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

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
Thiago Franco de Moraes
1 parent c06ff6da
Showing 16 changed files with 190 additions and 173 deletions Show diff stats
.gitignore
invesalius/data/converters.py
invesalius/data/cursor_actors.py
invesalius/data/measures.py
invesalius/data/polydata_utils.py
invesalius/data/slice_.py
invesalius/data/slice_data.py
invesalius/data/styles.py
invesalius/data/surface.py
invesalius/data/surface_process.py
invesalius/data/viewer_slice.py
invesalius/data/viewer_volume.py
invesalius/data/volume.py
invesalius/data/watershed_process.py
invesalius/gui/dicom_preview_panel.py
invesalius/reader/dicom_reader.py
@@ -20,3 +20,7 @@ invesalius/reader/*.pyc
 *.so
 tags
 *.c
+
+build
+*.patch
+*.tgz
@@ -43,16 +43,16 @@ def to_vtk(n_array, spacing, slice_number, orientation):
     image = vtk.vtkImageData()
     image.SetOrigin(0, 0, 0)
     image.SetSpacing(spacing)
-    image.SetNumberOfScalarComponents(1)
     image.SetDimensions(dx, dy, dz)
+    # SetNumberOfScalarComponents and SetScalrType were replaced by
+    # AllocateScalars
+    #  image.SetNumberOfScalarComponents(1)
+    #  image.SetScalarType(numpy_support.get_vtk_array_type(n_array.dtype))
+    image.AllocateScalars(numpy_support.get_vtk_array_type(n_array.dtype), 1)
     image.SetExtent(extent)
-    image.SetScalarType(numpy_support.get_vtk_array_type(n_array.dtype))
-    image.AllocateScalars()
     image.GetPointData().SetScalars(v_image)
-    image.Update()
  
     image_copy = vtk.vtkImageData()
     image_copy.DeepCopy(image)
-    image_copy.Update()
  
     return image_copy
@@ -55,19 +55,19 @@ def to_vtk(n_array, spacing, slice_number, orientation):
     image = vtk.vtkImageData()
     image.SetOrigin(0, 0, 0)
     image.SetSpacing(spacing)
-    image.SetNumberOfScalarComponents(1)
     image.SetDimensions(dx, dy, dz)
     image.SetExtent(extent)
-    image.SetScalarType(numpy_support.get_vtk_array_type(n_array.dtype))
-    image.AllocateScalars()
-    image.Update()
+    #  image.SetNumberOfScalarComponents(1)
+    #  image.SetScalarType(numpy_support.get_vtk_array_type(n_array.dtype))
+    image.AllocateScalars(numpy_support.get_vtk_array_type(n_array.dtype), 1)
+    #  image.Update()
     image.GetCellData().SetScalars(v_image)
     image.GetPointData().SetScalars(v_image)
-    image.Update()
+    #  image.Update()
  
     image_copy = vtk.vtkImageData()
     image_copy.DeepCopy(image)
-    image_copy.Update()
+    #  image_copy.Update()
  
     return image_copy
  
@@ -224,7 +224,7 @@ class CursorBase(object):
         img_colours_mask = vtk.vtkImageMapToColors()
         img_colours_mask.SetLookupTable(lut_mask)
         img_colours_mask.SetOutputFormatToRGBA()
-        img_colours_mask.SetInput(imagedata)
+        img_colours_mask.SetInputData(imagedata)
         img_colours_mask.Update()
  
         return img_colours_mask.GetOutput()
@@ -274,12 +274,12 @@ class CursorCircle(CursorBase):
         circle_ci = self._set_colour(circle_i, self.colour)
  
         if self.mapper is None:
-            self.actor.SetInput(circle_ci)
+            self.actor.SetInputData(circle_ci)
             self.actor.InterpolateOff()
             self.actor.PickableOff()
             self.actor.SetDisplayExtent(circle_ci.GetExtent())
         else:
-            self.mapper.SetInput(circle_ci)
+            self.mapper.SetInputData(circle_ci)
             self.mapper.BorderOn()
  
             self.mapper.SetOrientation(ORIENTATION[self.orientation])
@@ -347,12 +347,12 @@ class CursorRectangle(CursorBase):
         rectangle_ci = self._set_colour(rectangle_i, self.colour)
  
         if self.mapper is None:
-            self.actor.SetInput(rectangle_ci)
+            self.actor.SetInputData(rectangle_ci)
             self.actor.InterpolateOff()
             self.actor.PickableOff()
             self.actor.SetDisplayExtent(rectangle_ci.GetExtent())
         else:
-            self.mapper.SetInput(rectangle_ci)
+            self.mapper.SetInputData(rectangle_ci)
             self.mapper.BorderOn()
             self.mapper.SetOrientation(ORIENTATION[self.orientation])
  
@@ -341,8 +341,8 @@ class CrossPointRepresentation(object):
         sv.SetPoint2(p4)
  
         cruz = vtk.vtkAppendPolyData()
-        cruz.AddInput(sv.GetOutput())
-        cruz.AddInput(sh.GetOutput())
+        cruz.AddInputData(sv.GetOutput())
+        cruz.AddInputData(sh.GetOutput())
  
         c = vtk.vtkCoordinate()
         c.SetCoordinateSystemToWorld()
@@ -563,9 +563,11 @@ class AngularMeasure(object):
         arc = self.DrawArc()
  
         line = vtk.vtkAppendPolyData()
-        line.AddInput(line1.GetOutput())
-        line.AddInput(line2.GetOutput())
-        line.AddInput(arc.GetOutput())
+        line.AddInputConnection(line1.GetOutputPort())
+        line.AddInputConnection(line2.GetOutputPort())
+        line.AddInputConnection(arc.GetOutputPort())
+
+        print line
  
         c = vtk.vtkCoordinate()
         c.SetCoordinateSystemToWorld()
@@ -36,7 +36,7 @@ def ApplyDecimationFilter(polydata, reduction_factor):
     # Important: vtkQuadricDecimation presented better results than
     # vtkDecimatePro
     decimation = vtk.vtkQuadricDecimation()
-    decimation.SetInput(polydata)
+    decimation.SetInputData(polydata)
     decimation.SetTargetReduction(reduction_factor)
     decimation.GetOutput().ReleaseDataFlagOn()
     decimation.AddObserver("ProgressEvent", lambda obj, evt:
@@ -48,7 +48,7 @@ def ApplySmoothFilter(polydata, iterations, relaxation_factor):
     Smooth given vtkPolyData surface, based on iteration and relaxation_factor.
     """
     smoother = vtk.vtkSmoothPolyDataFilter()
-    smoother.SetInput(polydata)
+    smoother.SetInputData(polydata)
     smoother.SetNumberOfIterations(iterations)
     smoother.SetFeatureAngle(80)
     smoother.SetRelaxationFactor(relaxation_factor)
@@ -69,7 +69,7 @@ def FillSurfaceHole(polydata):
     # Filter used to detect and fill holes. Only fill
     print "Filling polydata"
     filled_polydata = vtk.vtkFillHolesFilter()
-    filled_polydata.SetInput(polydata)
+    filled_polydata.SetInputData(polydata)
     filled_polydata.SetHoleSize(500)
     return filled_polydata.GetOutput()
  
@@ -79,7 +79,7 @@ def CalculateSurfaceVolume(polydata):
     """
     # Filter used to calculate volume and area from a polydata
     measured_polydata = vtk.vtkMassProperties()
-    measured_polydata.SetInput(polydata)
+    measured_polydata.SetInputData(polydata)
     return measured_polydata.GetVolume()
  
 def CalculateSurfaceArea(polydata):
@@ -88,7 +88,7 @@ def CalculateSurfaceArea(polydata):
     """
     # Filter used to calculate volume and area from a polydata
     measured_polydata = vtk.vtkMassProperties()
-    measured_polydata.SetInput(polydata)
+    measured_polydata.SetInputData(polydata)
     return measured_polydata.GetSurfaceArea()
  
 def Merge(polydata_list):
@@ -96,11 +96,11 @@ def Merge(polydata_list):
  
     for polydata in polydata_list:
         triangle = vtk.vtkTriangleFilter()
-        triangle.SetInput(polydata)
-        append.AddInput(triangle.GetOutput())
+        triangle.SetInputData(polydata)
+        append.AddInputData(triangle.GetOutput())
  
     clean = vtk.vtkCleanPolyData()
-    clean.SetInput(append.GetOutput())
+    clean.SetInputData(append.GetOutput())
  
     return append.GetOutput()
  
@@ -112,7 +112,7 @@ def Export(polydata, filename, bin=False):
         writer.SetDataModeToBinary()
     else:
         writer.SetDataModeToAscii()
-    writer.SetInput(polydata)
+    writer.SetInputData(polydata)
     writer.Write()
  
 def Import(filename):
@@ -130,7 +130,7 @@ def JoinSeedsParts(polydata, point_id_list):
     from vtkPolyData.
     """
     conn = vtk.vtkPolyDataConnectivityFilter()
-    conn.SetInput(polydata)
+    conn.SetInputData(polydata)
     conn.SetExtractionModeToPointSeededRegions()
     UpdateProgress = vu.ShowProgress(1 + len(point_id_list))
     pos = 1
@@ -145,7 +145,6 @@ def JoinSeedsParts(polydata, point_id_list):
  
     result = vtk.vtkPolyData()
     result.DeepCopy(conn.GetOutput())
-    result.Update()
     return result
  
 def SelectLargestPart(polydata):
@@ -153,7 +152,7 @@ def SelectLargestPart(polydata):
     """
     UpdateProgress = vu.ShowProgress(1)
     conn = vtk.vtkPolyDataConnectivityFilter()
-    conn.SetInput(polydata)
+    conn.SetInputData(polydata)
     conn.SetExtractionModeToLargestRegion()
     conn.AddObserver("ProgressEvent", lambda obj, evt:
                   UpdateProgress(conn, "Getting largest part..."))
@@ -161,14 +160,13 @@ def SelectLargestPart(polydata):
  
     result = vtk.vtkPolyData()
     result.DeepCopy(conn.GetOutput())
-    result.Update()
     return result
  
 def SplitDisconectedParts(polydata):
     """
     """
     conn = vtk.vtkPolyDataConnectivityFilter()
-    conn.SetInput(polydata)
+    conn.SetInputData(polydata)
     conn.SetExtractionModeToAllRegions()
     conn.Update()
  
@@ -191,7 +189,6 @@ def SplitDisconectedParts(polydata):
  
         p = vtk.vtkPolyData()
         p.DeepCopy(conn.GetOutput())
-        p.Update()
  
         polydata_collection.append(p)
         if progress:
@@ -964,18 +964,18 @@ class Slice(object):
         img = self.buffer_slices[orientation].vtk_image
         original_orientation = Project().original_orientation
         cast = vtk.vtkImageCast()
-        cast.SetInput(img)
+        cast.SetInputData(img)
         cast.SetOutputScalarTypeToDouble() 
         cast.ClampOverflowOn()
         cast.Update()
  
         #if (original_orientation == const.AXIAL):
         flip = vtk.vtkImageFlip()
-        flip.SetInput(cast.GetOutput())
+        flip.SetInputConnection(cast.GetOutputPort())
         flip.SetFilteredAxis(1)
         flip.FlipAboutOriginOn()
         flip.Update()
-        widget.SetInput(flip.GetOutput())
+        widget.SetInputConnection(flip.GetOutputPort())
         #else:
             #widget.SetInput(cast.GetOutput())
  
@@ -1044,7 +1044,7 @@ class Slice(object):
                 i += 1
  
             colorer = vtk.vtkImageMapToColors()
-            colorer.SetInput(image)
+            colorer.SetInputData(image)
             colorer.SetLookupTable(lut)
             colorer.SetOutputFormatToRGB()
             colorer.Update()
@@ -1059,12 +1059,12 @@ class Slice(object):
  
             colorer = vtk.vtkImageMapToColors()
             colorer.SetLookupTable(lut)
-            colorer.SetInput(image)
+            colorer.SetInputData(image)
             colorer.SetOutputFormatToRGB()
             colorer.Update()
         else:
             colorer = vtk.vtkImageMapToWindowLevelColors()
-            colorer.SetInput(image)
+            colorer.SetInputData(image)
             colorer.SetWindow(self.window_width)
             colorer.SetLevel(self.window_level)
             colorer.SetOutputFormatToRGB()
@@ -1148,7 +1148,7 @@ class Slice(object):
             img_colours_bg = vtk.vtkImageMapToColors()
             img_colours_bg.SetOutputFormatToRGB()
             img_colours_bg.SetLookupTable(lut_bg)
-            img_colours_bg.SetInput(imagedata)
+            img_colours_bg.SetInputData(imagedata)
             img_colours_bg.Update()
  
             return img_colours_bg.GetOutput()
@@ -1179,7 +1179,7 @@ class Slice(object):
         img_colours_mask = vtk.vtkImageMapToColors()
         img_colours_mask.SetLookupTable(lut_mask)
         img_colours_mask.SetOutputFormatToRGBA()
-        img_colours_mask.SetInput(imagedata)
+        img_colours_mask.SetInputData(imagedata)
         img_colours_mask.Update()
         # self.img_colours_mask = img_colours_mask
  
@@ -1211,7 +1211,7 @@ class Slice(object):
         img_colours_mask = vtk.vtkImageMapToColors()
         img_colours_mask.SetLookupTable(lut_mask)
         img_colours_mask.SetOutputFormatToRGBA()
-        img_colours_mask.SetInput(imagedata)
+        img_colours_mask.SetInputData(imagedata)
         img_colours_mask.Update()
         # self.img_colours_mask = img_colours_mask
  
@@ -1225,8 +1225,8 @@ class Slice(object):
         blend_imagedata.SetBlendModeToNormal()
         # blend_imagedata.SetOpacity(0, 1.0)
         blend_imagedata.SetOpacity(1, 0.8)
-        blend_imagedata.SetInput(imagedata)
-        blend_imagedata.AddInput(mask)
+        blend_imagedata.SetInputData(imagedata)
+        blend_imagedata.AddInputData(mask)
         blend_imagedata.Update()
  
         return blend_imagedata.GetOutput()
@@ -55,7 +55,7 @@ class SliceData(object):
  
     def __create_line_actor(self, line):
         line_mapper = vtk.vtkPolyDataMapper2D()
-        line_mapper.SetInput(line.GetOutput())
+        line_mapper.SetInputConnection(line.GetOutputPort())
  
         line_actor = vtk.vtkActor2D()
         line_actor.SetMapper(line_mapper)
@@ -59,10 +59,14 @@ WATERSHED_OPERATIONS = {_(&quot;Erase&quot;): BRUSH_ERASE,
                         _("Background"): BRUSH_BACKGROUND,}
  
 def get_LUT_value(data, window, level):
-    return np.piecewise(data,
-                        [data <= (level - 0.5 - (window-1)/2),
-                         data > (level - 0.5 + (window-1)/2)],
-                        [0, window, lambda data: ((data - (level - 0.5))/(window-1) + 0.5)*(window)])
+    shape = data.shape
+    data_ = data.ravel()
+    data = np.piecewise(data_,
+                        [data_ <= (level - 0.5 - (window-1)/2),
+                         data_ > (level - 0.5 + (window-1)/2)],
+                        [0, window, lambda data_: ((data_ - (level - 0.5))/(window-1) + 0.5)*(window)])
+    data.shape = shape
+    return data
  
 class BaseImageInteractorStyle(vtk.vtkInteractorStyleImage):
     def __init__(self, viewer):
@@ -42,6 +42,8 @@ try:
 except ImportError:
     import data.ca_smoothing as ca_smoothing
  
+# TODO: Verificar ReleaseDataFlagOn and SetSource 
+
 class Surface():
     """
     Represent both vtkPolyData and associated properties.
@@ -240,12 +242,13 @@ class SurfaceManager():
                                   name=None, colour=None,
                                   transparency=None, volume=None):
         normals = vtk.vtkPolyDataNormals()
-        normals.SetInput(polydata)
+        normals.SetInputData(polydata)
         normals.SetFeatureAngle(80)
         normals.AutoOrientNormalsOn()
+        normals.Update()
  
         mapper = vtk.vtkPolyDataMapper()
-        mapper.SetInput(normals.GetOutput())
+        mapper.SetInputData(normals.GetOutput())
         mapper.ScalarVisibilityOff()
         mapper.ImmediateModeRenderingOn() # improve performance
  
@@ -289,11 +292,12 @@ class SurfaceManager():
         # The following lines have to be here, otherwise all volumes disappear
         if not volume:
             triangle_filter = vtk.vtkTriangleFilter()
-            triangle_filter.SetInput(polydata)
+            triangle_filter.SetInputData(polydata)
             triangle_filter.Update()
  
             measured_polydata = vtk.vtkMassProperties()
-            measured_polydata.SetInput(triangle_filter.GetOutput())
+            measured_polydata.SetInputConnection(triangle_filter.GetOutputPort())
+            measured_polydata.Update()
             volume =  measured_polydata.GetVolume()
             surface.volume = volume
             print ">>>>", surface.volume
@@ -338,19 +342,19 @@ class SurfaceManager():
             surface = surface_dict[key]
             # Map polygonal data (vtkPolyData) to graphics primitives.
             normals = vtk.vtkPolyDataNormals()
-            normals.SetInput(surface.polydata)
+            normals.SetInputData(surface.polydata)
             normals.SetFeatureAngle(80)
             normals.AutoOrientNormalsOn()
-            normals.GetOutput().ReleaseDataFlagOn()
+            #  normals.GetOutput().ReleaseDataFlagOn()
  
 	    # Improve performance
             stripper = vtk.vtkStripper()
-            stripper.SetInput(normals.GetOutput())
+            stripper.SetInputData(normals.GetOutput())
             stripper.PassThroughCellIdsOn()
             stripper.PassThroughPointIdsOn()
  
             mapper = vtk.vtkPolyDataMapper()
-            mapper.SetInput(stripper.GetOutput())
+            mapper.SetInputData(stripper.GetOutput())
             mapper.ScalarVisibilityOff()
             mapper.ImmediateModeRenderingOn() # improve performance
  
@@ -490,30 +494,30 @@ class SurfaceManager():
                 break
  
         polydata_append = vtk.vtkAppendPolyData()
-        polydata_append.ReleaseDataFlagOn()
+        #  polydata_append.ReleaseDataFlagOn()
         t = n_pieces
         while t:
             filename_polydata = q_out.get()
  
             reader = vtk.vtkXMLPolyDataReader()
             reader.SetFileName(filename_polydata)
-            reader.ReleaseDataFlagOn()
+            #  reader.ReleaseDataFlagOn()
             reader.Update()
-            reader.GetOutput().ReleaseDataFlagOn()
+            #  reader.GetOutput().ReleaseDataFlagOn()
  
             polydata = reader.GetOutput()
-            polydata.SetSource(None)
+            #  polydata.SetSource(None)
  
-            polydata_append.AddInput(polydata)
+            polydata_append.AddInputData(polydata)
             del reader
             del polydata
             t -= 1
  
         polydata_append.Update()
-        polydata_append.GetOutput().ReleaseDataFlagOn()
+        #  polydata_append.GetOutput().ReleaseDataFlagOn()
         polydata = polydata_append.GetOutput()
         #polydata.Register(None)
-        polydata.SetSource(None)
+        #  polydata.SetSource(None)
         del polydata_append
  
         if algorithm == 'ca_smoothing':
@@ -521,31 +525,31 @@ class SurfaceManager():
             normals_ref = weakref.ref(normals)
             normals_ref().AddObserver("ProgressEvent", lambda obj,evt:
                                       UpdateProgress(normals_ref(), _("Creating 3D surface...")))
-            normals.SetInput(polydata)
-            normals.ReleaseDataFlagOn()
+            normals.SetInputData(polydata)
+            #  normals.ReleaseDataFlagOn()
             #normals.SetFeatureAngle(80)
             #normals.AutoOrientNormalsOn()
             normals.ComputeCellNormalsOn()
-            normals.GetOutput().ReleaseDataFlagOn()
+            #  normals.GetOutput().ReleaseDataFlagOn()
             normals.Update()
             del polydata
             polydata = normals.GetOutput()
-            polydata.SetSource(None)
+            #  polydata.SetSource(None)
             del normals
  
             clean = vtk.vtkCleanPolyData()
-            clean.ReleaseDataFlagOn()
-            clean.GetOutput().ReleaseDataFlagOn()
+            #  clean.ReleaseDataFlagOn()
+            #  clean.GetOutput().ReleaseDataFlagOn()
             clean_ref = weakref.ref(clean)
             clean_ref().AddObserver("ProgressEvent", lambda obj,evt:
                             UpdateProgress(clean_ref(), _("Creating 3D surface...")))
-            clean.SetInput(polydata)
+            clean.SetInputData(polydata)
             clean.PointMergingOn()
             clean.Update()
  
             del polydata
             polydata = clean.GetOutput()
-            polydata.SetSource(None)
+            #  polydata.SetSource(None)
             del clean
  
             try:
@@ -556,7 +560,7 @@ class SurfaceManager():
                                                  options['max distance'],
                                                  options['min weight'],
                                                  options['steps'])
-            polydata.SetSource(None)
+            #  polydata.SetSource(None)
             polydata.DebugOn()
  
         else:
@@ -565,7 +569,7 @@ class SurfaceManager():
             smoother_ref = weakref.ref(smoother)
             smoother_ref().AddObserver("ProgressEvent", lambda obj,evt:
                             UpdateProgress(smoother_ref(), _("Creating 3D surface...")))
-            smoother.SetInput(polydata)
+            smoother.SetInputData(polydata)
             smoother.SetNumberOfIterations(smooth_iterations)
             smoother.SetRelaxationFactor(smooth_relaxation_factor)
             smoother.SetFeatureAngle(80)
@@ -575,21 +579,21 @@ class SurfaceManager():
             smoother.FeatureEdgeSmoothingOn()
             #smoother.NormalizeCoordinatesOn()
             #smoother.NonManifoldSmoothingOn()
-            smoother.ReleaseDataFlagOn()
-            smoother.GetOutput().ReleaseDataFlagOn()
+            #  smoother.ReleaseDataFlagOn()
+            #  smoother.GetOutput().ReleaseDataFlagOn()
             smoother.Update()
             del polydata
             polydata = smoother.GetOutput()
             #polydata.Register(None)
-            polydata.SetSource(None)
+            #  polydata.SetSource(None)
             del smoother
  
  
         if decimate_reduction:
             print "Decimating", decimate_reduction
             decimation = vtk.vtkQuadricDecimation()
-            decimation.ReleaseDataFlagOn()
-            decimation.SetInput(polydata)
+            #  decimation.ReleaseDataFlagOn()
+            decimation.SetInputData(polydata)
             decimation.SetTargetReduction(decimate_reduction)
             decimation_ref = weakref.ref(decimation)
             decimation_ref().AddObserver("ProgressEvent", lambda obj,evt:
@@ -597,31 +601,31 @@ class SurfaceManager():
             #decimation.PreserveTopologyOn()
             #decimation.SplittingOff()
             #decimation.BoundaryVertexDeletionOff()
-            decimation.GetOutput().ReleaseDataFlagOn()
+            #  decimation.GetOutput().ReleaseDataFlagOn()
             decimation.Update()
             del polydata
             polydata = decimation.GetOutput()
             #polydata.Register(None)
-            polydata.SetSource(None)
+            #  polydata.SetSource(None)
             del decimation
  
         to_measure = polydata
         #to_measure.Register(None)
-        to_measure.SetSource(None)
+        #  to_measure.SetSource(None)
  
         if keep_largest:
             conn = vtk.vtkPolyDataConnectivityFilter()
-            conn.SetInput(polydata)
+            conn.SetInputData(polydata)
             conn.SetExtractionModeToLargestRegion()
             conn_ref = weakref.ref(conn)
             conn_ref().AddObserver("ProgressEvent", lambda obj,evt:
                     UpdateProgress(conn_ref(), _("Creating 3D surface...")))
             conn.Update()
-            conn.GetOutput().ReleaseDataFlagOn()
+            #  conn.GetOutput().ReleaseDataFlagOn()
             del polydata
             polydata = conn.GetOutput()
             #polydata.Register(None)
-            polydata.SetSource(None)
+            #  polydata.SetSource(None)
             del conn
  
         #Filter used to detect and fill holes. Only fill boundary edges holes.
@@ -629,59 +633,59 @@ class SurfaceManager():
         #polydata_utils.FillSurfaceHole, we need to review this.
         if fill_holes:
             filled_polydata = vtk.vtkFillHolesFilter()
-            filled_polydata.ReleaseDataFlagOn()
-            filled_polydata.SetInput(polydata)
+            #  filled_polydata.ReleaseDataFlagOn()
+            filled_polydata.SetInputData(polydata)
             filled_polydata.SetHoleSize(300)
             filled_polydata_ref = weakref.ref(filled_polydata)
             filled_polydata_ref().AddObserver("ProgressEvent", lambda obj,evt:
                     UpdateProgress(filled_polydata_ref(), _("Creating 3D surface...")))
             filled_polydata.Update()
-            filled_polydata.GetOutput().ReleaseDataFlagOn()
+            #  filled_polydata.GetOutput().ReleaseDataFlagOn()
             del polydata
             polydata = filled_polydata.GetOutput()
             #polydata.Register(None)
-            polydata.SetSource(None)
+            #  polydata.SetSource(None)
             polydata.DebugOn()
             del filled_polydata
  
         normals = vtk.vtkPolyDataNormals()
-        normals.ReleaseDataFlagOn()
+        #  normals.ReleaseDataFlagOn()
         normals_ref = weakref.ref(normals)
         normals_ref().AddObserver("ProgressEvent", lambda obj,evt:
                         UpdateProgress(normals_ref(), _("Creating 3D surface...")))
-        normals.SetInput(polydata)
+        normals.SetInputData(polydata)
         normals.SetFeatureAngle(80)
         normals.AutoOrientNormalsOn()
-        normals.GetOutput().ReleaseDataFlagOn()
+        #  normals.GetOutput().ReleaseDataFlagOn()
         normals.Update()
         del polydata
         polydata = normals.GetOutput()
         #polydata.Register(None)
-        polydata.SetSource(None)
+        #  polydata.SetSource(None)
         del normals
  
         # Improve performance
         stripper = vtk.vtkStripper()
-        stripper.ReleaseDataFlagOn()
+        #  stripper.ReleaseDataFlagOn()
         stripper_ref = weakref.ref(stripper)
         stripper_ref().AddObserver("ProgressEvent", lambda obj,evt:
                         UpdateProgress(stripper_ref(), _("Creating 3D surface...")))
-        stripper.SetInput(polydata)
+        stripper.SetInputData(polydata)
         stripper.PassThroughCellIdsOn()
         stripper.PassThroughPointIdsOn()
-        stripper.GetOutput().ReleaseDataFlagOn()
+        #  stripper.GetOutput().ReleaseDataFlagOn()
         stripper.Update()
         del polydata
         polydata = stripper.GetOutput()
         #polydata.Register(None)
-        polydata.SetSource(None)
+        #  polydata.SetSource(None)
         del stripper
  
         # Map polygonal data (vtkPolyData) to graphics primitives.
         mapper = vtk.vtkPolyDataMapper()
-        mapper.SetInput(polydata)
+        mapper.SetInputData(polydata)
         mapper.ScalarVisibilityOff()
-        mapper.ReleaseDataFlagOn()
+        #  mapper.ReleaseDataFlagOn()
         mapper.ImmediateModeRenderingOn() # improve performance
  
         # Represent an object (geometry & properties) in the rendered scene
@@ -720,8 +724,8 @@ class SurfaceManager():
  
         # The following lines have to be here, otherwise all volumes disappear
         measured_polydata = vtk.vtkMassProperties()
-        measured_polydata.ReleaseDataFlagOn()
-        measured_polydata.SetInput(to_measure)
+        #  measured_polydata.ReleaseDataFlagOn()
+        measured_polydata.SetInputData(to_measure)
         volume =  float(measured_polydata.GetVolume())
         surface.volume = volume
         self.last_surface_index = surface.index
@@ -858,14 +862,15 @@ class SurfaceManager():
             if filetype in (const.FILETYPE_STL, const.FILETYPE_PLY):
                 # Invert normals
                 normals = vtk.vtkPolyDataNormals()
-                normals.SetInput(polydata)
+                normals.SetInputData(polydata)
                 normals.SetFeatureAngle(80)
                 normals.AutoOrientNormalsOn()
-                normals.GetOutput().ReleaseDataFlagOn()
+                #  normals.GetOutput().ReleaseDataFlagOn()
                 normals.UpdateInformation()
+                normals.Update()
                 polydata = normals.GetOutput()
  
             filename = filename.encode(wx.GetDefaultPyEncoding())
             writer.SetFileName(filename)
-            writer.SetInput(polydata)
+            writer.SetInputData(polydata)
             writer.Write()
@@ -26,7 +26,7 @@ def ResampleImage3D(imagedata, value):
     resolution = (height/(extent[1]-extent[0])+1)*spacing[1]
  
     resample = vtk.vtkImageResample()
-    resample.SetInput(imagedata)
+    resample.SetInputData(imagedata)
     resample.SetAxisMagnificationFactor(0, resolution)
     resample.SetAxisMagnificationFactor(1, resolution)
  
@@ -106,7 +106,7 @@ class SurfaceProcess(multiprocessing.Process):
                                            "AXIAL")
  
                 gauss = vtk.vtkImageGaussianSmooth()
-                gauss.SetInput(image)
+                gauss.SetInputData(image)
                 gauss.SetRadiusFactor(0.3)
                 gauss.ReleaseDataFlagOn()
                 gauss.Update()
@@ -125,7 +125,7 @@ class SurfaceProcess(multiprocessing.Process):
             image = ResampleImage3D(image, self.imagedata_resolution)
  
         flip = vtk.vtkImageFlip()
-        flip.SetInput(image)
+        flip.SetInputData(image)
         flip.SetFilteredAxis(1)
         flip.FlipAboutOriginOn()
         flip.ReleaseDataFlagOn()
@@ -148,7 +148,7 @@ class SurfaceProcess(multiprocessing.Process):
         #if self.mode == "CONTOUR":
         #print "Contour"
         contour = vtk.vtkContourFilter()
-        contour.SetInput(image)
+        contour.SetInputData(image)
         #contour.SetInput(flip.GetOutput())
         if self.from_binary:
             contour.SetValue(0, 127) # initial threshold
@@ -202,7 +202,7 @@ class SurfaceProcess(multiprocessing.Process):
  
         filename = tempfile.mktemp(suffix='_%s.vtp' % (self.pid))
         writer = vtk.vtkXMLPolyDataWriter()
-        writer.SetInput(polydata)
+        writer.SetInputData(polydata)
         writer.SetFileName(filename)
         writer.Write()
  
@@ -753,6 +753,7 @@ class Viewer(wx.Panel):
                 image = vtk.vtkRenderLargeImage()
                 image.SetInput(ren)
                 image.SetMagnification(1)
+                image.Update()
  
                 image = image.GetOutput()
  
@@ -769,8 +770,8 @@ class Viewer(wx.Panel):
                 elif (filetype == const.FILETYPE_TIF):
                     writer = vtk.vtkTIFFWriter()
                     filename = "%s.tif"%filename.strip(".tif")
-                
-                writer.SetInput(image)
+
+                writer.SetInputData(image)
                 writer.SetFileName(filename)
                 writer.Write()
  
@@ -919,7 +920,7 @@ class Viewer(wx.Panel):
         c.SetCoordinateSystemToWorld()
  
         cross_mapper = vtk.vtkPolyDataMapper()
-        cross_mapper.SetInput(cross.GetOutput())
+        cross_mapper.SetInputConnection(cross.GetOutputPort())
         #cross_mapper.SetTransformCoordinate(c)
  
         p = vtk.vtkProperty()
@@ -1176,7 +1177,7 @@ class Viewer(wx.Panel):
         border_size = self.mip_ctrls.border_spin.GetValue()
         image = self.slice_.GetSlices(self.orientation, index,
                                       self.number_slices, inverted, border_size)
-        self.slice_data.actor.SetInput(image)
+        self.slice_data.actor.SetInputData(image)
         for actor in self.actors_by_slice_number.get(self.slice_data.number, []):
             self.slice_data.renderer.RemoveActor(actor)
         for actor in self.actors_by_slice_number.get(index, []):
@@ -318,6 +318,7 @@ class Viewer(wx.Panel):
                 image = vtk.vtkRenderLargeImage()
                 image.SetInput(self.ren)
                 image.SetMagnification(1)
+                image.Update()
  
                 image = image.GetOutput()
  
@@ -333,12 +334,12 @@ class Viewer(wx.Panel):
                 elif (filetype == const.FILETYPE_TIF):
                     writer = vtk.vtkTIFFWriter()
                     filename = "%s.tif"%filename.strip(".tif")
-                
-                writer.SetInput(image)
+
+                writer.SetInputData(image)
                 writer.SetFileName(filename)
                 writer.Write()
         Publisher.sendMessage('End busy cursor')
- 
+
     def OnCloseProject(self, pubsub_evt):
         if self.raycasting_volume:
             self.raycasting_volume = False
@@ -224,7 +224,7 @@ class Volume():
         # Update convolution filter
         original_imagedata = self.imagedata.GetOutput()
         imagedata = self.ApplyConvolution(original_imagedata)
-        self.volume_mapper.SetInput(imagedata)
+        self.volume_mapper.SetInputData(imagedata)
  
         # Update other information
         self.SetShading()
@@ -484,7 +484,7 @@ class Volume():
                 update_progress = vtk_utils.ShowProgress(number_filters)
             for filter in self.config['convolutionFilters']:
                 convolve = vtk.vtkImageConvolve()
-                convolve.SetInput(imagedata)
+                convolve.SetInputData(imagedata)
                 convolve.SetKernel5x5([i/60.0 for i in Kernels[filter]])
                 convolve.ReleaseDataFlagOn()
  
@@ -530,7 +530,7 @@ class Volume():
         update_progress= vtk_utils.ShowProgress(2 + number_filters) 
         # Flip original vtkImageData
         flip = vtk.vtkImageFlip()
-        flip.SetInput(image)
+        flip.SetInputData(image)
         flip.SetFilteredAxis(1)
         flip.FlipAboutOriginOn()
         flip.ReleaseDataFlagOn()
@@ -545,7 +545,7 @@ class Volume():
         self.scale = scale
  
         cast = vtk.vtkImageShiftScale()
-        cast.SetInput(image)
+        cast.SetInputData(image)
         cast.SetShift(abs(scale[0]))
         cast.SetOutputScalarTypeToUnsignedShort()
         cast.ReleaseDataFlagOn()
@@ -589,7 +589,7 @@ class Volume():
                 self.volume_mapper = volume_mapper
  
         self.SetTypeRaycasting()
-        volume_mapper.SetInput(image2)
+        volume_mapper.SetInputData(image2)
  
         # TODO: Look to this
         #volume_mapper_hw = vtk.vtkVolumeTextureMapper3D()
@@ -657,7 +657,7 @@ class Volume():
         image = self.image
         r = int(image.GetScalarRange()[1] - image.GetScalarRange()[0])
         accumulate = vtk.vtkImageAccumulate()
-        accumulate.SetInput(image)
+        accumulate.SetInputData(image)
         accumulate.SetComponentExtent(0, r -1, 0, 0, 0, 0)
         accumulate.SetComponentOrigin(image.GetScalarRange()[0], 0, 0)
         accumulate.ReleaseDataFlagOn()
-import numpy as np
-from scipy import ndimage
-from scipy.ndimage import watershed_ift, generate_binary_structure
-from skimage.morphology import watershed
-from skimage import filter
-
-
-def get_LUT_value(data, window, level):
-    return np.piecewise(data, 
-                        [data <= (level - 0.5 - (window-1)/2),
-                         data > (level - 0.5 + (window-1)/2)],
-                        [0, 255, lambda data: ((data - (level - 0.5))/(window-1) + 0.5)*(255-0)])
-
-
-
-def do_watershed(image, markers,  tfile, shape, bstruct, algorithm, mg_size, use_ww_wl, wl, ww, q):
-    mask = np.memmap(tfile, shape=shape, dtype='uint8', mode='r+')
-                
-    if use_ww_wl:
-        if algorithm == 'Watershed':
-            tmp_image = ndimage.morphological_gradient(
-                           get_LUT_value(image, ww, wl).astype('uint16'),
-                           mg_size)
-            tmp_mask = watershed(tmp_image, markers.astype('int16'), bstruct)
-        else:
-            tmp_image = get_LUT_value(image, ww, wl).astype('uint16')
-            #tmp_image = ndimage.gaussian_filter(tmp_image, self.config.mg_size)
-            #tmp_image = ndimage.morphological_gradient(
-                           #get_LUT_value(image, ww, wl).astype('uint16'),
-                           #self.config.mg_size)
-            tmp_mask = watershed_ift(tmp_image, markers.astype('int16'), bstruct)
-    else:
-        if algorithm == 'Watershed':
-            tmp_image = ndimage.morphological_gradient((image - image.min()).astype('uint16'), mg_size)
-            tmp_mask = watershed(tmp_image, markers.astype('int16'), bstruct)
-        else:
-            tmp_image = (image - image.min()).astype('uint16')
-            #tmp_image = ndimage.gaussian_filter(tmp_image, self.config.mg_size)
-            #tmp_image = ndimage.morphological_gradient((image - image.min()).astype('uint16'), self.config.mg_size)
-            tmp_mask = watershed_ift(tmp_image, markers.astype('int8'), bstruct)
-    mask[:] = tmp_mask
-    mask.flush()
-    q.put(1)
+import numpy as np
+from scipy import ndimage
+from scipy.ndimage import watershed_ift, generate_binary_structure
+from skimage.morphology import watershed
+from skimage import filter
+
+
+def get_LUT_value(data, window, level):
+    shape = data.shape
+    data_ = data.ravel()
+    data = np.piecewise(data_,
+                        [data_ <= (level - 0.5 - (window-1)/2),
+                         data_ > (level - 0.5 + (window-1)/2)],
+                        [0, window, lambda data_: ((data_ - (level - 0.5))/(window-1) + 0.5)*(window)])
+    data.shape = shape
+    return data
+
+
+def do_watershed(image, markers,  tfile, shape, bstruct, algorithm, mg_size, use_ww_wl, wl, ww, q):
+    mask = np.memmap(tfile, shape=shape, dtype='uint8', mode='r+')
+                
+    if use_ww_wl:
+        if algorithm == 'Watershed':
+            tmp_image = ndimage.morphological_gradient(
+                           get_LUT_value(image, ww, wl).astype('uint16'),
+                           mg_size)
+            tmp_mask = watershed(tmp_image, markers.astype('int16'), bstruct)
+        else:
+            tmp_image = get_LUT_value(image, ww, wl).astype('uint16')
+            #tmp_image = ndimage.gaussian_filter(tmp_image, self.config.mg_size)
+            #tmp_image = ndimage.morphological_gradient(
+                           #get_LUT_value(image, ww, wl).astype('uint16'),
+                           #self.config.mg_size)
+            tmp_mask = watershed_ift(tmp_image, markers.astype('int16'), bstruct)
+    else:
+        if algorithm == 'Watershed':
+            tmp_image = ndimage.morphological_gradient((image - image.min()).astype('uint16'), mg_size)
+            tmp_mask = watershed(tmp_image, markers.astype('int16'), bstruct)
+        else:
+            tmp_image = (image - image.min()).astype('uint16')
+            #tmp_image = ndimage.gaussian_filter(tmp_image, self.config.mg_size)
+            #tmp_image = ndimage.morphological_gradient((image - image.min()).astype('uint16'), self.config.mg_size)
+            tmp_mask = watershed_ift(tmp_image, markers.astype('int8'), bstruct)
+    mask[:] = tmp_mask
+    mask.flush()
+    q.put(1)
@@ -848,12 +848,12 @@ class SingleImagePreview(wx.Panel):
         window_level = dicom.image.level
         window_width = dicom.image.window
         colorer = vtk.vtkImageMapToWindowLevelColors()
-        colorer.SetInput(rdicom.GetOutput())
+        colorer.SetInputConnection(rdicom.GetOutputPort())
         colorer.SetWindow(float(window_width))
         colorer.SetLevel(float(window_level))
  
         # PLOT IMAGE INTO VIEWER
-        self.actor.SetInput(colorer.GetOutput())
+        self.actor.SetInputData(colorer.GetOutput())
         self.renderer.ResetCamera()
         self.interactor.Render()
  
@@ -195,14 +195,14 @@ class LoadDicom:
                 window = 2000.0 
  
             colorer = vtk.vtkImageMapToWindowLevelColors()
-            colorer.SetInput(rvtk.GetOutput())
+            colorer.SetInputConnection(rvtk.GetOutputPort())
             colorer.SetWindow(float(window))
             colorer.SetLevel(float(level))
             colorer.SetOutputFormatToRGB()
             colorer.Update()           
  
             resample = vtk.vtkImageResample()
-            resample.SetInput(colorer.GetOutput())
+            resample.SetInputConnection(colorer.GetOutputPort())
             resample.SetAxisMagnificationFactor ( 0, 0.25 )
             resample.SetAxisMagnificationFactor ( 1, 0.25 )
             resample.SetAxisMagnificationFactor ( 2, 1 )    
@@ -211,7 +211,7 @@ class LoadDicom:
             thumbnail_path = tempfile.mktemp()
  
             write_png = vtk.vtkPNGWriter()
-            write_png.SetInput(resample.GetOutput())
+            write_png.SetInputConnection(resample.GetOutputPort())
             write_png.SetFileName(thumbnail_path)
             write_png.Write()
...	...	@@ -20,3 +20,7 @@ invesalius/reader/*.pyc
20	20	*.so
21	21	tags
22	22	*.c
	23	+
	24	+build
	25	+*.patch
	26	+*.tgz
...	...
...	...	@@ -43,16 +43,16 @@ def to_vtk(n_array, spacing, slice_number, orientation):
43	43	image = vtk.vtkImageData()
44	44	image.SetOrigin(0, 0, 0)
45	45	image.SetSpacing(spacing)
46		- image.SetNumberOfScalarComponents(1)
47	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	52	image.SetExtent(extent)
49		- image.SetScalarType(numpy_support.get_vtk_array_type(n_array.dtype))
50		- image.AllocateScalars()
51	53	image.GetPointData().SetScalars(v_image)
52		- image.Update()
53	54
54	55	image_copy = vtk.vtkImageData()
55	56	image_copy.DeepCopy(image)
56		- image_copy.Update()
57	57
58	58	return image_copy
...	...
...	...	@@ -55,19 +55,19 @@ def to_vtk(n_array, spacing, slice_number, orientation):
55	55	image = vtk.vtkImageData()
56	56	image.SetOrigin(0, 0, 0)
57	57	image.SetSpacing(spacing)
58		- image.SetNumberOfScalarComponents(1)
59	58	image.SetDimensions(dx, dy, dz)
60	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	64	image.GetCellData().SetScalars(v_image)
65	65	image.GetPointData().SetScalars(v_image)
66		- image.Update()
	66	+ # image.Update()
67	67
68	68	image_copy = vtk.vtkImageData()
69	69	image_copy.DeepCopy(image)
70		- image_copy.Update()
	70	+ # image_copy.Update()
71	71
72	72	return image_copy
73	73
...	...	@@ -224,7 +224,7 @@ class CursorBase(object):
224	224	img_colours_mask = vtk.vtkImageMapToColors()
225	225	img_colours_mask.SetLookupTable(lut_mask)
226	226	img_colours_mask.SetOutputFormatToRGBA()
227		- img_colours_mask.SetInput(imagedata)
	227	+ img_colours_mask.SetInputData(imagedata)
228	228	img_colours_mask.Update()
229	229
230	230	return img_colours_mask.GetOutput()
...	...	@@ -274,12 +274,12 @@ class CursorCircle(CursorBase):
274	274	circle_ci = self._set_colour(circle_i, self.colour)
275	275
276	276	if self.mapper is None:
277		- self.actor.SetInput(circle_ci)
	277	+ self.actor.SetInputData(circle_ci)
278	278	self.actor.InterpolateOff()
279	279	self.actor.PickableOff()
280	280	self.actor.SetDisplayExtent(circle_ci.GetExtent())
281	281	else:
282		- self.mapper.SetInput(circle_ci)
	282	+ self.mapper.SetInputData(circle_ci)
283	283	self.mapper.BorderOn()
284	284
285	285	self.mapper.SetOrientation(ORIENTATION[self.orientation])
...	...	@@ -347,12 +347,12 @@ class CursorRectangle(CursorBase):
347	347	rectangle_ci = self._set_colour(rectangle_i, self.colour)
348	348
349	349	if self.mapper is None:
350		- self.actor.SetInput(rectangle_ci)
	350	+ self.actor.SetInputData(rectangle_ci)
351	351	self.actor.InterpolateOff()
352	352	self.actor.PickableOff()
353	353	self.actor.SetDisplayExtent(rectangle_ci.GetExtent())
354	354	else:
355		- self.mapper.SetInput(rectangle_ci)
	355	+ self.mapper.SetInputData(rectangle_ci)
356	356	self.mapper.BorderOn()
357	357	self.mapper.SetOrientation(ORIENTATION[self.orientation])
358	358
...	...
...	...	@@ -341,8 +341,8 @@ class CrossPointRepresentation(object):
341	341	sv.SetPoint2(p4)
342	342
343	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	347	c = vtk.vtkCoordinate()
348	348	c.SetCoordinateSystemToWorld()
...	...	@@ -563,9 +563,11 @@ class AngularMeasure(object):
563	563	arc = self.DrawArc()
564	564
565	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	572	c = vtk.vtkCoordinate()
571	573	c.SetCoordinateSystemToWorld()
...	...
...	...	@@ -36,7 +36,7 @@ def ApplyDecimationFilter(polydata, reduction_factor):
36	36	# Important: vtkQuadricDecimation presented better results than
37	37	# vtkDecimatePro
38	38	decimation = vtk.vtkQuadricDecimation()
39		- decimation.SetInput(polydata)
	39	+ decimation.SetInputData(polydata)
40	40	decimation.SetTargetReduction(reduction_factor)
41	41	decimation.GetOutput().ReleaseDataFlagOn()
42	42	decimation.AddObserver("ProgressEvent", lambda obj, evt:
...	...	@@ -48,7 +48,7 @@ def ApplySmoothFilter(polydata, iterations, relaxation_factor):
48	48	Smooth given vtkPolyData surface, based on iteration and relaxation_factor.
49	49	"""
50	50	smoother = vtk.vtkSmoothPolyDataFilter()
51		- smoother.SetInput(polydata)
	51	+ smoother.SetInputData(polydata)
52	52	smoother.SetNumberOfIterations(iterations)
53	53	smoother.SetFeatureAngle(80)
54	54	smoother.SetRelaxationFactor(relaxation_factor)
...	...	@@ -69,7 +69,7 @@ def FillSurfaceHole(polydata):
69	69	# Filter used to detect and fill holes. Only fill
70	70	print "Filling polydata"
71	71	filled_polydata = vtk.vtkFillHolesFilter()
72		- filled_polydata.SetInput(polydata)
	72	+ filled_polydata.SetInputData(polydata)
73	73	filled_polydata.SetHoleSize(500)
74	74	return filled_polydata.GetOutput()
75	75
...	...	@@ -79,7 +79,7 @@ def CalculateSurfaceVolume(polydata):
79	79	"""
80	80	# Filter used to calculate volume and area from a polydata
81	81	measured_polydata = vtk.vtkMassProperties()
82		- measured_polydata.SetInput(polydata)
	82	+ measured_polydata.SetInputData(polydata)
83	83	return measured_polydata.GetVolume()
84	84
85	85	def CalculateSurfaceArea(polydata):
...	...	@@ -88,7 +88,7 @@ def CalculateSurfaceArea(polydata):
88	88	"""
89	89	# Filter used to calculate volume and area from a polydata
90	90	measured_polydata = vtk.vtkMassProperties()
91		- measured_polydata.SetInput(polydata)
	91	+ measured_polydata.SetInputData(polydata)
92	92	return measured_polydata.GetSurfaceArea()
93	93
94	94	def Merge(polydata_list):
...	...	@@ -96,11 +96,11 @@ def Merge(polydata_list):
96	96
97	97	for polydata in polydata_list:
98	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	102	clean = vtk.vtkCleanPolyData()
103		- clean.SetInput(append.GetOutput())
	103	+ clean.SetInputData(append.GetOutput())
104	104
105	105	return append.GetOutput()
106	106
...	...	@@ -112,7 +112,7 @@ def Export(polydata, filename, bin=False):
112	112	writer.SetDataModeToBinary()
113	113	else:
114	114	writer.SetDataModeToAscii()
115		- writer.SetInput(polydata)
	115	+ writer.SetInputData(polydata)
116	116	writer.Write()
117	117
118	118	def Import(filename):
...	...	@@ -130,7 +130,7 @@ def JoinSeedsParts(polydata, point_id_list):
130	130	from vtkPolyData.
131	131	"""
132	132	conn = vtk.vtkPolyDataConnectivityFilter()
133		- conn.SetInput(polydata)
	133	+ conn.SetInputData(polydata)
134	134	conn.SetExtractionModeToPointSeededRegions()
135	135	UpdateProgress = vu.ShowProgress(1 + len(point_id_list))
136	136	pos = 1
...	...	@@ -145,7 +145,6 @@ def JoinSeedsParts(polydata, point_id_list):
145	145
146	146	result = vtk.vtkPolyData()
147	147	result.DeepCopy(conn.GetOutput())
148		- result.Update()
149	148	return result
150	149
151	150	def SelectLargestPart(polydata):
...	...	@@ -153,7 +152,7 @@ def SelectLargestPart(polydata):
153	152	"""
154	153	UpdateProgress = vu.ShowProgress(1)
155	154	conn = vtk.vtkPolyDataConnectivityFilter()
156		- conn.SetInput(polydata)
	155	+ conn.SetInputData(polydata)
157	156	conn.SetExtractionModeToLargestRegion()
158	157	conn.AddObserver("ProgressEvent", lambda obj, evt:
159	158	UpdateProgress(conn, "Getting largest part..."))
...	...	@@ -161,14 +160,13 @@ def SelectLargestPart(polydata):
161	160
162	161	result = vtk.vtkPolyData()
163	162	result.DeepCopy(conn.GetOutput())
164		- result.Update()
165	163	return result
166	164
167	165	def SplitDisconectedParts(polydata):
168	166	"""
169	167	"""
170	168	conn = vtk.vtkPolyDataConnectivityFilter()
171		- conn.SetInput(polydata)
	169	+ conn.SetInputData(polydata)
172	170	conn.SetExtractionModeToAllRegions()
173	171	conn.Update()
174	172
...	...	@@ -191,7 +189,6 @@ def SplitDisconectedParts(polydata):
191	189
192	190	p = vtk.vtkPolyData()
193	191	p.DeepCopy(conn.GetOutput())
194		- p.Update()
195	192
196	193	polydata_collection.append(p)
197	194	if progress:
...	...
...	...	@@ -964,18 +964,18 @@ class Slice(object):
964	964	img = self.buffer_slices[orientation].vtk_image
965	965	original_orientation = Project().original_orientation
966	966	cast = vtk.vtkImageCast()
967		- cast.SetInput(img)
	967	+ cast.SetInputData(img)
968	968	cast.SetOutputScalarTypeToDouble()
969	969	cast.ClampOverflowOn()
970	970	cast.Update()
971	971
972	972	#if (original_orientation == const.AXIAL):
973	973	flip = vtk.vtkImageFlip()
974		- flip.SetInput(cast.GetOutput())
	974	+ flip.SetInputConnection(cast.GetOutputPort())
975	975	flip.SetFilteredAxis(1)
976	976	flip.FlipAboutOriginOn()
977	977	flip.Update()
978		- widget.SetInput(flip.GetOutput())
	978	+ widget.SetInputConnection(flip.GetOutputPort())
979	979	#else:
980	980	#widget.SetInput(cast.GetOutput())
981	981
...	...	@@ -1044,7 +1044,7 @@ class Slice(object):
1044	1044	i += 1
1045	1045
1046	1046	colorer = vtk.vtkImageMapToColors()
1047		- colorer.SetInput(image)
	1047	+ colorer.SetInputData(image)
1048	1048	colorer.SetLookupTable(lut)
1049	1049	colorer.SetOutputFormatToRGB()
1050	1050	colorer.Update()
...	...	@@ -1059,12 +1059,12 @@ class Slice(object):
1059	1059
1060	1060	colorer = vtk.vtkImageMapToColors()
1061	1061	colorer.SetLookupTable(lut)
1062		- colorer.SetInput(image)
	1062	+ colorer.SetInputData(image)
1063	1063	colorer.SetOutputFormatToRGB()
1064	1064	colorer.Update()
1065	1065	else:
1066	1066	colorer = vtk.vtkImageMapToWindowLevelColors()
1067		- colorer.SetInput(image)
	1067	+ colorer.SetInputData(image)
1068	1068	colorer.SetWindow(self.window_width)
1069	1069	colorer.SetLevel(self.window_level)
1070	1070	colorer.SetOutputFormatToRGB()
...	...	@@ -1148,7 +1148,7 @@ class Slice(object):
1148	1148	img_colours_bg = vtk.vtkImageMapToColors()
1149	1149	img_colours_bg.SetOutputFormatToRGB()
1150	1150	img_colours_bg.SetLookupTable(lut_bg)
1151		- img_colours_bg.SetInput(imagedata)
	1151	+ img_colours_bg.SetInputData(imagedata)
1152	1152	img_colours_bg.Update()
1153	1153
1154	1154	return img_colours_bg.GetOutput()
...	...	@@ -1179,7 +1179,7 @@ class Slice(object):
1179	1179	img_colours_mask = vtk.vtkImageMapToColors()
1180	1180	img_colours_mask.SetLookupTable(lut_mask)
1181	1181	img_colours_mask.SetOutputFormatToRGBA()
1182		- img_colours_mask.SetInput(imagedata)
	1182	+ img_colours_mask.SetInputData(imagedata)
1183	1183	img_colours_mask.Update()
1184	1184	# self.img_colours_mask = img_colours_mask
1185	1185
...	...	@@ -1211,7 +1211,7 @@ class Slice(object):
1211	1211	img_colours_mask = vtk.vtkImageMapToColors()
1212	1212	img_colours_mask.SetLookupTable(lut_mask)
1213	1213	img_colours_mask.SetOutputFormatToRGBA()
1214		- img_colours_mask.SetInput(imagedata)
	1214	+ img_colours_mask.SetInputData(imagedata)
1215	1215	img_colours_mask.Update()
1216	1216	# self.img_colours_mask = img_colours_mask
1217	1217
...	...	@@ -1225,8 +1225,8 @@ class Slice(object):
1225	1225	blend_imagedata.SetBlendModeToNormal()
1226	1226	# blend_imagedata.SetOpacity(0, 1.0)
1227	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	1230	blend_imagedata.Update()
1231	1231
1232	1232	return blend_imagedata.GetOutput()
...	...
...	...	@@ -55,7 +55,7 @@ class SliceData(object):
55	55
56	56	def __create_line_actor(self, line):
57	57	line_mapper = vtk.vtkPolyDataMapper2D()
58		- line_mapper.SetInput(line.GetOutput())
	58	+ line_mapper.SetInputConnection(line.GetOutputPort())
59	59
60	60	line_actor = vtk.vtkActor2D()
61	61	line_actor.SetMapper(line_mapper)
...	...
...	...	@@ -59,10 +59,14 @@ WATERSHED_OPERATIONS = {_("Erase"): BRUSH_ERASE,
59	59	_("Background"): BRUSH_BACKGROUND,}
60	60
61	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	71	class BaseImageInteractorStyle(vtk.vtkInteractorStyleImage):
68	72	def __init__(self, viewer):
...	...
...	...	@@ -42,6 +42,8 @@ try:
42	42	except ImportError:
43	43	import data.ca_smoothing as ca_smoothing
44	44
	45	+# TODO: Verificar ReleaseDataFlagOn and SetSource
	46	+
45	47	class Surface():
46	48	"""
47	49	Represent both vtkPolyData and associated properties.
...	...	@@ -240,12 +242,13 @@ class SurfaceManager():
240	242	name=None, colour=None,
241	243	transparency=None, volume=None):
242	244	normals = vtk.vtkPolyDataNormals()
243		- normals.SetInput(polydata)
	245	+ normals.SetInputData(polydata)
244	246	normals.SetFeatureAngle(80)
245	247	normals.AutoOrientNormalsOn()
	248	+ normals.Update()
246	249
247	250	mapper = vtk.vtkPolyDataMapper()
248		- mapper.SetInput(normals.GetOutput())
	251	+ mapper.SetInputData(normals.GetOutput())
249	252	mapper.ScalarVisibilityOff()
250	253	mapper.ImmediateModeRenderingOn() # improve performance
251	254
...	...	@@ -289,11 +292,12 @@ class SurfaceManager():
289	292	# The following lines have to be here, otherwise all volumes disappear
290	293	if not volume:
291	294	triangle_filter = vtk.vtkTriangleFilter()
292		- triangle_filter.SetInput(polydata)
	295	+ triangle_filter.SetInputData(polydata)
293	296	triangle_filter.Update()
294	297
295	298	measured_polydata = vtk.vtkMassProperties()
296		- measured_polydata.SetInput(triangle_filter.GetOutput())
	299	+ measured_polydata.SetInputConnection(triangle_filter.GetOutputPort())
	300	+ measured_polydata.Update()
297	301	volume = measured_polydata.GetVolume()
298	302	surface.volume = volume
299	303	print ">>>>", surface.volume
...	...	@@ -338,19 +342,19 @@ class SurfaceManager():
338	342	surface = surface_dict[key]
339	343	# Map polygonal data (vtkPolyData) to graphics primitives.
340	344	normals = vtk.vtkPolyDataNormals()
341		- normals.SetInput(surface.polydata)
	345	+ normals.SetInputData(surface.polydata)
342	346	normals.SetFeatureAngle(80)
343	347	normals.AutoOrientNormalsOn()
344		- normals.GetOutput().ReleaseDataFlagOn()
	348	+ # normals.GetOutput().ReleaseDataFlagOn()
345	349
346	350	# Improve performance
347	351	stripper = vtk.vtkStripper()
348		- stripper.SetInput(normals.GetOutput())
	352	+ stripper.SetInputData(normals.GetOutput())
349	353	stripper.PassThroughCellIdsOn()
350	354	stripper.PassThroughPointIdsOn()
351	355
352	356	mapper = vtk.vtkPolyDataMapper()
353		- mapper.SetInput(stripper.GetOutput())
	357	+ mapper.SetInputData(stripper.GetOutput())
354	358	mapper.ScalarVisibilityOff()
355	359	mapper.ImmediateModeRenderingOn() # improve performance
356	360
...	...	@@ -490,30 +494,30 @@ class SurfaceManager():
490	494	break
491	495
492	496	polydata_append = vtk.vtkAppendPolyData()
493		- polydata_append.ReleaseDataFlagOn()
	497	+ # polydata_append.ReleaseDataFlagOn()
494	498	t = n_pieces
495	499	while t:
496	500	filename_polydata = q_out.get()
497	501
498	502	reader = vtk.vtkXMLPolyDataReader()
499	503	reader.SetFileName(filename_polydata)
500		- reader.ReleaseDataFlagOn()
	504	+ # reader.ReleaseDataFlagOn()
501	505	reader.Update()
502		- reader.GetOutput().ReleaseDataFlagOn()
	506	+ # reader.GetOutput().ReleaseDataFlagOn()
503	507
504	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	512	del reader
509	513	del polydata
510	514	t -= 1
511	515
512	516	polydata_append.Update()
513		- polydata_append.GetOutput().ReleaseDataFlagOn()
	517	+ # polydata_append.GetOutput().ReleaseDataFlagOn()
514	518	polydata = polydata_append.GetOutput()
515	519	#polydata.Register(None)
516		- polydata.SetSource(None)
	520	+ # polydata.SetSource(None)
517	521	del polydata_append
518	522
519	523	if algorithm == 'ca_smoothing':
...	...	@@ -521,31 +525,31 @@ class SurfaceManager():
521	525	normals_ref = weakref.ref(normals)
522	526	normals_ref().AddObserver("ProgressEvent", lambda obj,evt:
523	527	UpdateProgress(normals_ref(), _("Creating 3D surface...")))
524		- normals.SetInput(polydata)
525		- normals.ReleaseDataFlagOn()
	528	+ normals.SetInputData(polydata)
	529	+ # normals.ReleaseDataFlagOn()
526	530	#normals.SetFeatureAngle(80)
527	531	#normals.AutoOrientNormalsOn()
528	532	normals.ComputeCellNormalsOn()
529		- normals.GetOutput().ReleaseDataFlagOn()
	533	+ # normals.GetOutput().ReleaseDataFlagOn()
530	534	normals.Update()
531	535	del polydata
532	536	polydata = normals.GetOutput()
533		- polydata.SetSource(None)
	537	+ # polydata.SetSource(None)
534	538	del normals
535	539
536	540	clean = vtk.vtkCleanPolyData()
537		- clean.ReleaseDataFlagOn()
538		- clean.GetOutput().ReleaseDataFlagOn()
	541	+ # clean.ReleaseDataFlagOn()
	542	+ # clean.GetOutput().ReleaseDataFlagOn()
539	543	clean_ref = weakref.ref(clean)
540	544	clean_ref().AddObserver("ProgressEvent", lambda obj,evt:
541	545	UpdateProgress(clean_ref(), _("Creating 3D surface...")))
542		- clean.SetInput(polydata)
	546	+ clean.SetInputData(polydata)
543	547	clean.PointMergingOn()
544	548	clean.Update()
545	549
546	550	del polydata
547	551	polydata = clean.GetOutput()
548		- polydata.SetSource(None)
	552	+ # polydata.SetSource(None)
549	553	del clean
550	554
551	555	try:
...	...	@@ -556,7 +560,7 @@ class SurfaceManager():
556	560	options['max distance'],
557	561	options['min weight'],
558	562	options['steps'])
559		- polydata.SetSource(None)
	563	+ # polydata.SetSource(None)
560	564	polydata.DebugOn()
561	565
562	566	else:
...	...	@@ -565,7 +569,7 @@ class SurfaceManager():
565	569	smoother_ref = weakref.ref(smoother)
566	570	smoother_ref().AddObserver("ProgressEvent", lambda obj,evt:
567	571	UpdateProgress(smoother_ref(), _("Creating 3D surface...")))
568		- smoother.SetInput(polydata)
	572	+ smoother.SetInputData(polydata)
569	573	smoother.SetNumberOfIterations(smooth_iterations)
570	574	smoother.SetRelaxationFactor(smooth_relaxation_factor)
571	575	smoother.SetFeatureAngle(80)
...	...	@@ -575,21 +579,21 @@ class SurfaceManager():
575	579	smoother.FeatureEdgeSmoothingOn()
576	580	#smoother.NormalizeCoordinatesOn()
577	581	#smoother.NonManifoldSmoothingOn()
578		- smoother.ReleaseDataFlagOn()
579		- smoother.GetOutput().ReleaseDataFlagOn()
	582	+ # smoother.ReleaseDataFlagOn()
	583	+ # smoother.GetOutput().ReleaseDataFlagOn()
580	584	smoother.Update()
581	585	del polydata
582	586	polydata = smoother.GetOutput()
583	587	#polydata.Register(None)
584		- polydata.SetSource(None)
	588	+ # polydata.SetSource(None)
585	589	del smoother
586	590
587	591
588	592	if decimate_reduction:
589	593	print "Decimating", decimate_reduction
590	594	decimation = vtk.vtkQuadricDecimation()
591		- decimation.ReleaseDataFlagOn()
592		- decimation.SetInput(polydata)
	595	+ # decimation.ReleaseDataFlagOn()
	596	+ decimation.SetInputData(polydata)
593	597	decimation.SetTargetReduction(decimate_reduction)
594	598	decimation_ref = weakref.ref(decimation)
595	599	decimation_ref().AddObserver("ProgressEvent", lambda obj,evt:
...	...	@@ -597,31 +601,31 @@ class SurfaceManager():
597	601	#decimation.PreserveTopologyOn()
598	602	#decimation.SplittingOff()
599	603	#decimation.BoundaryVertexDeletionOff()
600		- decimation.GetOutput().ReleaseDataFlagOn()
	604	+ # decimation.GetOutput().ReleaseDataFlagOn()
601	605	decimation.Update()
602	606	del polydata
603	607	polydata = decimation.GetOutput()
604	608	#polydata.Register(None)
605		- polydata.SetSource(None)
	609	+ # polydata.SetSource(None)
606	610	del decimation
607	611
608	612	to_measure = polydata
609	613	#to_measure.Register(None)
610		- to_measure.SetSource(None)
	614	+ # to_measure.SetSource(None)
611	615
612	616	if keep_largest:
613	617	conn = vtk.vtkPolyDataConnectivityFilter()
614		- conn.SetInput(polydata)
	618	+ conn.SetInputData(polydata)
615	619	conn.SetExtractionModeToLargestRegion()
616	620	conn_ref = weakref.ref(conn)
617	621	conn_ref().AddObserver("ProgressEvent", lambda obj,evt:
618	622	UpdateProgress(conn_ref(), _("Creating 3D surface...")))
619	623	conn.Update()
620		- conn.GetOutput().ReleaseDataFlagOn()
	624	+ # conn.GetOutput().ReleaseDataFlagOn()
621	625	del polydata
622	626	polydata = conn.GetOutput()
623	627	#polydata.Register(None)
624		- polydata.SetSource(None)
	628	+ # polydata.SetSource(None)
625	629	del conn
626	630
627	631	#Filter used to detect and fill holes. Only fill boundary edges holes.
...	...	@@ -629,59 +633,59 @@ class SurfaceManager():
629	633	#polydata_utils.FillSurfaceHole, we need to review this.
630	634	if fill_holes:
631	635	filled_polydata = vtk.vtkFillHolesFilter()
632		- filled_polydata.ReleaseDataFlagOn()
633		- filled_polydata.SetInput(polydata)
	636	+ # filled_polydata.ReleaseDataFlagOn()
	637	+ filled_polydata.SetInputData(polydata)
634	638	filled_polydata.SetHoleSize(300)
635	639	filled_polydata_ref = weakref.ref(filled_polydata)
636	640	filled_polydata_ref().AddObserver("ProgressEvent", lambda obj,evt:
637	641	UpdateProgress(filled_polydata_ref(), _("Creating 3D surface...")))
638	642	filled_polydata.Update()
639		- filled_polydata.GetOutput().ReleaseDataFlagOn()
	643	+ # filled_polydata.GetOutput().ReleaseDataFlagOn()
640	644	del polydata
641	645	polydata = filled_polydata.GetOutput()
642	646	#polydata.Register(None)
643		- polydata.SetSource(None)
	647	+ # polydata.SetSource(None)
644	648	polydata.DebugOn()
645	649	del filled_polydata
646	650
647	651	normals = vtk.vtkPolyDataNormals()
648		- normals.ReleaseDataFlagOn()
	652	+ # normals.ReleaseDataFlagOn()
649	653	normals_ref = weakref.ref(normals)
650	654	normals_ref().AddObserver("ProgressEvent", lambda obj,evt:
651	655	UpdateProgress(normals_ref(), _("Creating 3D surface...")))
652		- normals.SetInput(polydata)
	656	+ normals.SetInputData(polydata)
653	657	normals.SetFeatureAngle(80)
654	658	normals.AutoOrientNormalsOn()
655		- normals.GetOutput().ReleaseDataFlagOn()
	659	+ # normals.GetOutput().ReleaseDataFlagOn()
656	660	normals.Update()
657	661	del polydata
658	662	polydata = normals.GetOutput()
659	663	#polydata.Register(None)
660		- polydata.SetSource(None)
	664	+ # polydata.SetSource(None)
661	665	del normals
662	666
663	667	# Improve performance
664	668	stripper = vtk.vtkStripper()
665		- stripper.ReleaseDataFlagOn()
	669	+ # stripper.ReleaseDataFlagOn()
666	670	stripper_ref = weakref.ref(stripper)
667	671	stripper_ref().AddObserver("ProgressEvent", lambda obj,evt:
668	672	UpdateProgress(stripper_ref(), _("Creating 3D surface...")))
669		- stripper.SetInput(polydata)
	673	+ stripper.SetInputData(polydata)
670	674	stripper.PassThroughCellIdsOn()
671	675	stripper.PassThroughPointIdsOn()
672		- stripper.GetOutput().ReleaseDataFlagOn()
	676	+ # stripper.GetOutput().ReleaseDataFlagOn()
673	677	stripper.Update()
674	678	del polydata
675	679	polydata = stripper.GetOutput()
676	680	#polydata.Register(None)
677		- polydata.SetSource(None)
	681	+ # polydata.SetSource(None)
678	682	del stripper
679	683
680	684	# Map polygonal data (vtkPolyData) to graphics primitives.
681	685	mapper = vtk.vtkPolyDataMapper()
682		- mapper.SetInput(polydata)
	686	+ mapper.SetInputData(polydata)
683	687	mapper.ScalarVisibilityOff()
684		- mapper.ReleaseDataFlagOn()
	688	+ # mapper.ReleaseDataFlagOn()
685	689	mapper.ImmediateModeRenderingOn() # improve performance
686	690
687	691	# Represent an object (geometry & properties) in the rendered scene
...	...	@@ -720,8 +724,8 @@ class SurfaceManager():
720	724
721	725	# The following lines have to be here, otherwise all volumes disappear
722	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	729	volume = float(measured_polydata.GetVolume())
726	730	surface.volume = volume
727	731	self.last_surface_index = surface.index
...	...	@@ -858,14 +862,15 @@ class SurfaceManager():
858	862	if filetype in (const.FILETYPE_STL, const.FILETYPE_PLY):
859	863	# Invert normals
860	864	normals = vtk.vtkPolyDataNormals()
861		- normals.SetInput(polydata)
	865	+ normals.SetInputData(polydata)
862	866	normals.SetFeatureAngle(80)
863	867	normals.AutoOrientNormalsOn()
864		- normals.GetOutput().ReleaseDataFlagOn()
	868	+ # normals.GetOutput().ReleaseDataFlagOn()
865	869	normals.UpdateInformation()
	870	+ normals.Update()
866	871	polydata = normals.GetOutput()
867	872
868	873	filename = filename.encode(wx.GetDefaultPyEncoding())
869	874	writer.SetFileName(filename)
870		- writer.SetInput(polydata)
	875	+ writer.SetInputData(polydata)
871	876	writer.Write()
...	...
...	...	@@ -26,7 +26,7 @@ def ResampleImage3D(imagedata, value):
26	26	resolution = (height/(extent[1]-extent[0])+1)*spacing[1]
27	27
28	28	resample = vtk.vtkImageResample()
29		- resample.SetInput(imagedata)
	29	+ resample.SetInputData(imagedata)
30	30	resample.SetAxisMagnificationFactor(0, resolution)
31	31	resample.SetAxisMagnificationFactor(1, resolution)
32	32
...	...	@@ -106,7 +106,7 @@ class SurfaceProcess(multiprocessing.Process):
106	106	"AXIAL")
107	107
108	108	gauss = vtk.vtkImageGaussianSmooth()
109		- gauss.SetInput(image)
	109	+ gauss.SetInputData(image)
110	110	gauss.SetRadiusFactor(0.3)
111	111	gauss.ReleaseDataFlagOn()
112	112	gauss.Update()
...	...	@@ -125,7 +125,7 @@ class SurfaceProcess(multiprocessing.Process):
125	125	image = ResampleImage3D(image, self.imagedata_resolution)
126	126
127	127	flip = vtk.vtkImageFlip()
128		- flip.SetInput(image)
	128	+ flip.SetInputData(image)
129	129	flip.SetFilteredAxis(1)
130	130	flip.FlipAboutOriginOn()
131	131	flip.ReleaseDataFlagOn()
...	...	@@ -148,7 +148,7 @@ class SurfaceProcess(multiprocessing.Process):
148	148	#if self.mode == "CONTOUR":
149	149	#print "Contour"
150	150	contour = vtk.vtkContourFilter()
151		- contour.SetInput(image)
	151	+ contour.SetInputData(image)
152	152	#contour.SetInput(flip.GetOutput())
153	153	if self.from_binary:
154	154	contour.SetValue(0, 127) # initial threshold
...	...	@@ -202,7 +202,7 @@ class SurfaceProcess(multiprocessing.Process):
202	202
203	203	filename = tempfile.mktemp(suffix='_%s.vtp' % (self.pid))
204	204	writer = vtk.vtkXMLPolyDataWriter()
205		- writer.SetInput(polydata)
	205	+ writer.SetInputData(polydata)
206	206	writer.SetFileName(filename)
207	207	writer.Write()
208	208
...	...