1 # -*- coding: iso-8859-1 -*-
2 # Copyright (C) 2007-2023 CEA, EDF
4 # This library is free software; you can redistribute it and/or
5 # modify it under the terms of the GNU Lesser General Public
6 # License as published by the Free Software Foundation; either
7 # version 2.1 of the License, or (at your option) any later version.
9 # This library is distributed in the hope that it will be useful,
10 # but WITHOUT ANY WARRANTY; without even the implied warranty of
11 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
12 # Lesser General Public License for more details.
14 # You should have received a copy of the GNU Lesser General Public
15 # License along with this library; if not, write to the Free Software
16 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
18 # See http://www.salome-platform.org/ or email : webmaster.salome@opencascade.com
20 # Author : Anthony GEAY (CEA/DEN/DM2S/STMF/LGLS)
22 # http://www-vis.lbl.gov/NERSC/Software/ensight/doc/OnlineHelp/UM-C11.pdf
24 from medcoupling import *
25 from CaseIO import CaseIO
28 class CaseReader(CaseIO):
29 """ Converting a file in the Case format (Ensight) to the MED format.
30 A new file with the same base name and the .med extension is created.
34 def New(cls,fileName):
35 """ Static constructor. """
36 return CaseReader(fileName)
39 def __init__(self,fileName):
42 self._fileName=fileName
43 self._dirName=os.path.dirname(self._fileName)
46 def __traduceMesh(self,name,typ,coords,cells):
47 """ Convert a CASE mesh into a MEDCouplingUMesh. """
48 name = name.decode("ascii")
50 coo=np.array(coords,dtype="float64") ; coo=coo.reshape(nbCoords,3)
51 coo=DataArrayDouble(coo) ; coo=coo.fromNoInterlace()
52 ct=self.dictMCTyp2[typ]
53 m=MEDCouplingUMesh(name,MEDCouplingUMesh.GetDimensionOfGeometricType(ct))
55 nbNodesPerCell=MEDCouplingMesh.GetNumberOfNodesOfGeometricType(ct)
56 cI=DataArrayInt(len(cells)+1) ; cI.iota() ; cI*=nbNodesPerCell+1
58 cells2=cells.reshape(len(cells),nbNodesPerCell)
59 c2=DataArrayInt(np.array(cells2,dtype="int{}".format(MEDCouplingSizeOfIDs())) )
60 c=DataArrayInt(len(cells),nbNodesPerCell+1) ; c[:,0]=ct ; c[:,1:]=c2-1 ; c.rearrange(1)
61 m.setConnectivity(c,cI,True)
65 def __traduceMeshForPolyhed(self,name,coords,arr0,arr1,arr2):
67 coo=np.array(coords,dtype="float64") ; coo=coo.reshape(nbCoords,3)
68 coo=DataArrayDouble(coo) ; coo=coo.fromNoInterlace()
69 m=MEDCouplingUMesh(name,3)
73 arr0mc0=DataArrayInt(arr0) ; arr0mc0.computeOffsetsFull()
74 arr0mc1=DataArrayInt(arr0).deepCopy()
75 arr0mc2=DataArrayInt(len(arr0),2) ; arr0mc2[:,0]=DataArrayInt(arr0)-1 ; arr0mc2[:,1]=1 ; arr0mc2.rearrange(1) ; arr0mc2.computeOffsetsFull()
76 arr0mc3=DataArrayInt.Range(0,2*len(arr0),2).buildExplicitArrByRanges(arr0mc2)
77 arr1mc0=DataArrayInt(arr1) ; arr1mc0.computeOffsetsFull()
78 arr1mc1=arr1mc0[arr0mc0] ; arr1mc1[1:]+=arr0mc0[1:]
79 arr1mc2=DataArrayInt(arr1).deepCopy() ; arr1mc2+=1 ; arr1mc2.computeOffsetsFull()
80 arr2mc0=(arr1mc2[1:])[arr0mc3]
82 c=DataArrayInt(arr1.size+arr2.size)
83 c[arr1mc1[:-1]]=NORM_POLYHED
85 a=arr2mc0.buildUnion(arr1mc1[:-1]).buildComplement(len(c))
86 c[a]=DataArrayInt(arr2)
88 m.setConnectivity(c,arr1mc1,True)
92 def __traduceMeshForPolygon(self,name,coords,arr0,arr1):
94 coo=np.array(coords,dtype="float64") ; coo=coo.reshape(nbCoords,3)
95 coo=DataArrayDouble(coo) ; coo=coo.fromNoInterlace()
96 m=MEDCouplingUMesh(name,2)
99 arr0_0=DataArrayInt(arr0+1) ; arr0_0.computeOffsetsFull()
100 arr0_1=DataArrayInt(len(arr0),2) ; arr0_1[:,1]=DataArrayInt(arr0) ; arr0_1[:,0]=1 ; arr0_1.rearrange(1) ; arr0_1.computeOffsetsFull()
101 arr0_2=DataArrayInt.Range(1,2*len(arr0),2).buildExplicitArrByRanges(arr0_1)
102 c=DataArrayInt(len(arr0)+len(arr1)) ; c[:]=0 ; c[arr0_0[:-1]]=NORM_POLYGON
103 c[arr0_2]=DataArrayInt(arr1-1)
105 m.setConnectivity(c,arr0_0,True)
109 def __convertGeo2MED(self,geoFileName):
110 """ Convert all the geometry (all the meshes) contained in the CASE file into MEDCouplingUMesh'es. """
111 fd=open(os.path.join(self._dirName,geoFileName),"r+b") ; fd.seek(0,2) ; end=fd.tell() ; fd.seek(0) ; title=fd.read(80)
112 title=title.strip().lower()
113 if b"binary" not in title:
114 raise Exception("Error only binary geo files are supported for the moment !")
117 if b"fortran" in title:
118 mcmeshes=self.__convertGeo2MEDFortran(fd,end) ; zeType=False
120 mcmeshes=self.__convertGeo2MEDC(fd,end)
123 ms.resize(len(mcmeshes))
124 for i,m in enumerate(mcmeshes):
126 mlm.setMeshAtLevel(0,m)
127 ms.setMeshAtPos(i,mlm)
129 return mcmeshes,ms,zeType
131 def __convertGeo2MEDFortran(self,fd,end):
133 fd.read(80) # comment 1
134 fd.read(80) # comment 2
135 fd.read(80) # node id
136 fd.read(80) # element id
138 elt=fd.read(80) ; elt=elt.strip() ; pos=fd.tell()
142 while abs(pos-end)>8 and b"part" in typ:
143 if b"part" not in elt:
144 raise Exception("Error on reading mesh fortran #1 !")
145 fd.seek(fd.tell()+4)# skip #
146 tmp=fd.read(80) ; meshName=tmp.split("P")[-1]
148 if b"coordinates" not in tmp:
149 raise Exception("Error on reading mesh fortran #2 !")
152 pos+=76 # what else ?
156 nbNodes=np.memmap(fd,dtype='>i4',mode='r',offset=int(pos),shape=(1,)).tolist()[0]
157 pos+=12 # what else ?
158 a=np.memmap(fd,dtype='>f4',mode='r',offset=int(pos),shape=(nbNodes))
159 b=np.memmap(fd,dtype='>f4',mode='r',offset=int(pos+nbNodes*4+2*4),shape=(nbNodes))
160 c=np.memmap(fd,dtype='>f4',mode='r',offset=int(pos+nbNodes*2*4+4*4),shape=(nbNodes))
161 coo=np.zeros(dtype=">f4",shape=(nbNodes*3))
162 coo[:nbNodes]=a ; coo[nbNodes:2*nbNodes]=b ; coo[2*nbNodes:]=c
163 coo=coo.reshape(nbNodes,3)
164 pos+=nbNodes*3*4 ; fd.seek(pos)#np.array(0,dtype='float%i'%(typeOfCoo)).nbytes
165 typ=fd.read(80).strip() ; pos=fd.tell()
167 for k in self.dictMCTyp2:
174 nbCellsOfType=np.memmap(fd,dtype='>i4',mode='r',offset=int(pos),shape=(1,)).tolist()[0]
175 pos+=4 # for the number of cells
176 pos+=2*4 # because it's great !
177 nbNodesPerCell=MEDCouplingMesh.GetNumberOfNodesOfGeometricType(self.dictMCTyp2[zeK])
178 nodalConn=np.memmap(fd,dtype='>i4',mode='r',offset=pos,shape=(nbCellsOfType,nbNodesPerCell))
179 meshName=meshName.strip()
180 mcmeshes2.append(self.__traduceMesh(meshName,zeK,coo,nodalConn))
181 pos+=nbNodesPerCell*nbCellsOfType*4
183 fd.seek(pos) ;elt=fd.read(80) ; typ=elt[:] ; pos+=80
187 #coo=mcmeshes2[0].getCoords() ; name=mcmeshes2[0].getName()
188 #for itmesh in mcmeshes2: itmesh.setCoords(coo)
189 #m=MEDCouplingUMesh.MergeUMeshesOnSameCoords(mcmeshes2) ; m.setName(name)
193 def __convertGeo2MEDC(self,fd,end):
195 #name=fd.readline().strip() ; fd.readline() ; fd.readline()
197 descrip=fd.read(80).strip() ; fd.read(80) ; fd.read(80)
200 elt=fd.read(80) ; elt=elt.strip() ; pos+=80
202 if b"part" not in elt:
203 raise Exception("Error on reading mesh #1 !")
205 meshName=fd.read(80).strip()
206 if fd.read(len("coordinates"))!=b"coordinates":
207 raise Exception("Error on reading mesh #2 !")
209 typeOfCoo=np.memmap(fd,dtype='byte',mode='r',offset=int(pos),shape=(1)).tolist()[0]
211 nbNodes=np.memmap(fd,dtype='int32',mode='r',offset=int(pos),shape=(1,)).tolist()[0]
213 coo=np.memmap(fd,dtype='float32',mode='r',offset=int(pos),shape=(nbNodes,3))
214 pos+=nbNodes*3*4 ; fd.seek(pos)#np.array(0,dtype='float%i'%(typeOfCoo)).nbytes
215 typ=fd.read(80).strip() ; pos=fd.tell()
217 while pos!=end and typ!=b"part":
218 if typ[0]==0: pos+=1; continue
219 mctyp=self.dictMCTyp2[typ]
220 nbCellsOfType=np.memmap(fd,dtype='int32',mode='r',offset=int(pos),shape=(1,)).tolist()[0]
222 if mctyp!=NORM_POLYHED and mctyp!=NORM_POLYGON:
223 nbNodesPerCell=MEDCouplingMesh.GetNumberOfNodesOfGeometricType(mctyp)
224 cells=np.memmap(fd,dtype='int32',mode='r',offset=pos,shape=(nbCellsOfType,nbNodesPerCell))
225 pos+=nbCellsOfType*nbNodesPerCell*4
227 mcmeshes2.append(self.__traduceMesh(meshName,typ,coo,cells))
228 elif mctyp==NORM_POLYHED:
229 nbOfFacesPerCell=np.memmap(fd,dtype='int32',mode='r',offset=int(pos),shape=(nbCellsOfType,))
231 szOfNbOfNodesPerFacePerCellArr=int(nbOfFacesPerCell.sum())
232 arr1=np.memmap(fd,dtype='int32',mode='r',offset=int(pos),shape=(szOfNbOfNodesPerFacePerCellArr,))#arr1 -> nbOfNodesPerFacePerCellArr
233 pos+=szOfNbOfNodesPerFacePerCellArr*4
234 szOfNodesPerFacePerCellArr=arr1.sum()
235 arr2=np.memmap(fd,dtype='int32',mode='r',offset=int(pos),shape=(szOfNodesPerFacePerCellArr,))#arr2 -> nodesPerFacePerCellArr
236 pos+=szOfNodesPerFacePerCellArr*4 ; fd.seek(pos)
237 mcmeshes2.append(self.__traduceMeshForPolyhed(meshName,coo,nbOfFacesPerCell,arr1,arr2))
240 nbOfNodesPerCell=np.memmap(fd,dtype='int32',mode='r',offset=int(pos),shape=(nbCellsOfType,))
242 szOfNbOfNodesPerCellArr=int(nbOfNodesPerCell.sum())
243 arr1=np.memmap(fd,dtype='int32',mode='r',offset=int(pos),shape=(szOfNbOfNodesPerCellArr,))
244 pos+=szOfNbOfNodesPerCellArr*4 ; fd.seek(pos)
245 mcmeshes2.append(self.__traduceMeshForPolygon(meshName,coo,nbOfNodesPerCell,arr1))
247 elt=fd.read(80) ; elt=elt.strip() ; typ=elt[:] ; pos+=80
251 coo=mcmeshes2[0].getCoords() ; name=mcmeshes2[0].getName()
252 for itmesh in mcmeshes2: itmesh.setCoords(coo)
253 m=MEDCouplingUMesh.MergeUMeshesOnSameCoords(mcmeshes2) ; m.setName(name)
259 def __convertField(self,mlfields, mcmeshes, fileName, fieldName, discr, nbCompo, locId, it):
260 """ Convert the fields. """
261 stars=re.search("[\*]+",fileName).group()
262 st="%0"+str(len(stars))+"i"
263 trueFileName=fileName.replace(stars,st%(it))
264 fd=open(os.path.join(self._dirName,trueFileName),"r+b") ; fd.seek(0,2) ; end=fd.tell() ; fd.seek(0)
265 name=fd.read(80).strip().split(b" ")[0].decode("ascii")
267 raise Exception("ConvertField : mismatch")
269 st=fd.read(80) ; st=st.strip() ; pos=fd.tell()
272 raise Exception("ConvertField : mismatch #2")
273 fdisc=MEDCouplingFieldDiscretization.New(self.discSpatial2[discr])
274 meshId=np.memmap(fd,dtype='int32',mode='r',offset=int(pos),shape=(1)).tolist()[0]-1
275 if meshId >= len( mcmeshes ):
277 nbOfValues=fdisc.getNumberOfTuples(mcmeshes[meshId])
278 vals2=DataArrayDouble(nbOfValues,nbCompo)
280 st=fd.read(80).strip() ; pos=fd.tell()
282 while pos!=end and st!=b"part":
283 if st!=b"coordinates":
284 nbOfValsOfTyp=mcmeshes[meshId].getNumberOfCellsWithType(self.dictMCTyp2[st])
286 nbOfValsOfTyp=nbOfValues
288 vals=np.memmap(fd,dtype='float32',mode='r',offset=int(pos),shape=(nbOfValsOfTyp,nbCompo))#np.memmap(fd,dtype='int32',mode='r',offset=159,shape=(1))
289 vals2[offset:offset+nbOfValsOfTyp]=DataArrayDouble(np.array(vals,dtype='float64')).fromNoInterlace()
290 pos+=nbOfValsOfTyp*nbCompo*4 ; fd.seek(pos)
291 st=fd.read(80) ; st=st.strip() ; pos=fd.tell()
292 offset+=nbOfValsOfTyp
294 f=MEDCouplingFieldDouble(self.discSpatial2[discr],ONE_TIME) ; f.setName("%s_%s"%(fieldName,mcmeshes[meshId].getName()))
295 f.setMesh(mcmeshes[meshId]) ; f.setArray(vals2) ; f.setTime(float(it),it,-1)
296 f.checkConsistencyLight()
297 mlfields[locId+meshId].appendFieldNoProfileSBT(f)
300 def __convertFieldFortran(self,mlfields, mcmeshes, fileName, fieldName, discr, nbCompo, locId, it):
301 """ Convert the fields. """
302 if re.search("[\*]+",fileName):
303 stars=re.search("[\*]+",fileName).group()
304 st="%0"+str(len(stars))+"i"
305 trueFileName=fileName.replace(stars,st%(it))
308 trueFileName=fileName
310 fd=open(os.path.join(self._dirName,trueFileName),"r+b") ; fd.seek(0,2) ; end=fd.tell() ; fd.seek(0)
312 if fieldName not in name:
313 raise Exception("ConvertField : mismatch")
315 st=fd.read(80) ; st=st.strip() ; pos=fd.tell()
316 if b"part" not in st:
317 raise Exception("ConvertField : mismatch #2")
318 st=fd.read(80).strip() ; pos=fd.tell()
322 while pos!=end and b"part" not in st:
323 fdisc=MEDCouplingFieldDiscretization.New(self.discSpatial2[discr])
324 nbOfValues=fdisc.getNumberOfTuples(mcmeshes[nbTurn])
325 vals2=DataArrayDouble(nbOfValues,nbCompo)
326 pos+=24 # I love it again !
327 nbOfValsOfTyp=np.memmap(fd,dtype='>i4',mode='r',offset=pos,shape=(1)).tolist()[0]/4
329 vals=np.zeros(dtype=">f4",shape=(nbOfValsOfTyp*nbCompo))
330 for iii in range(nbCompo):
331 valsTmp=np.memmap(fd,dtype='>f4',mode='r',offset=int(pos),shape=(nbOfValsOfTyp))
332 vals[iii*nbOfValsOfTyp:(iii+1)*nbOfValsOfTyp]=valsTmp
334 pos+=2*4 ## hey hey, that is the ultimate class !
335 vals2.setInfoOnComponent(iii,chr(ord('X')+iii))
340 vals=vals.reshape(nbOfValsOfTyp,nbCompo)
341 vals2[offset:offset+nbOfValsOfTyp]=DataArrayDouble(np.array(vals,dtype='float64')).fromNoInterlace()
344 st=fd.read(80) ; st=st.strip() ; pos=fd.tell()
345 st=fd.read(80) ; st=st.strip() ; pos=fd.tell()
347 f=MEDCouplingFieldDouble(self.discSpatial2[discr],ONE_TIME) ; f.setName("%s_%s"%(fieldName,mcmeshes[nbTurn].getName()))
348 f.setMesh(mcmeshes[nbTurn]) ; f.setArray(vals2) ; f.setTime(float(it),it,-1)
349 f.checkConsistencyLight()
350 mlfields[locId+nbTurn].appendFieldNoProfileSBT(f)
355 def loadInMEDFileDS(self):
356 """ Load a CASE file into a MEDFileData object. """
357 f=open(self._fileName)
359 ind=lines.index("GEOMETRY\n")
361 raise Exception("Error with file %s"%(fname))
362 geoName=re.match("model:([\W]*)([\w\.]+)",lines[ind+1]).group(2)
363 m1,m2,typeOfFile=self.__convertGeo2MED(geoName)
364 fieldsInfo=[] ; nbOfTimeSteps=0
365 if "VARIABLE\n" in lines:
366 ind=lines.index("VARIABLE\n")
368 if "TIME\n" in lines:
369 end=lines.index("TIME\n")
371 for i in range(ind + 1,end):
372 m=re.match("^([\w]+)[\s]+per[\s]+([\w]+)[\s]*\:[\s]*[0-9]*[\s]*([\w]+)[\s]+([\S]+)$",lines[i])
374 if m.groups()[0]=="constant":
376 spatialDisc=m.groups()[1] ; fieldName=m.groups()[2] ; nbOfCompo=self.dictCompo2[m.groups()[0]] ; fieldFileName=m.groups()[3]
377 if "*" in fieldFileName:
378 fieldsInfo.append((fieldName,spatialDisc,nbOfCompo,fieldFileName))
382 expr=re.compile("number[\s]+of[\s]+steps[\s]*\:[\s]*([\d]+)")
383 tmp = [line for line in lines if expr.search(line)]
385 nbOfTimeSteps = int(expr.search(tmp[0]).group(1))
386 expr=re.compile("filename[\s]+start[\s]+number[\s]*\:[\s]*([\d]+)")
387 startIt = int(expr.search([line for line in lines if expr.search(line)][0]).group(1))
388 expr=re.compile("filename[\s]+increment[\s]*\:[\s]*([\d]+)")
389 incrIt = int(expr.search([line for line in lines if expr.search(line)][0]).group(1))
397 mlfields=MEDFileFields()
398 mlfields.resize(len(fieldsInfo)*len(m1))
400 for field in fieldsInfo:
402 mlfields.setFieldAtPos(i,MEDFileFieldMultiTS())
406 for ts in range(nbOfTimeSteps):
408 for field in fieldsInfo:
410 self.__convertField(mlfields,m1,field[3],field[0],field[1],field[2],i,curIt);
412 self.__convertFieldFortran(mlfields,m1,field[3],field[0],field[1],field[2],i,curIt)
420 del mlfields[[x for x in range(len(mlfields)) if len(mlfields[x]) == 0]]
421 ret.setFields(mlfields)