1 # -*- coding: iso-8859-1 -*-
2 # Copyright (C) 2007-2016 CEA/DEN, EDF R&D
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 MEDLoader 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):
41 self._fileName=fileName
42 self._dirName=os.path.dirname(self._fileName)
45 def __traduceMesh(self,name,typ,coords,cells):
46 """ Convert a CASE mesh into a MEDCouplingUMesh. """
48 coo=np.array(coords,dtype="float64") ; coo=coo.reshape(nbCoords,3)
49 coo=DataArrayDouble(coo) ; coo=coo.fromNoInterlace()
50 ct=self.dictMCTyp2[typ]
51 m=MEDCouplingUMesh(name,MEDCouplingUMesh.GetDimensionOfGeometricType(ct))
53 nbNodesPerCell=MEDCouplingMesh.GetNumberOfNodesOfGeometricType(ct)
54 cI=DataArrayInt(len(cells)+1) ; cI.iota() ; cI*=nbNodesPerCell+1
56 cells2=cells.reshape(len(cells),nbNodesPerCell)
57 if cells2.dtype=='int32':
58 c2=DataArrayInt(cells2)
60 c2=DataArrayInt(np.array(cells2,dtype="int32"))
62 c=DataArrayInt(len(cells),nbNodesPerCell+1) ; c[:,0]=ct ; c[:,1:]=c2-1 ; c.rearrange(1)
63 m.setConnectivity(c,cI,True)
67 def __traduceMeshForPolyhed(self,name,coords,arr0,arr1,arr2):
69 coo=np.array(coords,dtype="float64") ; coo=coo.reshape(nbCoords,3)
70 coo=DataArrayDouble(coo) ; coo=coo.fromNoInterlace()
71 m=MEDCouplingUMesh(name,3)
75 arr0mc0=DataArrayInt(arr0) ; arr0mc0.computeOffsetsFull()
76 arr0mc1=DataArrayInt(arr0).deepCopy()
77 arr0mc2=DataArrayInt(len(arr0),2) ; arr0mc2[:,0]=DataArrayInt(arr0)-1 ; arr0mc2[:,1]=1 ; arr0mc2.rearrange(1) ; arr0mc2.computeOffsetsFull()
78 arr0mc3=DataArrayInt.Range(0,2*len(arr0),2).buildExplicitArrByRanges(arr0mc2)
79 arr1mc0=DataArrayInt(arr1) ; arr1mc0.computeOffsetsFull()
80 arr1mc1=arr1mc0[arr0mc0] ; arr1mc1[1:]+=arr0mc0[1:]
81 arr1mc2=DataArrayInt(arr1).deepCopy() ; arr1mc2+=1 ; arr1mc2.computeOffsetsFull()
82 arr2mc0=(arr1mc2[1:])[arr0mc3]
84 c=DataArrayInt(arr1.size+arr2.size)
85 c[arr1mc1[:-1]]=NORM_POLYHED
87 a=arr2mc0.buildUnion(arr1mc1[:-1]).buildComplement(len(c))
88 c[a]=DataArrayInt(arr2)
90 m.setConnectivity(c,arr1mc1,True)
94 def __traduceMeshForPolygon(self,name,coords,arr0,arr1):
96 coo=np.array(coords,dtype="float64") ; coo=coo.reshape(nbCoords,3)
97 coo=DataArrayDouble(coo) ; coo=coo.fromNoInterlace()
98 m=MEDCouplingUMesh(name,2)
101 arr0_0=DataArrayInt(arr0+1) ; arr0_0.computeOffsetsFull()
102 arr0_1=DataArrayInt(len(arr0),2) ; arr0_1[:,1]=DataArrayInt(arr0) ; arr0_1[:,0]=1 ; arr0_1.rearrange(1) ; arr0_1.computeOffsetsFull()
103 arr0_2=DataArrayInt.Range(1,2*len(arr0),2).buildExplicitArrByRanges(arr0_1)
104 c=DataArrayInt(len(arr0)+len(arr1)) ; c[:]=0 ; c[arr0_0[:-1]]=NORM_POLYGON
105 c[arr0_2]=DataArrayInt(arr1-1)
107 m.setConnectivity(c,arr0_0,True)
111 def __convertGeo2MED(self,geoFileName):
112 """ Convert all the geometry (all the meshes) contained in the CASE file into MEDCouplingUMesh'es. """
113 fd=open(os.path.join(self._dirName,geoFileName),"r+b") ; fd.seek(0,2) ; end=fd.tell() ; fd.seek(0) ; title=fd.read(80)
114 title=title.strip().lower()
115 if "binary" not in title:
116 raise Exception("Error only binary geo files are supported for the moment !")
119 if "fortran" in title:
120 mcmeshes=self.__convertGeo2MEDFortran(fd,end) ; zeType=False
122 mcmeshes=self.__convertGeo2MEDC(fd,end)
125 ms.resize(len(mcmeshes))
126 for i,m in enumerate(mcmeshes):
128 mlm.setMeshAtLevel(0,m)
129 ms.setMeshAtPos(i,mlm)
131 return mcmeshes,ms,zeType
133 def __convertGeo2MEDFortran(self,fd,end):
135 fd.read(80) # comment 1
136 fd.read(80) # comment 2
137 fd.read(80) # node id
138 fd.read(80) # element id
140 elt=fd.read(80) ; elt=elt.strip() ; pos=fd.tell()
144 while abs(pos-end)>8 and "part" in typ:
145 if "part" not in elt:
146 raise Exception("Error on reading mesh fortran #1 !")
147 fd.seek(fd.tell()+4)# skip #
148 tmp=fd.read(80) ; meshName=tmp.split("P")[-1]
150 if "coordinates" not in tmp:
151 raise Exception("Error on reading mesh fortran #2 !")
154 pos+=76 # what else ?
158 nbNodes=np.memmap(fd,dtype='>i4',mode='r',offset=int(pos),shape=(1,)).tolist()[0]
159 pos+=12 # what else ?
160 a=np.memmap(fd,dtype='>f4',mode='r',offset=int(pos),shape=(nbNodes))
161 b=np.memmap(fd,dtype='>f4',mode='r',offset=int(pos+nbNodes*4+2*4),shape=(nbNodes))
162 c=np.memmap(fd,dtype='>f4',mode='r',offset=int(pos+nbNodes*2*4+4*4),shape=(nbNodes))
163 coo=np.zeros(dtype=">f4",shape=(nbNodes*3))
164 coo[:nbNodes]=a ; coo[nbNodes:2*nbNodes]=b ; coo[2*nbNodes:]=c
165 coo=coo.reshape(nbNodes,3)
166 pos+=nbNodes*3*4 ; fd.seek(pos)#np.array(0,dtype='float%i'%(typeOfCoo)).nbytes
167 typ=fd.read(80).strip() ; pos=fd.tell()
169 for k in self.dictMCTyp2:
176 nbCellsOfType=np.memmap(fd,dtype='>i4',mode='r',offset=int(pos),shape=(1,)).tolist()[0]
177 pos+=4 # for the number of cells
178 pos+=2*4 # because it's great !
179 nbNodesPerCell=MEDCouplingMesh.GetNumberOfNodesOfGeometricType(self.dictMCTyp2[zeK])
180 nodalConn=np.memmap(fd,dtype='>i4',mode='r',offset=pos,shape=(nbCellsOfType,nbNodesPerCell))
181 meshName=meshName.strip()
182 mcmeshes2.append(self.__traduceMesh(meshName,zeK,coo,nodalConn))
183 pos+=nbNodesPerCell*nbCellsOfType*4
185 fd.seek(pos) ;elt=fd.read(80) ; typ=elt[:] ; pos+=80
189 #coo=mcmeshes2[0].getCoords() ; name=mcmeshes2[0].getName()
190 #for itmesh in mcmeshes2: itmesh.setCoords(coo)
191 #m=MEDCouplingUMesh.MergeUMeshesOnSameCoords(mcmeshes2) ; m.setName(name)
195 def __convertGeo2MEDC(self,fd,end):
197 #name=fd.readline().strip() ; fd.readline() ; fd.readline()
199 descrip=fd.read(80).strip() ; fd.read(80) ; fd.read(80)
202 elt=fd.read(80) ; elt=elt.strip() ; pos+=80
204 if "part" not in elt:
205 raise Exception("Error on reading mesh #1 !")
207 meshName=fd.read(80).strip()
208 if fd.read(len("coordinates"))!="coordinates":
209 raise Exception("Error on reading mesh #2 !")
211 typeOfCoo=np.memmap(fd,dtype='byte',mode='r',offset=int(pos),shape=(1)).tolist()[0]
213 nbNodes=np.memmap(fd,dtype='int32',mode='r',offset=int(pos),shape=(1,)).tolist()[0]
215 coo=np.memmap(fd,dtype='float32',mode='r',offset=int(pos),shape=(nbNodes,3))
216 pos+=nbNodes*3*4 ; fd.seek(pos)#np.array(0,dtype='float%i'%(typeOfCoo)).nbytes
217 typ=fd.read(80).strip() ; pos=fd.tell()
219 while pos!=end and typ!="part":
220 if typ[0]=='\0': pos+=1; continue
221 mctyp=self.dictMCTyp2[typ]
222 nbCellsOfType=np.memmap(fd,dtype='int32',mode='r',offset=int(pos),shape=(1,)).tolist()[0]
224 if mctyp!=NORM_POLYHED and mctyp!=NORM_POLYGON:
225 nbNodesPerCell=MEDCouplingMesh.GetNumberOfNodesOfGeometricType(mctyp)
226 cells=np.memmap(fd,dtype='int32',mode='r',offset=pos,shape=(nbCellsOfType,nbNodesPerCell))
227 pos+=nbCellsOfType*nbNodesPerCell*4
229 mcmeshes2.append(self.__traduceMesh(meshName,typ,coo,cells))
230 elif mctyp==NORM_POLYHED:
231 nbOfFacesPerCell=np.memmap(fd,dtype='int32',mode='r',offset=int(pos),shape=(nbCellsOfType,))
233 szOfNbOfNodesPerFacePerCellArr=int(nbOfFacesPerCell.sum())
234 arr1=np.memmap(fd,dtype='int32',mode='r',offset=int(pos),shape=(szOfNbOfNodesPerFacePerCellArr,))#arr1 -> nbOfNodesPerFacePerCellArr
235 pos+=szOfNbOfNodesPerFacePerCellArr*4
236 szOfNodesPerFacePerCellArr=arr1.sum()
237 arr2=np.memmap(fd,dtype='int32',mode='r',offset=int(pos),shape=(szOfNodesPerFacePerCellArr,))#arr2 -> nodesPerFacePerCellArr
238 pos+=szOfNodesPerFacePerCellArr*4 ; fd.seek(pos)
239 mcmeshes2.append(self.__traduceMeshForPolyhed(meshName,coo,nbOfFacesPerCell,arr1,arr2))
242 nbOfNodesPerCell=np.memmap(fd,dtype='int32',mode='r',offset=int(pos),shape=(nbCellsOfType,))
244 szOfNbOfNodesPerCellArr=int(nbOfNodesPerCell.sum())
245 arr1=np.memmap(fd,dtype='int32',mode='r',offset=int(pos),shape=(szOfNbOfNodesPerCellArr,))
246 pos+=szOfNbOfNodesPerCellArr*4 ; fd.seek(pos)
247 mcmeshes2.append(self.__traduceMeshForPolygon(meshName,coo,nbOfNodesPerCell,arr1))
249 elt=fd.read(80) ; elt=elt.strip() ; typ=elt[:] ; pos+=80
253 coo=mcmeshes2[0].getCoords() ; name=mcmeshes2[0].getName()
254 for itmesh in mcmeshes2: itmesh.setCoords(coo)
255 m=MEDCouplingUMesh.MergeUMeshesOnSameCoords(mcmeshes2) ; m.setName(name)
261 def __convertField(self,mlfields, mcmeshes, fileName, fieldName, discr, nbCompo, locId, it):
262 """ Convert the fields. """
263 stars=re.search("[\*]+",fileName).group()
264 st="%0"+str(len(stars))+"i"
265 trueFileName=fileName.replace(stars,st%(it))
266 fd=open(os.path.join(self._dirName,trueFileName),"r+b") ; fd.seek(0,2) ; end=fd.tell() ; fd.seek(0)
267 name=fd.read(80).strip().split(" ")[0]
269 raise Exception("ConvertField : mismatch")
271 st=fd.read(80) ; st=st.strip() ; pos=fd.tell()
274 raise Exception("ConvertField : mismatch #2")
275 fdisc=MEDCouplingFieldDiscretization.New(self.discSpatial2[discr])
276 meshId=np.memmap(fd,dtype='int32',mode='r',offset=int(pos),shape=(1)).tolist()[0]-1
277 if meshId >= len( mcmeshes ):
279 nbOfValues=fdisc.getNumberOfTuples(mcmeshes[meshId])
280 vals2=DataArrayDouble(nbOfValues,nbCompo)
282 st=fd.read(80).strip() ; pos=fd.tell()
284 while pos!=end and st!="part":
285 if st!="coordinates":
286 nbOfValsOfTyp=mcmeshes[meshId].getNumberOfCellsWithType(self.dictMCTyp2[st])
288 nbOfValsOfTyp=nbOfValues
290 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))
291 vals2[offset:offset+nbOfValsOfTyp]=DataArrayDouble(np.array(vals,dtype='float64')).fromNoInterlace()
292 pos+=nbOfValsOfTyp*nbCompo*4 ; fd.seek(pos)
293 st=fd.read(80) ; st=st.strip() ; pos=fd.tell()
294 offset+=nbOfValsOfTyp
296 f=MEDCouplingFieldDouble(self.discSpatial2[discr],ONE_TIME) ; f.setName("%s_%s"%(fieldName,mcmeshes[meshId].getName()))
297 f.setMesh(mcmeshes[meshId]) ; f.setArray(vals2) ; f.setTime(float(it),it,-1)
298 f.checkConsistencyLight()
299 mlfields[locId+meshId].appendFieldNoProfileSBT(f)
302 def __convertFieldFortran(self,mlfields, mcmeshes, fileName, fieldName, discr, nbCompo, locId, it):
303 """ Convert the fields. """
304 if re.search("[\*]+",fileName):
305 stars=re.search("[\*]+",fileName).group()
306 st="%0"+str(len(stars))+"i"
307 trueFileName=fileName.replace(stars,st%(it))
310 trueFileName=fileName
312 fd=open(os.path.join(self._dirName,trueFileName),"r+b") ; fd.seek(0,2) ; end=fd.tell() ; fd.seek(0)
314 if fieldName not in name:
315 raise Exception("ConvertField : mismatch")
317 st=fd.read(80) ; st=st.strip() ; pos=fd.tell()
319 raise Exception("ConvertField : mismatch #2")
320 st=fd.read(80).strip() ; pos=fd.tell()
324 while pos!=end and "part" not in st:
325 fdisc=MEDCouplingFieldDiscretization.New(self.discSpatial2[discr])
326 nbOfValues=fdisc.getNumberOfTuples(mcmeshes[nbTurn])
327 vals2=DataArrayDouble(nbOfValues,nbCompo)
328 pos+=24 # I love it again !
329 nbOfValsOfTyp=np.memmap(fd,dtype='>i4',mode='r',offset=pos,shape=(1)).tolist()[0]/4
331 vals=np.zeros(dtype=">f4",shape=(nbOfValsOfTyp*nbCompo))
332 for iii in range(nbCompo):
333 valsTmp=np.memmap(fd,dtype='>f4',mode='r',offset=int(pos),shape=(nbOfValsOfTyp))
334 vals[iii*nbOfValsOfTyp:(iii+1)*nbOfValsOfTyp]=valsTmp
336 pos+=2*4 ## hey hey, that is the ultimate class !
337 vals2.setInfoOnComponent(iii,chr(ord('X')+iii))
342 vals=vals.reshape(nbOfValsOfTyp,nbCompo)
343 vals2[offset:offset+nbOfValsOfTyp]=DataArrayDouble(np.array(vals,dtype='float64')).fromNoInterlace()
346 st=fd.read(80) ; st=st.strip() ; pos=fd.tell()
347 st=fd.read(80) ; st=st.strip() ; pos=fd.tell()
349 f=MEDCouplingFieldDouble(self.discSpatial2[discr],ONE_TIME) ; f.setName("%s_%s"%(fieldName,mcmeshes[nbTurn].getName()))
350 f.setMesh(mcmeshes[nbTurn]) ; f.setArray(vals2) ; f.setTime(float(it),it,-1)
351 f.checkConsistencyLight()
352 mlfields[locId+nbTurn].appendFieldNoProfileSBT(f)
357 def loadInMEDFileDS(self):
358 """ Load a CASE file into a MEDFileData object. """
359 f=file(self._fileName)
361 ind=lines.index("GEOMETRY\n")
363 raise Exception("Error with file %s"%(fname))
364 geoName=re.match("model:([\W]*)([\w\.]+)",lines[ind+1]).group(2)
365 m1,m2,typeOfFile=self.__convertGeo2MED(geoName)
366 fieldsInfo=[] ; nbOfTimeSteps=0
367 if "VARIABLE\n" in lines:
368 ind=lines.index("VARIABLE\n")
370 if "TIME\n" in lines:
371 end=lines.index("TIME\n")
373 for i in range(ind + 1,end):
374 m=re.match("^([\w]+)[\s]+\per[\s]+([\w]+)[\s]*\:[\s]*[0-9]*[\s]*([\w]+)[\s]+([\S]+)$",lines[i])
376 if m.groups()[0]=="constant":
378 spatialDisc=m.groups()[1] ; fieldName=m.groups()[2] ; nbOfCompo=self.dictCompo2[m.groups()[0]] ; fieldFileName=m.groups()[3]
379 if fieldFileName.endswith("*"):
380 fieldsInfo.append((fieldName,spatialDisc,nbOfCompo,fieldFileName))
384 expr=re.compile("number[\s]+of[\s]+steps[\s]*\:[\s]*([\d]+)")
385 tmp = [line for line in lines if expr.search(line)]
387 nbOfTimeSteps = int(expr.search(tmp[0]).group(1))
388 expr=re.compile("filename[\s]+start[\s]+number[\s]*\:[\s]*([\d]+)")
389 startIt = int(expr.search([line for line in lines if expr.search(line)][0]).group(1))
390 expr=re.compile("filename[\s]+increment[\s]*\:[\s]*([\d]+)")
391 incrIt = int(expr.search([line for line in lines if expr.search(line)][0]).group(1))
399 mlfields=MEDFileFields()
400 mlfields.resize(len(fieldsInfo)*len(m1))
402 for field in fieldsInfo:
404 mlfields.setFieldAtPos(i,MEDFileFieldMultiTS())
408 for ts in range(nbOfTimeSteps):
410 for field in fieldsInfo:
412 self.__convertField(mlfields,m1,field[3],field[0],field[1],field[2],i,curIt);
414 self.__convertFieldFortran(mlfields,m1,field[3],field[0],field[1],field[2],i,curIt)
422 del mlfields[[x for x in range(len(mlfields)) if len(mlfields[x]) == 0]]
423 ret.setFields(mlfields)