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Commit 19c511ef7177e0b53cfb1e843140e0c6bfc966ed

Authored by tfmoraes
1 parent cfadc616
Exists in master and in 67 other branches 3d_inter_style, MIPs, beta3, beta4, brush_pix, canvas_reeng, canvas_text, casmoothing_cython, clean, command-line, cython_threshold, debian_cython, editor_improvements, encoding, ff_mask, ff_mask_improv, ffill_gui, ffill_segmentation, fill_holes_auto, fixes_pre_beta5, floodfill, get_pixel, import_mesh, interactor_style, inv3.0.1, mactoolbar, mactoolbar_bkp, manual_v3.1, mask_boolean_op, mask_boolean_op_bkp, mask_copy, mask_greatest_component, measure, measure_canvas, measure_improvements, measure_placement_test, measure_spacing, orientation, phoenix, region_growing_confidence, remote, remove_local_wxpython, rmatsuda-fix_ref_MTC, rmatsuda-fix_remove_marker_bug, rmatsuda-trigger_bug_fix, rotvol, segmentation_menu, select_part, smoothing_bin, smoothing_bin_pll, surface_area, threshold_history, user_guide_en, usp-navegador, vti, vtk6, watershed, watershed_improvements, watershed_improvements_bkp, watershed_merge, workdir, wwwlgui, wx2.9_mac, wxgtk3, wxgtk3_b5, wxgtk3_bkp, xmartlabs-command-line

ENH: Some tests with smoothing in surface generation

Showing 1 changed file with 30 additions and 26 deletions   Show diff stats
invesalius/data/surface_process.py
  Diff comments   View file @19c511e
@@ -50,32 +50,32 @@ class SurfaceProcess(multiprocessing.Process): @@ -50,32 +50,32 @@ class SurfaceProcess(multiprocessing.Process):
50 self.pipe.send([prog, msg]) 50 self.pipe.send([prog, msg])
51 51
52 def CreateSurface(self, roi): 52 def CreateSurface(self, roi):
53 - smoothed = ndimage.gaussian_filter(self.mask[roi], (1, 1, 1)) 53 + smoothed = numpy.array(self.mask[roi])
54 image = imagedata_utils.to_vtk(smoothed, self.spacing, roi.start, 54 image = imagedata_utils.to_vtk(smoothed, self.spacing, roi.start,
55 "AXIAL") 55 "AXIAL")
56 56
57 # Create vtkPolyData from vtkImageData 57 # Create vtkPolyData from vtkImageData
58 - print "Generating Polydata"  
59 - if self.mode == "CONTOUR":  
60 - print "Contour"  
61 - contour = vtk.vtkContourFilter()  
62 - contour.SetInput(image)  
63 - contour.SetValue(0, 127.5) # initial threshold  
64 - contour.ComputeScalarsOn()  
65 - contour.ComputeGradientsOn()  
66 - contour.ComputeNormalsOn()  
67 - polydata = contour.GetOutput()  
68 - else: #mode == "GRAYSCALE":  
69 - mcubes = vtk.vtkMarchingCubes()  
70 - mcubes.SetInput(image)  
71 - mcubes.SetValue(0, 127.5)  
72 - mcubes.ComputeScalarsOn()  
73 - mcubes.ComputeGradientsOn()  
74 - mcubes.ComputeNormalsOn()  
75 - polydata = mcubes.GetOutput() 58 + #print "Generating Polydata"
  59 + #if self.mode == "CONTOUR":
  60 + #print "Contour"
  61 + #contour = vtk.vtkContourFilter()
  62 + #contour.SetInput(image)
  63 + #contour.SetValue(0, 127.5) # initial threshold
  64 + #contour.ComputeScalarsOn()
  65 + #contour.ComputeGradientsOn()
  66 + #contour.ComputeNormalsOn()
  67 + #polydata = contour.GetOutput()
  68 + #else: #mode == "GRAYSCALE":
  69 + mcubes = vtk.vtkDiscreteMarchingCubes()
  70 + mcubes.SetInput(image)
  71 + mcubes.SetValue(0, 255)
  72 + mcubes.ComputeScalarsOn()
  73 + mcubes.ComputeGradientsOn()
  74 + mcubes.ComputeNormalsOn()
  75 + polydata = mcubes.GetOutput()
76 76
77 print "Decimating" 77 print "Decimating"
78 - if self.decimate_reduction: 78 + if not self.decimate_reduction:
79 decimation = vtk.vtkDecimatePro() 79 decimation = vtk.vtkDecimatePro()
80 decimation.SetInput(polydata) 80 decimation.SetInput(polydata)
81 decimation.SetTargetReduction(self.decimate_reduction) 81 decimation.SetTargetReduction(self.decimate_reduction)
@@ -83,19 +83,23 @@ class SurfaceProcess(multiprocessing.Process): @@ -83,19 +83,23 @@ class SurfaceProcess(multiprocessing.Process):
83 decimation.SplittingOff() 83 decimation.SplittingOff()
84 polydata = decimation.GetOutput() 84 polydata = decimation.GetOutput()
85 85
86 - print "Smoothing"  
87 if self.smooth_iterations and self.smooth_relaxation_factor: 86 if self.smooth_iterations and self.smooth_relaxation_factor:
88 - smoother = vtk.vtkSmoothPolyDataFilter() 87 + print "Smoothing"
  88 + smoother = vtk.vtkWindowedSincPolyDataFilter()
89 smoother.SetInput(polydata) 89 smoother.SetInput(polydata)
90 smoother.SetNumberOfIterations(self.smooth_iterations) 90 smoother.SetNumberOfIterations(self.smooth_iterations)
91 - smoother.SetFeatureAngle(80)  
92 - smoother.SetRelaxationFactor(self.smooth_relaxation_factor)  
93 - smoother.FeatureEdgeSmoothingOn() 91 + smoother.SetFeatureAngle(120)
  92 + smoother.SetNumberOfIterations(30)
94 smoother.BoundarySmoothingOn() 93 smoother.BoundarySmoothingOn()
  94 + smoother.SetPassBand(0.1)
  95 + smoother.FeatureEdgeSmoothingOn()
  96 + smoother.NonManifoldSmoothingOn()
  97 + smoother.NormalizeCoordinatesOn()
  98 + smoother.Update()
95 polydata = smoother.GetOutput() 99 polydata = smoother.GetOutput()
96 100
97 print "Saving" 101 print "Saving"
98 - filename = tempfile.mktemp() 102 + filename = tempfile.mktemp(suffix='_%s.vtp' % (self.pid))
99 writer = vtk.vtkXMLPolyDataWriter() 103 writer = vtk.vtkXMLPolyDataWriter()
100 writer.SetInput(polydata) 104 writer.SetInput(polydata)
101 writer.SetFileName(filename) 105 writer.SetFileName(filename)