def transformToData(scale, offset, timeOffset=0, timeScale=1, isPerspective=0):
""" Returns a transform, formatted to sofa data given voxelsize, rigid position (offset), time and camera parameters
"""
return concat(offset[:3]) + ' ' + concat(
quat.to_euler(offset[3:]) * 180. / math.pi) + ' ' + concat(
scale) + ' ' + str(timeOffset) + ' ' + str(timeScale) + ' ' + str(
int(isPerspective))
def addGaussPointSampler(self, shapeFunction, nbPoints, **kwargs):
shapeFunctionPath = shapeFunction.shapeFunction.getLinkPath()
samplerArgs = dict()
samplerArgs.update(kwargs)
if not self.labelImage is None:
samplerArgs["mask"] = self.labelImage.getImagePath() + ".image"
samplerArgs["maskLabels"] = concat(self.labels)
self.sampler = self.node.createObject(
"ImageGaussPointSampler",
template=shapeFunction.prefix + "ImageR," +
(self.labelImage.template()
if not self.labelImage is None else "ImageUC"),
name="sampler",
evaluateShapeFunction=False,
indices=shapeFunctionPath + ".indices",
weights=shapeFunctionPath + ".weights",
transform=shapeFunctionPath + ".transform",
method="2",
order=self.type[2:],
targetNumber=nbPoints,
**samplerArgs)
if shapeFunction.prefix == "Branching":
celloffsets = self.node.createObject(
"BranchingCellOffsetsFromPositions",
template=shapeFunction.prefix + "ImageUC",
name="cell",
position=self.sampler.getLinkPath() + ".position",
src=self.labelImage.getImagePath(),
labels=concat(self.labels))
self.cell = celloffsets.getLinkPath() + ".cell"
def subsetFromDeformable(self, deformable, indices):
if not deformable.topology is None:
topo = deformable.topology.getLinkPath()
self.meshLoader = self.node.createObject(
"MeshSubsetEngine",
template="Vec3",
name='MeshSubsetEngine',
inputPosition=topo + '.position',
inputTriangles=topo + '.triangles',
inputQuads=topo + '.quads',
indices=concat(indices))
self.topology = self.node.createObject("MeshTopology",
name="topology",
src="@" +
self.meshLoader.name)
if not deformable.dofs is None:
deformable.node.addChild(self.node)
self.dofs = self.node.createObject("MechanicalObject",
template="Vec3",
name="dofs")
self.mapping = self.node.createObject(
"SubsetMapping",
name='mapping',
indices=concat(indices),
input='@' + deformable.node.getPathName(),
output="@.")
def addModel(node,resolution,tr,useQuads=False, smooth=False,drawPlain=False):
# node.createObject("MeshObjLoader", name="loader", filename="mesh/sphere_"+resolution+".obj", triangulate="1", scale="1 1 1")
# node.createObject("Mesh", src="@loader", name="mesh")
# node.createObject("SurfacePressureForceField", pressure="1E2", volumeConservationMode='1', drawForceScale="0.00001")
if useQuads:
node.createObject("GridMeshCreator", name="loader" ,filename="nofile", resolution=concat(resolution), trianglePattern="0", translation="0 0 "+str(tr), rotation="0 0 0", scale3d="0.2 1 0" )
node.createObject("QuadSetTopologyContainer", name="mesh", src="@loader" )
else:
node.createObject("GridMeshCreator", name="loader", filename="nofile", resolution=concat(resolution), trianglePattern="1", translation="0 0 "+str(tr), rotation="0 0 0", scale3d="0.2 1 0" )
node.createObject("MeshTopology", name="mesh", src="@loader" )
node.createObject("MechanicalObject", src="@loader" )
node.createObject("BarycentricShapeFunction" )
node.createObject("UniformMass", totalMass="1000")
g = 0.0
node.createObject("BoxROI", name="box1", box=concat([g-0.005,-0.005,-0.005+tr,1.005-g,0.005 ,0.005+tr]) )
node.createObject("FixedConstraint", indices="@[-1].indices" )
node.createObject("BoxROI", name="box2", box=concat([g-0.005,0.995,-0.005+tr,1.005-g,1.005 ,0.005+tr]) )
# node.createObject("FixedConstraint", indices="@[-1].indices" )
node.createObject("ConstantForceField", template="Vec3d", points="@[-1].indices", totalForce="-3 -3 0")
node.createObject("PartialFixedConstraint", fixedDirections="0 0 1", fixAll=True )
Fnode = node.createChild("F")
GPsampler = Fnode.createObject("TopologyGaussPointSampler", name="sampler", inPosition="@../loader.position", method="0", order="2" if useQuads else "1", orientation="0 0 25", useLocalOrientation="0")
Fnode.createObject("MechanicalObject", template="F321" )
Fnode.createObject("LinearMapping", template="Vec3d,F321", showDeformationGradientScale="0.0", showDeformationGradientStyle="1")
Enode = Fnode.createChild("E")
Enode.createObject("MechanicalObject", template="E321", name="E")
Enode.createObject("GreenStrainMapping", template="F321,E321" )
# Enode.createObject("CorotationalStrainMapping", template="F321,E321", method="polar", geometricStiffness=True)
if smooth:
Esnode = Enode.createChild("Es")
# Esnode.createObject("HatShapeFunction", nbRef="4", param="0.5", position=GPsampler.getLinkPath()+".position" )
Esnode.createObject("ShepardShapeFunction", nbRef="4", position=GPsampler.getLinkPath()+".position" )
Esnode.createObject("GridMeshCreator", name="sampler" ,filename="nofile", resolution=concat([2*r for r in resolution]), trianglePattern="0", translation="0 0 "+str(tr), rotation="0 0 0", scale3d="0.2 1 0" )
Esnode.createObject("GaussPointSmoother", name="GP", position="@sampler.position", showSamplesScale=0, inputVolume=GPsampler.getLinkPath()+".volume", inputTransforms=GPsampler.getLinkPath()+".transforms" )
Esnode.createObject("MechanicalObject", template="E321", name="E" )
Esnode.createObject("LinearStrainMapping", template="E321,E321", indices="@GP.indices", weights="@GP.weights")
Esnode.createObject("HookeForceField", template="E321", name="ff", youngModulus="3000.0", poissonRatio="0.4", viscosity="0" )
else:
# Enode.createObject("HookeOrthotropicForceField", template="E321", youngModulusX="200", youngModulusY="20", poissonRatioXY="0.4", shearModulusXY="3.6", viscosity="0")
Enode.createObject("HookeForceField", template="E321", name="ff", youngModulus="3000.0", poissonRatio="0.4", viscosity="0" )
vnode = node.createChild("Visual")
if drawPlain:
vnode.createObject("VisualModel", color="0.8 0.8 1 1")
else:
vnode.createObject("VisualModel", color="0.8 0.8 1 1",edges="@../mesh.edges",position="@../mesh.position")
vnode.createObject("IdentityMapping" )
def __addMesh(self, mesh, closingValue=None, roiIndices=list(), roiValue=list(), name=None):
""" some code factorization between addMeshLoader and addExternMesh
"""
args = dict()
if not closingValue is None: # close mesh if closingValue is defined
meshPath = mesh.mesh.getLinkPath()
mesh.mesh = self.node.createObject(
"MeshClosingEngine",
name="closer_" + name,
inputPosition=meshPath + ".position",
inputTriangles=meshPath + ".triangles",
)
mesh.roiValue = [closingValue]
mesh.roiIndices = mesh.mesh.getLinkPath() + ".indices"
elif len(roiIndices) != 0 and len(roiValue) != 0:
mesh.roiValue = roiValue
args = dict()
for i, roi in enumerate(roiIndices):
args["indices" + str(i + 1)] = concat(roi)
mesh.mergeROIs = self.node.createObject(
"MergeROIs", name="mergeROIs_" + name, nbROIs=len(roiIndices), **args
)
mesh.roiIndices = mesh.mergeROIs.getLinkPath() + ".roiIndices"
# use mergeROIs to potentially combine other rois (from meshclosing, boxRois, etc.)
# but here, roiIndices reformating to "[i,j,..] [k,l,..]" would work..
self.meshes[name] = mesh
self.meshSeq.append(name)
def addMeshToImage(self, voxelSize):
args = dict()
i = 1
for name in self.meshSeq:
mesh = self.meshes[name]
if mesh.mesh is None:
Sofa.msg_error("Image.API", "addMeshToImage : no mesh for " + name)
return
meshPath = mesh.mesh.getLinkPath()
args["position" + str(i)] = meshPath + ".position"
args["triangles" + str(i)] = meshPath + ".triangles"
args["value" + str(i)] = mesh.value
if mesh.insideValue is None:
args["fillInside" + str(i)] = False
else:
args["insideValue" + str(i)] = mesh.insideValue
if not mesh.roiIndices is None and len(mesh.roiValue) != 0:
args["roiIndices" + str(i)] = mesh.roiIndices
args["roiValue" + str(i)] = concat(mesh.roiValue)
i += 1
self.image = self.node.createObject(
"MeshToImageEngine",
template=self.template(),
name="image",
voxelSize=voxelSize,
padSize=1,
subdiv=8,
rotateImage=False,
nbMeshes=len(self.meshes),
**args
)
def read(self, filenamePrefix=None, directory="", **kwargs):
filename = self.getFilename(filenamePrefix, directory)
data = dict()
with open(filename, 'r') as f:
data.update(json.load(f))
self.type = data['type']
self.sampler = self.node.createObject(
'GaussPointContainer',
name='GPContainer',
volumeDim=data['volumeDim'],
inputVolume=data['inputVolume'],
position=data['position'],
**kwargs)
if not self.labelImage is None and not self.labels is None:
if self.labelImage.prefix == "Branching":
celloffsets = self.node.createObject(
"BranchingCellOffsetsFromPositions",
template=self.labelImage.template(),
name="cell",
position=self.sampler.getLinkPath() + ".position",
src=self.labelImage.getImagePath(),
labels=concat(self.labels))
self.cell = celloffsets.getLinkPath() + ".cell"
if printLog:
Sofa.msg_info("Flexible.API.Behavior",
'Imported Gauss Points from ' + filename)
def loadMesh(self,
meshPath,
offset=[0, 0, 0, 0, 0, 0, 1],
scale=[1, 1, 1],
triangulate=False):
r = Quaternion.to_euler(offset[3:]) * 180.0 / math.pi
self.meshLoader = SofaPython.Tools.meshLoader(self.node,
meshPath,
translation=concat(
offset[:3]),
rotation=concat(r),
scale3d=concat(scale),
triangulate=triangulate)
self.topology = self.node.createObject("MeshTopology",
name="topology",
src="@" + self.meshLoader.name)
def addMapping(self,
dofRigidNode=None,
dofAffineNode=None,
labelImage=None,
labels=None,
useGlobalIndices=False,
useIndexLabelPairs=False,
assemble=True,
isMechanical=True):
cell = ''
if not labelImage is None and not labels is None: # use labels to select specific voxels in branching image
if labelImage.prefix == 'Branching':
position = "@" + self.topology.name + ".position" if not self.topology is None else "@" + self.visual.name + ".position"
offsets = self.node.createObject(
"BranchingCellOffsetsFromPositions",
template=labelImage.template(),
name="cell",
position=position,
image=labelImage.getImagePath() + ".image",
transform=labelImage.getImagePath() + ".transform",
labels=concat(labels),
useGlobalIndices=useGlobalIndices,
useIndexLabelPairs=useIndexLabelPairs)
cell = offsets.getLinkPath() + ".cell"
self.mapping = insertLinearMapping(self.node,
dofRigidNode,
dofAffineNode,
cell,
assemble,
isMechanical=isMechanical)
def addBeam(node,resolution,tr,smooth=False,drawPlain=False):
node.createObject("RegularGrid", name="mesh", n=concat(resolution), min=concat([-0.2+tr,-0.2,-1]), max=concat([0.2+tr,0.2,1]))
node.createObject("MechanicalObject", template="Vec3", name="dofs" )
node.createObject("BoxROI", template="Vec3d", position="@mesh.position", box=concat([-1+tr,-1,-1.1,1+tr,1,-0.99]) )
node.createObject("FixedConstraint", indices="@[-1].indices" )
node.createObject("BoxROI", template="Vec3d", position="@mesh.position", box=concat([-1+tr,-1,0.99,1+tr,1,1.1]), drawBoxes="1" )
node.createObject("ConstantForceField", template="Vec3d", points="@[-1].indices", totalForce="0 -3 0")
# node.createObject("ConstantForceField", template="Vec3d", points="@[-1].indices", totalForce="0 -6 0")
# node.createObject("ConstantForceField", template="Vec3d", points="@[-1].indices", totalForce="0 0 100")
node.createObject("UniformMass", totalMass="10" )
# node.createObject("HexahedronFEMForceField", youngModulus="1000.0" ,poissonRatio="0", method="polar", updateStiffnessMatrix="false" )
node.createObject("BarycentricShapeFunction", nbRef="8" )
Fnode = node.createChild("F")
GPsampler = Fnode.createObject("TopologyGaussPointSampler", name="sampler", inPosition="@../mesh.position", showSamplesScale="0", method="0", order="2" )
Fnode.createObject("MechanicalObject", template="F331", name="F" )
mapping = Fnode.createObject("LinearMapping", name="FMapping", template="Vec3d,F331" )
Enode = Fnode.createChild("E")
Enode.createObject("MechanicalObject", template="E331", name="E" )
# Enode.createObject("CorotationalStrainMapping", template="F331,E331", method="svd", geometricStiffness=True)
Enode.createObject("GreenStrainMapping", template="F331,E331", geometricStiffness=True)
if smooth:
Esnode = Enode.createChild("Es")
# Esnode.createObject("HatShapeFunction", nbRef="8", param="0.5", position=GPsampler.getLinkPath()+".position" )
Esnode.createObject("ShepardShapeFunction", nbRef="8", position=GPsampler.getLinkPath()+".position" )
Esnode.createObject("RegularGrid", name="sampler", n=concat([2*r for r in resolution]), min=concat([-0.2+tr,-0.2,-1]), max=concat([0.2+tr,0.2,1]))
Esnode.createObject("GaussPointSmoother", name="GP", position="@sampler.position", inputVolume=GPsampler.getLinkPath()+".volume", inputTransforms=GPsampler.getLinkPath()+".transforms" )
Esnode.createObject("MechanicalObject", template="E331", name="E" )
Esnode.createObject("LinearStrainMapping", template="E331,E331", indices="@GP.indices", weights="@GP.weights")
Esnode.createObject("HookeForceField", template="E331", name="ff", youngModulus="3000.0", poissonRatio="0.3", viscosity="0" )
else:
Enode.createObject("HookeForceField", template="E331", name="ff", youngModulus="3000.0", poissonRatio="0.3", viscosity="0" )
vnode = node.createChild("Visual")
if drawPlain:
vnode.createObject("VisualModel", color="0.8 0.8 1 1")
else:
vnode.createObject("VisualModel", color="0.8 0.8 1 1",edges="@../mesh.edges",position="@../mesh.position")
vnode.createObject("IdentityMapping" )
def addVisualCylinder(self, radius=0.01, color=[1, 1, 1, 1]):
if not self.dofs is None:
d = Deformable(self.node, "Visual")
d.visual = d.node.createObject("OglCylinderModel",
name="model",
radius=radius,
color=concat(color))
return d
def createSceneAndController(rootNode):
rootNode.createObject('RequiredPlugin', pluginName="Flexible")
rootNode.createObject('RequiredPlugin', pluginName="Compliant")
rootNode.createObject('RequiredPlugin', pluginName="ContactMapping")
rootNode.createObject('BackgroundSetting', color='1 1 1')
rootNode.createObject('VisualStyle', displayFlags='showBehavior')
rootNode.dt = 0.01
rootNode.gravity = [0, -10, 0]
rootNode.createObject('CompliantImplicitSolver', name="odesolver")
# rootNode.createObject('SequentialSolver', name="numsolver", iterations =10, precision=1e-14)
rootNode.createObject('LDLTSolver', name="numsolver")
# rootNode.createObject('MinresSolver', name="numsolver", iterations =10, precision=1e-14)
# rootNode.createObject('EulerImplicitSolver')
# rootNode.createObject('CGSolver', tolerance="1.0e-9" ,threshold="1.0e-9" )
pos = [[0, 0, 0], [0, 1, 0], [0.1, 1, 0], [0.1, 0.5, 0], [0.2, 0.5, 0],
[0.2, 1, 0], [0.3, 1, 0], [0.3, 0, 0]]
edges = [[i, i + 1] for i in xrange(len(pos) - 1)]
rootNode.createObject('Mesh',
name="mesh",
position=lconcat(pos),
lines=lconcat(edges))
rootNode.createObject('MechanicalObject',
template="Vec3d",
name="DOFs",
src="@mesh")
rootNode.createObject('UniformMass', name="mass", totalMass="2")
rootNode.createObject('FixedConstraint',
name="FixedConstraint",
indices=concat([1, 2, 3, 4, 5, 6]))
# rootNode.createObject('UniformVelocityDampingForceField',dampingCoefficient="0.1")
rootNode.createObject('RestShapeSpringsForceField',
points="0 7",
stiffness="10")
Lnode = rootNode.createChild("L")
Lnode.createObject('MechanicalObject', template="Vec1")
Lnode.createObject('LengthMapping',
template="Vec3,Vec1",
edges="@../mesh.lines",
offset="-3.3",
geometricStiffness=1)
Lnode.createObject('UniformCompliance',
compliance=1E-2,
rayleighStiffness=1,
isCompliance='0')
Vnode = rootNode.createChild("visual")
Vnode.createObject('VisualModel', edges="@../mesh.lines")
Vnode.createObject('IdentityMapping')
def addSkinning(self,
armatureNode,
indices,
weights,
assemble=True,
isMechanical=True):
""" Add skinning (linear) mapping based on the armature (Rigid3) in armatureNode using
"""
self.mapping = self.node.createObject("LinearMapping",
template="Rigid3,Vec3",
name="mapping",
input="@" +
armatureNode.getPathName(),
indices=concat(indices),
weights=concat(weights),
assemble=assemble,
mapForces=isMechanical,
mapConstraints=isMechanical,
mapMasses=isMechanical)
def loadVisual(self,
meshPath,
offset=[0, 0, 0, 0, 0, 0, 1],
scale=[1, 1, 1],
color=[1, 1, 1, 1],
**kwargs):
r = Quaternion.to_euler(offset[3:]) * 180.0 / math.pi
self.visual = self.node.createObject("VisualModel",
name="model",
filename=meshPath,
translation=concat(offset[:3]),
rotation=concat(r),
scale3d=concat(scale),
color=concat(color),
putOnlyTexCoords=True,
computeTangents=True,
**kwargs)
# self.visual = self.node.createObject("VisualModel", name="model", filename=meshPath, translation=concat(offset[:3]) , rotation=concat(r), scale3d=concat(scale), color=concat(color), **kwargs)
self.visual.setColor(
color[0], color[1], color[2], color[3]
) # the previous assignement fails when reloading a scene..
self.normals = self.visual
def addMeshLoader(
self,
meshFile,
value,
insideValue=None,
closingValue=None,
roiIndices=list(),
roiValue=list(),
name=None,
offset=[0, 0, 0, 0, 0, 0, 1],
scale=[1, 1, 1],
):
mesh = Image.Mesh(value, insideValue)
_name = name if not name is None else os.path.splitext(os.path.basename(meshFile))[0]
mesh.mesh = SofaPython.Tools.meshLoader(
self.node,
meshFile,
name="meshLoader_" + _name,
triangulate=True,
translation=concat(offset[:3]),
rotation=concat(Quaternion.to_euler(offset[3:]) * 180.0 / math.pi),
scale3d=concat(scale),
)
self.__addMesh(mesh, closingValue, roiIndices, roiValue, _name)
def addGaussPointSampler(self, shapeFunction, nbPoints, **kwargs):
shapeFunctionPath = shapeFunction.shapeFunction.getLinkPath()
samplerArgs = dict()
samplerArgs.update(kwargs)
if not self.labelImage is None:
samplerArgs["mask"]=self.labelImage.getImagePath()+".image"
samplerArgs["maskLabels"]=concat(self.labels)
self.sampler = self.node.createObject(
"ImageGaussPointSampler",
template=shapeFunction.prefix+"ImageR,"+(self.labelImage.template() if not self.labelImage is None else "ImageUC"),
name="sampler",
indices=shapeFunctionPath+".indices", weights=shapeFunctionPath+".weights", transform=shapeFunctionPath+".transform",
method="2", order=self.type[2:], targetNumber=nbPoints,
**samplerArgs)
if shapeFunction.prefix == "Branching":
celloffsets = self.node.createObject("BranchingCellOffsetsFromPositions", template=shapeFunction.prefix+"ImageUC", name="cell", position =self.sampler.getLinkPath()+".position", src=self.labelImage.getImagePath(), labels=concat(self.labels))
self.cell = celloffsets.getLinkPath()+".cell"
def visualFromDeformable(self, deformable, color=[1, 1, 1, 1]):
deformable.node.addChild(self.node)
self.visual = self.node.createObject(
"VisualModel",
name="model",
filename="@" + deformable.meshLoader.getPathName() + ".filename",
color=concat(color))
self.visual.setColor(
color[0], color[1], color[2], color[3]
) # the previous assignement fails when reloading a scene..
self.mapping = self.node.createObject("IdentityMapping",
name="mapping",
input='@' +
deformable.node.getPathName(),
output="@.",
mapForces=False,
mapConstraints=False,
mapMasses=False)
self.normals = self.visual
def addMeshToImage(self, voxelSize):
args=dict()
i=1
for name in self.meshSeq:
mesh = self.meshes[name]
if mesh.mesh is None:
Sofa.msg_error('Image.API',"addMeshToImage : no mesh for "+ name)
return
meshPath = mesh.mesh.getLinkPath()
args["position"+str(i)]=meshPath+".position"
args["triangles"+str(i)]=meshPath+".triangles"
args["value"+str(i)]=mesh.value
if mesh.insideValue is None:
args["fillInside"+str(i)]=False
else:
args["insideValue"+str(i)]=mesh.insideValue
if not mesh.roiIndices is None and len(mesh.roiValue)!=0 :
args["roiIndices"+str(i)]=mesh.roiIndices
args["roiValue"+str(i)]=concat(mesh.roiValue)
i+=1
self.image = self.node.createObject('MeshToImageEngine', template=self.template(), name="image", voxelSize=voxelSize, padSize=1, subdiv=8, rotateImage=False, nbMeshes=len(self.meshes), **args)
def __addMesh(self, mesh, closingValue=None, roiIndices=list(), roiValue=list(), name=None):
""" some code factorization between addMeshLoader and addExternMesh
"""
args=dict()
if not closingValue is None : # close mesh if closingValue is defined
meshPath = mesh.mesh.getLinkPath()
mesh.mesh = self.node.createObject("MeshClosingEngine", name="closer_"+name, inputPosition=meshPath+".position", inputTriangles=meshPath+".triangles")
mesh.roiValue=[closingValue]
mesh.roiIndices=mesh.mesh.getLinkPath()+".indices"
elif len(roiIndices)!=0 and len(roiValue)!=0 :
mesh.roiValue=roiValue
args=dict()
for i,roi in enumerate(roiIndices):
args["indices"+str(i+1)]=concat(roi)
mesh.mergeROIs = self.node.createObject('MergeROIs', name="mergeROIs_"+name, nbROIs=len(roiIndices), **args)
mesh.roiIndices=mesh.mergeROIs.getLinkPath()+".roiIndices"
# use mergeROIs to potentially combine other rois (from meshclosing, boxRois, etc.)
# but here, roiIndices reformating to "[i,j,..] [k,l,..]" would work..
self.meshes[name] = mesh
self.meshSeq.append(name)
def loadMesh(self, meshPath, offset = [0,0,0,0,0,0,1], scale=[1,1,1], triangulate=False):
r = Quaternion.to_euler(offset[3:]) * 180.0 / math.pi
self.meshLoader = SofaPython.Tools.meshLoader(self.node, meshPath, translation=concat(offset[:3]) , rotation=concat(r), scale3d=concat(scale), triangulate=triangulate)
self.topology = self.node.createObject("MeshTopology", name="topology", src="@"+self.meshLoader.name )
def read(self, filenamePrefix=None, directory="", **kwargs):
filename = self.getFilename(filenamePrefix,directory)
data = dict()
with open(filename,'r') as f:
data.update(json.load(f))
self.type = data['type']
self.sampler = self.node.createObject('GaussPointContainer',name='GPContainer', volumeDim=data['volumeDim'], inputVolume=data['inputVolume'], position=data['position'], **kwargs)
if not self.labelImage is None and not self.labels is None:
if self.labelImage.prefix == "Branching":
celloffsets = self.node.createObject("BranchingCellOffsetsFromPositions", template=self.labelImage.template(), name="cell", position =self.sampler.getLinkPath()+".position", src=self.labelImage.getImagePath(), labels=concat(self.labels))
self.cell = celloffsets.getLinkPath()+".cell"
if printLog:
Sofa.msg_info("Flexible.API.Behavior",'Imported Gauss Points from '+filename)
def addSkinning(self, armatureNode, indices, weights, assemble=True, isMechanical=True):
""" Add skinning (linear) mapping based on the armature (Rigid3) in armatureNode using
"""
self.mapping = self.node.createObject("LinearMapping", template="Rigid3,Vec3", name="mapping", input="@"+armatureNode.getPathName(), indices=concat(indices), weights=concat(weights), assemble=assemble, mapForces=isMechanical, mapConstraints=isMechanical, mapMasses=isMechanical)
def addMapping(self, dofRigidNode=None, dofAffineNode=None, labelImage=None, labels=None, useGlobalIndices=False, useIndexLabelPairs=False, assemble=True, isMechanical=True):
cell = ''
if not labelImage is None and not labels is None : # use labels to select specific voxels in branching image
if labelImage.prefix=='Branching':
position="@"+self.topology.name+".position" if not self.topology is None else "@"+self.visual.name+".position"
offsets = self.node.createObject("BranchingCellOffsetsFromPositions", template=labelImage.template(), name="cell", position =position, image=labelImage.getImagePath()+".image", transform=labelImage.getImagePath()+".transform", labels=concat(labels), useGlobalIndices=useGlobalIndices, useIndexLabelPairs=useIndexLabelPairs)
cell = offsets.getLinkPath()+".cell"
self.mapping = insertLinearMapping(self.node, dofRigidNode, dofAffineNode, cell, assemble, isMechanical=isMechanical)
def subsetFromDeformables(self, deformableIndicesList = list() ):
args=dict()
inputs=[]
indexPairs=[]
i=1
mapTopo = True
mapDofs = True
for s,ind in deformableIndicesList:
s.node.addChild(self.node)
if s.dofs is None:
mapDofs = False
else:
if not ind is None:
for p in ind:
indexPairs+=[i-1,p]
else: # no roi -> take all points. Warning: does not work if parent dofs are not initialized
size = len(s.dofs.position)
if size==0:
Sofa.msg_error("Flexible.API.Deformable","subsetFromDeformables: no dof from "+ s.name)
for p in xrange(size):
indexPairs+=[i-1,p]
if s.topology is None:
mapTopo = False
else:
if not ind is None:
subset = self.node.createObject("MeshSubsetEngine", template = "Vec3", name='MeshSubsetEngine_'+s.name, inputPosition=s.topology.getLinkPath()+'.position', inputTriangles=s.topology.getLinkPath()+'.triangles', inputQuads=s.topology.getLinkPath()+'.quads', indices=concat(ind))
path = '@'+subset.name
else: # map all
path = s.topology.getLinkPath()
args["position"+str(i)]=path+".position"
args["triangles"+str(i)]=path+".triangles"
args["quads"+str(i)]=path+".quads"
inputs.append('@'+s.node.getPathName())
i+=1
if mapTopo:
self.meshLoader = self.node.createObject('MergeMeshes', name='MergeMeshes', nbMeshes=len(inputs), **args )
self.topology = self.node.createObject("MeshTopology", name="topology", src="@"+self.meshLoader.name )
if mapDofs:
self.dofs = self.node.createObject("MechanicalObject", template = "Vec3", name="dofs")
self.mapping = self.node.createObject("SubsetMultiMapping", name='mapping', indexPairs=concat(indexPairs), input=concat(inputs),output="@.")
def subsetFromDeformable(self, deformable, indices ):
if not deformable.topology is None:
topo = deformable.topology.getLinkPath()
self.meshLoader = self.node.createObject("MeshSubsetEngine", template = "Vec3", name='MeshSubsetEngine', inputPosition=topo+'.position', inputTriangles=topo+'.triangles', inputQuads=topo+'.quads', indices=concat(indices))
self.topology = self.node.createObject("MeshTopology", name="topology", src="@"+self.meshLoader.name)
if not deformable.dofs is None:
deformable.node.addChild(self.node)
self.dofs = self.node.createObject("MechanicalObject", template = "Vec3", name="dofs")
self.mapping = self.node.createObject("SubsetMapping", name='mapping', indices=concat(indices), input='@'+deformable.node.getPathName(),output="@.")
def visualFromDeformable(self, deformable, color=[1,1,1,1]):
deformable.node.addChild(self.node)
self.visual = self.node.createObject("VisualModel", name="model", filename="@"+deformable.meshLoader.getPathName()+".filename", color=concat(color))
self.visual.setColor(color[0],color[1],color[2],color[3]) # the previous assignement fails when reloading a scene..
self.mapping = self.node.createObject("IdentityMapping", name="mapping", input='@'+deformable.node.getPathName(),output="@.", mapForces=False, mapConstraints=False, mapMasses=False )
self.normals = self.visual
def addModel(node,
resolution,
tr,
useQuads=False,
smooth=False,
drawPlain=False):
# node.createObject("MeshObjLoader", name="loader", filename="mesh/sphere_"+resolution+".obj", triangulate="1", scale="1 1 1")
# node.createObject("Mesh", src="@loader", name="mesh")
# node.createObject("SurfacePressureForceField", pressure="1E2", volumeConservationMode='1', drawForceScale="0.00001")
if useQuads:
node.createObject("GridMeshCreator",
name="loader",
filename="nofile",
resolution=concat(resolution),
trianglePattern="0",
translation="0 0 " + str(tr),
rotation="0 0 0",
scale3d="0.2 1 0")
node.createObject("QuadSetTopologyContainer",
name="mesh",
src="@loader")
else:
node.createObject("GridMeshCreator",
name="loader",
filename="nofile",
resolution=concat(resolution),
trianglePattern="1",
translation="0 0 " + str(tr),
rotation="0 0 0",
scale3d="0.2 1 0")
node.createObject("MeshTopology", name="mesh", src="@loader")
node.createObject("MechanicalObject", src="@loader")
node.createObject("BarycentricShapeFunction")
node.createObject("UniformMass", totalMass="1000")
g = 0.0
node.createObject("BoxROI",
name="box1",
box=concat([
g - 0.005, -0.005, -0.005 + tr, 1.005 - g, 0.005,
0.005 + tr
]))
node.createObject("FixedConstraint", indices="@[-1].indices")
node.createObject("BoxROI",
name="box2",
box=concat([
g - 0.005, 0.995, -0.005 + tr, 1.005 - g, 1.005,
0.005 + tr
]))
# node.createObject("FixedConstraint", indices="@[-1].indices" )
node.createObject("ConstantForceField",
template="Vec3d",
points="@[-1].indices",
totalForce="-3 -3 0")
node.createObject("PartialFixedConstraint",
fixedDirections="0 0 1",
fixAll=True)
Fnode = node.createChild("F")
GPsampler = Fnode.createObject("TopologyGaussPointSampler",
name="sampler",
inPosition="@../loader.position",
method="0",
order="2" if useQuads else "1",
orientation="0 0 25",
useLocalOrientation="0")
Fnode.createObject("MechanicalObject", template="F321")
Fnode.createObject("LinearMapping",
template="Vec3d,F321",
showDeformationGradientScale="0.0",
showDeformationGradientStyle="1")
Enode = Fnode.createChild("E")
Enode.createObject("MechanicalObject", template="E321", name="E")
Enode.createObject("GreenStrainMapping", template="F321,E321")
# Enode.createObject("CorotationalStrainMapping", template="F321,E321", method="polar", geometricStiffness=True)
if smooth:
Esnode = Enode.createChild("Es")
# Esnode.createObject("HatShapeFunction", nbRef="4", param="0.5", position=GPsampler.getLinkPath()+".position" )
Esnode.createObject("ShepardShapeFunction",
nbRef="4",
position=GPsampler.getLinkPath() + ".position")
Esnode.createObject("GridMeshCreator",
name="sampler",
filename="nofile",
resolution=concat([2 * r for r in resolution]),
trianglePattern="0",
translation="0 0 " + str(tr),
rotation="0 0 0",
scale3d="0.2 1 0")
Esnode.createObject("GaussPointSmoother",
name="GP",
position="@sampler.position",
showSamplesScale=0,
inputVolume=GPsampler.getLinkPath() + ".volume",
inputTransforms=GPsampler.getLinkPath() +
".transforms")
Esnode.createObject("MechanicalObject", template="E321", name="E")
Esnode.createObject("LinearStrainMapping",
template="E321,E321",
indices="@GP.indices",
weights="@GP.weights")
Esnode.createObject("HookeForceField",
template="E321",
name="ff",
youngModulus="3000.0",
poissonRatio="0.4",
viscosity="0")
else:
# Enode.createObject("HookeOrthotropicForceField", template="E321", youngModulusX="200", youngModulusY="20", poissonRatioXY="0.4", shearModulusXY="3.6", viscosity="0")
Enode.createObject("HookeForceField",
template="E321",
name="ff",
youngModulus="3000.0",
poissonRatio="0.4",
viscosity="0")
vnode = node.createChild("Visual")
if drawPlain:
vnode.createObject("VisualModel", color="0.8 0.8 1 1")
else:
vnode.createObject("VisualModel",
color="0.8 0.8 1 1",
edges="@../mesh.edges",
position="@../mesh.position")
vnode.createObject("IdentityMapping")
def addMeshLoader(self, meshFile, value, insideValue=None, closingValue=None, roiIndices=list(), roiValue=list(), name=None, offset = [0,0,0,0,0,0,1], scale=[1,1,1]):
mesh = Image.Mesh(value, insideValue)
_name = name if not name is None else os.path.splitext(os.path.basename(meshFile))[0]
mesh.mesh = SofaPython.Tools.meshLoader(self.node, meshFile, name="meshLoader_"+_name, triangulate=True, translation=concat(offset[:3]) , rotation=concat(Quaternion.to_euler(offset[3:]) * 180.0 / math.pi), scale3d=concat(scale))
self.__addMesh(mesh,closingValue,roiIndices,roiValue,_name)
def transformToData(scale,offset,timeOffset=0,timeScale=1,isPerspective=0):
""" Returns a transform, formatted to sofa data given voxelsize, rigid position (offset), time and camera parameters
"""
return concat(offset[:3])+' '+concat(quat.to_euler(offset[3:])*180./math.pi)+' '+concat(scale)+' '+str(timeOffset)+' '+str(timeScale)+' '+str(int(isPerspective))
def loadVisual(self, meshPath, offset = [0,0,0,0,0,0,1], scale=[1,1,1], color=[1,1,1,1],**kwargs):
r = Quaternion.to_euler(offset[3:]) * 180.0 / math.pi
self.visual = self.node.createObject("VisualModel", name="model", filename=meshPath, translation=concat(offset[:3]) , rotation=concat(r), scale3d=concat(scale), color=concat(color), putOnlyTexCoords=True,computeTangents=True,**kwargs)
# self.visual = self.node.createObject("VisualModel", name="model", filename=meshPath, translation=concat(offset[:3]) , rotation=concat(r), scale3d=concat(scale), color=concat(color), **kwargs)
self.visual.setColor(color[0],color[1],color[2],color[3]) # the previous assignement fails when reloading a scene..
self.normals = self.visual
def addVisualCylinder(self,radius=0.01, color=[1,1,1,1]):
if not self.dofs is None:
d = Deformable(self.node,"Visual")
d.visual = d.node.createObject("OglCylinderModel", name="model",radius=radius, color=concat(color))
return d
def createScene(root):
# root node setup
root.createObject('RequiredPlugin', pluginName='Flexible')
root.createObject('RequiredPlugin', pluginName='Compliant')
root.createObject('VisualStyle', displayFlags="showBehavior")
root.createObject('CompliantAttachButtonSetting')
root.createObject('BackgroundSetting', color='1 1 1')
# simuation parameters
root.dt = 1e-1
root.gravity = [0, 0, 0]
# ode solver
ode = root.createObject(
'CompliantImplicitSolver',
neglecting_compliance_forces_in_geometric_stiffness=False,
stabilization="pre-stabilization")
# numerical solver
# root.createObject('LDLTSolver', name="numsolver")
root.createObject('SequentialSolver',
name='numsolver',
iterations=250,
precision=1e-14,
iterateOnBilaterals=True)
# root.createObject('LDLTResponse', name='response')
# root.createObject('LUResponse', name='response')
# scene node
scene = root.createChild('scene')
# script variables
nbLink = 7
linkSize = 2
# links creation
links = []
# rigid bodies
for i in xrange(nbLink):
body = StructuralAPI.RigidBody(root, "link-{0}".format(i))
body.setManually(offset=[0, -1. * linkSize * i, 0, 0, 0, 0, 1],
inertia_forces=False)
body.dofs.showObject = True
body.dofs.showObjectScale = 0.25 * linkSize
body.addVisualModel("mesh/cylinder.obj",
scale3d=[.3, .1 * linkSize, .3],
offset=[0, -0.5 * linkSize, 0, 0, 0, 0, 1])
links.append(body)
# attach first link
links[0].setFixed()
# joints creation
points = []
for i in xrange(nbLink - 1):
off1 = links[i].addOffset("offset-{0}-{1}".format(i, i + 1),
[0, -0.5 * linkSize, 0, 0, 0, 0, 1])
off2 = links[i + 1].addOffset("offset-{0}-{1}".format(i + 1, i),
[0, 0.5 * linkSize, 0, 0, 0, 0, 1])
j = StructuralAPI.HingeRigidJoint(2,
"joint-{0}-{1}".format(i, i + 1),
off1.node,
off2.node,
isCompliance=False,
compliance=1E-5)
#StructuralAPI.BallAndSocketRigidJoint("joint-{0}-{1}".format(i, i+1), off1.node, off2.node, isCompliance=True, compliance=0)
j.addLimits(0, .8, compliance=1E-15)
points.append(links[i].addAbsoluteMappedPoint(
"point-{0}-{1}".format(i, i + 1),
[0.5, -1. * linkSize * i - 0.25 * linkSize, 0]))
points.append(links[i + 1].addAbsoluteMappedPoint(
"point-{0}-{1}".format(i + 1, i),
[0.5, -1. * linkSize * (i + 1) + 0.25 * linkSize, 0]))
points.append(links[nbLink - 1].addAbsoluteMappedPoint(
"point-{0}".format(nbLink),
[0.5, -1. * linkSize * (nbLink - 1) - 0.5 * linkSize, 0]))
# rod
rodNode = scene.createChild('rod')
rodNode.createObject('MechanicalObject',
name='dofs',
template="Vec3",
position=concat([0.5, 0.5 * linkSize, 0]))
rodNode.createObject('UniformMass', name="mass", totalMass="1")
rodNode.createObject('RestShapeSpringsForceField',
points="0",
stiffness="1E3")
fullrodNode = rodNode.createChild('fullrod')
input = '@' + rodNode.getPathName() + ' '
indexPairs = '0 0 '
edges = ''
for i, p in enumerate(points):
input += '@' + p.node.getPathName() + ' '
indexPairs += str(i + 1) + ' 0 '
edges += str(i) + ' ' + str(i + 1) + ' '
p.node.addChild(fullrodNode)
fullrodNode.createObject('MechanicalObject',
template="Vec3",
showObject=True,
showObjectScale=0.1,
showColor="0 1 0 1",
drawMode=1)
fullrodNode.createObject('SubsetMultiMapping',
template="Vec3,Vec3",
name="mapping",
input=input,
output='@./',
indexPairs=indexPairs)
Lnode = fullrodNode.createChild("L")
Lnode.createObject('MechanicalObject', template="Vec1")
Lnode.createObject('LengthMapping',
template="Vec3,Vec1",
edges=edges,
offset=str(-nbLink * linkSize),
geometricStiffness=1)
Lnode.createObject('UniformCompliance',
compliance=1E-10,
rayleighStiffness=0,
isCompliance='1')
Vnode = fullrodNode.createChild("visual")
Vnode.createObject('VisualModel', edges=edges)
Vnode.createObject('IdentityMapping')
