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[tools/medcoupling.git] / src / MEDLoader / Swig / CaseReader.py
1 #  -*- coding: iso-8859-1 -*-
2 # Copyright (C) 2007-2016  CEA/DEN, EDF R&D
3 #
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.
8 #
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.
13 #
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
17 #
18 # See http://www.salome-platform.org/ or email : webmaster.salome@opencascade.com
19 #
20 # Author : Anthony GEAY (CEA/DEN/DM2S/STMF/LGLS)
21
22 # http://www-vis.lbl.gov/NERSC/Software/ensight/doc/OnlineHelp/UM-C11.pdf
23 import numpy as np
24 from MEDLoader import *
25 from CaseIO import CaseIO
26 import sys,re,os
27
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.
31     """
32
33     @classmethod
34     def New(cls,fileName):
35         """ Static constructor. """
36         return CaseReader(fileName)
37         pass
38
39     def __init__(self,fileName):
40         """ Constructor """
41         self._fileName=fileName
42         self._dirName=os.path.dirname(self._fileName)
43         pass
44
45     def __traduceMesh(self,name,typ,coords,cells):
46         """ Convert a CASE mesh into a MEDCouplingUMesh. """
47         nbCoords=len(coords)
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))
52         m.setCoords(coo)
53         nbNodesPerCell=MEDCouplingMesh.GetNumberOfNodesOfGeometricType(ct)
54         cI=DataArrayInt(len(cells)+1) ; cI.iota() ; cI*=nbNodesPerCell+1
55         #
56         cells2=cells.reshape(len(cells),nbNodesPerCell)
57         if cells2.dtype=='int32':
58             c2=DataArrayInt(cells2)
59         else:
60             c2=DataArrayInt(np.array(cells2,dtype="int32"))
61             pass
62         c=DataArrayInt(len(cells),nbNodesPerCell+1) ; c[:,0]=ct ; c[:,1:]=c2-1 ; c.rearrange(1)
63         m.setConnectivity(c,cI,True)
64         m.checkConsistency()
65         return m
66
67     def __traduceMeshForPolyhed(self,name,coords,arr0,arr1,arr2):
68         nbCoords=len(coords)
69         coo=np.array(coords,dtype="float64") ; coo=coo.reshape(nbCoords,3)
70         coo=DataArrayDouble(coo) ; coo=coo.fromNoInterlace()
71         m=MEDCouplingUMesh(name,3)
72         m.setCoords(coo)
73         #
74         arr2=arr2[:]-1
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]
83         #
84         c=DataArrayInt(arr1.size+arr2.size)
85         c[arr1mc1[:-1]]=NORM_POLYHED
86         c[arr2mc0]=-1
87         a=arr2mc0.buildUnion(arr1mc1[:-1]).buildComplement(len(c))
88         c[a]=DataArrayInt(arr2)
89         #
90         m.setConnectivity(c,arr1mc1,True)
91         m.checkConsistency()
92         return m
93
94     def __traduceMeshForPolygon(self,name,coords,arr0,arr1):
95         nbCoords=len(coords)
96         coo=np.array(coords,dtype="float64") ; coo=coo.reshape(nbCoords,3)
97         coo=DataArrayDouble(coo) ; coo=coo.fromNoInterlace()
98         m=MEDCouplingUMesh(name,2)
99         m.setCoords(coo)
100         #
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)
106         #
107         m.setConnectivity(c,arr0_0,True)
108         m.checkConsistency()
109         return m
110
111     def __convertGeo2MED(self,geoFileName):
112         """ Convert all the geometry (all the meshes) contained in teh 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 !")
117             pass
118         zeType=True
119         if "fortran" in title:
120             mcmeshes=self.__convertGeo2MEDFortran(fd,end) ; zeType=False
121         else:
122             mcmeshes=self.__convertGeo2MEDC(fd,end)
123         #
124         ms=MEDFileMeshes()
125         ms.resize(len(mcmeshes))
126         for i,m in enumerate(mcmeshes):
127             mlm=MEDFileUMesh()
128             mlm.setMeshAtLevel(0,m)
129             ms.setMeshAtPos(i,mlm)
130             pass
131         return mcmeshes,ms,zeType
132
133     def __convertGeo2MEDFortran(self,fd,end):
134         mcmeshes=[]
135         fd.read(80) # comment 1
136         fd.read(80) # comment 2
137         fd.read(80) # node id
138         fd.read(80) # element id
139         pos=fd.tell()
140         elt=fd.read(80) ; elt=elt.strip() ; pos=fd.tell()
141         mcmeshes2=[]
142         typ="part"
143         nbOfTurn=0
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]
149             tmp=fd.read(80)
150             if "coordinates" not in tmp:
151                 raise Exception("Error on reading mesh fortran #2 !")
152             pos=fd.tell() # 644
153             if nbOfTurn==0:
154                 pos+=76 # what else ?
155             else:
156                 pos+=40
157                 pass
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()
168             zeK=""
169             for k in self.dictMCTyp2:
170                 if k in typ:
171                     zeK=k
172                     break
173                     pass
174                 pass
175             pos+=8*4 # yeh man !
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
184             if abs(pos-end)>8:
185                 fd.seek(pos) ;elt=fd.read(80) ; typ=elt[:] ; pos+=80
186                 pass
187             nbOfTurn+=1
188             pass
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)
192         #mcmeshes.append(m)
193         return mcmeshes2
194
195     def __convertGeo2MEDC(self,fd,end):
196         #fd.readline()
197         #name=fd.readline().strip() ; fd.readline() ; fd.readline()
198         name=fd.read(80)
199         descrip=fd.read(80).strip() ; fd.read(80) ; fd.read(80)
200         pos=fd.tell()
201         mcmeshes=[]
202         elt=fd.read(80) ; elt=elt.strip() ; pos+=80
203         while pos!=end:
204             if "part" not in elt:
205                 raise Exception("Error on reading mesh #1 !")
206             fd.seek(fd.tell()+4)
207             meshName=fd.read(80).strip()
208             if fd.read(len("coordinates"))!="coordinates":
209                 raise Exception("Error on reading mesh #2 !")
210             pos=fd.tell()
211             typeOfCoo=np.memmap(fd,dtype='byte',mode='r',offset=int(pos),shape=(1)).tolist()[0]
212             pos+=1+17*4
213             nbNodes=np.memmap(fd,dtype='int32',mode='r',offset=int(pos),shape=(1,)).tolist()[0]
214             pos+=4
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()
218             mcmeshes2=[]
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]
223                 pos+=4
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
228                     fd.seek(pos)
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,))
232                     pos+=nbCellsOfType*4
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))
240                     pass
241                 else:
242                     nbOfNodesPerCell=np.memmap(fd,dtype='int32',mode='r',offset=int(pos),shape=(nbCellsOfType,))
243                     pos+=nbCellsOfType*4
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))
248                 if pos!=end:
249                     elt=fd.read(80) ; elt=elt.strip() ; typ=elt[:] ; pos+=80
250                     pass
251                 pass
252             if mcmeshes2:
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)
256                 mcmeshes.append(m)
257             pass
258         return mcmeshes
259
260
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]
268         if name!=fieldName:
269             raise Exception("ConvertField : mismatch")
270         pos=fd.tell()
271         st=fd.read(80) ; st=st.strip() ; pos=fd.tell()
272         while pos!=end:
273             if st!="part":
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 ):
278                 return
279             nbOfValues=fdisc.getNumberOfTuples(mcmeshes[meshId])
280             vals2=DataArrayDouble(nbOfValues,nbCompo)
281             fd.seek(pos+4)
282             st=fd.read(80).strip() ; pos=fd.tell()
283             offset=0
284             while pos!=end and st!="part":
285                 if st!="coordinates":
286                     nbOfValsOfTyp=mcmeshes[meshId].getNumberOfCellsWithType(self.dictMCTyp2[st])
287                 else:
288                     nbOfValsOfTyp=nbOfValues
289                     pass
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
295                 pass
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)
300             pass
301
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))
308             pass
309         else:
310             trueFileName=fileName
311             pass
312         fd=open(os.path.join(self._dirName,trueFileName),"r+b") ; fd.seek(0,2) ; end=fd.tell() ; fd.seek(0)
313         name=fd.read(80)
314         if fieldName not in name:
315             raise Exception("ConvertField : mismatch")
316         pos=fd.tell()
317         st=fd.read(80) ; st=st.strip() ; pos=fd.tell()
318         if "part" not in st:
319             raise Exception("ConvertField : mismatch #2")
320         st=fd.read(80).strip() ; pos=fd.tell()
321         pos+=12 # I love it
322         offset=0
323         nbTurn=0
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
330             pos+=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
335                 pos+=nbOfValsOfTyp*4
336                 pos+=2*4 ## hey hey, that is the ultimate class !
337                 vals2.setInfoOnComponent(iii,chr(ord('X')+iii))
338                 pass
339             if pos>end:
340                 pos=end
341                 pass
342             vals=vals.reshape(nbOfValsOfTyp,nbCompo)
343             vals2[offset:offset+nbOfValsOfTyp]=DataArrayDouble(np.array(vals,dtype='float64')).fromNoInterlace()
344             if pos!=end:
345                 fd.seek(pos)
346                 st=fd.read(80) ; st=st.strip() ; pos=fd.tell()
347                 st=fd.read(80) ; st=st.strip() ; pos=fd.tell()
348                 pass
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)
353             nbTurn+=1
354             pass
355         pass
356
357     def loadInMEDFileDS(self):
358         """ Load a CASE file into a MEDFileData object. """
359         f=file(self._fileName)
360         lines=f.readlines()
361         ind=lines.index("GEOMETRY\n")
362         if ind==-1:
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")
369             end=len(lines)-1
370             if "TIME\n" in lines:
371                 end=lines.index("TIME\n")
372                 pass
373             for i in xrange(ind + 1,end):
374                 m=re.match("^([\w]+)[\s]+\per[\s]+([\w]+)[\s]*\:[\s]*[0-9]*[\s]*([\w]+)[\s]+([\S]+)$",lines[i])
375                 if m:
376                     if m.groups()[0]=="constant":
377                         continue
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))
381                     pass
382                 pass
383
384             expr=re.compile("number[\s]+of[\s]+steps[\s]*\:[\s]*([\d]+)")
385             tmp = [line for line in lines if expr.search(line)]
386             if tmp:
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))
392             else:
393                 nbOfTimeSteps=1
394                 startIt=0
395                 incrIt=1
396                 pass
397             curIt=startIt
398             pass
399         mlfields=MEDFileFields()
400         mlfields.resize(len(fieldsInfo)*len(m1))
401         i=0
402         for field in fieldsInfo:
403             for m in m1:
404                 mlfields.setFieldAtPos(i,MEDFileFieldMultiTS())
405                 i+=1
406                 pass
407             pass
408         for ts in range(nbOfTimeSteps):
409             i=0
410             for field in fieldsInfo:
411                 if typeOfFile:
412                     self.__convertField(mlfields,m1,field[3],field[0],field[1],field[2],i,curIt);
413                 else:
414                     self.__convertFieldFortran(mlfields,m1,field[3],field[0],field[1],field[2],i,curIt)
415                     pass
416                 i+=len(m1)
417                 pass
418             curIt+=incrIt
419             pass
420         ret=MEDFileData()
421         ret.setMeshes(m2)
422         del mlfields[[x for x in range(len(mlfields)) if len(mlfields[x]) == 0]]
423         ret.setFields(mlfields)
424         return ret
425
426     pass