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$EndElements

liverVolumeSurfacePython

"""
liverVolumeSurfacePython
is based on the scene 
/home/zahra/sofa/Work/test/liverVolumeSurface.scn
but it uses the SofaPython plugin. 
Further informations on the usage of the plugin can be found in 
sofa/applications/plugins/SofaPython/doc/SofaPython.pdf
To lance the scene, type 
runSofa /home/zahra/sofa/Work/test/liverVolumeSurfacePython.scn

The current file has been written by the python script
/home/zahra/sofa/Sofa17.06/src/applications/plugins/SofaPython/scn2python.py
Author of scn2python.py: Christoph PAULUS, christoph.paulus@inria.fr
"""




""" errors you may encounter:
    
    [FATAL]   [SofaPython] SP_CALL_MODULEFUNC
Traceback (most recent call last):
  File "/home/zahra/sofa/Work/test/liverSurface_controller.py", line 121, in onBeginAnimationStep
    current_S_Fine = open('/home/zahra/sofa/Work/Exported/Fine_surface/LiverSurfaceFine_'+str(j[self.ind2])+'_0_'+str(i[self.ind1])+'_0.gmsh')
IOError: [Errno 2] No such file or directory: '/home/zahra/sofa/Work/Exported/Fine_surface/LiverSurfaceFine_111_0_-200_0.gmsh'

while you know that the path and the file name is true, follow the below format for mewsh exporter:
    
        Liver.createObject('MeshExporter', exportEveryNumberOfSteps='1', quads='0', name='meshExporter3', format='gmsh', exportAtEnd='0', filename='/home/zahra/sofa/Work/Exported/Fine_volume/LiverVolumeFine_111_0_-120_0', exportAtBegin='0', tetras='1', hexas='0', edges='0', triangles='0', listening='0')
"""


import Sofa


#### deleting the contents of the saved mesh folders from previous run

#
#import os, shutil
#folder1 = '/home/zahra/sofa/Work/Exported/Fine_volume'
#for the_file in os.listdir(folder1):
#    file_path = os.path.join(folder1, the_file)
#    try:
#        if os.path.isfile(file_path):
#            os.unlink(file_path)
#        #elif os.path.isdir(file_path): shutil.rmtree(file_path)
#    except Exception as e:
#        print(e)
# 
#folder2 = '/home/zahra/sofa/Work/Exported/Fine_surface'
#for the_file in os.listdir(folder2):
#    file_path = os.path.join(folder2, the_file)
#    try:
#        if os.path.isfile(file_path):
#            os.unlink(file_path)
#        #elif os.path.isdir(file_path): shutil.rmtree(file_path)
#    except Exception as e:
#        print(e)
#        
#folder3 = '/home/zahra/sofa/Work/Exported/Coarse_volume'
#for the_file in os.listdir(folder3):
#    file_path = os.path.join(folder3, the_file)
#    try:
#        if os.path.isfile(file_path):
#            os.unlink(file_path)
#        #elif os.path.isdir(file_path): shutil.rmtree(file_path)
#    except Exception as e:
#        print(e) 
#folder4 = '/home/zahra/sofa/Work/Exported/Coarse_surface'
#for the_file in os.listdir(folder4):
#    file_path = os.path.join(folder4, the_file)
#    try:
#        if os.path.isfile(file_path):
#            os.unlink(file_path)
#        #elif os.path.isdir(file_path): shutil.rmtree(file_path)
#    except Exception as e:
#        print(e)




def createScene(rootNode):
    rootNode.createObject('RequiredPlugin', name='SofaPython')
    mySimulation = liverVolumeSurface(rootNode,[])
    return 0;

class liverVolumeSurface (Sofa.PythonScriptController):

    def initGraph(self,rootNode):

        # rootNode
        rootNode.createObject('DefaultPipeline', name='CollisionPipeline', verbose='0')
        rootNode.createObject('BruteForceDetection', name='N2')
        rootNode.createObject('DefaultContactManager', name='collision response', response='default')
        rootNode.createObject('DiscreteIntersection', name='discreteIntersection1')
      #  rootNode.createObject('PythonScriptController', classname="controller", filename='liverSurface_controller.py')
      # rootNode.createObject('PythonScriptController', classname="controller", filename='liverVolumeSurface_restStateController.py')
       # rootNode.createObject('PythonScriptController', classname="controller", filename='liverVolumeSurface_controller.py')
     
        # rootNode/Liver
        Liver = rootNode.createChild('Liver')
        Liver.depend = 'topo dofs'
        Liver.createObject('EulerImplicitSolver', name='cg_odesolver', printLog='0')
        Liver.createObject('CGLinearSolver', threshold='1e-09', tolerance='1e-09', name='linear solver', iterations='25', template='GraphScattered')
        Liver.createObject('MeshGmshLoader', tetrahedraGroups='  -1 0 38144', name='loader', filename='/home/zahra/SOFAFORUM/InputLiverVolumeCoarse.gmsh',flipNormals='1')
        Liver.createObject('TetrahedronSetTopologyContainer', triangles='@loader.triangles', position='@loader.position', edges='@loader.edges', name='topo', tetrahedra='@loader.tetras')
        Liver.createObject('MechanicalObject', force='0 0 0', name='dofs', template='Vec3d', position='@loader.position', velocity='0 0 0', externalForce='0 0 0', restScale='1')
        Liver.createObject('TetrahedronSetGeometryAlgorithms', drawColorEdges='0.4 1 0.298039 1', showIndicesScale='0.01', name='GeomAlgo', showPointIndices='0', template='Vec3d',flipNormals='1')
        Liver.createObject('DiagonalMass', massDensity='1', name='computed using mass density', template='Vec3d')
        Liver.createObject('TetrahedralCorotationalFEMForceField', poissonRatio='0.3', name='FEM', computeGlobalMatrix='0', method='large', template='Vec3d', youngModulus='120')
        Liver.createObject('PlaneForceField', name='planeFF0', template='Vec3d', normal='0 1 0', draw='1', drawSize='8')
      #  Liver.createObject('ConstantForceField', indices='109', name='constantFF0', template='Vec3d', forces='0 50 0')
        Liver.createObject('ConstantForceField', indices='', name='constantFF0', template='Vec3d', forces='')
        Liver.createObject('FixedConstraint', indices='0 11 17 16 15 14 4 3 45 95 42 40 38 39 53 62 61 60 4 63 59 125 24 20 19 9', showObject='0', drawSize='0', name='fixedConstraint0', template='Vec3d')
      #  Liver.createObject('MeshExporter', exportEveryNumberOfSteps='1', quads='0', name='meshExporter0', format='gmsh', exportAtEnd='1', filename='/home/zahra/sofa/Work/Exported/Fine_volume/LiverVolumeFine_'+str(Liver.getObject('constantFF0').findData('forces').value[0])+'_'+str(Liver.getObject('constantFF0').findData('indices').value[0]), exportAtBegin='0', tetras='1', hexas='0', edges='0', triangles='0', listening='0')
      #  Liver.createObject('MeshExporter', exportEveryNumberOfSteps='1', quads='0', name='meshExporter0', format='gmsh', exportAtEnd='1', filename='/home/zahra/LiverFor2ndPaperTest/LiverMeshes/LiverUndeformedVolumeCoarse', exportAtBegin='0', tetras='1', hexas='0', edges='0', triangles='0', listening='0')
        Liver.createObject('TetrahedronSetTopologyModifier', name='tetrahedronSetTopologyModifier9')
        Liver.createObject('TetrahedronSetTopologyAlgorithms', name='tetrahedronSetTopologyAlgorithms10', template='Vec3d')
#        Liver.createObject('OglModel', sfactor='GL_SRC_ALPHA', blendEquation='GL_FUNC_ADD', name='oglModelFineVisu', template='ExtVec3f', dfactor='GL_ONE_MINUS_SRC_ALPHA', material='Default Diffuse 1 0.7 0.2 0.2 1 Ambient 1 0.2 0.2 0.2 1 Specular 0 1 1 1 1 Emissive 0 0 0 0 0 Shininess 0 45 ', primitiveType='DEFAULT')       
#        Liver.createObject('BarycentricMapping', input='@dofs', name='BarycentricMapfineVisu', template='Vec3d,ExtVec3f', output='@oglModelFineVisu/')
#  
#
        # rootNode/Liver/surface_fine
        surface_fine = Liver.createChild('surface_fine')
        surface_fine.createObject('TriangleSetTopologyContainer', name='triangleSetTopologyContainer0')
        surface_fine.createObject('TriangleSetTopologyModifier', name='triangleSetTopologyModifier1')
        surface_fine.createObject('TriangleSetTopologyAlgorithms', name='triangleSetTopologyAlgorithms2', template='Vec3d')
        surface_fine.createObject('TriangleSetGeometryAlgorithms', name='triangleSetGeometryAlgorithms3', template='Vec3d',flipNormals='1')
        surface_fine.createObject('Tetra2TriangleTopologicalMapping', input='@../', name='tetra2TriangleTopologicalMapping4', output='@./')
     #   surface_fine.createObject('TriangularFEMForceField', name='triangularFEMFF5', template='Vec3d', poissonRatio='0.3', youngModulus='60')
        surface_fine.createObject('TriangularBendingSprings', name='triangularBendingSprings6', template='Vec3d', stiffness="30", damping="1")
        surface_fine.createObject('TTriangleModel', name='tTriangleModel15', template='Vec3d')
      #  surface_fine.createObject('TrianglePressureForceField', name='trianglePressureFF22', template='Vec3d')
      #  surface_fine.createObject('MeshExporter', exportEveryNumberOfSteps='1', quads='0', name='meshExporter1', format='gmsh', exportAtEnd='1', filename='/home/zahra/LiverFor2ndPaperTest/LiverMeshes/LiverUndeformedSurfaceCoarsefinal', exportAtBegin='0', tetras='0', hexas='0', edges='0', triangles='1', listening='0')
        surface_fine.createObject('OglModel', sfactor='GL_SRC_ALPHA', blendEquation='GL_FUNC_ADD', name='oglModelSurfacefine', template='ExtVec3f', dfactor='GL_ONE_MINUS_SRC_ALPHA', material='Default Diffuse 1 0.7 0.2 0.2 1 Ambient 1 0.2 0.2 0.2 1 Specular 0 1 1 1 1 Emissive 0 0 0 0 0 Shininess 0 45 ', primitiveType='DEFAULT',)       
        surface_fine.createObject('BarycentricMapping', input='@../', name='BarycentricMapSurfaceCoarse', template='Vec3d,ExtVec3f', output='@oglModelSurfacefine/')

     #   surface_fine.createObject('MeshExporter', exportEveryNumberOfSteps='1', quads='0', name='meshExporter1', format='gmsh', exportAtEnd='1', filename='', exportAtBegin='0', tetras='0', hexas='0', edges='0', triangles='1', listening='0')

#        # rootNode/Liver/surface_fine/visu_surface_fine
#        visu_surface_fine = surface_fine.createChild('visu_surface_fine')
#        visu_surface_fine.createObject('OglModel', filename='/home/zahra/LiverFor2ndPaperTest/LiverMeshes/LiverSurfaceCoarseUnconnectedNodesCleansed140_fromSOFA.gmsh', sfactor='GL_SRC_ALPHA', blendEquation='GL_FUNC_ADD', name='oglModel18', template='ExtVec3f', dfactor='GL_ONE_MINUS_SRC_ALPHA', material='Default Diffuse 1 0.1 0.0 0.9 1 Ambient 1 0.2 0.2 0.2 1 Specular 0 1 1 1 1 Emissive 0 0 0 0 0 Shininess 0 45 ', primitiveType='DEFAULT')
#        visu_surface_fine.createObject('BarycentricMapping', input='@../../dofs', name='BarycentricMap1', template='Vec3d,ExtVec3f', output='@oglModel18/')

        return 0;