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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         CaseIO.__init__(self)
42         self._fileName=fileName
43         self._dirName=os.path.dirname(self._fileName)
44         pass
45
46     def __traduceMesh(self,name,typ,coords,cells):
47         """ Convert a CASE mesh into a MEDCouplingUMesh. """
48         nbCoords=len(coords)
49         coo=np.array(coords,dtype="float64") ; coo=coo.reshape(nbCoords,3)
50         coo=DataArrayDouble(coo) ; coo=coo.fromNoInterlace()
51         ct=self.dictMCTyp2[typ]
52         m=MEDCouplingUMesh(str(name),MEDCouplingUMesh.GetDimensionOfGeometricType(ct))
53         m.setCoords(coo)
54         nbNodesPerCell=MEDCouplingMesh.GetNumberOfNodesOfGeometricType(ct)
55         cI=DataArrayInt(len(cells)+1) ; cI.iota() ; cI*=nbNodesPerCell+1
56         #
57         cells2=cells.reshape(len(cells),nbNodesPerCell)
58         if cells2.dtype=='int32':
59             c2=DataArrayInt(cells2)
60         else:
61             c2=DataArrayInt(np.array(cells2,dtype="int32"))
62             pass
63         c=DataArrayInt(len(cells),nbNodesPerCell+1) ; c[:,0]=ct ; c[:,1:]=c2-1 ; c.rearrange(1)
64         m.setConnectivity(c,cI,True)
65         m.checkConsistency()
66         return m
67
68     def __traduceMeshForPolyhed(self,name,coords,arr0,arr1,arr2):
69         nbCoords=len(coords)
70         coo=np.array(coords,dtype="float64") ; coo=coo.reshape(nbCoords,3)
71         coo=DataArrayDouble(coo) ; coo=coo.fromNoInterlace()
72         m=MEDCouplingUMesh(name,3)
73         m.setCoords(coo)
74         #
75         arr2=arr2[:]-1
76         arr0mc0=DataArrayInt(arr0) ; arr0mc0.computeOffsetsFull()
77         arr0mc1=DataArrayInt(arr0).deepCopy()
78         arr0mc2=DataArrayInt(len(arr0),2) ; arr0mc2[:,0]=DataArrayInt(arr0)-1 ; arr0mc2[:,1]=1 ; arr0mc2.rearrange(1) ; arr0mc2.computeOffsetsFull()
79         arr0mc3=DataArrayInt.Range(0,2*len(arr0),2).buildExplicitArrByRanges(arr0mc2)
80         arr1mc0=DataArrayInt(arr1) ; arr1mc0.computeOffsetsFull()
81         arr1mc1=arr1mc0[arr0mc0] ; arr1mc1[1:]+=arr0mc0[1:]
82         arr1mc2=DataArrayInt(arr1).deepCopy() ; arr1mc2+=1 ; arr1mc2.computeOffsetsFull()
83         arr2mc0=(arr1mc2[1:])[arr0mc3]
84         #
85         c=DataArrayInt(arr1.size+arr2.size)
86         c[arr1mc1[:-1]]=NORM_POLYHED
87         c[arr2mc0]=-1
88         a=arr2mc0.buildUnion(arr1mc1[:-1]).buildComplement(len(c))
89         c[a]=DataArrayInt(arr2)
90         #
91         m.setConnectivity(c,arr1mc1,True)
92         m.checkConsistency()
93         return m
94
95     def __traduceMeshForPolygon(self,name,coords,arr0,arr1):
96         nbCoords=len(coords)
97         coo=np.array(coords,dtype="float64") ; coo=coo.reshape(nbCoords,3)
98         coo=DataArrayDouble(coo) ; coo=coo.fromNoInterlace()
99         m=MEDCouplingUMesh(name,2)
100         m.setCoords(coo)
101         #
102         arr0_0=DataArrayInt(arr0+1) ; arr0_0.computeOffsetsFull()
103         arr0_1=DataArrayInt(len(arr0),2) ; arr0_1[:,1]=DataArrayInt(arr0) ; arr0_1[:,0]=1 ; arr0_1.rearrange(1) ; arr0_1.computeOffsetsFull()
104         arr0_2=DataArrayInt.Range(1,2*len(arr0),2).buildExplicitArrByRanges(arr0_1)
105         c=DataArrayInt(len(arr0)+len(arr1)) ; c[:]=0 ; c[arr0_0[:-1]]=NORM_POLYGON
106         c[arr0_2]=DataArrayInt(arr1-1)
107         #
108         m.setConnectivity(c,arr0_0,True)
109         m.checkConsistency()
110         return m
111
112     def __convertGeo2MED(self,geoFileName):
113         """ Convert all the geometry (all the meshes) contained in the CASE file into MEDCouplingUMesh'es. """
114         fd=open(os.path.join(self._dirName,geoFileName),"r+b") ; fd.seek(0,2) ; end=fd.tell() ; fd.seek(0) ; title=fd.read(80)
115         title=title.strip().lower()
116         if b"binary" not in title:
117             raise Exception("Error only binary geo files are supported for the moment !")
118             pass
119         zeType=True
120         if b"fortran" in title:
121             mcmeshes=self.__convertGeo2MEDFortran(fd,end) ; zeType=False
122         else:
123             mcmeshes=self.__convertGeo2MEDC(fd,end)
124         #
125         ms=MEDFileMeshes()
126         ms.resize(len(mcmeshes))
127         for i,m in enumerate(mcmeshes):
128             mlm=MEDFileUMesh()
129             mlm.setMeshAtLevel(0,m)
130             ms.setMeshAtPos(i,mlm)
131             pass
132         return mcmeshes,ms,zeType
133
134     def __convertGeo2MEDFortran(self,fd,end):
135         mcmeshes=[]
136         fd.read(80) # comment 1
137         fd.read(80) # comment 2
138         fd.read(80) # node id
139         fd.read(80) # element id
140         pos=fd.tell()
141         elt=fd.read(80) ; elt=elt.strip() ; pos=fd.tell()
142         mcmeshes2=[]
143         typ=b"part"
144         nbOfTurn=0
145         while abs(pos-end)>8 and b"part" in typ:
146             if b"part" not in elt:
147                 raise Exception("Error on reading mesh fortran #1 !")
148             fd.seek(fd.tell()+4)# skip #
149             tmp=fd.read(80) ; meshName=tmp.split("P")[-1]
150             tmp=fd.read(80)
151             if b"coordinates" not in tmp:
152                 raise Exception("Error on reading mesh fortran #2 !")
153             pos=fd.tell() # 644
154             if nbOfTurn==0:
155                 pos+=76 # what else ?
156             else:
157                 pos+=40
158                 pass
159             nbNodes=np.memmap(fd,dtype='>i4',mode='r',offset=int(pos),shape=(1,)).tolist()[0]
160             pos+=12 # what else ?
161             a=np.memmap(fd,dtype='>f4',mode='r',offset=int(pos),shape=(nbNodes))
162             b=np.memmap(fd,dtype='>f4',mode='r',offset=int(pos+nbNodes*4+2*4),shape=(nbNodes))
163             c=np.memmap(fd,dtype='>f4',mode='r',offset=int(pos+nbNodes*2*4+4*4),shape=(nbNodes))
164             coo=np.zeros(dtype=">f4",shape=(nbNodes*3))
165             coo[:nbNodes]=a ; coo[nbNodes:2*nbNodes]=b ; coo[2*nbNodes:]=c
166             coo=coo.reshape(nbNodes,3)
167             pos+=nbNodes*3*4 ; fd.seek(pos)#np.array(0,dtype='float%i'%(typeOfCoo)).nbytes
168             typ=fd.read(80).strip() ; pos=fd.tell()
169             zeK=b""
170             for k in self.dictMCTyp2:
171                 if k in typ:
172                     zeK=k
173                     break
174                     pass
175                 pass
176             pos+=8*4 # yeh man !
177             nbCellsOfType=np.memmap(fd,dtype='>i4',mode='r',offset=int(pos),shape=(1,)).tolist()[0]
178             pos+=4 # for the number of cells
179             pos+=2*4 # because it's great !
180             nbNodesPerCell=MEDCouplingMesh.GetNumberOfNodesOfGeometricType(self.dictMCTyp2[zeK])
181             nodalConn=np.memmap(fd,dtype='>i4',mode='r',offset=pos,shape=(nbCellsOfType,nbNodesPerCell))
182             meshName=meshName.strip()
183             mcmeshes2.append(self.__traduceMesh(meshName,zeK,coo,nodalConn))
184             pos+=nbNodesPerCell*nbCellsOfType*4
185             if abs(pos-end)>8:
186                 fd.seek(pos) ;elt=fd.read(80) ; typ=elt[:] ; pos+=80
187                 pass
188             nbOfTurn+=1
189             pass
190         #coo=mcmeshes2[0].getCoords() ; name=mcmeshes2[0].getName()
191         #for itmesh in mcmeshes2: itmesh.setCoords(coo)
192         #m=MEDCouplingUMesh.MergeUMeshesOnSameCoords(mcmeshes2) ; m.setName(name)
193         #mcmeshes.append(m)
194         return mcmeshes2
195
196     def __convertGeo2MEDC(self,fd,end):
197         #fd.readline()
198         #name=fd.readline().strip() ; fd.readline() ; fd.readline()
199         name=fd.read(80)
200         descrip=fd.read(80).strip() ; fd.read(80) ; fd.read(80)
201         pos=fd.tell()
202         mcmeshes=[]
203         elt=fd.read(80) ; elt=elt.strip() ; pos+=80
204         while pos!=end:
205             if b"part" not in elt:
206                 raise Exception("Error on reading mesh #1 !")
207             fd.seek(fd.tell()+4)
208             meshName=fd.read(80).strip()
209             if fd.read(len("coordinates"))!=b"coordinates":
210                 raise Exception("Error on reading mesh #2 !")
211             pos=fd.tell()
212             typeOfCoo=np.memmap(fd,dtype='byte',mode='r',offset=int(pos),shape=(1)).tolist()[0]
213             pos+=1+17*4
214             nbNodes=np.memmap(fd,dtype='int32',mode='r',offset=int(pos),shape=(1,)).tolist()[0]
215             pos+=4
216             coo=np.memmap(fd,dtype='float32',mode='r',offset=int(pos),shape=(nbNodes,3))
217             pos+=nbNodes*3*4 ; fd.seek(pos)#np.array(0,dtype='float%i'%(typeOfCoo)).nbytes
218             typ=fd.read(80).strip() ; pos=fd.tell()
219             mcmeshes2=[]
220             while pos!=end and typ!=b"part":
221                 if typ[0]=='\0': pos+=1; continue
222                 mctyp=self.dictMCTyp2[typ]
223                 nbCellsOfType=np.memmap(fd,dtype='int32',mode='r',offset=int(pos),shape=(1,)).tolist()[0]
224                 pos+=4
225                 if mctyp!=NORM_POLYHED and mctyp!=NORM_POLYGON:
226                     nbNodesPerCell=MEDCouplingMesh.GetNumberOfNodesOfGeometricType(mctyp)
227                     cells=np.memmap(fd,dtype='int32',mode='r',offset=pos,shape=(nbCellsOfType,nbNodesPerCell))
228                     pos+=nbCellsOfType*nbNodesPerCell*4
229                     fd.seek(pos)
230                     mcmeshes2.append(self.__traduceMesh(meshName,typ,coo,cells))
231                 elif mctyp==NORM_POLYHED:
232                     nbOfFacesPerCell=np.memmap(fd,dtype='int32',mode='r',offset=int(pos),shape=(nbCellsOfType,))
233                     pos+=nbCellsOfType*4
234                     szOfNbOfNodesPerFacePerCellArr=int(nbOfFacesPerCell.sum())
235                     arr1=np.memmap(fd,dtype='int32',mode='r',offset=int(pos),shape=(szOfNbOfNodesPerFacePerCellArr,))#arr1 -> nbOfNodesPerFacePerCellArr
236                     pos+=szOfNbOfNodesPerFacePerCellArr*4
237                     szOfNodesPerFacePerCellArr=arr1.sum()
238                     arr2=np.memmap(fd,dtype='int32',mode='r',offset=int(pos),shape=(szOfNodesPerFacePerCellArr,))#arr2 -> nodesPerFacePerCellArr
239                     pos+=szOfNodesPerFacePerCellArr*4 ; fd.seek(pos)
240                     mcmeshes2.append(self.__traduceMeshForPolyhed(meshName,coo,nbOfFacesPerCell,arr1,arr2))
241                     pass
242                 else:
243                     nbOfNodesPerCell=np.memmap(fd,dtype='int32',mode='r',offset=int(pos),shape=(nbCellsOfType,))
244                     pos+=nbCellsOfType*4
245                     szOfNbOfNodesPerCellArr=int(nbOfNodesPerCell.sum())
246                     arr1=np.memmap(fd,dtype='int32',mode='r',offset=int(pos),shape=(szOfNbOfNodesPerCellArr,))
247                     pos+=szOfNbOfNodesPerCellArr*4  ; fd.seek(pos)
248                     mcmeshes2.append(self.__traduceMeshForPolygon(meshName,coo,nbOfNodesPerCell,arr1))
249                 if pos!=end:
250                     elt=fd.read(80) ; elt=elt.strip() ; typ=elt[:] ; pos+=80
251                     pass
252                 pass
253             if mcmeshes2:
254                 coo=mcmeshes2[0].getCoords() ; name=mcmeshes2[0].getName()
255                 for itmesh in mcmeshes2: itmesh.setCoords(coo)
256                 m=MEDCouplingUMesh.MergeUMeshesOnSameCoords(mcmeshes2) ; m.setName(name)
257                 mcmeshes.append(m)
258             pass
259         return mcmeshes
260
261
262     def __convertField(self,mlfields, mcmeshes, fileName, fieldName, discr, nbCompo, locId, it):
263         """ Convert the fields. """
264         stars=re.search("[\*]+",fileName).group()
265         st="%0"+str(len(stars))+"i"
266         trueFileName=fileName.replace(stars,st%(it))
267         fd=open(os.path.join(self._dirName,trueFileName),"r+b") ; fd.seek(0,2) ; end=fd.tell() ; fd.seek(0)
268         name=fd.read(80).strip().split(b" ")[0]
269         if name!=fieldName:
270             raise Exception("ConvertField : mismatch")
271         pos=fd.tell()
272         st=fd.read(80) ; st=st.strip() ; pos=fd.tell()
273         while pos!=end:
274             if st!=b"part":
275                 raise Exception("ConvertField : mismatch #2")
276             fdisc=MEDCouplingFieldDiscretization.New(self.discSpatial2[discr])
277             meshId=np.memmap(fd,dtype='int32',mode='r',offset=int(pos),shape=(1)).tolist()[0]-1
278             if meshId >= len( mcmeshes ):
279                 return
280             nbOfValues=fdisc.getNumberOfTuples(mcmeshes[meshId])
281             vals2=DataArrayDouble(nbOfValues,nbCompo)
282             fd.seek(pos+4)
283             st=fd.read(80).strip() ; pos=fd.tell()
284             offset=0
285             while pos!=end and st!=b"part":
286                 if st!=b"coordinates":
287                     nbOfValsOfTyp=mcmeshes[meshId].getNumberOfCellsWithType(self.dictMCTyp2[st])
288                 else:
289                     nbOfValsOfTyp=nbOfValues
290                     pass
291                 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))
292                 vals2[offset:offset+nbOfValsOfTyp]=DataArrayDouble(np.array(vals,dtype='float64')).fromNoInterlace()
293                 pos+=nbOfValsOfTyp*nbCompo*4 ; fd.seek(pos)
294                 st=fd.read(80) ; st=st.strip() ; pos=fd.tell()
295                 offset+=nbOfValsOfTyp
296                 pass
297             f=MEDCouplingFieldDouble(self.discSpatial2[discr],ONE_TIME) ; f.setName("%s_%s"%(fieldName,mcmeshes[meshId].getName()))
298             f.setMesh(mcmeshes[meshId]) ; f.setArray(vals2) ; f.setTime(float(it),it,-1)
299             f.checkConsistencyLight()
300             mlfields[locId+meshId].appendFieldNoProfileSBT(f)
301             pass
302
303     def __convertFieldFortran(self,mlfields, mcmeshes, fileName, fieldName, discr, nbCompo, locId, it):
304         """ Convert the fields. """
305         if re.search("[\*]+",fileName):
306             stars=re.search("[\*]+",fileName).group()
307             st="%0"+str(len(stars))+"i"
308             trueFileName=fileName.replace(stars,st%(it))
309             pass
310         else:
311             trueFileName=fileName
312             pass
313         fd=open(os.path.join(self._dirName,trueFileName),"r+b") ; fd.seek(0,2) ; end=fd.tell() ; fd.seek(0)
314         name=fd.read(80)
315         if fieldName not in name:
316             raise Exception("ConvertField : mismatch")
317         pos=fd.tell()
318         st=fd.read(80) ; st=st.strip() ; pos=fd.tell()
319         if b"part" not in st:
320             raise Exception("ConvertField : mismatch #2")
321         st=fd.read(80).strip() ; pos=fd.tell()
322         pos+=12 # I love it
323         offset=0
324         nbTurn=0
325         while pos!=end and b"part" not in st:
326             fdisc=MEDCouplingFieldDiscretization.New(self.discSpatial2[discr])
327             nbOfValues=fdisc.getNumberOfTuples(mcmeshes[nbTurn])
328             vals2=DataArrayDouble(nbOfValues,nbCompo)
329             pos+=24 # I love it again !
330             nbOfValsOfTyp=np.memmap(fd,dtype='>i4',mode='r',offset=pos,shape=(1)).tolist()[0]/4
331             pos+=4
332             vals=np.zeros(dtype=">f4",shape=(nbOfValsOfTyp*nbCompo))
333             for iii in range(nbCompo):
334                 valsTmp=np.memmap(fd,dtype='>f4',mode='r',offset=int(pos),shape=(nbOfValsOfTyp))
335                 vals[iii*nbOfValsOfTyp:(iii+1)*nbOfValsOfTyp]=valsTmp
336                 pos+=nbOfValsOfTyp*4
337                 pos+=2*4 ## hey hey, that is the ultimate class !
338                 vals2.setInfoOnComponent(iii,chr(ord('X')+iii))
339                 pass
340             if pos>end:
341                 pos=end
342                 pass
343             vals=vals.reshape(nbOfValsOfTyp,nbCompo)
344             vals2[offset:offset+nbOfValsOfTyp]=DataArrayDouble(np.array(vals,dtype='float64')).fromNoInterlace()
345             if pos!=end:
346                 fd.seek(pos)
347                 st=fd.read(80) ; st=st.strip() ; pos=fd.tell()
348                 st=fd.read(80) ; st=st.strip() ; pos=fd.tell()
349                 pass
350             f=MEDCouplingFieldDouble(self.discSpatial2[discr],ONE_TIME) ; f.setName("%s_%s"%(fieldName,mcmeshes[nbTurn].getName()))
351             f.setMesh(mcmeshes[nbTurn]) ; f.setArray(vals2) ; f.setTime(float(it),it,-1)
352             f.checkConsistencyLight()
353             mlfields[locId+nbTurn].appendFieldNoProfileSBT(f)
354             nbTurn+=1
355             pass
356         pass
357
358     def loadInMEDFileDS(self):
359         """ Load a CASE file into a MEDFileData object. """
360         f=open(self._fileName)
361         lines=f.readlines()
362         ind=lines.index("GEOMETRY\n")
363         if ind==-1:
364             raise Exception("Error with file %s"%(fname))
365         geoName=re.match("model:([\W]*)([\w\.]+)",lines[ind+1]).group(2)
366         m1,m2,typeOfFile=self.__convertGeo2MED(geoName)
367         fieldsInfo=[] ; nbOfTimeSteps=0
368         if "VARIABLE\n" in lines:
369             ind=lines.index("VARIABLE\n")
370             end=len(lines)-1
371             if "TIME\n" in lines:
372                 end=lines.index("TIME\n")
373                 pass
374             for i in range(ind + 1,end):
375                 m=re.match("^([\w]+)[\s]+\per[\s]+([\w]+)[\s]*\:[\s]*[0-9]*[\s]*([\w]+)[\s]+([\S]+)$",lines[i])
376                 if m:
377                     if m.groups()[0]=="constant":
378                         continue
379                     spatialDisc=m.groups()[1] ; fieldName=m.groups()[2] ; nbOfCompo=self.dictCompo2[m.groups()[0]] ; fieldFileName=m.groups()[3]
380                     if fieldFileName.endswith("*"):
381                       fieldsInfo.append((fieldName,spatialDisc,nbOfCompo,fieldFileName))
382                     pass
383                 pass
384
385             expr=re.compile("number[\s]+of[\s]+steps[\s]*\:[\s]*([\d]+)")
386             tmp = [line for line in lines if expr.search(line)]
387             if tmp:
388                 nbOfTimeSteps = int(expr.search(tmp[0]).group(1))
389                 expr=re.compile("filename[\s]+start[\s]+number[\s]*\:[\s]*([\d]+)")
390                 startIt = int(expr.search([line for line in lines if expr.search(line)][0]).group(1))
391                 expr=re.compile("filename[\s]+increment[\s]*\:[\s]*([\d]+)")
392                 incrIt = int(expr.search([line for line in lines if expr.search(line)][0]).group(1))
393             else:
394                 nbOfTimeSteps=1
395                 startIt=0
396                 incrIt=1
397                 pass
398             curIt=startIt
399             pass
400         mlfields=MEDFileFields()
401         mlfields.resize(len(fieldsInfo)*len(m1))
402         i=0
403         for field in fieldsInfo:
404             for m in m1:
405                 mlfields.setFieldAtPos(i,MEDFileFieldMultiTS())
406                 i+=1
407                 pass
408             pass
409         for ts in range(nbOfTimeSteps):
410             i=0
411             for field in fieldsInfo:
412                 if typeOfFile:
413                     self.__convertField(mlfields,m1,field[3],field[0],field[1],field[2],i,curIt);
414                 else:
415                     self.__convertFieldFortran(mlfields,m1,field[3],field[0],field[1],field[2],i,curIt)
416                     pass
417                 i+=len(m1)
418                 pass
419             curIt+=incrIt
420             pass
421         ret=MEDFileData()
422         ret.setMeshes(m2)
423         del mlfields[[x for x in range(len(mlfields)) if len(mlfields[x]) == 0]]
424         ret.setFields(mlfields)
425         return ret
426
427     pass