How to VTKexport PointSetTopologyContainer points

[mbarrow]

I am not sure but this may be a bug?

I have been able to assign the position and values of my data to a PointSetTopologyContainer, but I cannot write this object with VTKExporter. I am unable to assign values to “pointsDataField”, even though I see the values I want in PointSetTopologyContainer.points .

What should I do?

Here is the snippet of my .scn showing my issue

<PointSetTopologyContainer name="wee" src="@youngM" points="@youngM.values" position="@LMap.restPosition"/>
<VTKExporter filename="poo.vtu" edges="1"  position="@wee.position" pointsDataFields="@wee.points" XMLformat="1" exportAtBegin="true" overwrite="true"/>

[Hugo]

Hi @mbarrow

I just tested this:

<Node name="root" dt="0.01" gravity="0 -9.81 0">
    <Mesh name="mesh" filename="mesh/dragon.obj" />
    <MeshObjLoader name="loader" filename="mesh/dragon.obj" />
    <MechanicalObject src="@loader" template="Vec3f" name="mecha" showObject="1" />
    <TetrahedronSetTopologyContainer src="@loader" name="topo" />
    <VTKExporter filename="example.vtk" listening="true" edges="0" triangles="1" quads="0" tetras="0" pointsDataFields="topo.points" exportAtBegin="1" />
</Node>

and it exports the “points” as a dataField in the vtk format.
Are the component in the same order than in your scene (first the Container then later in the scene the exporter) ?

Hugo

[mbarrow]

Hi Hugo, that didn’t work for me. The vtk exporter won’t populate if I don’t use a mesh as a source for point data.

I am trying to export the data created dynamically in an example .scn. Specifically

sofa/v17.12/src/applications/plugins/Flexible/examples/demos/steak.scn

I am trying to save the youngM points and corresponding rest positions, which are generated dynamically in that .scn file

So, I want to output a set of points in a vtk file for the “E” node. Here are my non-working lines of code in the “E” node of steak.scn. With this extra context, can you help?

...
<Node   name="E"   >
          <ImageValuesFromPositions name="youngM" position="@../sampler.position" image="@../../../youngM.outputImage"     transform="@../../../extruder.outputTransform" />
  
          <MechanicalObject  template="E332" name="E"  />
  <!--        <GreenStrainMapping template="F332,E332"  /> -->
              <CorotationalStrainMapping template="F332,E332" geometricStiffness="false" method="svd" />
          <HookeForceField  template="E332" name="ff" youngModulus="@youngM.values" poissonRatio="0" viscosity="0"  />
<PointSetTopologyContainer name="wee" src="@youngM" points="@youngM.values" />
                  <VTKExporter filename="poo.vtu" edges="1"  position="@wee.position" pointsDataFields="@wee.points" XMLformat="1" exportAtBegin="true" overwrite="true"/>
      </Node>

[mbarrow]

Hello Hugo, I think there is indeed some kind of bug.

Position is showing the youngs modulus values in the X column of the three column position vector. Y and Z are all 0’s. This is wrong and should not be possible because I have not set position to be youngs modulus in the XML.

I need this feature to work, what are my options?

[Hugo]

Hi @mjbarrow

could you post the full node for my understanding?
this should not be hard to fix

[mbarrow]

Hi Hugo, thanks for getting back to me and trying to help.

I made a modification to steak.scn but I thought it may save time to dump the steak.scn here along with the modifications.

the topology you suggested looks ok, it has position vectors and youngs modulus values which I wish to export to a vtk file if I inspect the nodes with runSofa. But the VTKExporter won’t pick up on the youngs modulus values no matter what I try and I can’t write them out.

<?xml version="1.0"?>
<Node 	name="Root" gravity="0 -9.81 0 " dt="0.1"  > 
    <RequiredPlugin pluginName="Flexible"/>
    <RequiredPlugin pluginName="image"/>
    <VisualStyle displayFlags="showVisual showBehavior" />
    <DefaultAnimationLoop />
    <DefaultVisualManagerLoop />
    <EulerImplicitSolver  rayleighStiffness="0.1" rayleighMass="0.1" />
    <CGLinearSolver template="GraphScattered" iterations="10" threshold="1e-008" /> <!-- MB demo meat params (less plausible jiggle jiggle, but do work) -->

    <ImageContainer name="loader" filename="data/steak-seg-highres.ppm" drawBB="false" />
    <ImageFilter name="selectchannel" src="@loader" filter="21" param="0"/>
    <ImageFilter name="extruder" inputImage="@selectchannel.outputImage" filter="20" param="-5 -3.75 -1 64 64 15 0.15 0.15 0.15 0" inputTransform="-5 -3.75 0 0 0 0 0.025 0.025 0.8 0 1 0"/>
    <!--<ImageContainer name="image" image="@extruder.outputImage" transform="@extruder.outputTransform" drawBB="false"/>-->
    <ImageContainer name="image" image="@extruder.outputImage" transform="@extruder.outputTransform" drawBB="false"/>
    <TransferFunction name="youngM" template="ImageUC,ImageD" inputImage="@extruder.outputImage" param="0 0 1 20000 254 5000 255 15000000000"/>
    <ImageViewer template="ImageD" name="viewer" image="@youngM.outputImage" transform="@extruder.outputTransform" />

    <TransferFunction name="densityTF" template="ImageUC,ImageD" inputImage="@extruder.outputImage" param="0 0 1 0.01"/>

    <Node 	name="Flexible"   >
        <ImageSampler template="ImageUC" name="sampler" src="@../image" method="1" param="50" fixedPosition="" showSamplesScale="0"/>
        <MergeMeshes name="merged" nbMeshes="2" position1="@sampler.fixedPosition"  position2="@sampler.position" /> 
        <MechanicalObject template="Affine" name="dof" src="@merged" showObject="1" showObjectScale=".1"/>
        <VoronoiShapeFunction name="SF" template="ShapeFunctiond,ImageD" image="@../youngM.outputImage" transform="@../extruder.outputTransform" nbRef="2" method="0" bias="true" printLog="false" />
        <Node 	name="behavior"   >
            <ImageGaussPointSampler name="sampler" indices="@../SF.indices" weights="@../SF.weights" transform="@../SF.transform" method="2" order="1" showSamplesScale="0" printLog="1" targetNumber="200" />
            <MechanicalObject template="F331" name="F" />
            <!-- <MLSMapping template="Affine,F331"   showDeformationGradientScale="0.1"/> -->
            <LinearMapping template="Affine,F331" name="Lmap"  showDeformationGradientScale="0.1"/> <!-- MB swap MLS for linear -->

            <Node 	name="E"   >
				
				<ImageValuesFromPositions name="youngM" position="@../sampler.position" image="@../../../youngM.outputImage" transform="@../../../extruder.outputTransform" />

				<MechanicalObject  template="E331" name="E"  /> 
                <CorotationalStrainMapping template="F331,E331"   method="svd" geometricStiffness="1"/>
				<HookeForceField  template="E332" name="ff" youngModulus="@youngM.values" poissonRatio="0" viscosity="0"  />

				<!-- MB: Broken? -->
				<TetrahedronSetTopologyContainer src="@youngM" name="wee" points="@youngM.values" position="@Lmap.restPosition"/>
				 <VTKExporter filename="poo.vtu" edges="1" triangles="1" quads="1" hexas="1" tetras="1"  position="@wee.position" cellsDataFields="@wee.points"      pointsDataFields="@youngM.values" XMLformat="1" exportAtBegin="true" overwrite="true"/>
			
			</Node>
        </Node>

        <Node 	name="collision"   >
            <MeshObjLoader name="MeshLoader" filename="data/steak.obj"/>
            <Mesh src="@MeshLoader" name="mesh" /> 
            <MechanicalObject template="Vec3d" name="pts"  />
            <UniformMass totalMass="250" />
            <BoxROI template="Vec3d" box="0 -2 0 5 2 5"  position="@mesh.position" /> 
            <RestShapeSpringsForceField template="Vec3d" points="@[-1].indices" stiffness="1E3"/> 
            <LinearMapping template="Affine,Vec3d"/>
        </Node> 

        <Node 	name="visual"   >
            <OglModel template="ExtVec3f" name="Visual" fileMesh="data/steak.obj" texturename="data/steak.png" normals="0"/>
            <LinearMapping template="Affine,ExtVec3f"/>
        </Node>

    </Node>

</Node>

[Hugo]

Hi @mjbarrow,

you are actually using Flexible which uses an API a bit different from SOFA (decoupling the numerical integration, the mechanical law etc.). This is why the VTKExporter is not very usable in your case. Moreover, the simulation is based on Frame approach, with Voronoi shape functions. There is therefore no topology assiociated (usually required by VTKExporter).

In your particular case, I would recommand to export it using python:
python script “exportPositionYoungModulus.py”

import Sofa
import sys

class WriterController(Sofa.PythonScriptController):

    def bwdInitGraph(self,node):
        self.nodeWithYoungModulus = node.getChild('Flexible').getChild('behavior').getChild('E')
        self.MO = self.nodeWithYoungModulus.getObject('E')
        self.containerYM = self.nodeWithYoungModulus.getObject('youngM')

        position = self.MO.findData('position').value
        youngModulus = self.containerYM.findData('values').value

        thefile = open('exportPositionYoungModulus.txt', 'w')
        
        for i in range (0, len(position)-1) :
            thefile.write("%s\n" % position[i])
        
        for i in range (0, len(position)-1) :
            thefile.write("%s\n" % youngModulus[i])
        
        return 0

and add the PythonController in your scene:

<PythonScriptController name="WriterController" filename="exportPositionYoungModulus.py" classname="WriterController"/>

Let me know if it suits you.
Best,

Hugo

[mbarrow]

Hi Hugo, this is promising. I have a final confusion my side.

Each entry of the ‘position’ list is 24 elements long.

Is this to be expected? If so how can I convert to x,y,z?

Thanks

[mbarrow]

Hugo, I took a quite different approach to the python using some example python code in the Flexible plugin directory. It seems to sample the modulus image using a mesh, but I’m not sure if it really does the right thing. Could you confirm I am on the right path here? I’ve supplied the code for the python container.

Thanks.

import os
import Sofa
import json
from numpy import indices

# helper functions
def getNode(rootNode, path):
     currentNode = rootNode
     pathComponents = path.split('/')
     for c in pathComponents:
         if len(c)==0: # for leading '/' and in case of '//'
             continue
         if c=='..':
         	currentNode = currentNode.getParents()[0]
         else:
	         currentNode = currentNode.getChild(c)
	         if currentNode is None:
	             print "SofaPython.Tools.findNode: can't find node at", path
	             return None
     return currentNode

#  variables; self.variables[0][0] = path to mesh self.variables[0][0] = path to pts
class Modulus_Log(Sofa.PythonScriptController):
	def createGraph(self,node):
		meshpath = self.variables[0][0]
		ptspath = self.variables[1][0]
		self.outfile= self.variables[2][0]

		[path,obj]=ptspath.rsplit('/',1)					#get path to 'pts' object as supplied to the script
		self.movingpts=getNode(node,path).getObject(obj)	
		self.mynode = node.createChild('DataLogging')
		self.mesh = self.mynode.createObject('TriangleSetTopologyContainer',name='mesh', src='@../'+meshpath) 
		self.youngsIndices=self.mynode.createObject(	'ImageValuesFromPositions',
														template='ImageUI',
														name='youngsIndices', 
														position='@mesh.position',						 
														image='@../../sampler.region', 
														transform='@../../sampler.transform' ,			
														interpolation='0'							)
                self.mynode.createObject('IdentityMapping',input='@../'+ptspath, output='@.')
		return 0
	
	#Log data that you want in a decent format. you could use vtk json whatever.
	def cleanup(self):
		#get mapped youngs modulus values (mapped from an image sampler to the closest exterior points of mesh) and log them out.
		youngMidx = self.youngsIndices.findData('values').value
		allYM = self.ffield.findData('youngModulus').value		
		YM = [allYM[int(item[0])] for index, item in enumerate(youngMidx)]
		#get displaced mesh point positions and log those out too
		ptsXYZ=self.movingpts.getData('position').value
		rptsXYZ=self.movingpts.getData('rest_position').value
		T = self.mesh.getData('triangles').value
		print('logging out data...')
		output = dict()
		output['rest_position']=rptsXYZ
		output['position']=ptsXYZ
		output['triangles']=T
		output['youngsM']=YM
			
		with open(self.outfile,'w') as file:
			try:
				json.dump(output, file)
			except IOError:
				raise
		if self.outfile[0] != '/':
			print('saved simulation results to\n: \t'+os.getcwd()+'/'+self.outfile)
		else:
			print('saved simulation results to\n: \t'+self.outfile)

[Hugo]

Hi @mjbarrow

in my case, the script does not work due to “self.variable”
what is this suppose to be? it seems undefined

[mbarrow]

Hi Hugo, sorry I was tired when I posted that, the self.variables should come from the python controller node in the scn. The first is to the collision mesh and the second is just a file name for some output JSON

<PythonScriptController filename="steaklog.py" classname="Modulus_Log" variables="../../collision/mesh ../../collision/pts youngsdata.json"/>

Is this the answer to your question?

Let me know, thanks

[Author]

Posts