309 lines
No EOL
11 KiB
Python
309 lines
No EOL
11 KiB
Python
"""
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Rendering of 3D TIFF stacks with VTK
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"""
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import os
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from argparse import ArgumentParser
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import vtk
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import mp_color_map
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def get_ox_map():
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files = ["/home/grogan/oxygen_solution_loc_0.vti",
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"/home/grogan/oxygen_solution_loc_1.vti",
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"/home/grogan/oxygen_solution_loc_2.vti",
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"/home/grogan/oxygen_solution_loc_3.vti"]
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offsets = [(0.0,0.0), (40.0, 0.0), (40.0, 40.0), (0.0, 40.0)]
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ox_actors = []
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for idx, eachFile in enumerate(files):
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reader = vtk.vtkXMLImageDataReader()
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reader.SetFileName(eachFile)
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reader.Update()
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reader.GetOutput().GetPointData().SetScalars(reader.GetOutput().GetPointData().GetArray("oxygen"))
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plane = vtk.vtkPlane()
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plane.SetOrigin(0.0, 0, 3)
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plane.SetNormal(0, 0, 1)
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cutter = vtk.vtkCutter()
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cutter.SetInputData(reader.GetOutput())
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cutter.SetCutFunction(plane)
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cutter.GenerateCutScalarsOn()
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cutter.Update()
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trans = vtk.vtkTransform()
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trans.Scale(42.375, 42.375, 42.375)
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transf = vtk.vtkTransformFilter()
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transf.SetInputData(cutter.GetOutput())
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transf.SetTransform(trans)
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transf.Update()
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trans1 = vtk.vtkTransform()
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trans1.Translate(42.375*offsets[idx][0], 42.375*offsets[idx][1], 0.0)
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transf2 = vtk.vtkTransformFilter()
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transf2.SetInputData(transf.GetOutput())
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transf2.SetTransform(trans1)
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transf2.Update()
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warp = vtk.vtkWarpScalar()
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warp.SetInputData(transf2.GetOutput())
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warp.SetScaleFactor(0.15*42.375)
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warp.Update()
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scaled_ctf = vtk.vtkColorTransferFunction()
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scalar_range = [0, 0]
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warp.GetOutput().GetPointData().GetArray("oxygen").GetRange(scalar_range)
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for idx in range(256):
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color = [0, 0, 0]
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mp_color_map.get_ctf().GetColor(float(idx)/255.0, color)
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scaled_ctf.AddRGBPoint(scalar_range[0] + float(idx)*(scalar_range[1]-scalar_range[0])/255.0,
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color[0], color[1], color[2])
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ox_mapper = vtk.vtkPolyDataMapper()
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ox_mapper.SetInputData(warp.GetOutput())
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ox_mapper.ScalarVisibilityOn()
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ox_mapper.SetLookupTable(scaled_ctf)
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ox_mapper.SelectColorArray("oxygen")
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ox_mapper.SetScalarModeToUsePointFieldData()
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ox_mapper.SetColorModeToMapScalars()
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#ox_mapper.ScalarVisibilityOn()
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ox_actor = vtk.vtkActor()
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ox_actor.SetMapper(ox_mapper)
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ox_actor.GetProperty().SetColor(0.0, 1.0, 0.0)
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ox_actor.GetProperty().SetOpacity(0.5)
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ox_actors.append(ox_actor)
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scale_bar = vtk.vtkScalarBarActor()
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scale_bar.SetLookupTable(scaled_ctf);
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#scale_bar.SetTitle("Oxygen Tension (mmHg)");
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scale_bar.SetOrientationToVertical();
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scale_bar.GetPositionCoordinate().SetCoordinateSystemToNormalizedViewport();
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scale_bar.GetPositionCoordinate().SetValue(0.23, 0.27);
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scale_bar.SetWidth(0.08);
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scale_bar.SetHeight(0.6);
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#scale_bar.SetAnnotationTextScalingOff()
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#scale_bar.UnconstrainedFontSizeOn()
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scale_bar.GetTitleTextProperty().ItalicOff();
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scale_bar.GetLabelTextProperty().ItalicOff();
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scale_bar.GetTitleTextProperty().BoldOff();
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scale_bar.GetLabelTextProperty().BoldOff();
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scale_bar.GetTitleTextProperty().ShadowOff();
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scale_bar.GetLabelTextProperty().ShadowOff();
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scale_bar.SetLabelFormat("%.2g");
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scale_bar.GetTitleTextProperty().SetFontSize(15)
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scale_bar.GetLabelTextProperty().SetFontSize(15)
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scale_bar.GetTitleTextProperty().SetColor(1.0, 1.0, 1.0);
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scale_bar.GetLabelTextProperty().SetColor(1.0, 1.0, 1.0);
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return ox_actors, scale_bar
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def add_cells():
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cell_files = ["/scratch/jgrogan/TBME_16_Work/Simulations/BioHigh_15x/Bio3d_1/results_from_time_0/results_20.vtu",
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"/scratch/jgrogan/TBME_16_Work/Simulations/BioHigh_15x/Bio3d_1/results_from_time_0/results_100.vtu",
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"/scratch/jgrogan/TBME_16_Work/Simulations/BioHigh_15x/Bio3d_1/results_from_time_0/results_150.vtu"]
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cell_actors = []
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for eachFile in cell_files:
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reader = vtk.vtkXMLUnstructuredGridReader()
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reader.SetFileName(eachFile)
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reader.Update()
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spheres = vtk.vtkSphereSource()
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spheres.SetRadius(0.6)
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spheres.SetPhiResolution(8)
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spheres.SetThetaResolution(8)
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glyph = vtk.vtkGlyph3D()
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glyph.SetInputData(reader.GetOutput());
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glyph.SetSourceConnection(spheres.GetOutputPort());
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glyph.ClampingOff();
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glyph.SetScaleModeToScaleByScalar();
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glyph.SetScaleFactor(0.8);
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glyph.Update();
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trans = vtk.vtkTransform()
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trans.Scale(42.375, 42.375, 42.375)
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transf = vtk.vtkTransformFilter()
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transf.SetInputData(glyph.GetOutput())
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transf.SetTransform(trans)
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transf.Update()
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scaled_ctf = vtk.vtkColorTransferFunction()
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scalar_range = [0, 0]
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reader.GetOutput().GetPointData().GetArray("Cell types").GetRange(scalar_range)
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for idx in range(256):
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color = [0, 0, 0]
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mp_color_map.get_disc_ctf().GetColor(float(idx)/255.0, color)
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scaled_ctf.AddRGBPoint(scalar_range[0] + float(idx)*(scalar_range[1]-scalar_range[0])/255.0,
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color[0], color[1], color[2])
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mapper = vtk.vtkPolyDataMapper();
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mapper.SetInputData(transf.GetOutput());
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mapper.SetLookupTable(scaled_ctf);
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mapper.ScalarVisibilityOn();
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mapper.SelectColorArray("Cell types");
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mapper.SetScalarModeToUsePointFieldData();
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mapper.SetColorModeToMapScalars();
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actor = vtk.vtkActor();
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actor.SetMapper(mapper);
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actor.GetProperty().SetOpacity(0.8);
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cell_actors.append(actor)
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return cell_actors
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# if(!this->mDataLabel.empty() and this->mShowScaleBar)
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# {
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# this->mpScaleBar->SetLookupTable(p_scaled_ctf);
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# this->mpScaleBar->SetTitle(this->mDataLabel.c_str());
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# pRenderer->AddActor(this->mpScaleBar);
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# }
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def render_image(image_path, threshold = 20.0):
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"""
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Render the 3D stack with VTK
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"""
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input_files = []
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for eachFile in os.listdir(image_path):
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if eachFile.endswith(".vti"):
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input_files.append(image_path + "/"+eachFile)
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renderer = vtk.vtkRenderer()
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renderer.SetBackground(20.0/255.0,30.0/255.0,48.0/255.0);
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renderer.SetBackground2(36.0/255.0,59.0/255.0,85.0/255.0);
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for eachImage in input_files:
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reader= vtk.vtkXMLImageDataReader()
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reader.SetFileName(eachImage)
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reader.Update()
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volume_mapper = vtk.vtkVolumeRayCastMapper()
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volume_mapper.SetInputData(reader.GetOutput())
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composite_function = vtk.vtkVolumeRayCastCompositeFunction()
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volume_mapper.SetVolumeRayCastFunction(composite_function)
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color_transfer_func = vtk.vtkColorTransferFunction()
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color_transfer_func.AddRGBPoint(0, 0.0, 1.0, 0.0 )
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color_transfer_func.AddRGBPoint(threshold-1, 0.0, 1.0, 0.0 )
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color_transfer_func.AddRGBPoint(threshold, 1.0, 0.0, 0.0 )
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color_transfer_func.AddRGBPoint(255.0, 1.0, 0.0, 0.0 )
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opacity_transfer_func = vtk.vtkPiecewiseFunction()
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opacity_transfer_func.AddPoint(0, 0.0 )
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opacity_transfer_func.AddPoint(threshold-1.0, 0.0 )
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#opacity_transfer_func.AddPoint(threshold, 1.0 )
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opacity_transfer_func.AddPoint(255.0, 0.1 )
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volume_properties = vtk.vtkVolumeProperty()
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volume_properties.SetColor( color_transfer_func )
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volume_properties.SetScalarOpacity( opacity_transfer_func )
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volume = vtk.vtkVolume()
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volume.SetMapper(volume_mapper)
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volume.SetProperty(volume_properties)
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renderer.AddVolume(volume)
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# textActor = vtk.vtkTextActor()
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# textActor.SetTextScaleModeToNone()
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# textActor.SetDisplayPosition(200, 300)
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# textActor.SetInput("Oxygen Tension (mmHg)")
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# tprop = textActor.GetTextProperty()
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# tprop.SetFontSize(10)
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# tprop.SetFontFamilyToArial()
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# tprop.SetJustificationToCentered()
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# tprop.BoldOff()
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# tprop.ItalicOff()
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# tprop.ShadowOff()
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# tprop.SetColor(1, 1, 1)
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# #renderer.AddActor2D(textActor)
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renderer.ResetCamera()
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render_window = vtk.vtkRenderWindow()
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window_interactor = vtk.vtkRenderWindowInteractor()
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render_window.AddRenderer(renderer)
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window_interactor.SetRenderWindow(render_window)
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render_window.SetSize(170, 177)
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render_window.Render()
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ox_actors, scale_bar_actor = get_ox_map()
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#renderer.AddActor(scale_bar_actor)
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render_window.Render()
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renderer.GetActiveCamera().Elevation(-33.0)
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renderer.GetActiveCamera().Zoom(1.0)
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position = list(renderer.GetActiveCamera().GetFocalPoint())
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#position[0] = position[0] - 750
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#position[1] = position[1] - 105
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renderer.GetActiveCamera().SetFocalPoint(position)
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renderer.ResetCameraClippingRange()
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render_window.Render()
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window_to_image_filter = vtk.vtkWindowToImageFilter()
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window_to_image_filter.SetInput(render_window)
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writer = vtk.vtkTIFFWriter()
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extension = ".tiff"
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writer.SetInputConnection(window_to_image_filter.GetOutputPort())
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writer.SetFileName("vtk_animation_0"+extension)
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writer.Write()
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num_samples = 1
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for idx in range(num_samples):
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if idx==0:
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for eachActor in ox_actors:
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renderer.AddActor(eachActor)
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renderer.GetActiveCamera().OrthogonalizeViewUp()
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#time.sleep(0.02)
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#renderer.GetActiveCamera().Dolly(1.002))
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render_window.Render()
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window_to_image_filter.Modified()
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writer.SetFileName("vtk_animation_"+str(idx+1)+extension)
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writer.Write()
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renderer.RemoveActor(ox_actors[0])
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render_window.Render()
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window_to_image_filter.Modified()
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writer.SetFileName("vtk_animation_"+str(num_samples+1)+extension)
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writer.Write()
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cell_actors = add_cells()
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renderer.AddActor(cell_actors[0])
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render_window.Render()
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window_to_image_filter.Modified()
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writer.SetFileName("vtk_animation_"+str(num_samples+2)+extension)
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writer.Write()
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renderer.RemoveActor(cell_actors[0])
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renderer.AddActor(cell_actors[1])
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render_window.Render()
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window_to_image_filter.Modified()
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writer.SetFileName("vtk_animation_"+str(num_samples+3)+extension)
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writer.Write()
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renderer.RemoveActor(cell_actors[1])
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renderer.AddActor(cell_actors[2])
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render_window.Render()
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window_to_image_filter.Modified()
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writer.SetFileName("vtk_animation_"+str(num_samples+4)+extension)
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writer.Write()
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window_interactor.Start()
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if __name__ == "__main__":
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parser = ArgumentParser()
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parser.add_argument("-i", "--input_file", type=str, help='vtk input file')
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args = parser.parse_args()
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render_image(args.input_file) |