medcoupling 9.13.0__cp39-cp39-win_amd64.whl → 9.15.0__cp39-cp39-win_amd64.whl

vtk2medcoupling.py

@@ -1,6 +1,6 @@
 #! /usr/bin/env python3
 #  -*- coding: utf-8 -*-
-# Copyright (C) 2020-2024  CEA, EDF
+# Copyright (C) 2020-2025  CEA, EDF
 #
 # This library is free software; you can redistribute it and/or
 # modify it under the terms of the GNU Lesser General Public
@@ -24,17 +24,263 @@ import vtk
 from vtk.util import numpy_support
 import medcoupling as mc
 import numpy as np
+import logging
+
+logger = None
+
+
+def getLogger():
+    global logger
+    if logger is None:
+        logging.basicConfig(level=logging.INFO)
+        logger = logging.getLogger()
+    return logger
+
+
+def setLogLevel(lev):
+    getLogger().setLevel(lev)
+
 
 def mesh_convertor(fileName):
-    #vtk.vtkDataSetReader()
+    # vtk.vtkDataSetReader()
     reader = vtk.vtkXMLUnstructuredGridReader()
     reader.SetFileName(fileName)
     reader.Update()
     ug = reader.GetOutput()
-    return mesh_convertor_mem(ug),ug
-    
-def mesh_convertor_mem(ug):
+    return mesh_convertor_mem(ug), ug
+
+
+def mesh_convertor_mem(ug, dimRequested=-1):
+    """
+    Main entry
+    """
     from distutils.version import LooseVersion
+
+    vtkVersion = vtk.vtkVersion().GetVTKVersion()
+    getLogger().debug(f"VTK version : {vtkVersion}")
+    if LooseVersion(vtkVersion) <= LooseVersion("9.3.0"):
+        return mesh_convertor_mem_93(ug, dimRequested)
+    else:
+        return mesh_convertor_mem_94(ug, dimRequested)
+
+
+def get_coarse_data_from_VTK_unstructuredGrid93(ug):
+    facesLoc = numpy_support.vtk_to_numpy(ug.GetFaceLocations())
+    faces = numpy_support.vtk_to_numpy(ug.GetFaces())
+    return facesLoc, faces
+
+
+def generate_polyhedrons_mesh_from_VTK_UnstructuredGrid_93(ug):
+    """
+    Returns from vtkUnstructuredGrid instance MEDCouplingMesh containing only polyhedra cells
+    """
+    facesLoc, faces = get_coarse_data_from_VTK_unstructuredGrid93(ug)
+    facesLocMed = mc.DataArrayInt(facesLoc)
+    facesMed = mc.DataArrayInt(faces)
+    cellIdsPolyh = facesLocMed.findIdsNotEqual(-1)
+    facesLocCpy = facesLocMed[:]
+    #
+    polyhStart = facesLocCpy[cellIdsPolyh]
+    polyhStart.pushBackSilent(len(facesMed))
+    a, b = mc.DataArrayInt64.FromVTKInternalReprOfPolyedra(facesMed, polyhStart)
+    m = mc.MEDCoupling1DGTUMesh("mesh", mc.NORM_POLYHED)
+    m.setNodalConnectivity(a, b)
+    return m.buildUnstructured()
+
+
+def generate_polyhedrons_mesh_from_VTK_UnstructuredGrid_94(ug):
+    facesLoc = (
+        ug.GetPolyhedronFaceLocations()
+    )  # vtkCellArray.SetData(offsets,connectivity)
+    facesLoc_o = mc.DataArrayInt(numpy_support.vtk_to_numpy(facesLoc.GetOffsetsArray()))
+    facesLoc_c = mc.DataArrayInt(
+        numpy_support.vtk_to_numpy(facesLoc.GetConnectivityArray())
+    )
+
+    faces = ug.GetPolyhedronFaces()
+    faces_o = mc.DataArrayInt(numpy_support.vtk_to_numpy(faces.GetOffsetsArray()))
+    faces_c = mc.DataArrayInt(numpy_support.vtk_to_numpy(faces.GetConnectivityArray()))
+
+    nbFacesPerCell = facesLoc_o.deltaShiftIndex()
+    polyhedronsCellIds = nbFacesPerCell.findIdsNotEqual(0)
+
+    _, facesLoc_o_eff = mc.DataArrayInt.ExtractFromIndexedArrays(
+        polyhedronsCellIds, facesLoc_c, facesLoc_o
+    )
+
+    a, b = mc.DataArrayInt64.FromVTK94InternalReprOfPolyedra(
+        faces_c, faces_o, facesLoc_o_eff
+    )
+
+    m = mc.MEDCoupling1DGTUMesh("mesh", mc.NORM_POLYHED)
+    m.setNodalConnectivity(a, b)
+    return m.buildUnstructured()
+
+
+def from_93_to_94_coarse_VTK_data(ug):
+    facesLoc, faces, _ = get_coarse_data_from_VTK_unstructuredGrid93(ug)
+    facesLocMed = mc.DataArrayInt(facesLoc)
+    facesMed = mc.DataArrayInt(faces)
+    cellIdsPolyh = facesLocMed.findIdsNotEqual(-1)
+    nbFacesPerPolyh = facesMed[facesLocMed[cellIdsPolyh]]
+    facesLoc_o = mc.DataArrayInt(len(facesLocMed))
+    facesLoc_o[:] = 0
+    facesLoc_o[cellIdsPolyh] = nbFacesPerPolyh
+    facesLoc_o.computeOffsetsFull()
+    faceLocMedNoMinusOne = facesLocMed[cellIdsPolyh]
+    faceLocMedNoMinusOne.pushBackSilent(len(facesMed))
+    faces_c, faces_o = mc.DataArrayInt64.FromVTK93To94FacesInternaReprOfPolyedra(
+        facesMed, faceLocMedNoMinusOne
+    )
+    nbFacesInPolyhedra = facesLoc_o[-1]
+    facesLoc_c = mc.DataArrayInt(nbFacesInPolyhedra)
+    facesLoc_c.iota()
+    return facesLoc_o, facesLoc_c, faces_o, faces_c
+
+
+def get_coarse_data_from_VTK_unstructuredGrid_94(ug):
+    facesLoc = ug.GetPolyhedronFaceLocations()
+    facesLoc_o = numpy_support.vtk_to_numpy(facesLoc.GetOffsetsArray())
+    facesLoc_c = numpy_support.vtk_to_numpy(facesLoc.GetConnectivityArray())
+
+    faces = ug.GetPolyhedronFaces()
+    faces_o = numpy_support.vtk_to_numpy(faces.GetOffsetsArray())
+    faces_c = numpy_support.vtk_to_numpy(faces.GetConnectivityArray())
+    return facesLoc_o, facesLoc_c, faces_o, faces_c
+
+
+def mesh_convertor_mem_gen(ug, dimRequested, callback_for_polyedrons):
+    coords = mc.DataArrayDouble(
+        np.array(numpy_support.vtk_to_numpy(ug.GetPoints().GetData()), dtype=np.float64)
+    )
+    cells = ug.GetCells()
+    offsets = numpy_support.vtk_to_numpy(cells.GetOffsetsArray())
+    ci = mc.DataArrayInt(np.array(offsets, dtype=np.int64))[:]
+    conn = mc.DataArrayInt(
+        np.array(
+            numpy_support.vtk_to_numpy(cells.GetConnectivityArray()), dtype=np.int64
+        )
+    )
+    types = numpy_support.vtk_to_numpy(ug.GetCellTypesArray())
+    ct = mc.DataArrayInt(
+        np.array(types, dtype="int{}".format(mc.MEDCouplingSizeOfIDs()))
+    )[:]
+    vtk2med = mc.DataArrayInt(mc.vtk2med_cell_types())
+    ctdim = ct[:]
+    ct.transformWithIndArr(vtk2med)
+
+    activeType = vtk2med.findIdsNotEqual(-1)
+    vtk2dim = vtk2med[:]
+    vtk2dim[activeType] = mc.DataArrayInt(
+        [
+            mc.MEDCouplingUMesh.GetDimensionOfGeometricType(int(elt))
+            for elt in vtk2med[activeType]
+        ]
+    )
+    ctdim.transformWithIndArr(vtk2dim)
+    dims = ctdim.getDifferentValues().getValues()
+    getLogger().debug(f"Available dimensions : {dims}")
+    zeDim = dimRequested
+    if zeDim < 0:
+        zeDim = max(dims)
+    else:
+        if zeDim not in dims:
+            raise RuntimeError(
+                f"{zeDim} not in detected dimension of vtkUnstructuredGrid instance : {dims}"
+            )
+    getLogger().debug(f"Filtering on dimension : {zeDim}")
+    selectedCells = ctdim.findIdsEqual(zeDim)
+    conn1, ci1 = mc.DataArrayInt.ExtractFromIndexedArrays(selectedCells, conn, ci)
+    ct1 = ct[selectedCells]
+
+    classicalCells = ct1.findIdsNotEqual(mc.NORM_POLYHED)
+    isPostWithPoly = ct1.presenceOfValue(mc.NORM_POLYHED)
+    resu = []
+    resu2 = []
+    if not classicalCells.empty():
+        getLogger().debug(f"Presence of {len(classicalCells)} classical cells")
+        conn2, ci2 = mc.DataArrayInt.ExtractFromIndexedArrays(
+            classicalCells, conn1, ci1
+        )
+        ct2 = ct1[classicalCells]
+        m = mc.MEDCouplingUMesh("mesh", zeDim)
+        # insert geo type in connectivity
+        a = ci2.deltaShiftIndex()
+        a2 = a + 1
+        a2.computeOffsetsFull()
+        b = mc.DataArrayInt(len(a))
+        b[:] = 1
+        c = mc.DataArrayInt.Meld([b, a])
+        c.rearrange(1)
+        c.computeOffsetsFull()
+        d = mc.DataArrayInt(len(classicalCells))
+        d.iota()
+        d *= 2
+        d += 1
+        d2 = d.buildExplicitArrByRanges(c)
+        d3 = mc.DataArrayInt(len(conn2) + len(classicalCells))
+        d3[:] = -1
+        idsForGeoType = d2.buildComplement(len(conn2) + len(classicalCells))
+        d3[idsForGeoType] = ct2
+        d3[d2] = conn2
+        #
+        m.setConnectivity(d3, a2, True)
+        m.setCoords(coords)
+        resu2.append(classicalCells)
+        resu.append(m)
+
+    if isPostWithPoly:
+        getLogger().debug(f"Presence of polyhedrons cells")
+        resu2.append(ct1.findIdsEqual(mc.NORM_POLYHED))
+        m = callback_for_polyedrons(ug)
+        m.setCoords(coords)
+        resu.append(m)
+
+    resu2 = mc.DataArrayInt.Aggregate(resu2)
+    resu = mc.MEDCouplingUMesh.MergeUMeshesOnSameCoords(resu)
+    ren = resu2.invertArrayO2N2N2O(len(resu2))
+    ret = resu[ren]
+    return ret
+
+
+def mesh_convertor_mem_93(ug, dimRequested=-1):
+    getLogger().debug(f"Reader 9.3")
+    return mesh_convertor_mem_gen(
+        ug, dimRequested, generate_polyhedrons_mesh_from_VTK_UnstructuredGrid_93
+    )
+
+
+def mesh_convertor_mem_94(ug, dimRequested=-1):
+    getLogger().debug(f"Reader 9.4")
+    return mesh_convertor_mem_gen(
+        ug, dimRequested, generate_polyhedrons_mesh_from_VTK_UnstructuredGrid_94
+    )
+
+
+def mesh_convertor_mem_93_legacy(ug):
+    def patchForPolyedra(polyhedCellIds, ug, mesh):
+        """
+        Method in charge to change the connectivity of polyedra contained in mesh using ug vtkUnstructuredGrid.
+
+        :param in polyhedCellIds: mc.DataArrayInt of cells ids in mesh to be patched
+        :param in ug: vtkUnstructuredGrid containing polyhedra
+        :param in-out mesh: mc.MEDCouplingUMesh. 3D Mesh whose polyedra cells connectivity will be modified
+        """
+        facesLoc = mc.DataArrayInt(numpy_support.vtk_to_numpy(ug.GetFaceLocations()))
+        faces = mc.DataArrayInt(numpy_support.vtk_to_numpy(ug.GetFaces()))
+        facesLoc = facesLoc[polyhedCellIds]
+        facesLoc = mc.DataArrayInt.Aggregate([facesLoc, mc.DataArrayInt([len(faces)])])
+        connForPoly, facesLoc = mc.DataArrayInt.FromVTKInternalReprOfPolyedra(
+            faces, facesLoc
+        )
+        meshPoly = mc.MEDCoupling1DGTUMesh(mesh.getName(), mc.NORM_POLYHED)
+        meshPoly.setCoords(mesh.getCoords())
+        meshPoly.setNodalConnectivity(connForPoly, facesLoc)
+        mesh[polyhedCellIds] = meshPoly.buildUnstructured()
+        pass
+
+    from distutils.version import LooseVersion
+
     #
     pts = numpy_support.vtk_to_numpy(ug.GetPoints().GetData())
     #
@@ -42,31 +288,41 @@ def mesh_convertor_mem(ug):
     ctvtk = numpy_support.vtk_to_numpy(ug.GetCellTypesArray())
     conn = numpy_support.vtk_to_numpy(ug.GetCells().GetData())
     #
-    ct=mc.DataArrayInt(np.array(ctvtk,dtype="int{}".format(mc.MEDCouplingSizeOfIDs())))[:]
-    c=mc.DataArrayInt(conn)[:]
-    ci=mc.DataArrayInt(cla)[:]
+    ct = mc.DataArrayInt(
+        np.array(ctvtk, dtype="int{}".format(mc.MEDCouplingSizeOfIDs()))
+    )[:]
+    c = mc.DataArrayInt(conn)[:]
+    ci = mc.DataArrayInt(cla)[:]
     # for pv580
     if LooseVersion(vtk.vtkVersion().GetVTKVersion()) >= LooseVersion("8.90.0"):
-        ci = ci.deltaShiftIndex()+1
+        ci = ci.deltaShiftIndex() + 1
         ci.computeOffsetsFull()
     #
     vtk2med = mc.DataArrayInt(mc.vtk2med_cell_types())
     #
     ct.transformWithIndArr(vtk2med)
-    c[ci]=ct
-    ci = mc.DataArrayInt.Aggregate([ci,mc.DataArrayInt([len(c)])])
+    c[ci] = ct
+    ci = mc.DataArrayInt.Aggregate([ci, mc.DataArrayInt([len(c)])])
     #
     gtv = ct.getDifferentValues().getValues()
-    dimArray = mc.DataArrayInt(len(gtv)) ; dimArray[:] = -1
-    for i,gt in enumerate(gtv):
+    dimArray = mc.DataArrayInt(len(gtv))
+    dimArray[:] = -1
+    for i, gt in enumerate(gtv):
         dimArray[i] = mc.MEDCouplingUMesh.GetDimensionOfGeometricType(gt)
     dim = dimArray.getMaxValueInArray()
     if not dimArray.isUniform(dim):
-        raise RuntimeError("The input vtkUnstructuredGrid instance is not a single level mesh ! need to split it !")
+        raise RuntimeError(
+            "The input vtkUnstructuredGrid instance is not a single level mesh ! need to split it !"
+        )
     #
-    m=mc.MEDCouplingUMesh("mesh",dim)
-    m.setCoords(mc.DataArrayDouble(np.array(pts,dtype=np.float64)))
-    m.setConnectivity(c,ci,True)
+    m = mc.MEDCouplingUMesh("mesh", dim)
+    m.setCoords(mc.DataArrayDouble(np.array(pts, dtype=np.float64)))
+    m.setConnectivity(c, ci, True)
     m.checkConsistencyLight()
     #
+    if m.getMeshDimension() == 3:
+        polyhedCellIds = ct.findIdsEqual(mc.NORM_POLYHED)
+        if not polyhedCellIds.empty():
+            patchForPolyedra(polyhedCellIds, ug, m)
+    #
     return m

medcoupling-9.13.0.dist-info/RECORD

@@ -1,30 +0,0 @@
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-.\CaseWriter.py,sha256=BYosBK-cTq0nRWcWvpwox8Ha-ydJfQrJKTWRvud3HkM=,16368
-.\geom2medcoupling.py,sha256=PYs1yQlxycYd5jamSDvRG0kN74u327OiXMM3yLx9t6M=,4108
-.\hdf5.dll,sha256=I3A-7yoSrVezzpOPTijCJ4mlKCr9rl7uxo73vkmaYVc=,2956288
-.\interpkernel.dll,sha256=WVbnv6if7U2STQ84DCuDF3WAo7wml8wy0fxrkcUzqh8=,733696
-.\libxml2.dll,sha256=HUa_sIbRgg4fBXfQ72ZsZIGEjPVMKEyIpDdw5TTjvEI=,1407488
-.\medC.dll,sha256=4Mfq_Ira02DogCoLe808rZRTvpD35T9PqJHeNZPFMZ8=,5445632
-.\medcoupling.dll,sha256=jbJlIPu9xzH--CEEkvB4hylm9WlNPhZUJBeI1PwnI2Q=,2631680
-.\medcoupling.py,sha256=s4xGJq1Iss5zbeK9WJIsxHNsI55gv4cElLKBMDY2YYE=,810254
-.\MEDCouplingCompat.py,sha256=pcpmSeGEZNpVecuBCdmaOVplUXJXpGMkrGKMslSDYYo=,538877
-.\medcouplingremapper.dll,sha256=DJ3hQDeyDvP8Wi00EdNtmdCOWH4sIbKwcSAoaMnXCNI=,574464
-.\MEDCouplingRemapper.py,sha256=BuCmc-9KeZWFIZ6A23l-cYylo-_IxENH8GxRJYiTyi4=,563761
-.\medicoco.dll,sha256=CrbN31f1B6opTTuOeuINbMsKEP4npeiULtE3XDjSTEU=,19456
-.\medloader.dll,sha256=VAlM9TwXT6UoU3gwWFI_VbpVgH0z7SzD7PnJ3JPDnl8=,2010624
-.\MEDLoader.py,sha256=cCCwa2x1TVKQRW56zz-7m6zhNz8Dp5cWT-85RdvSVck=,771453
-.\MEDLoaderFinalize.py,sha256=USOqudg9lHQpfDzybNNmePqJLDF8VU4O4WDc7OL23vc=,2794
-.\MEDLoaderSplitter.py,sha256=5G612vtDORCcV7kxYWAxnireNIQY-miZowTv57ppTkA=,9357
-.\MEDPartitioner.py,sha256=cQIboO-wCLxay01TOARvvdDYzWRdeh2nq5-W2Raxh0c=,5798
-.\medpartitionercpp.dll,sha256=cC5IToN6oN7s5-Im7qcXxttvbYcchMoRbqUS-ouhoz8=,468480
-.\MEDRenumber.py,sha256=rywrn1niHDoTsLGJUlPz1xJhE725-GnndnPsccHUnEQ=,520363
-.\renumbercpp.dll,sha256=wKOJn8AwmeEwx9_2QOTxlR6byS4tU1Rhglhni2hRpOQ=,132608
-.\vtk2medcoupling.py,sha256=RfyXlfLiT_z8msaW75m_n65o7vLXvm00qCjT62Rugl8=,2775
-.\VTKReader.py,sha256=tRvp_wjkdxjs0Sli9S3A4OFC6EhiFpd05PD_9MXr4wo=,12601
-.\_medcoupling.pyd,sha256=Gv_iTHhefcovl9TUXXQcILEDPC58s__HsH4fmLmSAXs=,5433344
-.\_MEDCouplingCompat.pyd,sha256=phGFqefYTzljwVQEtd_HdMRuDP7DgaSIOgwkbTMcn-E=,3523072
-.\_MEDCouplingRemapper.pyd,sha256=eMiB7ibiz-sK4cICdHxyBS5N94M1QFH0t045m1LLqzE=,3629056
-.\_MEDLoader.pyd,sha256=4Pxu__12gnJEzGe0gFQuYKprsguEnFHUZsdzR-rEMrQ=,5248512
-.\_MEDPartitioner.pyd,sha256=RPzTIqBrUBgzRJE8KGC79-TvGNtjC7RKdxc-MVKGrkw=,76800
-.\_MEDRenumber.pyd,sha256=wKkGu2Y1Jjyc4syz_vWCiZNA0fB47ygaobdOqeBkpcM=,3530240