoint2(p4) 341 sv.SetPoint2(p4)
342 342
343 cruz = vtk.vtkAppendPolyData() 343 cruz = vtk.vtkAppendPolyData()
344 - cruz.AddInput(sv.GetOutput())  
345 - cruz.AddInput(sh.GetOutput()) 344 + cruz.AddInputData(sv.GetOutput())
  345 + cruz.AddInputData(sh.GetOutput())
346 346
347 c = vtk.vtkCoordinate() 347 c = vtk.vtkCoordinate()
348 c.SetCoordinateSystemToWorld() 348 c.SetCoordinateSystemToWorld()
@@ -563,9 +563,11 @@ class AngularMeasure(object): @@ -563,9 +563,11 @@ class AngularMeasure(object):
563 arc = self.DrawArc() 563 arc = self.DrawArc()
564 564
565 line = vtk.vtkAppendPolyData() 565 line = vtk.vtkAppendPolyData()
566 - line.AddInput(line1.GetOutput())  
567 - line.AddInput(line2.GetOutput())  
568 - line.AddInput(arc.GetOutput()) 566 + line.AddInputConnection(line1.GetOutputPort())
  567 + line.AddInputConnection(line2.GetOutputPort())
  568 + line.AddInputConnection(arc.GetOutputPort())
  569 +
  570 + print line
569 571
570 c = vtk.vtkCoordinate() 572 c = vtk.vtkCoordinate()
571 c.SetCoordinateSystemToWorld() 573 c.SetCoordinateSystemToWorld()
invesalius/data/polydata_utils.py
  Diff comments   View file @0317ac2
@@ -36,7 +36,7 @@ def ApplyDecimationFilter(polydata, reduction_factor): @@ -36,7 +36,7 @@ def ApplyDecimationFilter(polydata, reduction_factor):
36 # Important: vtkQuadricDecimation presented better results than 36 # Important: vtkQuadricDecimation presented better results than
37 # vtkDecimatePro 37 # vtkDecimatePro
38 decimation = vtk.vtkQuadricDecimation() 38 decimation = vtk.vtkQuadricDecimation()
39 - decimation.SetInput(polydata) 39 + decimation.SetInputData(polydata)
40 decimation.SetTargetReduction(reduction_factor) 40 decimation.SetTargetReduction(reduction_factor)
41 decimation.GetOutput().ReleaseDataFlagOn() 41 decimation.GetOutput().ReleaseDataFlagOn()
42 decimation.AddObserver("ProgressEvent", lambda obj, evt: 42 decimation.AddObserver("ProgressEvent", lambda obj, evt:
@@ -48,7 +48,7 @@ def ApplySmoothFilter(polydata, iterations, relaxation_factor): @@ -48,7 +48,7 @@ def ApplySmoothFilter(polydata, iterations, relaxation_factor):
48 Smooth given vtkPolyData surface, based on iteration and relaxation_factor. 48 Smooth given vtkPolyData surface, based on iteration and relaxation_factor.
49 """ 49 """
50 smoother = vtk.vtkSmoothPolyDataFilter() 50 smoother = vtk.vtkSmoothPolyDataFilter()
51 - smoother.SetInput(polydata) 51 + smoother.SetInputData(polydata)
52 smoother.SetNumberOfIterations(iterations) 52 smoother.SetNumberOfIterations(iterations)
53 smoother.SetFeatureAngle(80) 53 smoother.SetFeatureAngle(80)
54 smoother.SetRelaxationFactor(relaxation_factor) 54 smoother.SetRelaxationFactor(relaxation_factor)
@@ -69,7 +69,7 @@ def FillSurfaceHole(polydata): @@ -69,7 +69,7 @@ def FillSurfaceHole(polydata):
69 # Filter used to detect and fill holes. Only fill 69 # Filter used to detect and fill holes. Only fill
70 print "Filling polydata" 70 print "Filling polydata"
71 filled_polydata = vtk.vtkFillHolesFilter() 71 filled_polydata = vtk.vtkFillHolesFilter()
72 - filled_polydata.SetInput(polydata) 72 + filled_polydata.SetInputData(polydata)
73 filled_polydata.SetHoleSize(500) 73 filled_polydata.SetHoleSize(500)
74 return filled_polydata.GetOutput() 74 return filled_polydata.GetOutput()
75 75
@@ -79,7 +79,7 @@ def CalculateSurfaceVolume(polydata): @@ -79,7 +79,7 @@ def CalculateSurfaceVolume(polydata):
79 """ 79 """
80 # Filter used to calculate volume and area from a polydata 80 # Filter used to calculate volume and area from a polydata
81 measured_polydata = vtk.vtkMassProperties() 81 measured_polydata = vtk.vtkMassProperties()
82 - measured_polydata.SetInput(polydata) 82 + measured_polydata.SetInputData(polydata)
83 return measured_polydata.GetVolume() 83 return measured_polydata.GetVolume()
84 84
85 def CalculateSurfaceArea(polydata): 85 def CalculateSurfaceArea(polydata):
@@ -88,7 +88,7 @@ def CalculateSurfaceArea(polydata): @@ -88,7 +88,7 @@ def CalculateSurfaceArea(polydata):
88 """ 88 """
89 # Filter used to calculate volume and area from a polydata 89 # Filter used to calculate volume and area from a polydata
90 measured_polydata = vtk.vtkMassProperties() 90 measured_polydata = vtk.vtkMassProperties()
91 - measured_polydata.SetInput(polydata) 91 + measured_polydata.SetInputData(polydata)
92 return measured_polydata.GetSurfaceArea() 92 return measured_polydata.GetSurfaceArea()
93 93
94 def Merge(polydata_list): 94 def Merge(polydata_list):
@@ -96,11 +96,11 @@ def Merge(polydata_list): @@ -96,11 +96,11 @@ def Merge(polydata_list):
96 96
97 for polydata in polydata_list: 97 for polydata in polydata_list:
98 triangle = vtk.vtkTriangleFilter() 98 triangle = vtk.vtkTriangleFilter()
99 - triangle.SetInput(polydata)  
100 - append.AddInput(triangle.GetOutput()) 99 + triangle.SetInputData(polydata)
  100 + append.AddInputData(triangle.GetOutput())
101 101
102 clean = vtk.vtkCleanPolyData() 102 clean = vtk.vtkCleanPolyData()
103 - clean.SetInput(append.GetOutput()) 103 + clean.SetInputData(append.GetOutput())
104 104
105 return append.GetOutput() 105 return append.GetOutput()
106 106
@@ -112,7 +112,7 @@ def Export(polydata, filename, bin=False): @@ -112,7 +112,7 @@ def Export(polydata, filename, bin=False):
112 writer.SetDataModeToBinary() 112 writer.SetDataModeToBinary()
113 else: 113 else:
114 writer.SetDataModeToAscii() 114 writer.SetDataModeToAscii()
115 - writer.SetInput(polydata) 115 + writer.SetInputData(polydata)
116 writer.Write() 116 writer.Write()
117 117
118 def Import(filename): 118 def Import(filename):
@@ -130,7 +130,7 @@ def JoinSeedsParts(polydata, point_id_list): @@ -130,7 +130,7 @@ def JoinSeedsParts(polydata, point_id_list):
130 from vtkPolyData. 130 from vtkPolyData.
131 """ 131 """
132 conn = vtk.vtkPolyDataConnectivityFilter() 132 conn = vtk.vtkPolyDataConnectivityFilter()
133 - conn.SetInput(polydata) 133 + conn.SetInputData(polydata)
134 conn.SetExtractionModeToPointSeededRegions() 134 conn.SetExtractionModeToPointSeededRegions()
135 UpdateProgress = vu.ShowProgress(1 + len(point_id_list)) 135 UpdateProgress = vu.ShowProgress(1 + len(point_id_list))
136 pos = 1 136 pos = 1
@@ -145,7 +145,6 @@ def JoinSeedsParts(polydata, point_id_list): @@ -145,7 +145,6 @@ def JoinSeedsParts(polydata, point_id_list):
145 145
146 result = vtk.vtkPolyData() 146 result = vtk.vtkPolyData()
147 result.DeepCopy(conn.GetOutput()) 147 result.DeepCopy(conn.GetOutput())
148 - result.Update()  
149 return result 148 return result
150 149
151 def SelectLargestPart(polydata): 150 def SelectLargestPart(polydata):
@@ -153,7 +152,7 @@ def SelectLargestPart(polydata): @@ -153,7 +152,7 @@ def SelectLargestPart(polydata):
153 """ 152 """
154 UpdateProgress = vu.ShowProgress(1) 153 UpdateProgress = vu.ShowProgress(1)
155 conn = vtk.vtkPolyDataConnectivityFilter() 154 conn = vtk.vtkPolyDataConnectivityFilter()
156 - conn.SetInput(polydata) 155 + conn.SetInputData(polydata)
157 conn.SetExtractionModeToLargestRegion() 156 conn.SetExtractionModeToLargestRegion()
158 conn.AddObserver("ProgressEvent", lambda obj, evt: 157 conn.AddObserver("ProgressEvent", lambda obj, evt:
159 UpdateProgress(conn, "Getting largest part...")) 158 UpdateProgress(conn, "Getting largest part..."))
@@ -161,14 +160,13 @@ def SelectLargestPart(polydata): @@ -161,14 +160,13 @@ def SelectLargestPart(polydata):
161 160
162 result = vtk.vtkPolyData() 161 result = vtk.vtkPolyData()
163 result.DeepCopy(conn.GetOutput()) 162 result.DeepCopy(conn.GetOutput())
164 - result.Update()  
165 return result 163 return result
166 164
167 def SplitDisconectedParts(polydata): 165 def SplitDisconectedParts(polydata):
168 """ 166 """
169 """ 167 """
170 conn = vtk.vtkPolyDataConnectivityFilter() 168 conn = vtk.vtkPolyDataConnectivityFilter()
171 - conn.SetInput(polydata) 169 + conn.SetInputData(polydata)
172 conn.SetExtractionModeToAllRegions() 170 conn.SetExtractionModeToAllRegions()
173 conn.Update() 171 conn.Update()
174 172
@@ -191,7 +189,6 @@ def SplitDisconectedParts(polydata): @@ -191,7 +189,6 @@ def SplitDisconectedParts(polydata):
191 189
192 p = vtk.vtkPolyData() 190 p = vtk.vtkPolyData()
193 p.DeepCopy(conn.GetOutput()) 191 p.DeepCopy(conn.GetOutput())
194 - p.Update()  
195 192
196 polydata_collection.append(p) 193 polydata_collection.append(p)
197 if progress: 194 if progress:
invesalius/data/slice_.py
  Diff comments   View file @0317ac2
@@ -964,18 +964,18 @@ class Slice(object): @@ -964,18 +964,18 @@ class Slice(object):
964 img = self.buffer_slices[orientation].vtk_image 964 img = self.buffer_slices[orientation].vtk_image
965 original_orientation = Project().original_orientation 965 original_orientation = Project().original_orientation
966 cast = vtk.vtkImageCast() 966 cast = vtk.vtkImageCast()
967 - cast.SetInput(img) 967 + cast.SetInputData(img)
968 cast.SetOutputScalarTypeToDouble() 968 cast.SetOutputScalarTypeToDouble()
969 cast.ClampOverflowOn() 969 cast.ClampOverflowOn()
970 cast.Update() 970 cast.Update()
971 971
972 #if (original_orientation == const.AXIAL): 972 #if (original_orientation == const.AXIAL):
973 flip = vtk.vtkImageFlip() 973 flip = vtk.vtkImageFlip()
974 - flip.SetInput(cast.GetOutput()) 974 + flip.SetInputConnection(cast.GetOutputPort())
975 flip.SetFilteredAxis(1) 975 flip.SetFilteredAxis(1)
976 flip.FlipAboutOriginOn() 976 flip.FlipAboutOriginOn()
977 flip.Update() 977 flip.Update()
978 - widget.SetInput(flip.GetOutput()) 978 + widget.SetInputConnection(flip.GetOutputPort())
979 #else: 979 #else:
980 #widget.SetInput(cast.GetOutput()) 980 #widget.SetInput(cast.GetOutput())
981 981
@@ -1044,7 +1044,7 @@ class Slice(object): @@ -1044,7 +1044,7 @@ class Slice(object):
1044 i += 1 1044 i += 1
1045 1045
1046 colorer = vtk.vtkImageMapToColors() 1046 colorer = vtk.vtkImageMapToColors()
1047 - colorer.SetInput(image) 1047 + colorer.SetInputData(image)
1048 colorer.SetLookupTable(lut) 1048 colorer.SetLookupTable(lut)
1049 colorer.SetOutputFormatToRGB() 1049 colorer.SetOutputFormatToRGB()
1050 colorer.Update() 1050 colorer.Update()
@@ -1059,12 +1059,12 @@ class Slice(object): @@ -1059,12 +1059,12 @@ class Slice(object):
1059 1059
1060 colorer = vtk.vtkImageMapToColors() 1060 colorer = vtk.vtkImageMapToColors()
1061 colorer.SetLookupTable(lut) 1061 colorer.SetLookupTable(lut)
1062 - colorer.SetInput(image) 1062 + colorer.SetInputData(image)
1063 colorer.SetOutputFormatToRGB() 1063 colorer.SetOutputFormatToRGB()
1064 colorer.Update() 1064 colorer.Update()
1065 else: 1065 else:
1066 colorer = vtk.vtkImageMapToWindowLevelColors() 1066 colorer = vtk.vtkImageMapToWindowLevelColors()
1067 - colorer.SetInput(image) 1067 + colorer.SetInputData(image)
1068 colorer.SetWindow(self.window_width) 1068 colorer.SetWindow(self.window_width)
1069 colorer.SetLevel(self.window_level) 1069 colorer.SetLevel(self.window_level)
1070 colorer.SetOutputFormatToRGB() 1070 colorer.SetOutputFormatToRGB()
@@ -1148,7 +1148,7 @@ class Slice(object): @@ -1148,7 +1148,7 @@ class Slice(object):
1148 img_colours_bg = vtk.vtkImageMapToColors() 1148 img_colours_bg = vtk.vtkImageMapToColors()
1149 img_colours_bg.SetOutputFormatToRGB() 1149 img_colours_bg.SetOutputFormatToRGB()
1150 img_colours_bg.SetLookupTable(lut_bg) 1150 img_colours_bg.SetLookupTable(lut_bg)
1151 - img_colours_bg.SetInput(imagedata) 1151 + img_colours_bg.SetInputData(imagedata)
1152 img_colours_bg.Update() 1152 img_colours_bg.Update()
1153 1153
1154 return img_colours_bg.GetOutput() 1154 return img_colours_bg.GetOutput()
@@ -1179,7 +1179,7 @@ class Slice(object): @@ -1179,7 +1179,7 @@ class Slice(object):
1179 img_colours_mask = vtk.vtkImageMapToColors() 1179 img_colours_mask = vtk.vtkImageMapToColors()
1180 img_colours_mask.SetLookupTable(lut_mask) 1180 img_colours_mask.SetLookupTable(lut_mask)
1181 img_colours_mask.SetOutputFormatToRGBA() 1181 img_colours_mask.SetOutputFormatToRGBA()
1182 - img_colours_mask.SetInput(imagedata) 1182 + img_colours_mask.SetInputData(imagedata)
1183 img_colours_mask.Update() 1183 img_colours_mask.Update()
1184 # self.img_colours_mask = img_colours_mask 1184 # self.img_colours_mask = img_colours_mask
1185 1185
@@ -1211,7 +1211,7 @@ class Slice(object): @@ -1211,7 +1211,7 @@ class Slice(object):
1211 img_colours_mask = vtk.vtkImageMapToColors() 1211 img_colours_mask = vtk.vtkImageMapToColors()
1212 img_colours_mask.SetLookupTable(lut_mask) 1212 img_colours_mask.SetLookupTable(lut_mask)
1213 img_colours_mask.SetOutputFormatToRGBA() 1213 img_colours_mask.SetOutputFormatToRGBA()
1214 - img_colours_mask.SetInput(imagedata) 1214 + img_colours_mask.SetInputData(imagedata)
1215 img_colours_mask.Update() 1215 img_colours_mask.Update()
1216 # self.img_colours_mask = img_colours_mask 1216 # self.img_colours_mask = img_colours_mask
1217 1217
@@ -1225,8 +1225,8 @@ class Slice(object): @@ -1225,8 +1225,8 @@ class Slice(object):
1225 blend_imagedata.SetBlendModeToNormal() 1225 blend_imagedata.SetBlendModeToNormal()
1226 # blend_imagedata.SetOpacity(0, 1.0) 1226 # blend_imagedata.SetOpacity(0, 1.0)
1227 blend_imagedata.SetOpacity(1, 0.8) 1227 blend_imagedata.SetOpacity(1, 0.8)
1228 - blend_imagedata.SetInput(imagedata)  
1229 - blend_imagedata.AddInput(mask) 1228 + blend_imagedata.SetInputData(imagedata)
  1229 + blend_imagedata.AddInputData(mask)
1230 blend_imagedata.Update() 1230 blend_imagedata.Update()
1231 1231
1232 return blend_imagedata.GetOutput() 1232 return blend_imagedata.GetOutput()
invesalius/data/slice_data.py
  Diff comments   View file @0317ac2
@@ -55,7 +55,7 @@ class SliceData(object): @@ -55,7 +55,7 @@ class SliceData(object):
55 55
56 def __create_line_actor(self, line): 56 def __create_line_actor(self, line):
57 line_mapper = vtk.vtkPolyDataMapper2D() 57 line_mapper = vtk.vtkPolyDataMapper2D()
58 - line_mapper.SetInput(line.GetOutput()) 58 + line_mapper.SetInputConnection(line.GetOutputPort())
59 59
60 line_actor = vtk.vtkActor2D() 60 line_actor = vtk.vtkActor2D()
61 line_actor.SetMapper(line_mapper) 61 line_actor.SetMapper(line_mapper)
invesalius/data/styles.py
  Diff comments   View file @0317ac2
@@ -59,10 +59,14 @@ WATERSHED_OPERATIONS = {_("Erase"): BRUSH_ERASE, @@ -59,10 +59,14 @@ WATERSHED_OPERATIONS = {_("Erase"): BRUSH_ERASE,
59 _("Background"): BRUSH_BACKGROUND,} 59 _("Background"): BRUSH_BACKGROUND,}
60 60
61 def get_LUT_value(data, window, level): 61 def get_LUT_value(data, window, level):
62 - return np.piecewise(data,  
63 - [data <= (level - 0.5 - (window-1)/2),  
64 - data > (level - 0.5 + (window-1)/2)],  
65 - [0, window, lambda data: ((data - (level - 0.5))/(window-1) + 0.5)*(window)]) 62 + shape = data.shape
  63 + data_ = data.ravel()
  64 + data = np.piecewise(data_,
  65 + [data_ <= (level - 0.5 - (window-1)/2),
  66 + data_ > (level - 0.5 + (window-1)/2)],
  67 + [0, window, lambda data_: ((data_ - (level - 0.5))/(window-1) + 0.5)*(window)])
  68 + data.shape = shape
  69 + return data
66 70
67 class BaseImageInteractorStyle(vtk.vtkInteractorStyleImage): 71 class BaseImageInteractorStyle(vtk.vtkInteractorStyleImage):
68 def __init__(self, viewer): 72 def __init__(self, viewer):
invesalius/data/surface.py
  Diff comments   View file @0317ac2
@@ -42,6 +42,8 @@ try: @@ -42,6 +42,8 @@ try:
42 except ImportError: 42 except ImportError:
43 import data.ca_smoothing as ca_smoothing 43 import data.ca_smoothing as ca_smoothing
44 44
  45 +# TODO: Verificar ReleaseDataFlagOn and SetSource
  46 +
45 class Surface(): 47 class Surface():
46 """ 48 """
47 Represent both vtkPolyData and associated properties. 49 Represent both vtkPolyData and associated properties.
@@ -240,12 +242,13 @@ class SurfaceManager(): @@ -240,12 +242,13 @@ class SurfaceManager():
240 name=None, colour=None, 242 name=None, colour=None,
241 transparency=None, volume=None): 243 transparency=None, volume=None):
242 normals = vtk.vtkPolyDataNormals() 244 normals = vtk.vtkPolyDataNormals()
243 - normals.SetInput(polydata) 245 + normals.SetInputData(polydata)
244 normals.SetFeatureAngle(80) 246 normals.SetFeatureAngle(80)
245 normals.AutoOrientNormalsOn() 247 normals.AutoOrientNormalsOn()
  248 + normals.Update()
246 249
247 mapper = vtk.vtkPolyDataMapper() 250 mapper = vtk.vtkPolyDataMapper()
248 - mapper.SetInput(normals.GetOutput()) 251 + mapper.SetInputData(normals.GetOutput())
249 mapper.ScalarVisibilityOff() 252 mapper.ScalarVisibilityOff()
250 mapper.ImmediateModeRenderingOn() # improve performance 253 mapper.ImmediateModeRenderingOn() # improve performance
251 254
@@ -289,11 +292,12 @@ class SurfaceManager(): @@ -289,11 +292,12 @@ class SurfaceManager():
289 # The following lines have to be here, otherwise all volumes disappear 292 # The following lines have to be here, otherwise all volumes disappear
290 if not volume: 293 if not volume:
291 triangle_filter = vtk.vtkTriangleFilter() 294 triangle_filter = vtk.vtkTriangleFilter()
292 - triangle_filter.SetInput(polydata) 295 + triangle_filter.SetInputData(polydata)
293 triangle_filter.Update() 296 triangle_filter.Update()
294 297
295 measured_polydata = vtk.vtkMassProperties() 298 measured_polydata = vtk.vtkMassProperties()
296 - measured_polydata.SetInput(triangle_filter.GetOutput()) 299 + measured_polydata.SetInputConnection(triangle_filter.GetOutputPort())
  300 + measured_polydata.Update()
297 volume = measured_polydata.GetVolume() 301 volume = measured_polydata.GetVolume()
298 surface.volume = volume 302 surface.volume = volume
299 print ">>>>", surface.volume 303 print ">>>>", surface.volume
@@ -338,19 +342,19 @@ class SurfaceManager(): @@ -338,19 +342,19 @@ class SurfaceManager():
338 surface = surface_dict[key] 342 surface = surface_dict[key]
339 # Map polygonal data (vtkPolyData) to graphics primitives. 343 # Map polygonal data (vtkPolyData) to graphics primitives.
340 normals = vtk.vtkPolyDataNormals() 344 normals = vtk.vtkPolyDataNormals()
341 - normals.SetInput(surface.polydata) 345 + normals.SetInputData(surface.polydata)
342 normals.SetFeatureAngle(80) 346 normals.SetFeatureAngle(80)
343 normals.AutoOrientNormalsOn() 347 normals.AutoOrientNormalsOn()
344 - normals.GetOutput().ReleaseDataFlagOn() 348 + # normals.GetOutput().ReleaseDataFlagOn()
345 349
346 # Improve performance 350 # Improve performance
347 stripper = vtk.vtkStripper() 351 stripper = vtk.vtkStripper()
348 - stripper.SetInput(normals.GetOutput()) 352 + stripper.SetInputData(normals.GetOutput())
349 stripper.PassThroughCellIdsOn() 353 stripper.PassThroughCellIdsOn()
350 stripper.PassThroughPointIdsOn() 354 stripper.PassThroughPointIdsOn()
351 355
352 mapper = vtk.vtkPolyDataMapper() 356 mapper = vtk.vtkPolyDataMapper()
353 - mapper.SetInput(stripper.GetOutput()) 357 + mapper.SetInputData(stripper.GetOutput())
354 mapper.ScalarVisibilityOff() 358 mapper.ScalarVisibilityOff()
355 mapper.ImmediateModeRenderingOn() # improve performance 359 mapper.ImmediateModeRenderingOn() # improve performance
356 360
@@ -490,30 +494,30 @@ class SurfaceManager(): @@ -490,30 +494,30 @@ class SurfaceManager():
490 break 494 break
491 495
492 polydata_append = vtk.vtkAppendPolyData() 496 polydata_append = vtk.vtkAppendPolyData()
493 - polydata_append.ReleaseDataFlagOn() 497 + # polydata_append.ReleaseDataFlagOn()
494 t = n_pieces 498 t = n_pieces
495 while t: 499 while t:
496 filename_polydata = q_out.get() 500 filename_polydata = q_out.get()
497 501
498 reader = vtk.vtkXMLPolyDataReader() 502 reader = vtk.vtkXMLPolyDataReader()
499 reader.SetFileName(filename_polydata) 503 reader.SetFileName(filename_polydata)
500 - reader.ReleaseDataFlagOn() 504 + # reader.ReleaseDataFlagOn()
501 reader.Update() 505 reader.Update()
502 - reader.GetOutput().ReleaseDataFlagOn() 506 + # reader.GetOutput().ReleaseDataFlagOn()
503 507
504 polydata = reader.GetOutput() 508 polydata = reader.GetOutput()
505 - polydata.SetSource(None) 509 + # polydata.SetSource(None)
506 510
507 - polydata_append.AddInput(polydata) 511 + polydata_append.AddInputData(polydata)
508 del reader 512 del reader
509 del polydata 513 del polydata
510 t -= 1 514 t -= 1
511 515
512 polydata_append.Update() 516 polydata_append.Update()
513 - polydata_append.GetOutput().ReleaseDataFlagOn() 517 + # polydata_append.GetOutput().ReleaseDataFlagOn()
514 polydata = polydata_append.GetOutput() 518 polydata = polydata_append.GetOutput()
515 #polydata.Register(None) 519 #polydata.Register(None)
516 - polydata.SetSource(None) 520 + # polydata.SetSource(None)
517 del polydata_append 521 del polydata_append
518 522
519 if algorithm == 'ca_smoothing': 523 if algorithm == 'ca_smoothing':
@@ -521,31 +525,31 @@ class SurfaceManager(): @@ -521,31 +525,31 @@ class SurfaceManager():
521 normals_ref = weakref.ref(normals) 525 normals_ref = weakref.ref(normals)
522 normals_ref().AddObserver("ProgressEvent", lambda obj,evt: 526 normals_ref().AddObserver("ProgressEvent", lambda obj,evt:
523 UpdateProgress(normals_ref(), _("Creating 3D surface..."))) 527 UpdateProgress(normals_ref(), _("Creating 3D surface...")))
524 - normals.SetInput(polydata)  
525 - normals.ReleaseDataFlagOn() 528 + normals.SetInputData(polydata)
  529 + # normals.ReleaseDataFlagOn()
526 #normals.SetFeatureAngle(80) 530 #normals.SetFeatureAngle(80)
527 #normals.AutoOrientNormalsOn() 531 #normals.AutoOrientNormalsOn()
528 normals.ComputeCellNormalsOn() 532 normals.ComputeCellNormalsOn()
529 - normals.GetOutput().ReleaseDataFlagOn() 533 + # normals.GetOutput().ReleaseDataFlagOn()
530 normals.Update() 534 normals.Update()
531 del polydata 535 del polydata
532 polydata = normals.GetOutput() 536 polydata = normals.GetOutput()
533 - polydata.SetSource(None) 537 + # polydata.SetSource(None)
534 del normals 538 del normals
535 539
536 clean = vtk.vtkCleanPolyData() 540 clean = vtk.vtkCleanPolyData()
537 - clean.ReleaseDataFlagOn()  
538 - clean.GetOutput().ReleaseDataFlagOn() 541 + # clean.ReleaseDataFlagOn()
  542 + # clean.GetOutput().ReleaseDataFlagOn()
539 clean_ref = weakref.ref(clean) 543 clean_ref = weakref.ref(clean)
540 clean_ref().AddObserver("ProgressEvent", lambda obj,evt: 544 clean_ref().AddObserver("ProgressEvent", lambda obj,evt:
541 UpdateProgress(clean_ref(), _("Creating 3D surface..."))) 545 UpdateProgress(clean_ref(), _("Creating 3D surface...")))
542 - clean.SetInput(polydata) 546 + clean.SetInputData(polydata)
543 clean.PointMergingOn() 547 clean.PointMergingOn()
544 clean.Update() 548 clean.Update()
545 549
546 del polydata 550 del polydata
547 polydata = clean.GetOutput() 551 polydata = clean.GetOutput()
548 - polydata.SetSource(None) 552 + # polydata.SetSource(None)
549 del clean 553 del clean
550 554
551 try: 555 try:
@@ -556,7 +560,7 @@ class SurfaceManager(): @@ -556,7 +560,7 @@ class SurfaceManager():
556 options['max distance'], 560 options['max distance'],
557 options['min weight'], 561 options['min weight'],
558 options['steps']) 562 options['steps'])
559 - polydata.SetSource(None) 563 + # polydata.SetSource(None)
560 polydata.DebugOn() 564 polydata.DebugOn()
561 565
562 else: 566 else:
@@ -565,7 +569,7 @@ class SurfaceManager(): @@ -565,7 +569,7 @@ class SurfaceManager():
565 smoother_ref = weakref.ref(smoother) 569 smoother_ref = weakref.ref(smoother)
566 smoother_ref().AddObserver("ProgressEvent", lambda obj,evt: 570 smoother_ref().AddObserver("ProgressEvent", lambda obj,evt:
567 UpdateProgress(smoother_ref(), _("Creating 3D surface..."))) 571 UpdateProgress(smoother_ref(), _("Creating 3D surface...")))
568 - smoother.SetInput(polydata) 572 + smoother.SetInputData(polydata)
569 smoother.SetNumberOfIterations(smooth_iterations) 573 smoother.SetNumberOfIterations(smooth_iterations)
570 smoother.SetRelaxationFactor(smooth_relaxation_factor) 574 smoother.SetRelaxationFactor(smooth_relaxation_factor)
571 smoother.SetFeatureAngle(80) 575 smoother.SetFeatureAngle(80)
@@ -575,21 +579,21 @@ class SurfaceManager(): @@ -575,21 +579,21 @@ class SurfaceManager():
575 smoother.FeatureEdgeSmoothingOn() 579 smoother.FeatureEdgeSmoothingOn()
576 #smoother.NormalizeCoordinatesOn() 580 #smoother.NormalizeCoordinatesOn()
577 #smoother.NonManifoldSmoothingOn() 581 #smoother.NonManifoldSmoothingOn()
578 - smoother.ReleaseDataFlagOn()  
579 - smoother.GetOutput().ReleaseDataFlagOn() 582 + # smoother.ReleaseDataFlagOn()
  583 + # smoother.GetOutput().ReleaseDataFlagOn()
580 smoother.Update() 584 smoother.Update()
581 del polydata 585 del polydata
582 polydata = smoother.GetOutput() 586 polydata = smoother.GetOutput()
583 #polydata.Register(None) 587 #polydata.Register(None)
584 - polydata.SetSource(None) 588 + # polydata.SetSource(None)
585 del smoother 589 del smoother
586 590
587 591
588 if decimate_reduction: 592 if decimate_reduction:
589 print "Decimating", decimate_reduction 593 print "Decimating", decimate_reduction
590 decimation = vtk.vtkQuadricDecimation() 594 decimation = vtk.vtkQuadricDecimation()
591 - decimation.ReleaseDataFlagOn()  
592 - decimation.SetInput(polydata) 595 + # decimation.ReleaseDataFlagOn()
  596 + decimation.SetInputData(polydata)
593 decimation.SetTargetReduction(decimate_reduction) 597 decimation.SetTargetReduction(decimate_reduction)
594 decimation_ref = weakref.ref(decimation) 598 decimation_ref = weakref.ref(decimation)
595 decimation_ref().AddObserver("ProgressEvent", lambda obj,evt: 599 decimation_ref().AddObserver("ProgressEvent", lambda obj,evt:
@@ -597,31 +601,31 @@ class SurfaceManager(): @@ -597,31 +601,31 @@ class SurfaceManager():
597 #decimation.PreserveTopologyOn() 601 #decimation.PreserveTopologyOn()
598 #decimation.SplittingOff() 602 #decimation.SplittingOff()
599 #decimation.BoundaryVertexDeletionOff() 603 #decimation.BoundaryVertexDeletionOff()
600 - decimation.GetOutput().ReleaseDataFlagOn() 604 + # decimation.GetOutput().ReleaseDataFlagOn()
601 decimation.Update() 605 decimation.Update()
602 del polydata 606 del polydata
603 polydata = decimation.GetOutput() 607 polydata = decimation.GetOutput()
604 #polydata.Register(None) 608 #polydata.Register(None)
605 - polydata.SetSource(None) 609 + # polydata.SetSource(None)
606 del decimation 610 del decimation
607 611
608 to_measure = polydata 612 to_measure = polydata
609 #to_measure.Register(None) 613 #to_measure.Register(None)
610 - to_measure.SetSource(None) 614 + # to_measure.SetSource(None)
611 615
612 if keep_largest: 616 if keep_largest:
613 conn = vtk.vtkPolyDataConnectivityFilter() 617 conn = vtk.vtkPolyDataConnectivityFilter()
614 - conn.SetInput(polydata) 618 + conn.SetInputData(polydata)
615 conn.SetExtractionModeToLargestRegion() 619 conn.SetExtractionModeToLargestRegion()
616 conn_ref = weakref.ref(conn) 620 conn_ref = weakref.ref(conn)
617 conn_ref().AddObserver("ProgressEvent", lambda obj,evt: 621 conn_ref().AddObserver("ProgressEvent", lambda obj,evt:
618 UpdateProgress(conn_ref(), _("Creating 3D surface..."))) 622 UpdateProgress(conn_ref(), _("Creating 3D surface...")))
619 conn.Update() 623 conn.Update()
620 - conn.GetOutput().ReleaseDataFlagOn() 624 + # conn.GetOutput().ReleaseDataFlagOn()
621 del polydata 625 del polydata
622 polydata = conn.GetOutput() 626 polydata = conn.GetOutput()
623 #polydata.Register(None) 627 #polydata.Register(None)
624 - polydata.SetSource(None) 628 + # polydata.SetSource(None)
625 del conn 629 del conn
626 630
627 #Filter used to detect and fill holes. Only fill boundary edges holes. 631 #Filter used to detect and fill holes. Only fill boundary edges holes.
@@ -629,59 +633,59 @@ class SurfaceManager(): @@ -629,59 +633,59 @@ class SurfaceManager():
629 #polydata_utils.FillSurfaceHole, we need to review this. 633 #polydata_utils.FillSurfaceHole, we need to review this.
630 if fill_holes: 634 if fill_holes:
631 filled_polydata = vtk.vtkFillHolesFilter() 635 filled_polydata = vtk.vtkFillHolesFilter()
632 - filled_polydata.ReleaseDataFlagOn()  
633 - filled_polydata.SetInput(polydata) 636 + # filled_polydata.ReleaseDataFlagOn()
  637 + filled_polydata.SetInputData(polydata)
634 filled_polydata.SetHoleSize(300) 638 filled_polydata.SetHoleSize(300)
635 filled_polydata_ref = weakref.ref(filled_polydata) 639 filled_polydata_ref = weakref.ref(filled_polydata)
636 filled_polydata_ref().AddObserver("ProgressEvent", lambda obj,evt: 640 filled_polydata_ref().AddObserver("ProgressEvent", lambda obj,evt:
637 UpdateProgress(filled_polydata_ref(), _("Creating 3D surface..."))) 641 UpdateProgress(filled_polydata_ref(), _("Creating 3D surface...")))
638 filled_polydata.Update() 642 filled_polydata.Update()
639 - filled_polydata.GetOutput().ReleaseDataFlagOn() 643 + # filled_polydata.GetOutput().ReleaseDataFlagOn()
640 del polydata 644 del polydata
641 polydata = filled_polydata.GetOutput() 645 polydata = filled_polydata.GetOutput()
642 #polydata.Register(None) 646 #polydata.Register(None)
643 - polydata.SetSource(None) 647 + # polydata.SetSource(None)
644 polydata.DebugOn() 648 polydata.DebugOn()
645 del filled_polydata 649 del filled_polydata
646 650
647 normals = vtk.vtkPolyDataNormals() 651 normals = vtk.vtkPolyDataNormals()
648 - normals.ReleaseDataFlagOn() 652 + # normals.ReleaseDataFlagOn()
649 normals_ref = weakref.ref(normals) 653 normals_ref = weakref.ref(normals)
650 normals_ref().AddObserver("ProgressEvent", lambda obj,evt: 654 normals_ref().AddObserver("ProgressEvent", lambda obj,evt:
651 UpdateProgress(normals_ref(), _("Creating 3D surface..."))) 655 UpdateProgress(normals_ref(), _("Creating 3D surface...")))
652 - normals.SetInput(polydata) 656 + normals.SetInputData(polydata)
653 normals.SetFeatureAngle(80) 657 normals.SetFeatureAngle(80)
654 normals.AutoOrientNormalsOn() 658 normals.AutoOrientNormalsOn()
655 - normals.GetOutput().ReleaseDataFlagOn() 659 + # normals.GetOutput().ReleaseDataFlagOn()
656 normals.Update() 660 normals.Update()
657 del polydata 661 del polydata
658 polydata = normals.GetOutput() 662 polydata = normals.GetOutput()
659 #polydata.Register(None) 663 #polydata.Register(None)
660 - polydata.SetSource(None) 664 + # polydata.SetSource(None)
661 del normals 665 del normals
662 666
663 # Improve performance 667 # Improve performance
664 stripper = vtk.vtkStripper() 668 stripper = vtk.vtkStripper()
665 - stripper.ReleaseDataFlagOn() 669 + # stripper.ReleaseDataFlagOn()
666 stripper_ref = weakref.ref(stripper) 670 stripper_ref = weakref.ref(stripper)
667 stripper_ref().AddObserver("ProgressEvent", lambda obj,evt: 671 stripper_ref().AddObserver("ProgressEvent", lambda obj,evt:
668 UpdateProgress(stripper_ref(), _("Creating 3D surface..."))) 672 UpdateProgress(stripper_ref(), _("Creating 3D surface...")))
669 - stripper.SetInput(polydata) 673 + stripper.SetInputData(polydata)
670 stripper.PassThroughCellIdsOn() 674 stripper.PassThroughCellIdsOn()
671 stripper.PassThroughPointIdsOn() 675 stripper.PassThroughPointIdsOn()
672 - stripper.GetOutput().ReleaseDataFlagOn() 676 + # stripper.GetOutput().ReleaseDataFlagOn()
673 stripper.Update() 677 stripper.Update()
674 del polydata 678 del polydata
675 polydata = stripper.GetOutput() 679 polydata = stripper.GetOutput()
676 #polydata.Register(None) 680 #polydata.Register(None)
677 - polydata.SetSource(None) 681 + # polydata.SetSource(None)
678 del stripper 682 del stripper
679 683
680 # Map polygonal data (vtkPolyData) to graphics primitives. 684 # Map polygonal data (vtkPolyData) to graphics primitives.
681 mapper = vtk.vtkPolyDataMapper() 685 mapper = vtk.vtkPolyDataMapper()
682 - mapper.SetInput(polydata) 686 + mapper.SetInputData(polydata)
683 mapper.ScalarVisibilityOff() 687 mapper.ScalarVisibilityOff()
684 - mapper.ReleaseDataFlagOn() 688 + # mapper.ReleaseDataFlagOn()
685 mapper.ImmediateModeRenderingOn() # improve performance 689 mapper.ImmediateModeRenderingOn() # improve performance
686 690
687 # Represent an object (geometry & properties) in the rendered scene 691 # Represent an object (geometry & properties) in the rendered scene
@@ -720,8 +724,8 @@ class SurfaceManager(): @@ -720,8 +724,8 @@ class SurfaceManager():
720 724
721 # The following lines have to be here, otherwise all volumes disappear 725 # The following lines have to be here, otherwise all volumes disappear
722 measured_polydata = vtk.vtkMassProperties() 726 measured_polydata = vtk.vtkMassProperties()
723 - measured_polydata.ReleaseDataFlagOn()  
724 - measured_polydata.SetInput(to_measure) 727 + # measured_polydata.ReleaseDataFlagOn()
  728 + measured_polydata.SetInputData(to_measure)
725 volume = float(measured_polydata.GetVolume()) 729 volume = float(measured_polydata.GetVolume())
726 surface.volume = volume 730 surface.volume = volume
727 self.last_surface_index = surface.index 731 self.last_surface_index = surface.index
@@ -858,14 +862,15 @@ class SurfaceManager(): @@ -858,14 +862,15 @@ class SurfaceManager():
858 if filetype in (const.FILETYPE_STL, const.FILETYPE_PLY): 862 if filetype in (const.FILETYPE_STL, const.FILETYPE_PLY):
859 # Invert normals 863 # Invert normals
860 normals = vtk.vtkPolyDataNormals() 864 normals = vtk.vtkPolyDataNormals()
861 - normals.SetInput(polydata) 865 + normals.SetInputData(polydata)
862 normals.SetFeatureAngle(80) 866 normals.SetFeatureAngle(80)
863 normals.AutoOrientNormalsOn() 867 normals.AutoOrientNormalsOn()
864 - normals.GetOutput().ReleaseDataFlagOn() 868 + # normals.GetOutput().ReleaseDataFlagOn()
865 normals.UpdateInformation() 869 normals.UpdateInformation()
  870 + normals.Update()
866 polydata = normals.GetOutput() 871 polydata = normals.GetOutput()
867 872
868 filename = filename.encode(wx.GetDefaultPyEncoding()) 873 filename = filename.encode(wx.GetDefaultPyEncoding())
869 writer.SetFileName(filename) 874 writer.SetFileName(filename)
870 - writer.SetInput(polydata) 875 + writer.SetInputData(polydata)
871 writer.Write() 876 writer.Write()
invesalius/data/surface_process.py
  Diff comments   View file @0317ac2
@@ -26,7 +26,7 @@ def ResampleImage3D(imagedata, value): @@ -26,7 +26,7 @@ def ResampleImage3D(imagedata, value):
26 resolution = (height/(extent[1]-extent[0])+1)*spacing[1] 26 resolution = (height/(extent[1]-extent[0])+1)*spacing[1]
27 27
28 resample = vtk.vtkImageResample() 28 resample = vtk.vtkImageResample()
29 - resample.SetInput(imagedata) 29 + resample.SetInputData(imagedata)
30 resample.SetAxisMagnificationFactor(0, resolution) 30 resample.SetAxisMagnificationFactor(0, resolution)
31 resample.SetAxisMagnificationFactor(1, resolution) 31 resample.SetAxisMagnificationFactor(1, resolution)
32 32
@@ -106,7 +106,7 @@ class SurfaceProcess(multiprocessing.Process): @@ -106,7 +106,7 @@ class SurfaceProcess(multiprocessing.Process):
106 "AXIAL") 106 "AXIAL")
107 107
108 gauss = vtk.vtkImageGaussianSmooth() 108 gauss = vtk.vtkImageGaussianSmooth()
109 - gauss.SetInput(image) 109 + gauss.SetInputData(image)
110 gauss.SetRadiusFactor(0.3) 110 gauss.SetRadiusFactor(0.3)
111 gauss.ReleaseDataFlagOn() 111 gauss.ReleaseDataFlagOn()
112 gauss.Update() 112 gauss.Update()
@@ -125,7 +125,7 @@ class SurfaceProcess(multiprocessing.Process): @@ -125,7 +125,7 @@ class SurfaceProcess(multiprocessing.Process):
125 image = ResampleImage3D(image, self.imagedata_resolution) 125 image = ResampleImage3D(image, self.imagedata_resolution)
126 126
127 flip = vtk.vtkImageFlip() 127 flip = vtk.vtkImageFlip()
128 - flip.SetInput(image) 128 + flip.SetInputData(image)
129 flip.SetFilteredAxis(1) 129 flip.SetFilteredAxis(1)
130 flip.FlipAboutOriginOn() 130 flip.FlipAboutOriginOn()
131 flip.ReleaseDataFlagOn() 131 flip.ReleaseDataFlagOn()
@@ -148,7 +148,7 @@ class SurfaceProcess(multiprocessing.Process): @@ -148,7 +148,7 @@ class SurfaceProcess(multiprocessing.Process):
148 #if self.mode == "CONTOUR": 148 #if self.mode == "CONTOUR":
149 #print "Contour" 149 #print "Contour"
150 contour = vtk.vtkContourFilter() 150 contour = vtk.vtkContourFilter()
151 - contour.SetInput(image) 151 + contour.SetInputData(image)
152 #contour.SetInput(flip.GetOutput()) 152 #contour.SetInput(flip.GetOutput())
153 if self.from_binary: 153 if self.from_binary:
154 contour.SetValue(0, 127) # initial threshold 154 contour.SetValue(0, 127) # initial threshold
@@ -202,7 +202,7 @@ class SurfaceProcess(multiprocessing.Process): @@ -202,7 +202,7 @@ class SurfaceProcess(multiprocessing.Process):
202 202
203 filename = tempfile.mktemp(suffix='_%s.vtp' % (self.pid)) 203 filename = tempfile.mktemp(suffix='_%s.vtp' % (self.pid))
204 writer = vtk.vtkXMLPolyDataWriter() 204 writer = vtk.vtkXMLPolyDataWriter()
205 - writer.SetInput(polydata) 205 + writer.SetInputData(polydata)
206 writer.SetFileName(filename) 206 writer.SetFileName(filename)
207 writer.Write() 207 writer.Write()
208 208
invesalius/data/viewer_slice.py
  Diff comments   View file @0317ac2
@@ -753,6 +753,7 @@ class Viewer(wx.Panel): @@ -753,6 +753,7 @@ class Viewer(wx.Panel):
753 image = vtk.vtkRenderLargeImage() 753 image = vtk.vtkRenderLargeImage()
754 image.SetInput(ren) 754 image.SetInput(ren)
755 image.SetMagnification(1) 755 image.SetMagnification(1)
  756 + image.Update()
756 757
757 image = image.GetOutput() 758 image = image.GetOutput()
758 759
@@ -769,8 +770,8 @@ class Viewer(wx.Panel): @@ -769,8 +770,8 @@ class Viewer(wx.Panel):
769 elif (filetype == const.FILETYPE_TIF): 770 elif (filetype == const.FILETYPE_TIF):
770 writer = vtk.vtkTIFFWriter() 771 writer = vtk.vtkTIFFWriter()
771 filename = "%s.tif"%filename.strip(".tif") 772 filename = "%s.tif"%filename.strip(".tif")
772 -  
773 - writer.SetInput(image) 773 +
  774 + writer.SetInputData(image)
774 writer.SetFileName(filename) 775 writer.SetFileName(filename)
775 writer.Write() 776 writer.Write()
776 777
@@ -919,7 +920,7 @@ class Viewer(wx.Panel): @@ -919,7 +920,7 @@ class Viewer(wx.Panel):
919 c.SetCoordinateSystemToWorld() 920 c.SetCoordinateSystemToWorld()
920 921
921 cross_mapper = vtk.vtkPolyDataMapper() 922 cross_mapper = vtk.vtkPolyDataMapper()
922 - cross_mapper.SetInput(cross.GetOutput()) 923 + cross_mapper.SetInputConnection(cross.GetOutputPort())
923 #cross_mapper.SetTransformCoordinate(c) 924 #cross_mapper.SetTransformCoordinate(c)
924 925
925 p = vtk.vtkProperty() 926 p = vtk.vtkProperty()
@@ -1176,7 +1177,7 @@ class Viewer(wx.Panel): @@ -1176,7 +1177,7 @@ class Viewer(wx.Panel):
1176 border_size = self.mip_ctrls.border_spin.GetValue() 1177 border_size = self.mip_ctrls.border_spin.GetValue()
1177 image = self.slice_.GetSlices(self.orientation, index, 1178 image = self.slice_.GetSlices(self.orientation, index,
1178 self.number_slices, inverted, border_size) 1179 self.number_slices, inverted, border_size)
1179 - self.slice_data.actor.SetInput(image) 1180 + self.slice_data.actor.SetInputData(image)
1180 for actor in self.actors_by_slice_number.get(self.slice_data.number, []): 1181 for actor in self.actors_by_slice_number.get(self.slice_data.number, []):
1181 self.slice_data.renderer.RemoveActor(actor) 1182 self.slice_data.renderer.RemoveActor(actor)
1182 for actor in self.actors_by_slice_number.get(index, []): 1183 for actor in self.actors_by_slice_number.get(index, []):
invesalius/data/viewer_volume.py
  Diff comments   View file @0317ac2
@@ -318,6 +318,7 @@ class Viewer(wx.Panel): @@ -318,6 +318,7 @@ class Viewer(wx.Panel):
318 image = vtk.vtkRenderLargeImage() 318 image = vtk.vtkRenderLargeImage()
319 image.SetInput(self.ren) 319 image.SetInput(self.ren)
320 image.SetMagnification(1) 320 image.SetMagnification(1)
  321 + image.Update()
321 322
322 image = image.GetOutput() 323 image = image.GetOutput()
323 324
@@ -333,12 +334,12 @@ class Viewer(wx.Panel): @@ -333,12 +334,12 @@ class Viewer(wx.Panel):
333 elif (filetype == const.FILETYPE_TIF): 334 elif (filetype == const.FILETYPE_TIF):
334 writer = vtk.vtkTIFFWriter() 335 writer = vtk.vtkTIFFWriter()
335 filename = "%s.tif"%filename.strip(".tif") 336 filename = "%s.tif"%filename.strip(".tif")
336 -  
337 - writer.SetInput(image) 337 +
  338 + writer.SetInputData(image)
338 writer.SetFileName(filename) 339 writer.SetFileName(filename)
339 writer.Write() 340 writer.Write()
340 Publisher.sendMessage('End busy cursor') 341 Publisher.sendMessage('End busy cursor')
341 - 342 +
342 def OnCloseProject(self, pubsub_evt): 343 def OnCloseProject(self, pubsub_evt):
343 if self.raycasting_volume: 344 if self.raycasting_volume:
344 self.raycasting_volume = False 345 self.raycasting_volume = False
invesalius/data/volume.py
  Diff comments   View file @0317ac2
@@ -224,7 +224,7 @@ class Volume(): @@ -224,7 +224,7 @@ class Volume():
224 # Update convolution filter 224 # Update convolution filter
225 original_imagedata = self.imagedata.GetOutput() 225 original_imagedata = self.imagedata.GetOutput()
226 imagedata = self.ApplyConvolution(original_imagedata) 226 imagedata = self.ApplyConvolution(original_imagedata)
227 - self.volume_mapper.SetInput(imagedata) 227 + self.volume_mapper.SetInputData(imagedata)
228 228
229 # Update other information 229 # Update other information
230 self.SetShading() 230 self.SetShading()
@@ -484,7 +484,7 @@ class Volume(): @@ -484,7 +484,7 @@ class Volume():
484 update_progress = vtk_utils.ShowProgress(number_filters) 484 update_progress = vtk_utils.ShowProgress(number_filters)
485 for filter in self.config['convolutionFilters']: 485 for filter in self.config['convolutionFilters']:
486 convolve = vtk.vtkImageConvolve() 486 convolve = vtk.vtkImageConvolve()
487 - convolve.SetInput(imagedata) 487 + convolve.SetInputData(imagedata)
488 convolve.SetKernel5x5([i/60.0 for i in Kernels[filter]]) 488 convolve.SetKernel5x5([i/60.0 for i in Kernels[filter]])
489 convolve.ReleaseDataFlagOn() 489 convolve.ReleaseDataFlagOn()
490 490
@@ -530,7 +530,7 @@ class Volume(): @@ -530,7 +530,7 @@ class Volume():
530 update_progress= vtk_utils.ShowProgress(2 + number_filters) 530 update_progress= vtk_utils.ShowProgress(2 + number_filters)
531 # Flip original vtkImageData 531 # Flip original vtkImageData
532 flip = vtk.vtkImageFlip() 532 flip = vtk.vtkImageFlip()
533 - flip.SetInput(image) 533 + flip.SetInputData(image)
534 flip.SetFilteredAxis(1) 534 flip.SetFilteredAxis(1)
535 flip.FlipAboutOriginOn() 535 flip.FlipAboutOriginOn()
536 flip.ReleaseDataFlagOn() 536 flip.ReleaseDataFlagOn()
@@ -545,7 +545,7 @@ class Volume(): @@ -545,7 +545,7 @@ class Volume():
545 self.scale = scale 545 self.scale = scale
546 546
547 cast = vtk.vtkImageShiftScale() 547 cast = vtk.vtkImageShiftScale()
548 - cast.SetInput(image) 548 + cast.SetInputData(image)
549 cast.SetShift(abs(scale[0])) 549 cast.SetShift(abs(scale[0]))
550 cast.SetOutputScalarTypeToUnsignedShort() 550 cast.SetOutputScalarTypeToUnsignedShort()
551 cast.ReleaseDataFlagOn() 551 cast.ReleaseDataFlagOn()
@@ -589,7 +589,7 @@ class Volume(): @@ -589,7 +589,7 @@ class Volume():
589 self.volume_mapper = volume_mapper 589 self.volume_mapper = volume_mapper
590 590
591 self.SetTypeRaycasting() 591 self.SetTypeRaycasting()
592 - volume_mapper.SetInput(image2) 592 + volume_mapper.SetInputData(image2)
593 593
594 # TODO: Look to this 594 # TODO: Look to this
595 #volume_mapper_hw = vtk.vtkVolumeTextureMapper3D() 595 #volume_mapper_hw = vtk.vtkVolumeTextureMapper3D()
@@ -657,7 +657,7 @@ class Volume(): @@ -657,7 +657,7 @@ class Volume():
657 image = self.image 657 image = self.image
658 r = int(image.GetScalarRange()[1] - image.GetScalarRange()[0]) 658 r = int(image.GetScalarRange()[1] - image.GetScalarRange()[0])
659 accumulate = vtk.vtkImageAccumulate() 659 accumulate = vtk.vtkImageAccumulate()
660 - accumulate.SetInput(image) 660 + accumulate.SetInputData(image)
661 accumulate.SetComponentExtent(0, r -1, 0, 0, 0, 0) 661 accumulate.SetComponentExtent(0, r -1, 0, 0, 0, 0)
662 accumulate.SetComponentOrigin(image.GetScalarRange()[0], 0, 0) 662 accumulate.SetComponentOrigin(image.GetScalarRange()[0], 0, 0)
663 accumulate.ReleaseDataFlagOn() 663 accumulate.ReleaseDataFlagOn()
invesalius/data/watershed_process.py
  Diff comments   View file @0317ac2
1 -import numpy as np  
2 -from scipy import ndimage  
3 -from scipy.ndimage import watershed_ift, generate_binary_structure  
4 -from skimage.morphology import watershed  
5 -from skimage import filter  
6 -  
7 -  
8 -def get_LUT_value(data, window, level):  
9 - return np.piecewise(data,  
10 - [data <= (level - 0.5 - (window-1)/2),  
11 - data > (level - 0.5 + (window-1)/2)],  
12 - [0, 255, lambda data: ((data - (level - 0.5))/(window-1) + 0.5)*(255-0)])  
13 -  
14 -  
15 -  
16 -def do_watershed(image, markers, tfile, shape, bstruct, algorithm, mg_size, use_ww_wl, wl, ww, q):  
17 - mask = np.memmap(tfile, shape=shape, dtype='uint8', mode='r+')  
18 -  
19 - if use_ww_wl:  
20 - if algorithm == 'Watershed':  
21 - tmp_image = ndimage.morphological_gradient(  
22 - get_LUT_value(image, ww, wl).astype('uint16'),  
23 - mg_size)  
24 - tmp_mask = watershed(tmp_image, markers.astype('int16'), bstruct)  
25 - else:  
26 - tmp_image = get_LUT_value(image, ww, wl).astype('uint16')  
27 - #tmp_image = ndimage.gaussian_filter(tmp_image, self.config.mg_size)  
28 - #tmp_image = ndimage.morphological_gradient(  
29 - #get_LUT_value(image, ww, wl).astype('uint16'),  
30 - #self.config.mg_size)  
31 - tmp_mask = watershed_ift(tmp_image, markers.astype('int16'), bstruct)  
32 - else:  
33 - if algorithm == 'Watershed':  
34 - tmp_image = ndimage.morphological_gradient((image - image.min()).astype('uint16'), mg_size)  
35 - tmp_mask = watershed(tmp_image, markers.astype('int16'), bstruct)  
36 - else:  
37 - tmp_image = (image - image.min()).astype('uint16')  
38 - #tmp_image = ndimage.gaussian_filter(tmp_image, self.config.mg_size)  
39 - #tmp_image = ndimage.morphological_gradient((image - image.min()).astype('uint16'), self.config.mg_size)  
40 - tmp_mask = watershed_ift(tmp_image, markers.astype('int8'), bstruct)  
41 - mask[:] = tmp_mask  
42 - mask.flush()  
43 - q.put(1) 1 +import numpy as np
  2 +from scipy import ndimage
  3 +from scipy.ndimage import watershed_ift, generate_binary_structure
  4 +from skimage.morphology import watershed
  5 +from skimage import filter
  6 +
  7 +
  8 +def get_LUT_value(data, window, level):
  9 + shape = data.shape
  10 + data_ = data.ravel()
  11 + data = np.piecewise(data_,
  12 + [data_ <= (level - 0.5 - (window-1)/2),
  13 + data_ > (level - 0.5 + (window-1)/2)],
  14 + [0, window, lambda data_: ((data_ - (level - 0.5))/(window-1) + 0.5)*(window)])
  15 + data.shape = shape
  16 + return data
  17 +
  18 +
  19 +def do_watershed(image, markers, tfile, shape, bstruct, algorithm, mg_size, use_ww_wl, wl, ww, q):
  20 + mask = np.memmap(tfile, shape=shape, dtype='uint8', mode='r+')
  21 +
  22 + if use_ww_wl:
  23 + if algorithm == 'Watershed':
  24 + tmp_image = ndimage.morphological_gradient(
  25 + get_LUT_value(image, ww, wl).astype('uint16'),
  26 + mg_size)
  27 + tmp_mask = watershed(tmp_image, markers.astype('int16'), bstruct)
  28 + else:
  29 + tmp_image = get_LUT_value(image, ww, wl).astype('uint16')
  30 + #tmp_image = ndimage.gaussian_filter(tmp_image, self.config.mg_size)
  31 + #tmp_image = ndimage.morphological_gradient(
  32 + #get_LUT_value(image, ww, wl).astype('uint16'),
  33 + #self.config.mg_size)
  34 + tmp_mask = watershed_ift(tmp_image, markers.astype('int16'), bstruct)
  35 + else:
  36 + if algorithm == 'Watershed':
  37 + tmp_image = ndimage.morphological_gradient((image - image.min()).astype('uint16'), mg_size)
  38 + tmp_mask = watershed(tmp_image, markers.astype('int16'), bstruct)
  39 + else:
  40 + tmp_image = (image - image.min()).astype('uint16')
  41 + #tmp_image = ndimage.gaussian_filter(tmp_image, self.config.mg_size)
  42 + #tmp_image = ndimage.morphological_gradient((image - image.min()).astype('uint16'), self.config.mg_size)
  43 + tmp_mask = watershed_ift(tmp_image, markers.astype('int8'), bstruct)
  44 + mask[:] = tmp_mask
  45 + mask.flush()
  46 + q.put(1)
invesalius/gui/dicom_preview_panel.py
  Diff comments   View file @0317ac2
@@ -848,12 +848,12 @@ class SingleImagePreview(wx.Panel): @@ -848,12 +848,12 @@ class SingleImagePreview(wx.Panel):
848 window_level = dicom.image.level 848 window_level = dicom.image.level
849 window_width = dicom.image.window 849 window_width = dicom.image.window
850 colorer = vtk.vtkImageMapToWindowLevelColors() 850 colorer = vtk.vtkImageMapToWindowLevelColors()
851 - colorer.SetInput(rdicom.GetOutput()) 851 + colorer.SetInputConnection(rdicom.GetOutputPort())
852 colorer.SetWindow(float(window_width)) 852 colorer.SetWindow(float(window_width))
853 colorer.SetLevel(float(window_level)) 853 colorer.SetLevel(float(window_level))
854 854
855 # PLOT IMAGE INTO VIEWER 855 # PLOT IMAGE INTO VIEWER
856 - self.actor.SetInput(colorer.GetOutput()) 856 + self.actor.SetInputData(colorer.GetOutput())
857 self.renderer.ResetCamera() 857 self.renderer.ResetCamera()
858 self.interactor.Render() 858 self.interactor.Render()
859 859
invesalius/reader/dicom_reader.py
  Diff comments   View file @0317ac2
@@ -195,14 +195,14 @@ class LoadDicom: @@ -195,14 +195,14 @@ class LoadDicom:
195 window = 2000.0 195 window = 2000.0
196 196
197 colorer = vtk.vtkImageMapToWindowLevelColors() 197 colorer = vtk.vtkImageMapToWindowLevelColors()
198 - colorer.SetInput(rvtk.GetOutput()) 198 + colorer.SetInputConnection(rvtk.GetOutputPort())
199 colorer.SetWindow(float(window)) 199 colorer.SetWindow(float(window))
200 colorer.SetLevel(float(level)) 200 colorer.SetLevel(float(level))
201 colorer.SetOutputFormatToRGB() 201 colorer.SetOutputFormatToRGB()
202 colorer.Update() 202 colorer.Update()
203 203
204 resample = vtk.vtkImageResample() 204 resample = vtk.vtkImageResample()
205 - resample.SetInput(colorer.GetOutput()) 205 + resample.SetInputConnection(colorer.GetOutputPort())
206 resample.SetAxisMagnificationFactor ( 0, 0.25 ) 206 resample.SetAxisMagnificationFactor ( 0, 0.25 )
207 resample.SetAxisMagnificationFactor ( 1, 0.25 ) 207 resample.SetAxisMagnificationFactor ( 1, 0.25 )
208 resample.SetAxisMagnificationFactor ( 2, 1 ) 208 resample.SetAxisMagnificationFactor ( 2, 1 )
@@ -211,7 +211,7 @@ class LoadDicom: @@ -211,7 +211,7 @@ class LoadDicom:
211 thumbnail_path = tempfile.mktemp() 211 thumbnail_path = tempfile.mktemp()
212 212
213 write_png = vtk.vtkPNGWriter() 213 write_png = vtk.vtkPNGWriter()
214 - write_png.SetInput(resample.GetOutput()) 214 + write_png.SetInputConnection(resample.GetOutputPort())
215 write_png.SetFileName(thumbnail_path) 215 write_png.SetFileName(thumbnail_path)
216 write_png.Write() 216 write_png.Write()
217 217