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"Supporting" Fortran case file.
authorageay <ageay>
Fri, 31 Jan 2014 15:54:28 +0000 (15:54 +0000)
committerageay <ageay>
Fri, 31 Jan 2014 15:54:28 +0000 (15:54 +0000)
src/MEDLoader/Swig/CaseReader.py

index 87d2fbcce509e9a6f7d7ab9b2f37fa94c6690dab..7dc270e575a9f001027b8785af38cf2c2fc5eddb 100644 (file)
@@ -19,6 +19,7 @@
 #
 # Author Anthony GEAY (CEA/DEN/DM2S/STMF/LGLS)
 
+# http://www-vis.lbl.gov/NERSC/Software/ensight/doc/OnlineHelp/UM-C11.pdf
 import numpy as np
 from MEDLoader import *
 from CaseIO import CaseIO
@@ -53,7 +54,11 @@ class CaseReader(CaseIO):
         cI=DataArrayInt(len(cells)+1) ; cI.iota() ; cI*=nbNodesPerCell+1
         #
         cells2=cells.reshape(len(cells),nbNodesPerCell)
-        c2=DataArrayInt(cells2)
+        if cells2.dtype=='int32':
+            c2=DataArrayInt(cells2)
+        else:
+            c2=DataArrayInt(np.array(cells2,dtype="int32"))
+            pass
         c=DataArrayInt(len(cells),nbNodesPerCell+1) ; c[:,0]=ct ; c[:,1:]=c2-1 ; c.rearrange(1)
         m.setConnectivity(c,cI,True)
         m.checkCoherency2()
@@ -105,13 +110,96 @@ class CaseReader(CaseIO):
 
     def __convertGeo2MED(self,geoFileName):
         """ Convert all the geometry (all the meshes) contained in teh CASE file into MEDCouplingUMesh'es. """
-        fd=open(os.path.join(self._dirName,geoFileName),"r+b") ; fd.seek(0,2) ; end=fd.tell() ; fd.seek(0) ; fd.readline() ; fd.readline()
+        fd=open(os.path.join(self._dirName,geoFileName),"r+b") ; fd.seek(0,2) ; end=fd.tell() ; fd.seek(0) ; title=fd.read(80)
+        title=title.strip().lower()
+        if "binary" not in title:
+            raise Exception("Error only binary geo files are supported for the moment !")
+            pass
+        zeType=True
+        if "fortran" in title:
+            mcmeshes=self.__convertGeo2MEDFortran(fd,end) ; zeType=False
+        else:
+            mcmeshes=self.__convertGeo2MEDC(fd,end)
+        #
+        ms=MEDFileMeshes()
+        ms.resize(len(mcmeshes))
+        for i,m in enumerate(mcmeshes):
+            mlm=MEDFileUMesh()
+            mlm.setMeshAtLevel(0,m)
+            ms.setMeshAtPos(i,mlm)
+            pass
+        return mcmeshes,ms,zeType
+
+    def __convertGeo2MEDFortran(self,fd,end):
+        mcmeshes=[]
+        fd.read(80) # comment 1
+        fd.read(80) # comment 2
+        fd.read(80) # node id
+        fd.read(80) # element id
+        pos=fd.tell()
+        elt=fd.read(80) ; elt=elt.strip() ; pos=fd.tell()
+        mcmeshes2=[]
+        typ="part"
+        nbOfTurn=0
+        while abs(pos-end)>8 and "part" in typ:
+            if "part" not in elt:
+                raise Exception("Error on reading mesh fortran #1 !")
+            fd.seek(fd.tell()+4)# skip #
+            tmp=fd.read(80) ; meshName=tmp.split("P")[-1]
+            tmp=fd.read(80)
+            if "coordinates" not in tmp:
+                raise Exception("Error on reading mesh fortran #2 !")
+            pos=fd.tell() # 644
+            if nbOfTurn==0:
+                pos+=76 # what else ?
+            else:
+                pos+=40
+                pass
+            nbNodes=np.memmap(fd,dtype='>i4',mode='r',offset=int(pos),shape=(1,)).tolist()[0]
+            pos+=12 # what else ?
+            a=np.memmap(fd,dtype='>f4',mode='r',offset=int(pos),shape=(nbNodes))
+            b=np.memmap(fd,dtype='>f4',mode='r',offset=int(pos+nbNodes*4+2*4),shape=(nbNodes))
+            c=np.memmap(fd,dtype='>f4',mode='r',offset=int(pos+nbNodes*2*4+4*4),shape=(nbNodes))
+            coo=np.zeros(dtype=">f4",shape=(nbNodes*3))
+            coo[:nbNodes]=a ; coo[nbNodes:2*nbNodes]=b ; coo[2*nbNodes:]=c
+            coo=coo.reshape(nbNodes,3)
+            pos+=nbNodes*3*4 ; fd.seek(pos)#np.array(0,dtype='float%i'%(typeOfCoo)).nbytes
+            typ=fd.read(80).strip() ; pos=fd.tell()
+            zeK=""
+            for k in self.dictMCTyp2.keys():
+                if k in typ:
+                    zeK=k
+                    break
+                    pass
+                pass
+            pos+=8*4 # yeh man !
+            nbCellsOfType=np.memmap(fd,dtype='>i4',mode='r',offset=int(pos),shape=(1,)).tolist()[0]
+            pos+=4 # for the number of cells
+            pos+=2*4 # because it's great !
+            nbNodesPerCell=MEDCouplingMesh.GetNumberOfNodesOfGeometricType(self.dictMCTyp2[zeK])
+            nodalConn=np.memmap(fd,dtype='>i4',mode='r',offset=pos,shape=(nbCellsOfType,nbNodesPerCell))
+            meshName=meshName.strip()
+            mcmeshes2.append(self.__traduceMesh(meshName,zeK,coo,nodalConn))
+            pos+=nbNodesPerCell*nbCellsOfType*4
+            if abs(pos-end)>8:
+                fd.seek(pos) ;elt=fd.read(80) ; typ=elt[:] ; pos+=80 
+                pass
+            nbOfTurn+=1
+            pass
+        #coo=mcmeshes2[0].getCoords() ; name=mcmeshes2[0].getName()
+        #for itmesh in mcmeshes2: itmesh.setCoords(coo)
+        #m=MEDCouplingUMesh.MergeUMeshesOnSameCoords(mcmeshes2) ; m.setName(name)
+        #mcmeshes.append(m)
+        return mcmeshes2
+
+    def __convertGeo2MEDC(self,fd,end):
+        fd.readline()
         name=fd.readline().strip() ; fd.readline() ; fd.readline()
         pos=fd.tell()
         mcmeshes=[]
         elt=fd.read(80) ; elt=elt.strip() ; pos+=80
         while pos!=end:
-            if elt!="part":
+            if "part" not in elt:
                 raise Exception("Error on reading mesh #1 !")
             fd.seek(fd.tell()+4)
             meshName=fd.read(80).strip()
@@ -163,15 +251,8 @@ class CaseReader(CaseIO):
             m=MEDCouplingUMesh.MergeUMeshesOnSameCoords(mcmeshes2) ; m.setName(name)
             mcmeshes.append(m)
             pass
-        #
-        ms=MEDFileMeshes()
-        ms.resize(len(mcmeshes))
-        for i,m in enumerate(mcmeshes):
-            mlm=MEDFileUMesh()
-            mlm.setMeshAtLevel(0,m)
-            ms.setMeshAtPos(i,mlm)
-            pass
-        return mcmeshes,ms
+        return mcmeshes
+        
     
     def __convertField(self,mlfields, mcmeshes, fileName, fieldName, discr, nbCompo, locId, it):
         """ Convert the fields. """
@@ -211,6 +292,60 @@ class CaseReader(CaseIO):
             f.checkCoherency()
             mlfields[locId+meshId].appendFieldNoProfileSBT(f)
             pass
+
+    def __convertFieldFortran(self,mlfields, mcmeshes, fileName, fieldName, discr, nbCompo, locId, it):
+        """ Convert the fields. """
+        if re.search("[\*]+",fileName):
+            stars=re.search("[\*]+",fileName).group()
+            st="%0"+str(len(stars))+"i"
+            trueFileName=fileName.replace(stars,st%(it))
+            pass
+        else:
+            trueFileName=fileName
+            pass
+        fd=open(os.path.join(self._dirName,trueFileName),"r+b") ; fd.seek(0,2) ; end=fd.tell() ; fd.seek(0)
+        name=fd.read(80)
+        if fieldName not in name:
+            raise Exception("ConvertField : mismatch")
+        pos=fd.tell()
+        st=fd.read(80) ; st=st.strip() ; pos=fd.tell()
+        if "part" not in st:
+            raise Exception("ConvertField : mismatch #2")
+        st=fd.read(80).strip() ; pos=fd.tell()
+        pos+=12 # I love it
+        offset=0
+        nbTurn=0
+        while pos!=end and "part" not in st:
+            fdisc=MEDCouplingFieldDiscretization.New(self.discSpatial2[discr])
+            nbOfValues=fdisc.getNumberOfTuples(mcmeshes[nbTurn])
+            vals2=DataArrayDouble(nbOfValues,nbCompo)
+            pos+=24 # I love it again !
+            nbOfValsOfTyp=np.memmap(fd,dtype='>i4',mode='r',offset=pos,shape=(1)).tolist()[0]/4
+            pos+=4
+            vals=np.zeros(dtype=">f4",shape=(nbOfValsOfTyp*nbCompo))
+            for iii in xrange(nbCompo):
+                valsTmp=np.memmap(fd,dtype='>f4',mode='r',offset=int(pos),shape=(nbOfValsOfTyp))
+                vals[iii*nbOfValsOfTyp:(iii+1)*nbOfValsOfTyp]=valsTmp
+                pos+=nbOfValsOfTyp*4
+                pos+=2*4 ## hey hey, that is the ultimate class !
+                vals2.setInfoOnComponent(iii,chr(ord('X')+iii))
+                pass
+            if pos>end:
+                pos=end
+                pass
+            vals=vals.reshape(nbOfValsOfTyp,nbCompo)
+            vals2[offset:offset+nbOfValsOfTyp]=DataArrayDouble(np.array(vals,dtype='float64')).fromNoInterlace()
+            if pos!=end:
+                fd.seek(pos)
+                st=fd.read(80) ; st=st.strip() ; pos=fd.tell()
+                st=fd.read(80) ; st=st.strip() ; pos=fd.tell()
+                pass
+            f=MEDCouplingFieldDouble(self.discSpatial2[discr],ONE_TIME) ; f.setName("%s_%s"%(fieldName,mcmeshes[nbTurn].getName()))
+            f.setMesh(mcmeshes[nbTurn]) ; f.setArray(vals2) ; f.setTime(float(it),it,-1)
+            f.checkCoherency()
+            mlfields[locId+nbTurn].appendFieldNoProfileSBT(f)
+            nbTurn+=1
+            pass
         pass
     
     def loadInMEDFileDS(self):
@@ -221,26 +356,36 @@ class CaseReader(CaseIO):
         if ind==-1:
             raise Exception("Error with file %s"%(fname))
         geoName=re.match("model:([\W]*)([\w\.]+)",lines[ind+1]).group(2)
-        m1,m2=self.__convertGeo2MED(geoName)
-        ind=lines.index("VARIABLE\n")
+        m1,m2,typeOfFile=self.__convertGeo2MED(geoName)
         fieldsInfo=[]
-        for i in xrange(ind+1,lines.index("TIME\n")):
+        ind=lines.index("VARIABLE\n")
+        end=len(lines)-1
+        if "TIME\n" in lines:
+            end=lines.index("TIME\n")
+            pass
+        for i in xrange(ind+1,end):
             m=re.match("^([\w]+)[\s]+\per[\s]+([\w]+)[\s]*\:[\s]*([\w]+)[\s]+([\S]+)$",lines[i])
             if m:
+                if m.groups()[0]=="constant":
+                    continue
                 spatialDisc=m.groups()[1] ; fieldName=m.groups()[2] ; nbOfCompo=self.dictCompo2[m.groups()[0]] ; fieldFileName=m.groups()[3]
                 fieldsInfo.append((fieldName,spatialDisc,nbOfCompo,fieldFileName))
                 pass
             pass
         
         expr=re.compile("number[\s]+of[\s]+steps[\s]*\:[\s]*([\d]+)")
-        nbOfTimeSteps=int(expr.search(filter(expr.search,lines)[0]).group(1))
-        
-        expr=re.compile("filename[\s]+start[\s]+number[\s]*\:[\s]*([\d]+)")
-        startIt=int(expr.search(filter(expr.search,lines)[0]).group(1))
-        
-        expr=re.compile("filename[\s]+increment[\s]*\:[\s]*([\d]+)")
-        incrIt=int(expr.search(filter(expr.search,lines)[0]).group(1))
-        
+        tmp=filter(expr.search,lines)
+        if len(tmp)!=0:
+            nbOfTimeSteps=int(expr.search(filter(expr.search,lines)[0]).group(1))
+            expr=re.compile("filename[\s]+start[\s]+number[\s]*\:[\s]*([\d]+)")
+            startIt=int(expr.search(filter(expr.search,lines)[0]).group(1))
+            expr=re.compile("filename[\s]+increment[\s]*\:[\s]*([\d]+)")
+            incrIt=int(expr.search(filter(expr.search,lines)[0]).group(1))
+        else:
+            nbOfTimeSteps=1
+            startIt=0
+            incrIt=1
+            pass
         curIt=startIt
         mlfields=MEDFileFields()
         mlfields.resize(len(fieldsInfo)*len(m1))
@@ -254,7 +399,11 @@ class CaseReader(CaseIO):
         for ts in xrange(nbOfTimeSteps):
             i=0
             for field in fieldsInfo:
-                self.__convertField(mlfields,m1,field[3],field[0],field[1],field[2],i,curIt)
+                if typeOfFile:
+                    self.__convertField(mlfields,m1,field[3],field[0],field[1],field[2],i,curIt);
+                else:
+                    self.__convertFieldFortran(mlfields,m1,field[3],field[0],field[1],field[2],i,curIt)
+                    pass
                 i+=len(m1)
                 pass
             curIt+=incrIt