CGALi2vLungs example broken (2)

[markus-stoll]

CGALi2vLungs example was broken. First fixes: 479d7f3fb9ee0999f3ecfa4e57534f5c05020338

A problem with generateDVF operator remains. The problems seems to be that the generateDVF input parameter is passed as path-type e.g. "path(u'disp50.vtu')". Changing "physical='VTK'" to "physical='string'" for in share\alphabet\msml_operators\misc\generateDVF.xml would fix the problem....

msml_github/src/msml.py exec C:\Projekte\msml_github\examples\CGALi2vLungs\Lungs_new.xml -e nsofa

Couldn't import dot_parser, loading of dot files will not be possible. I-0: READING alphabet... (from frontend.py:214) I-0: found 22 xml files in the alphabet search path (from frontend.py:218) W-161: logical type segmentationImage requested, but does not exist (from sorts.py:99) W-161: logical type linearTetMesh requested, but does not exist (from sorts.py:99) W-161: logical type triangularMesh requested, but does not exist (from sorts.py:99) W-161: logical type linearTetMesh requested, but does not exist (from sorts.py:99) W-161: logical type triangularMesh requested, but does not exist (from sorts.py:99) W-161: logical type linearTetMesh, quadraticTetMesh requested, but does not exist (from sorts.py:99) W-161: logical type indexgroup requested, but does not exist (from sorts.py:99) W-161: logical type triangularMesh requested, but does not exist (from sorts.py:99) W-161: logical type triangularMesh requested, but does not exist (from sorts.py:99) W-161: logical type linearTetMesh+quadraticTetMesh requested, but does not exist (from sorts.py:99) W-161: logical type linearTetMesh+quadraticTetMesh requested, but does not exist (from sorts.py:99) W-161: logical type linearTetMesh+triangularMesh requested, but does not exist (from sorts.py:99) W-161: logical type linearTetMesh+triangularMesh requested, but does not exist (from sorts.py:99) W-161: logical type image requested, but does not exist (from sorts.py:99) W-161: logical type linearTetMesh requested, but does not exist (from sorts.py:99) W-161: logical type indexGroup requested, but does not exist (from sorts.py:99) W-161: logical type triangularMesh requested, but does not exist (from sorts.py:99) W-161: logical type segmentationImage requested, but does not exist (from sorts.py:99) W-161: logical type triangularMesh requested, but does not exist (from sorts.py:99) LOADING: msml.ext.cgal.CreateVolumeMeshi2v LOADING: msml.ext.cgal.CreateVolumeMeshs2v LOADING: msml.ext.misc.ApplyDVF LOADING: msml.ext.misc.ColorMeshPython LOADING: msml.ext.misc.computeIndicesFromBoxROI LOADING: msml.ext.misc.ConvertSTLToVTK LOADING: msml.ext.misc.ConvertVTKMeshToAbaqusMeshString LOADING: msml.ext.misc.ExtractAllSurfacesByMaterial LOADING: msml.ext.misc.GenerateDVF LOADING: msml.ext.misc.computeIndicesFromMaterialId LOADING: msml.ext.misc.VoxelizeSurfaceMesh LOADING: msml.ext.tetgen.CreateVolumeMeshPython E-182: OAConstraint: springMeshToFixed does not have an indices attribute defined (from alphabet.py:206) E-182: OAConstraint: supportingMesh does not have an indices attribute defined (from alphabet.py:206) W-161: logical type segmentationImage requested, but does not exist (from sorts.py:99) I-6161: Need convert value of <var segementation_voxel_image : <Sort: <class 'msml.sortdef.VTK'>, None> = case1_T00_labled.vti> (from base.py:446) W-161: logical type linearMesh requested, but does not exist (from sorts.py:99) I-6161: Need convert value of <var tet_only_mesh : <Sort: <class 'msml.sortdef.VTK'>, None> = case1_T00_tetmesh.vtk> (from base.py:446) W-161: logical type linearMesh requested, but does not exist (from sorts.py:99) I-6161: Need convert value of <var combo_mesh : <Sort: <class 'msml.sortdef.VTK'>, None> = case1_T00_mesh_combo.vtk> (from base.py:446) Execute: C:\Projekte\msml_github\examples\CGALi2vLungs\Lungs_new.xml in <bound method path.dirname of path(u'C:\Projekte\msml_github\examples\CGALi2vLungs\Lungs_new.xml')> I-6161: Need convert value of <var _gen001 : <Sort: <class 'msml.sortdef.MSMLFloat'>, None> = 18> (from base.py:446) I-6161: Need convert value of <var _gen002 : <Sort: <class 'msml.sortdef.MSMLFloat'>, None> = 3> (from base.py:446) I-6161: Need convert value of <var _gen003 : <Sort: <class 'msml.sortdef.MSMLFloat'>, None> = 3> (from base.py:446) I-6161: Need convert value of <var _gen004 : <Sort: <type 'bool'>, None> = false> (from base.py:446) I-6161: Need convert value of <var _gen005 : <Sort: <type 'bool'>, None> = false> (from base.py:446) I-6161: Need convert value of <var _gen006 : <Sort: <class 'msml.sortdef.MSMLFloat'>, None> = 12> (from base.py:446) I-6161: Need convert value of <var _gen007 : <Sort: <type 'bool'>, None> = false> (from base.py:446) I-6161: Need convert value of <var _gen008 : <Sort: <type 'bool'>, None> = false> (from base.py:446) I-6161: Need convert value of <var _gen009 : <Sort: <class 'msml.sortdef.MSMLFloat'>, None> = 20> (from base.py:446) I-6161: Need convert value of <var _gen010 : <Sort: <class 'msml.sortdef.MSMLInt'>, None> = 100> (from base.py:446) I-6161: Need convert value of <var _gen011 : <Sort: <class 'msml.sortdef.MSMLString'>, None> = elements> (from base.py:446) I-6161: Need convert value of <var _gen012 : <Sort: <class 'msml.sortdef.MSMLInt'>, None> = 50> (from base.py:446) I-6161: Need convert value of <var _gen013 : <Sort: <class 'msml.sortdef.MSMLString'>, None> = elements> (from base.py:446) I-6161: Need convert value of <var _gen014 : <Sort: <class 'msml.sortdef.MSMLInt'>, None> = 75> (from base.py:446) I-6161: Need convert value of <var _gen015 : <Sort: <class 'msml.sortdef.MSMLString'>, None> = faces> (from base.py:446) I-6161: Need convert value of <var _gen016 : <Sort: <class 'msml.sortdef.MSMLInt'>, None> = 75> (from base.py:446) I-6161: Need convert value of <var _gen017 : <Sort: <class 'msml.sortdef.MSMLString'>, None> = elements> (from base.py:446) I-6161: Need convert value of <var _gen018 : <Sort: <type 'bool'>, None> = false> (from base.py:446) I-6161: Need convert value of <var _gen019 : <Sort: <class 'msml.sortdef.MSMLString'>, None> = dvf01.vtk> (from base.py:446) I-6161: Need convert value of <var _gen020 : <Sort: <class 'msml.sortdef.MSMLInt'>, None> = 25> (from base.py:446) I-6161: Need convert value of <var _gen021 : <Sort: <class 'msml.sortdef.MSMLString'>, None> = elements> (from base.py:446) I-6161: Need convert value of <var _gen022 : <Sort: <class 'msml.sortdef.MSMLInt'>, None> = 50> (from base.py:446) I-6161: Need convert value of <var _gen023 : <Sort: <class 'msml.sortdef.MSMLString'>, None> = faces> (from base.py:446) I-6161: Need convert value of <var _gen024 : <Sort: <type 'bool'>, None> = false> (from base.py:446) I-6161: Need convert value of <var _gen025 : <Sort: <class 'msml.sortdef.MSMLListF'>, None> = -10 190 -10 1000 1000 1000> (from base.py:446) I-6161: Need convert value of <var _gen026 : <Sort: <class 'msml.sortdef.MSMLString'>, None> = points> (from base.py:446) F-0: Parameter name of Definiton mass is not specified in msml file. (from base.py:893) F-0: Parameter name of Definiton mass is not specified in msml file. (from base.py:893) F-0: Parameter name of Definiton mass is not specified in msml file. (from base.py:893) F-0: Parameter name of Definiton mass is not specified in msml file. (from base.py:893) E-0: Parameter forStep of Element fixedConstraint is not specified in definition. (from base.py:887) E-0: Parameter name of Element fixedConstraint is not specified in definition. (from base.py:887) F-0: Parameter time of Definiton fixedConstraint is not specified in msml file. (from base.py:893) E-0: Parameter name of Element surfacePressure is not specified in definition. (from base.py:887) F-0: Parameter time of Definiton surfacePressure is not specified in msml file. (from base.py:893) E-0: Parameter name of Element surfacePressure is not specified in definition. (from base.py:887) F-0: Parameter time of Definiton surfacePressure is not specified in msml file. (from base.py:893) D-1562: Reference <Reference+: <var _gen003 : <Sort: <class 'msml.sortdef.MSMLFloat'>, None> = 3.0> -> <Slot cell_radius_edge_ratio: <Sort: <class 'msml.sortdef.MSMLFloat'>, None>>> is valid (from runinit.py:271) D-1562: Reference <Reference+: <var _gen021 : <Sort: <class 'msml.sortdef.MSMLString'>, None> = elements> -> <Slot type: <Sort: <class 'msml.sortdef.MSMLString'>, None>>> is valid (from runinit.py:271) D-1562: Reference <Reference+: <var _gen004 : <Sort: <type 'bool'>, None> = False> -> <Slot odt: <Sort: <type 'bool'>, None>>> is valid (from runinit.py:271) D-1562: Reference <Reference+: <Slot indices: <Sort: <class 'msml.sortdef.MSMLListI'>, None>> -> <Slot mr_patMaterial04_indexgroup: <Sort: <class 'msml.sortdef.MSMLListI'>, None>>> is valid (from runinit.py:271) D-1562: Reference <Reference+: <var disp : <Sort: <class 'msml.sortdef.VTK'>, None> = None> -> <Slot RefMesh: <Sort: <class 'msml.sortdef.VTK'>, <class 'msml.sortdef.Mesh'>>>> is valid (from runinit.py:271) D-1562: Reference <Reference+: <var disp : <Sort: <class 'msml.sortdef.VTK'>, None> = None> -> <Slot data: <Sort: <class 'msml.sortdef.VTK'>, <class 'msml.sortdef.Mesh'>>>> is valid (from runinit.py:271) D-1562: Reference <Reference+: <var _gen022 : <Sort: <class 'msml.sortdef.MSMLInt'>, None> = 50> -> <Slot num: <Sort: <class 'msml.sortdef.MSMLInt'>, None>>> is valid (from runinit.py:271) D-1562: Reference <Reference+: <var _gen005 : <Sort: <type 'bool'>, None> = False> -> <Slot pertube: <Sort: <type 'bool'>, None>>> is valid (from runinit.py:271) D-1562: Reference <Reference+: <var _gen006 : <Sort: <class 'msml.sortdef.MSMLFloat'>, None> = 12.0> -> <Slot facet_size: <Sort: <class 'msml.sortdef.MSMLFloat'>, None>>> is valid (from runinit.py:271) D-1562: Reference <Reference+: <Slot meshOut: <Sort: <class 'msml.sortdef.VTK'>, None>> -> <Slot mesh: <Sort: <class 'msml.sortdef.VTK'>, None>>> is valid (from runinit.py:271) D-1562: Reference <Reference+: <Slot meshOut: <Sort: <class 'msml.sortdef.VTK'>, None>> -> <Slot mesh: <Sort: <class 'msml.sortdef.VTK'>, None>>> is valid (from runinit.py:271) D-1562: Reference <Reference+: <Slot meshOut: <Sort: <class 'msml.sortdef.VTK'>, None>> -> <Slot mesh: <Sort: <class 'msml.sortdef.VTK'>, None>>> is valid (from runinit.py:271) D-1562: Reference <Reference+: <Slot meshOut: <Sort: <class 'msml.sortdef.VTK'>, None>> -> <Slot mesh: <Sort: <class 'msml.sortdef.VTK'>, None>>> is valid (from runinit.py:271) D-1562: Reference <Reference+: <Slot meshOut: <Sort: <class 'msml.sortdef.VTK'>, None>> -> <Slot DeformedMesh: <Sort: <class 'msml.sortdef.VTK'>, None>>> is valid (from runinit.py:271) D-1562: Reference <Reference+: <Slot meshOut: <Sort: <class 'msml.sortdef.VTK'>, None>> -> <Slot mesh: <Sort: <class 'msml.sortdef.VTK'>, None>>> is valid (from runinit.py:271) D-1562: Reference <Reference+: <Slot meshOut: <Sort: <class 'msml.sortdef.VTK'>, None>> -> <Slot mesh: <Sort: <class 'msml.sortdef.VTK'>, None>>> is valid (from runinit.py:271) D-1562: Reference <Reference+: <Slot meshOut: <Sort: <class 'msml.sortdef.VTK'>, None>> -> <Slot mesh: <Sort: <class 'msml.sortdef.VTK'>, <class 'msml.sortdef.Mesh'>>>> is valid (from runinit.py:271) D-1562: Reference <Reference+: <Slot meshOut: <Sort: <class 'msml.sortdef.VTK'>, None>> -> <Slot mesh: <Sort: <class 'msml.sortdef.VTK'>, None>>> is valid (from runinit.py:271) D-1562: Reference <Reference+: <var _gen024 : <Sort: <type 'bool'>, None> = False> -> <Slot cut: <Sort: <type 'bool'>, None>>> is valid (from runinit.py:271) D-1562: Reference <Reference+: <var _gen007 : <Sort: <type 'bool'>, None> = False> -> <Slot lloyd: <Sort: <type 'bool'>, None>>> is valid (from runinit.py:271) I-1561: Reference <Reference+: <var combo_mesh : <Sort: <class 'msml.sortdef.VTK'>, None> = case1_T00_mesh_combo.vtk> -> <Slot meshOutFilename: <Sort: <class 'msml.sortdef.MSMLString'>, None>>> is invalid. Try to implicit conversion (from runinit.py:245) D-1562: Reference <Reference+: <var _gen025 : <Sort: <class 'msml.sortdef.MSMLListF'>, None> = [-10.0, 190.0, -10.0, 1000.0, 1000.0, 1000.0]> -> <Slot box: <Sort: <class 'msml.sortdef.MSMLListF'>, None>>> is valid (from runinit.py:271) D-1562: Reference <Reference+: <var _gen008 : <Sort: <type 'bool'>, None> = False> -> <Slot exude: <Sort: <type 'bool'>, None>>> is valid (from runinit.py:271) D-1562: Reference <Reference+: <var _gen026 : <Sort: <class 'msml.sortdef.MSMLString'>, None> = points> -> <Slot select: <Sort: <class 'msml.sortdef.MSMLString'>, None>>> is valid (from runinit.py:271) D-1562: Reference <Reference+: <var _gen009 : <Sort: <class 'msml.sortdef.MSMLFloat'>, None> = 20.0> -> <Slot facet_angle: <Sort: <class 'msml.sortdef.MSMLFloat'>, None>>> is valid (from runinit.py:271) D-1562: Reference <Reference+: <Slot mesh: <Sort: <class 'msml.sortdef.VTK'>, None>> -> <Slot meshIn: <Sort: <class 'msml.sortdef.VTK'>, None>>> is valid (from runinit.py:271) D-1562: Reference <Reference+: <var _gen010 : <Sort: <class 'msml.sortdef.MSMLInt'>, None> = 100> -> <Slot num: <Sort: <class 'msml.sortdef.MSMLInt'>, None>>> is valid (from runinit.py:271) D-1562: Reference <Reference+: <Slot indices: <Sort: <class 'msml.sortdef.MSMLListI'>, None>> -> <Slot mr_patMaterial01_indexgroup: <Sort: <class 'msml.sortdef.MSMLListI'>, None>>> is valid (from runinit.py:271) D-1562: Reference <Reference+: <var _gen011 : <Sort: <class 'msml.sortdef.MSMLString'>, None> = elements> -> <Slot type: <Sort: <class 'msml.sortdef.MSMLString'>, None>>> is valid (from runinit.py:271) D-1562: Reference <Reference+: <var _gen023 : <Sort: <class 'msml.sortdef.MSMLString'>, None> = faces> -> <Slot type: <Sort: <class 'msml.sortdef.MSMLString'>, None>>> is valid (from runinit.py:271) D-1562: Reference <Reference+: <var _gen012 : <Sort: <class 'msml.sortdef.MSMLInt'>, None> = 50> -> <Slot num: <Sort: <class 'msml.sortdef.MSMLInt'>, None>>> is valid (from runinit.py:271) D-1562: Reference <Reference+: <var _gen013 : <Sort: <class 'msml.sortdef.MSMLString'>, None> = elements> -> <Slot type: <Sort: <class 'msml.sortdef.MSMLString'>, None>>> is valid (from runinit.py:271) D-1562: Reference <Reference+: <var _gen014 : <Sort: <class 'msml.sortdef.MSMLInt'>, None> = 75> -> <Slot num: <Sort: <class 'msml.sortdef.MSMLInt'>, None>>> is valid (from runinit.py:271) D-1562: Reference <Reference+: <var _gen015 : <Sort: <class 'msml.sortdef.MSMLString'>, None> = faces> -> <Slot type: <Sort: <class 'msml.sortdef.MSMLString'>, None>>> is valid (from runinit.py:271) I-1561: Reference <Reference+: <var segementation_voxel_image : <Sort: <class 'msml.sortdef.VTK'>, None> = case1_T00_labled.vti> -> <Slot image: <Sort: <class 'msml.sortdef.VTI'>, None>>> is invalid. Try to implicit conversion (from runinit.py:245) D-1562: Reference <Reference+: <var _gen016 : <Sort: <class 'msml.sortdef.MSMLInt'>, None> = 75> -> <Slot num: <Sort: <class 'msml.sortdef.MSMLInt'>, None>>> is valid (from runinit.py:271) D-1562: Reference <Reference+: <var _gen017 : <Sort: <class 'msml.sortdef.MSMLString'>, None> = elements> -> <Slot type: <Sort: <class 'msml.sortdef.MSMLString'>, None>>> is valid (from runinit.py:271) D-1562: Reference <Reference+: <Slot indices: <Sort: <class 'msml.sortdef.MSMLListI'>, None>> -> <Slot mr_patMaterial02_indexgroup: <Sort: <class 'msml.sortdef.MSMLListI'>, None>>> is valid (from runinit.py:271) D-1562: Reference <Reference+: <var _gen018 : <Sort: <type 'bool'>, None> = False> -> <Slot multipleReferenceGrids: <Sort: <type 'bool'>, None>>> is valid (from runinit.py:271) D-1562: Reference <Reference+: <var _gen001 : <Sort: <class 'msml.sortdef.MSMLFloat'>, None> = 18.0> -> <Slot cell_size: <Sort: <class 'msml.sortdef.MSMLFloat'>, None>>> is valid (from runinit.py:271) I-1561: Reference <Reference+: <var tet_only_mesh : <Sort: <class 'msml.sortdef.VTK'>, None> = case1_T00_tetmesh.vtk> -> <Slot meshFilename: <Sort: <class 'msml.sortdef.MSMLString'>, None>>> is invalid. Try to implicit conversion (from runinit.py:245) D-1562: Reference <Reference+: <var _gen019 : <Sort: <class 'msml.sortdef.MSMLString'>, None> = dvf01.vtk> -> <Slot DVFFilename: <Sort: <class 'msml.sortdef.MSMLString'>, None>>> is valid (from runinit.py:271) D-1562: Reference <Reference+: <var _gen002 : <Sort: <class 'msml.sortdef.MSMLFloat'>, None> = 3.0> -> <Slot facet_distance: <Sort: <class 'msml.sortdef.MSMLFloat'>, None>>> is valid (from runinit.py:271) D-1562: Reference <Reference+: <var _gen020 : <Sort: <class 'msml.sortdef.MSMLInt'>, None> = 25> -> <Slot num: <Sort: <class 'msml.sortdef.MSMLInt'>, None>>> is valid (from runinit.py:271) D-1562: Reference <Reference+: <Slot indices: <Sort: <class 'msml.sortdef.MSMLListI'>, None>> -> <Slot mr_patMaterial03_indexgroup: <Sort: <class 'msml.sortdef.MSMLListI'>, None>>> is valid (from runinit.py:271) I-001: Executing operator of task {Task combo_mesh (converter_VTK_MSMLString)} with arguments {'i': 'C:\Projekte\msml_github\examples\CGALi2vLungs\case1_T00_mesh_combo.vtk'} (from runinit.py:170) I-001: Executing operator of task <PythonOperator: .> with arguments ['C:\Projekte\msml_github\examples\CGALi2vLungs\case1_T00_mesh_combo.vtk'] (from alphabet.py:437) I-002: --Executing operator of task <PythonOperator: .> done (from alphabet.py:439) I-002: --Executing operator of task {Task combo_mesh (converter_VTK_MSMLString)} done (from runinit.py:172) I-001: Executing operator of task {Task tet_only_mesh (converter_VTK_MSMLString)} with arguments {'i': 'C:\Projekte\msml_github\examples\CGALi2vLungs\case1_T00_tetmesh.vtk'} (from runinit.py:170) I-001: Executing operator of task <PythonOperator: .> with arguments ['C:\Projekte\msml_github\examples\CGALi2vLungs\case1_T00_tetmesh.vtk'] (from alphabet.py:437) I-002: --Executing operator of task <PythonOperator: .> done (from alphabet.py:439) I-002: --Executing operator of task {Task tet_only_mesh (converter_VTK_MSMLString)} done (from runinit.py:172) 'C:\Projekte\msml_github\examples\CGALi2vLungs\case1_T00_labled.vti'} with arguments {'i': 'C:\Projekte\msml_github\examples\CGALi2vLungs\case1_T00_labled.vti'} (from runinit.py:170) I-001: Executing operator of task <PythonOperator: .> with arguments ['C:\Projekte\msml_github\examples\CGALi2vLungs\case1_T00_labled.vti'] (from alphabet.py:437) I-002: --Executing operator of task <PythonOperator: .> done (from alphabet.py:439) I-002: --Executing operator of task {Task segementation_voxel_image (converter_VTK_VTI)} done (from runinit.py:172) I-001: Executing operator of task {Task VolumeMesher (mesherCGALi2v)} with arguments {'cell_size': 18.0, 'facet_distance': 3.0, 'cell_radius_edge_ratio': 3.0, 'image': 'C:\Projekte\msml_github\examples\CGALi2vLungs\case1_T00_labled.vti', 'odt': False, 'pertube': False, 'facet_size': 12.0, 'meshFilename': 'C:\Projekte\msml_github\examples\CGALi2vLungs\case1_T00_tetmesh.vtk', 'lloyd': False, 'exude': False, 'facet_angle': 20.0} (from runinit.py:170) I-001: Executing operator of task with arguments ['C:\Projekte\msml_github\examples\CGALi2vLungs\case1_T00_labled.vti', 'C:\Projekte\msml_github\examples\CGALi2vLungs\case1_T00_tetmesh.vtk', 20.0, 12.0, 3.0, 3.0, 18.0, False, False, False, False] (from alphabet.py:437) GetNumberOfTuples()=6160384 image->size()=6160384 wdim=1 I-002: --Executing operator of task done (from alphabet.py:439) I-002: --Executing operator of task {Task VolumeMesher (mesherCGALi2v)} done (from runinit.py:172) I-001: Executing operator of task {Task surfaceExtraction (ExtractAllSurfacesByMaterial)} with arguments {'meshOutFilename': 'C:\Projekte\msml_github\examples\CGALi2vLungs\case1_T00_mesh_combo.vtk', 'cut': False, 'meshIn': 'C:\Projekte\msml_github\examples\CGALi2vLungs\case1_T00_tetmesh.vtk'} (from runinit.py:170) I-001: Executing operator of task with arguments ['C:\Projekte\msml_github\examples\CGALi2vLungs\case1_T00_tetmesh.vtk', 'C:\Projekte\msml_github\examples\CGALi2vLungs\case1_T00_mesh_combo.vtk', False] (from alphabet.py:437) There are 27581 cells before thresholding. 5976 cells of MaterialId=25 found. There are 5976 cells after thresholding with 25 CellType is 5 2499 cells of MaterialId=50 found. There are 2499 cells after thresholding with 50 CellType is 5 2868 cells of MaterialId=75 found. There are 2868 cells after thresholding with 75 CellType is 5 16238 cells of MaterialId=100 found. There are 16238 cells after thresholding with 100 I-002: --Executing operator of task done (from alphabet.py:439) I-002: --Executing operator of task {Task surfaceExtraction (ExtractAllSurfacesByMaterial)} done (from runinit.py:172) I-001: Executing operator of task {Task bottomToIndexGroup (boxROIToIndexOperator)} with arguments {'box': [-10.0, 190.0, -10.0, 1000.0, 1000.0, 1000.0], 'mesh': 'C:\Projekte\msml_github\examples\CGALi2vLungs\case1_T00_mesh_combo.vtk', 'select': 'points'} (from runinit.py:170) I-001: Executing operator of task with arguments ['C:\Projekte\msml_github\examples\CGALi2vLungs\case1_T00_mesh_combo.vtk', [-10.0, 190.0, -10.0, 1000.0, 1000.0, 1000.0], 'points'] (from alphabet.py:437) CellType is 5 443 points found in boxI-002: --Executing operator of task done (from alphabet.py:439) I-002: --Executing operator of task {Task bottomToIndexGroup (boxROIToIndexOperator)} done (from runinit.py:172) I-001: Executing operator of task {Task bonesToIndexGroup (materialId-to-index)} with arguments {'num': 25, 'type': 'elements', 'mesh': 'C:\Projekte\msml_github\examples\CGALi2vLungs\case1_T00_mesh_combo.vtk'} (from runinit.py:170) I-001: Executing operator of task with arguments ['C:\Projekte\msml_github\examples\CGALi2vLungs\case1_T00_mesh_combo.vtk', 25, 'elements'] (from alphabet.py:437) I-002: --Executing operator of task done (from alphabet.py:439) I-002: --Executing operator of task {Task bonesToIndexGroup (materialId-to-index)} done (from runinit.py:172) I-001: Executing operator of task {Task lung2facesToIndexGroup (materialId-to-index)} with arguments {'num': 75, 'type': 'faces', 'mesh': 'C:\Projekte\msml_github\examples\CGALi2vLungs\case1_T00_mesh_combo.vtk'} (from runinit.py:170) I-001: Executing operator of task with arguments ['C:\Projekte\msml_github\examples\CGALi2vLungs\case1_T00_mesh_combo.vtk', 75, 'faces'] (from alphabet.py:437) I-002: --Executing operator of task done (from alphabet.py:439) I-002: --Executing operator of task {Task lung2facesToIndexGroup (materialId-to-index)} done (from runinit.py:172) I-001: Executing operator of task {Task lung1facesToIndexGroup (materialId-to-index)} with arguments {'num': 50, 'type': 'faces', 'mesh': 'C:\Projekte\msml_github\examples\CGALi2vLungs\case1_T00_mesh_combo.vtk'} (from runinit.py:170) I-001: Executing operator of task with arguments ['C:\Projekte\msml_github\examples\CGALi2vLungs\case1_T00_mesh_combo.vtk', 50, 'faces'] (from alphabet.py:437) I-002: --Executing operator of task done (from alphabet.py:439) I-002: --Executing operator of task {Task lung1facesToIndexGroup (materialId-to-index)} done (from runinit.py:172) I-001: Executing operator of task {Task bodyToIndexGroup (materialId-to-index)} with arguments {'num': 100, 'type': 'elements', 'mesh': 'C:\Projekte\msml_github\examples\CGALi2vLungs\case1_T00_mesh_combo.vtk'} (from runinit.py:170) I-001: Executing operator of task with arguments ['C:\Projekte\msml_github\examples\CGALi2vLungs\case1_T00_mesh_combo.vtk', 100, 'elements'] (from alphabet.py:437) I-002: --Executing operator of task done (from alphabet.py:439) I-002: --Executing operator of task {Task bodyToIndexGroup (materialId-to-index)} done (from runinit.py:172) I-001: Executing operator of task {Task lung2ToIndexGroup (materialId-to-index)} with arguments {'num': 75, 'type': 'elements', 'mesh': 'C:\Projekte\msml_github\examples\CGALi2vLungs\case1_T00_mesh_combo.vtk'} (from runinit.py:170) I-001: Executing operator of task with arguments ['C:\Projekte\msml_github\examples\CGALi2vLungs\case1_T00_mesh_combo.vtk', 75, 'elements'] (from alphabet.py:437) I-002: --Executing operator of task done (from alphabet.py:439) I-002: --Executing operator of task {Task lung2ToIndexGroup (materialId-to-index)} done (from runinit.py:172) I-001: Executing operator of task {Task lung1ToIndexGroup (materialId-to-index)} with arguments {'num': 50, 'type': 'elements', 'mesh': 'C:\Projekte\msml_github\examples\CGALi2vLungs\case1_T00_mesh_combo.vtk'} (from runinit.py:170) I-001: Executing operator of task with arguments ['C:\Projekte\msml_github\examples\CGALi2vLungs\case1_T00_mesh_combo.vtk', 50, 'elements'] (from alphabet.py:437) I-002: --Executing operator of task done (from alphabet.py:439) I-002: --Executing operator of task {Task lung1ToIndexGroup (materialId-to-index)} done (from runinit.py:172) Converting to sofa scn Lungs_new.scn I-252: Executing C:/Projekte/SOFA/Sofa/bin/SofaBatch.exe -l SOFACuda Lungs_new.scn_SOFA_batch.txt (from sofanew.py:100) I-616: Working directory: C:\Projekte\msml_github\examples\CGALi2vLungs (from sofanew.py:101)

SIMULATION (.scn:C:\Projekte\msml_github\examples\CGALi2vLungs\Lungs_new.scn, #steps:100, .simu:Lungs_new.scn.simu) Found 5116 float points LNG: 0 Found 48167 cells LNG: 0 LNG: 0 LNG: 0 LNG: 0 Data structure: SCALARS Read cell data: 48167 LNG: 1 CUDA: 4 device(s) found. CUDA: 0 : "Tesla C2075", 5375 MB, 112 cores at 1.147 GHz, revision 2.0 CUDA: 1 : "Tesla C2075", 5375 MB, 112 cores at 1.147 GHz, revision 2.0 CUDA: 2 : "Tesla C2075", 5375 MB, 112 cores at 1.147 GHz, revision 2.0 CUDA: 3 : "Tesla C2075", 5375 MB, 112 cores at 1.147 GHz, revision 2.0 CUDA: Using device 0 : "Tesla C2075" WARNING[root(GNode)]: Object type "DiagonalMass" creation Failed LOAD ERROR: Node initialization failed. WARNING[unnamed(WriteState)]: Error creating compressed file C:/Projekte/SOFA/Sofa//applications/projects/sofaBatch/simulation/Lungs_new.scn.simu_0_dofs_mstate.txt.gz Computing 100 iterations. 100 iterations done in 22.9418 s ( 4.35886 FPS). 100 iterations done in 22.9418 s ( 4.35886 FPS). C:/Projekte/SOFA/Sofa//applications/projects/sofaBatch/simulation/Lungs_new.scn.simu.simu file error I-001: Executing operator of task {Task dvf1 (generateDVF)} with arguments {'multipleReferenceGrids': False, 'RefMesh': path(u'disp50.vtu'), 'DeformedMesh': 'C:\Projekte\msml_github\examples\CGALi2vLungs\case1_T00_mesh_combo.vtk', 'DVFFilename': 'dvf01.vtk'} (from runinit.py:170) I-001: Executing operator of task with arguments [path(u'disp50.vtu'), 'dvf01.vtk', 'C:\Projekte\msml_github\examples\CGALi2vLungs\case1_T00_mesh_combo.vtk', False] (from alphabet.py:437) Traceback (most recent call last): File "C:\Projekte\msml_github\src\msml.py", line 36, in msml.frontend.main() File "C:\Projekte\msml_github\src\msml\frontend.py", line 274, in main app._exec() File "C:\Projekte\msml_github\src\msml\frontend.py", line 260, in _exec fn() File "C:\Projekte\msml_github\src\msml\frontend.py", line 211, in execution self.execute_msml_file(path(fil)) File "C:\Projekte\msml_github\src\msml\frontend.py", line 193, in execute_msml_file self.execute_msml(mfile) File "C:\Projekte\msml_github\src\msml\frontend.py", line 205, in execute_msml mem = exe.run() File "C:\Projekte\msml_github\src\msml\runinit.py", line 140, in run self._execute_operator_task(node) File "C:\Projekte\msml_github\src\msml\runinit.py", line 171, in _execute_operator_task result = task.operator(kwargs) File "C:\Projekte\msml_github\src\msml\model\alphabet.py", line 438, in call r = self._function(args) NotImplementedError: Wrong number or type of arguments for overloaded function 'GenerateDVF'. Possible C/C++ prototypes are: MSML::PostProcessingOperators::GenerateDVF(char const ,char const ,char const ,bool) MSML::PostProcessingOperators::GenerateDVF(char const ,char const ,char const ) MSML::PostProcessingOperators::GenerateDVF(vtkUnstructuredGrid ,vtkImageData ,vtkUnstructuredGrid *)

[markus-stoll]

any ideas? Shall a push my hack-fix "physical='string'" for RefMesh parameter?

[markus-stoll]

hack-fixed with 92124a63358ce8538f6e0ef5ac4fc50eb3616fc0 Better ideas?

[markus-stoll]

As discussed, I have reintroduced the problem. @areku: can you take a look at it d9e142d49869b48b0ac26e5f2d7287df55f736b7 ?

you can use the Lungs_new.xml example to call the GenerateDVF operator.

[wadoon]

SOFAExporter set the disp1 with wrong type (path.path, None) and not the type it has defined for this output request (VTK, Mesh).

This fixed it: self._memory['SOFAExporter'] = {request.id: VTK(str(filenameLastOutput))}

The build graph is ok: