107 lines
No EOL
5 KiB
Python
107 lines
No EOL
5 KiB
Python
import pickle
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import vtk
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import os
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from stack3d.study.components import StudyData, MouseData, TimepointData
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import stack3d.formats.unet
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def render_skeleton(work_dir, study_collection):
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for eachStudy in study_collection:
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print "Rendering Study: ", eachStudy.raw_data_path
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study_dir = work_dir + "/" + eachStudy.raw_data_path
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for eachMouse in eachStudy.mice:
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print "Rendering Mouse: ", eachMouse.raw_data_path
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mouse_dir = study_dir + "/" + eachMouse.raw_data_path
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for eachTimePoint in eachMouse.timepoints:
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print "Rendering Time: ", eachTimePoint.raw_data_path
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time_dir = mouse_dir + "/" + eachTimePoint.raw_data_path
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base_path = "/analysis_analysis/skeleton.vtp"
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if os.path.isfile(time_dir + base_path):
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reader = vtk.vtkXMLPolyDataReader()
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reader.SetFileName(time_dir + base_path)
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reader.Update()
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polydata = reader.GetOutput()
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cell_to_point = vtk.vtkCellDataToPointData()
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cell_to_point.SetInputData(polydata)
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cell_to_point.Update()
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tubes = vtk.vtkTubeFilter()
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tubes.SetInputData(cell_to_point.GetOutput())
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tubes.SetNumberOfSides(6)
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tubes.SetRadius(1.0)
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tubes.SetRadiusFactor(50.0)
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tubes.SetVaryRadiusToVaryRadiusByScalar()
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tubes.Update()
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mapper = vtk.vtkPolyDataMapper()
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mapper.SetInputData(tubes.GetOutput())
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mapper.ScalarVisibilityOff()
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actor = vtk.vtkActor()
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actor.SetMapper(mapper)
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actor.GetProperty().SetColor(1, 0, 0)
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textActor = vtk.vtkTextActor()
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textActor.SetTextScaleModeToProp()
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textActor.SetDisplayPosition(400, 50)
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inp_string = "Study: " + eachStudy.raw_data_path
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inp_string += " | Mouse: " + eachMouse.raw_data_path
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inp_string += " | Time: " + eachTimePoint.raw_data_path
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textActor.SetInput(inp_string)
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tprop = textActor.GetTextProperty()
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tprop.SetFontSize(24)
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tprop.SetFontFamilyToArial()
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tprop.SetJustificationToCentered()
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tprop.BoldOn()
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tprop.ItalicOn()
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tprop.ShadowOn()
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tprop.SetColor(0, 0, 1)
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cubesource = vtk.vtkCubeSource()
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cubesource.SetBounds(0, 4000, 0, 4000, 0, 70)
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cubesource.Update()
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cube_mapper = vtk.vtkPolyDataMapper()
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cube_mapper.SetInputConnection(cubesource.GetOutputPort())
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cube_mapper.ScalarVisibilityOff()
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cube_actor = vtk.vtkActor()
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cube_actor.SetMapper(cube_mapper)
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cube_actor.GetProperty().SetColor(0, 0, 0)
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cube_actor.GetProperty().SetOpacity(0.1)
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# Create a renderer, render window, and interactor
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renderer = vtk.vtkRenderer()
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renderer.SetBackground(1, 1, 1)
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renderer.AddActor2D(textActor)
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#renderer.GetActiveCamera().Zoom(1.0)
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renderWindow = vtk.vtkRenderWindow()
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renderWindow.SetSize(1200, 800)
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renderWindow.SetAlphaBitPlanes(1)
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renderWindow.AddRenderer(renderer)
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# renderWindowInteractor = vtk.vtkRenderWindowInteractor()
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# renderWindowInteractor.SetRenderWindow(renderWindow)
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# Add the actors to the scene
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renderer.AddActor(actor)
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renderer.AddActor(cube_actor)
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renderer.ResetCameraClippingRange()
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# Render and interact
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renderWindow.Render()
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#renderWindowInteractor.Start()
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window_to_image_filter = vtk.vtkWindowToImageFilter()
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window_to_image_filter.SetInput(renderWindow)
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window_to_image_filter.SetMagnification(1);
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window_to_image_filter.SetInputBufferTypeToRGBA()
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window_to_image_filter.ReadFrontBufferOff()
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writer = vtk.vtkTIFFWriter()
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writer.SetInputConnection(window_to_image_filter.GetOutputPort())
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writer.SetFileName(time_dir + "/analysis_analysis/rendering.tiff")
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writer.Write()
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work_dir = "/scratch/jgrogan/stack-working/study/"
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f = open(work_dir + "/study_collection.p", 'r')
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study_collection = pickle.load(f)
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render_skeleton(work_dir, study_collection) |