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‎README.md

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Original file line numberDiff line numberDiff line change
@@ -14,11 +14,11 @@ Note that the results displayed here are re-generated every time a push is made
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## Install dependencies
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To run the code in this repo you need FEniCS and gmsh with OpenCascade installed. The easiest way to do this is to either use the provided docker image, i.e
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```
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docker pull ghcr.io/computationalphysiology/ciucci-2024:v1.0.0
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docker pull ghcr.io/computationalphysiology/ciucci-2024:latest
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```
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You can create a new container using the command
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```
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docker run --name ciucci -w /home/shared -v $PWD:/home/shared -it ghcr.io/computationalphysiology/ciucci-2024:v1.0.0
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docker run --name ciucci -w /home/shared -v $PWD:/home/shared -it ghcr.io/computationalphysiology/ciucci-2024:latest
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```
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which will also share your current directory with the container. If you are interested you can also check out the [Dockerfile](Dockerfile) if you want to know how the image was created.
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‎code/create_paraview_figure.py

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# trace generated using paraview version 5.11.0
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# import paraview
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# paraview.compatibility.major = 5
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# paraview.compatibility.minor = 11
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#### import the simple module from the paraview
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from paraview.simple import *
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def main(filename, min_value, max_value, name, label, blocknr, figure_folder):
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#### disable automatic camera reset on 'Show'
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paraview.simple._DisableFirstRenderCameraReset()
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# create a new 'Xdmf3ReaderT'
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resultsxdmf = Xdmf3ReaderT(
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registrationName="results.xdmf",
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FileName=[
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filename,
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],
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)
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# get animation scene
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animationScene1 = GetAnimationScene()
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# get the time-keeper
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timeKeeper1 = GetTimeKeeper()
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# update animation scene based on data timesteps
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animationScene1.UpdateAnimationUsingDataTimeSteps()
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# get active view
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renderView1 = GetActiveViewOrCreate("RenderView")
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# # create a new 'Extract Block'
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extractBlock = ExtractBlock(registrationName="ExtractBlock", Input=resultsxdmf)
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# # Properties modified on extractBlock
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extractBlock.Selectors = [f"/Root/Block{blocknr}"]
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# show data in view
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extractBlockDisplay = Show(extractBlock, renderView1, "UnstructuredGridRepresentation")
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# get color transfer function/color map for 'sigma_xx'
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sigma_xxLUT = GetColorTransferFunction(name)
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# get opacity transfer function/opacity map for 'sigma_xx'
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sigma_xxPWF = GetOpacityTransferFunction(name)
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# trace defaults for the display properties.
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extractBlockDisplay.Representation = "Surface"
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extractBlockDisplay.ColorArrayName = ["POINTS", name]
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extractBlockDisplay.LookupTable = sigma_xxLUT
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extractBlockDisplay.SelectTCoordArray = "None"
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extractBlockDisplay.SelectNormalArray = "None"
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extractBlockDisplay.SelectTangentArray = "None"
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extractBlockDisplay.OSPRayScaleArray = name
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extractBlockDisplay.OSPRayScaleFunction = "PiecewiseFunction"
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extractBlockDisplay.SelectOrientationVectors = "None"
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extractBlockDisplay.ScaleFactor = 400.0
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extractBlockDisplay.SelectScaleArray = name
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extractBlockDisplay.GlyphType = "Arrow"
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extractBlockDisplay.GlyphTableIndexArray = name
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extractBlockDisplay.GaussianRadius = 20.0
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extractBlockDisplay.SetScaleArray = ["POINTS", name]
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extractBlockDisplay.ScaleTransferFunction = "PiecewiseFunction"
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extractBlockDisplay.OpacityArray = ["POINTS", name]
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extractBlockDisplay.OpacityTransferFunction = "PiecewiseFunction"
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extractBlockDisplay.DataAxesGrid = "GridAxesRepresentation"
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extractBlockDisplay.PolarAxes = "PolarAxesRepresentation"
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extractBlockDisplay.ScalarOpacityFunction = sigma_xxPWF
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extractBlockDisplay.ScalarOpacityUnitDistance = 120.50872400061667
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extractBlockDisplay.OpacityArrayName = ["POINTS", name]
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extractBlockDisplay.SelectInputVectors = [None, ""]
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extractBlockDisplay.WriteLog = ""
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# init the 'PiecewiseFunction' selected for 'ScaleTransferFunction'
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extractBlockDisplay.ScaleTransferFunction.Points = [
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2.5313084643816214e-16,
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0.0,
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0.5,
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0.0,
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2.531850565467864e-16,
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1.0,
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0.5,
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0.0,
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]
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# init the 'PiecewiseFunction' selected for 'OpacityTransferFunction'
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extractBlockDisplay.OpacityTransferFunction.Points = [
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2.5313084643816214e-16,
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0.0,
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0.5,
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0.0,
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2.531850565467864e-16,
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1.0,
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0.5,
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0.0,
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]
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# hide data in view
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Hide(resultsxdmf, renderView1)
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# show color bar/color legend
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extractBlockDisplay.SetScalarBarVisibility(renderView1, True)
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# update the view to ensure updated data information
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renderView1.Update()
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# get 2D transfer function for 'sigma_xx'
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sigma_xxTF2D = GetTransferFunction2D(name)
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animationScene1.GoToNext()
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# Rescale transfer function
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sigma_xxLUT.RescaleTransferFunction(-2.8939850330352783, 7.81556510925293)
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# Rescale transfer function
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sigma_xxPWF.RescaleTransferFunction(-2.8939850330352783, 7.81556510925293)
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# create a new 'Clip'
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clip1 = Clip(registrationName="Clip1", Input=extractBlock)
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clip1.ClipType = "Plane"
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clip1.HyperTreeGridClipper = "Plane"
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clip1.Scalars = ["POINTS", name]
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clip1.Value = 2.4607900381088257
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# show data in view
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clip1Display = Show(clip1, renderView1, "UnstructuredGridRepresentation")
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# trace defaults for the display properties.
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clip1Display.Representation = "Surface"
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clip1Display.ColorArrayName = ["POINTS", name]
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clip1Display.LookupTable = sigma_xxLUT
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clip1Display.SelectTCoordArray = "None"
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clip1Display.SelectNormalArray = "None"
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clip1Display.SelectTangentArray = "None"
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clip1Display.OSPRayScaleArray = name
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clip1Display.OSPRayScaleFunction = "PiecewiseFunction"
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clip1Display.SelectOrientationVectors = "None"
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clip1Display.ScaleFactor = 200.0
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clip1Display.SelectScaleArray = name
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clip1Display.GlyphType = "Arrow"
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clip1Display.GlyphTableIndexArray = name
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clip1Display.GaussianRadius = 10.0
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clip1Display.SetScaleArray = ["POINTS", name]
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clip1Display.ScaleTransferFunction = "PiecewiseFunction"
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clip1Display.OpacityArray = ["POINTS", name]
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clip1Display.OpacityTransferFunction = "PiecewiseFunction"
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clip1Display.DataAxesGrid = "GridAxesRepresentation"
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clip1Display.PolarAxes = "PolarAxesRepresentation"
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clip1Display.ScalarOpacityFunction = sigma_xxPWF
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clip1Display.ScalarOpacityUnitDistance = 80.35903137837035
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clip1Display.OpacityArrayName = ["POINTS", name]
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clip1Display.SelectInputVectors = [None, ""]
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clip1Display.WriteLog = ""
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# init the 'PiecewiseFunction' selected for 'ScaleTransferFunction'
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clip1Display.ScaleTransferFunction.Points = [
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-2.8062829971313477,
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0.0,
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0.5,
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0.0,
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7.81556510925293,
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1.0,
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0.5,
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0.0,
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]
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# init the 'PiecewiseFunction' selected for 'OpacityTransferFunction'
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clip1Display.OpacityTransferFunction.Points = [
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-2.8062829971313477,
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0.0,
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0.5,
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0.0,
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7.81556510925293,
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1.0,
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0.5,
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0.0,
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]
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# hide data in view
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Hide(extractBlock, renderView1)
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# show color bar/color legend
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clip1Display.SetScalarBarVisibility(renderView1, True)
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# update the view to ensure updated data information
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renderView1.Update()
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# set active source
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SetActiveSource(extractBlock)
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# toggle interactive widget visibility (only when running from the GUI)
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HideInteractiveWidgets(proxy=clip1.ClipType)
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# create a new 'Clip'
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clip2 = Clip(registrationName="Clip2", Input=extractBlock)
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clip2.ClipType = "Plane"
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clip2.HyperTreeGridClipper = "Plane"
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clip2.Scalars = ["POINTS", name]
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clip2.Value = 2.4607900381088257
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# Properties modified on clip2.ClipType
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clip2.ClipType.Normal = [0.0, 1.0, 0.0]
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# show data in view
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clip2Display = Show(clip2, renderView1, "UnstructuredGridRepresentation")
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# trace defaults for the display properties.
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clip2Display.Representation = "Surface"
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clip2Display.ColorArrayName = ["POINTS", name]
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clip2Display.LookupTable = sigma_xxLUT
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clip2Display.SelectTCoordArray = "None"
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clip2Display.SelectNormalArray = "None"
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clip2Display.SelectTangentArray = "None"
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clip2Display.OSPRayScaleArray = name
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clip2Display.OSPRayScaleFunction = "PiecewiseFunction"
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clip2Display.SelectOrientationVectors = "None"
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clip2Display.ScaleFactor = 400.0
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clip2Display.SelectScaleArray = name
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clip2Display.GlyphType = "Arrow"
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clip2Display.GlyphTableIndexArray = name
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clip2Display.GaussianRadius = 20.0
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clip2Display.SetScaleArray = ["POINTS", name]
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clip2Display.ScaleTransferFunction = "PiecewiseFunction"
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clip2Display.OpacityArray = ["POINTS", name]
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clip2Display.OpacityTransferFunction = "PiecewiseFunction"
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clip2Display.DataAxesGrid = "GridAxesRepresentation"
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clip2Display.PolarAxes = "PolarAxesRepresentation"
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clip2Display.ScalarOpacityFunction = sigma_xxPWF
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clip2Display.ScalarOpacityUnitDistance = 145.3794450275547
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clip2Display.OpacityArrayName = ["POINTS", name]
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clip2Display.SelectInputVectors = [None, ""]
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clip2Display.WriteLog = ""
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# init the 'PiecewiseFunction' selected for 'ScaleTransferFunction'
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clip2Display.ScaleTransferFunction.Points = [
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-2.363538980484009,
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0.0,
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0.5,
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0.0,
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6.50651741027832,
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1.0,
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0.5,
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0.0,
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]
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# init the 'PiecewiseFunction' selected for 'OpacityTransferFunction'
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clip2Display.OpacityTransferFunction.Points = [
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-2.363538980484009,
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0.0,
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0.5,
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0.0,
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6.50651741027832,
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1.0,
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0.5,
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0.0,
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]
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# hide data in view
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Hide(extractBlock, renderView1)
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# show color bar/color legend
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clip2Display.SetScalarBarVisibility(renderView1, True)
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# update the view to ensure updated data information
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renderView1.Update()
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# get color legend/bar for sigma_xxLUT in view renderView1
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sigma_xxLUTColorBar = GetScalarBar(sigma_xxLUT, renderView1)
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# Properties modified on sigma_xxLUTColorBar
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sigma_xxLUTColorBar.Title = label
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sigma_xxLUTColorBar.RangeLabelFormat = "%-#6.1f"
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# Apply a preset using its name. Note this may not work as expected when presets have duplicate names.
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sigma_xxLUT.ApplyPreset("Viridis (matplotlib)", True)
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# change scalar bar placement
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sigma_xxLUTColorBar.Orientation = "Horizontal"
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sigma_xxLUTColorBar.WindowLocation = "Any Location"
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sigma_xxLUTColorBar.Position = [0.3250956464379949, 0.7651456310679611]
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sigma_xxLUTColorBar.ScalarBarLength = 0.33
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# Rescale transfer function
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sigma_xxLUT.RescaleTransferFunction(min_value, max_value)
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# Rescale transfer function
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sigma_xxPWF.RescaleTransferFunction(min_value, max_value)
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# Rescale 2D transfer function
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sigma_xxTF2D.RescaleTransferFunction(min_value, max_value, 0.0, 1.0)
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# toggle interactive widget visibility (only when running from the GUI)
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HideInteractiveWidgets(proxy=clip2.ClipType)
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# get layout
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layout1 = GetLayout()
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# --------------------------------
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# saving layout sizes for layouts
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# layout/tab size in pixels
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layout1.SetSize(1516, 1030)
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# -----------------------------------
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# saving camera placements for views
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# current camera placement for renderView1
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renderView1.CameraPosition = [
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4527.975828521292,
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1143.9996458085711,
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1335.8353866420669,
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]
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renderView1.CameraFocalPoint = [
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-501.3331417934615,
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-126.6625437863954,
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-147.90241305746002,
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]
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renderView1.CameraViewUp = [
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-0.21900790347787114,
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0.9715903578242485,
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-0.08970905638326834,
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]
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renderView1.CameraParallelScale = 2044.5048300260873
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# export view
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ExportView(f"{figure_folder}/{name}.svg", view=renderView1)
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# ================================================================
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# addendum: following script captures some of the application
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# state to faithfully reproduce the visualization during playback
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# ================================================================
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# --------------------------------------------
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# uncomment the following to render all views
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# RenderAllViews()
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# alternatively, if you want to write images, you can use SaveScreenshot(...).
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if __name__ == "__main__":
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import argparse
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parser = argparse.ArgumentParser()
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parser.add_argument("--filename", type=str)
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parser.add_argument("--min_value", type=float)
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parser.add_argument("--max_value", type=float)
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parser.add_argument("--name", type=str)
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parser.add_argument("--label", type=str)
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parser.add_argument("--blocknr", type=int)
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parser.add_argument("--figure_folder", type=str)
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args = parser.parse_args()
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main(
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filename=args.filename,
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min_value=float(args.min_value),
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max_value=float(args.max_value),
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name=args.name,
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label=args.label,
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blocknr=int(args.blocknr),
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figure_folder=args.figure_folder,
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)
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# main(
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# filename="/Users/finsberg/local/src/cardiac-cancer/code/results4/cylinder_fine_varying_incomp/spring3000.0/results.xdmf",
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# min_value=0.0,
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# max_value=3.0,
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# name=name,
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# label="$\\sigma_{xx}$",
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# )
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# main(
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# filename="/Users/finsberg/local/src/cardiac-cancer/code/results4/cylinder_fine_incomp/spring3000.0/results.xdmf",
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# min_value=0.0,
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# max_value=3.0,
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# name="sigma_r",
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# label="$\\sigma_{xx}$",
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# blocknr=1,
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# )

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