Sync with cvs.cactuscode.org:/packages/FlexIO.

Mainly adding debug statements. One important fix for AMRwriter.cc to get the
min_ext[] and grid_placement_refinement[] attributes right again.


git-svn-id: http://svn.cactuscode.org/arrangements/CactusExternal/FlexIO/trunk@46 21a6bef8-4479-4f54-8f8d-0db94a2919ef

6 files changed, 140 insertions, 36 deletions

diff --git a/src/AMRwriter.cc b/src/AMRwriter.cc
index d46b57a..3f76648 100644
--- a/src/AMRwriter.cc
+++ b/src/AMRwriter.cc
@@ -20,6 +20,7 @@ void AMRwriter::writeAMRattributes(){
   // compute persistence
   
   persistence = levels[levels.getSize()-currentlevel-1].trefine;
+  if(persistence<=0) { fprintf(stderr,"Refinement *must* be >1... this isn't right!!!\n"); persistence=1;}
   level_timestep = currentstep/persistence;
   // compute from min-ext...
   // y-know... there is more point density near 0 in the float
@@ -36,7 +37,7 @@ void AMRwriter::writeAMRattributes(){
   for(int i=0;i<drank;i++) {
     currentdelta[i] = ddelta[i]/(levels[currentlevel]).srefine[i];
     ext[i] = currentorigin[i] + 
-      (double)((ddims[i]+1) * currentdelta[i]);
+      (double)((ddims[i]) * currentdelta[i]);
   }
   
   file.writeAttribute("level",IObase::Int32,1,&currentlevel);
@@ -100,8 +101,9 @@ void AMRwriter::setRefinement(int timerefinement,
 			      int spatialrefinement,
 			      int gridplacementrefinement){
   int tref=1,sref=1,gref=gridplacementrefinement;
-  int maxdepth=levels.getSize()+1;
+  int maxdepth=levels.getSize();
   // if gref==-1, then we need to multiply by maxdepth
+  /*  printf("maxdepth***********=%u\n",maxdepth); */
   for(int level=0;level<maxdepth;level++){
     setLevelRefinement(level,tref,sref,gref);
     tref*=timerefinement;
@@ -117,13 +119,13 @@ void AMRwriter::setRefinement(int timerefinement,
 void AMRwriter::setRefinement(int timerefinement,
 			      int *spatialrefinement,
 			      int *gridplacementrefinement){
-  int maxdepth = 1+levels.getSize();
+  int maxdepth = levels.getSize();
   int tref = 1;
   int *sref = new int[drank];
   int *gref = new int[drank];
   for(int i=0;i<drank;i++) 
   {     sref[i]=gref[i]=1;
-        if(gridplacementrefinement) gref[i]+=gridplacementrefinement[i];
+        if(gridplacementrefinement) gref[i]*=gridplacementrefinement[i];
   }
   for(int level=0;level<maxdepth;level++){
     setLevelRefinement(level,tref,sref,gref);
@@ -264,7 +266,7 @@ void AMRsetType(AMRFile afile,int numbertype){
   w->setType(IObase::Int2DataType(numbertype));
 }
 
-void AMRsetToplevelParameters(AMRFile afile,int rank, double *origin,
+void AMRsetTopLevelParameters(AMRFile afile,int rank, double *origin,
 			      double *delta, double timestep,int maxdepth){
   AMRwriter *w = (AMRwriter*)afile;
   w->setTopLevelParameters(rank,origin,delta,timestep,maxdepth);
@@ -302,12 +304,12 @@ void AMRsetScalarLevelRefinement(AMRFile afile,int level,
   w->setLevelRefinement(level,timerefinement,spatialrefinement,gridplacementrefinement);
 }
 
-void AMRlevel(AMRFile afile,int level){
+void AMRsetLevel(AMRFile afile,int level){
   AMRwriter *w = (AMRwriter*)afile;
   w->setLevel(level);
 }
 
-void AMRtime(AMRFile afile,int time){
+void AMRsetTime(AMRFile afile,int time){
   AMRwriter *w = (AMRwriter*)afile;
   w->setTime(time);
 }
diff --git a/src/AmrFileReader.cc b/src/AmrFileReader.cc
index 6047ce0..4207210 100644
--- a/src/AmrFileReader.cc
+++ b/src/AmrFileReader.cc
@@ -47,7 +47,9 @@ void AmrFileReader::buildInfoTable(){
     grids.append(g);
     if(g.level>maxlevel)
       maxlevel=g.level;
+    printf("Gridnum[%u] timestep=%u\n",i,g.timestep);
     if(!i){
+      printf("i=%u INITIALIZE TIME*********************\n",i);
       mintime = g.timestep;
       maxtime = g.timestep;
       maxtimeres = g.timerefinement;
diff --git a/src/AmrGridReader.cc b/src/AmrGridReader.cc
index 3ea8f90..a7eba1e 100644
--- a/src/AmrGridReader.cc
+++ b/src/AmrGridReader.cc
@@ -77,7 +77,7 @@ AmrGrid *AmrGridReader::getGridInfo(AmrGrid &g,int index){
   
 AmrGrid *AmrGridReader::getGridData(AmrGrid &g,int index){
   IObase::DataType atype;
-  // if(data) free(data); data=0; // make certain it is empty first
+  if(g.data) free(g.data); g.data=0; // make certain it is empty first
   g.data = malloc(g.nbytes);
   file.seek(index);
   file.readInfo(atype,g.rank,g.dims);
diff --git a/src/H5IO.cc b/src/H5IO.cc
index c611f0b..b4fd238 100644
--- a/src/H5IO.cc
+++ b/src/H5IO.cc
@@ -43,10 +43,11 @@ IObase::DataType H5IO::H5DataType2DataType(hid_t nt){
   
   typeclass = H5Tget_class(nt);
   typesize  = H5Tget_size(nt);
+  //fprintf(stderr,"class=%d size=%d\n",typeclass,typesize);
   
   switch(typeclass){
   case H5T_INTEGER:
-    printf("Int %d bytes\n",typesize);
+    // printf("Int %d bytes\n",typesize);
     switch(typesize){
     case 1:
       return Int8;
@@ -78,17 +79,18 @@ IObase::DataType H5IO::H5DataType2DataType(hid_t nt){
     puts("Cannot convert type Time");
     break;
   case H5T_STRING:
+    return Char8;
     //puts("String");
-    switch(typesize){
-    case 1:
-      return Char8;
-    case 2:
-      return Char16;
-    default:
-      printf("Cannot convert type for string element with %d bytes\n",
-	     typesize);
-      break;
-    }
+    //switch(typesize){
+    //case 1:
+    //  return Char8;
+    //case 2:
+    //  return Char16;
+    //default:
+    //  printf("Cannot convert type for string element with %d bytes\n",
+    //     typesize);
+    //  break;
+    //}
     break;
   case H5T_BITFIELD:
     puts("Cannot convert type Bitfield");
@@ -177,9 +179,9 @@ int H5IO::selectdataset(int i){
   // must iterate to select or for now just
   char dataname[128];
   //char dataname2[128];
-  sprintf(dataname,"H5IO-Dataset%09u",index); // was a KLUDGE!
-  //getdatasetname(index,dataname2);
-  //printf("Datasetname for dataset[%u]=[%s] [%s]\n",index,dataname,dataname2);
+  //sprintf(dataname,"H5IO-Dataset%09u",index); // was a KLUDGE!
+  getdatasetname(index,dataname);
+  //fprintf(stderr,"Datasetname for dataset[%u]=[%s] [%s]\n",index,dataname,dataname2);
   enddataset(); // close current dataset
   dataset = H5Dopen(file,dataname); // open a dataset
   if(!dataset) puts("error no dataset");
@@ -202,7 +204,30 @@ herr_t H5IOcounter(hid_t group_id,
 	       const char *member_name, 
 		      void *operator_data){
   int *count = (int*)operator_data;
-  (*count)++;
+  /* typedef struct H5G_stat_t {
+    unsigned long fileno[2];
+    unsigned long objno[2]; 
+    unsigned nlink; 
+    int type; 
+    time_t mtime; 
+    size_t linklen;
+    } H5G_stat_t */
+  H5G_stat_t objinfo;
+  // request info about the type of objects in root group
+  if(H5Gget_objinfo(group_id, 
+		 member_name,
+		 1 /* follow links */, 
+		    &objinfo)<0) {
+    //fprintf(stderr,"\tcounter: Bad Info [%s] count=%u\n",member_name,*count);
+    return 0; // error (probably bad symlink)
+  }
+  // only count objects that are datasets (not subgroups)
+  if(objinfo.type==H5G_DATASET){
+    // fprintf(stderr,"\tcounter: This is a dataset [%s] count=%u\n",member_name,*count);
+    (*count)++;
+  }
+  else
+    // fprintf(stderr,"\tcounter: **reject dataset [%s] count=%u\n",member_name,*count);
   return 0;
 }
 
@@ -214,6 +239,16 @@ herr_t H5IOgetname(hid_t group_id,
 			  const char *member_name, 
 			  void *operator_data){
   H5IO_getname_t *getn = (H5IO_getname_t*)operator_data;
+  // check type first (only respond if it is a dataset)
+  H5G_stat_t objinfo;
+  // request info about the type of objects in root group
+  if(H5Gget_objinfo(group_id, 
+		    member_name,
+		    1 /* follow links */, 
+		    &objinfo)<0) return 0; // error (probably bad symlink)
+  // only count objects that are datasets (not subgroups)
+  if(objinfo.type!=H5G_DATASET) 
+    return 0; // do not increment count if it isn't a dataset.
   if(getn->index==getn->count){
     strcpy(getn->name,member_name);
     return 1; // success
@@ -234,6 +269,7 @@ int H5IO::getndatasets(){
     //printf("getndatasets: nitems{%d}!=count{%d}\n",
     //	   nitems,count);
   //}
+  //fprintf(stderr,"getndatasets:=%u\n",count);
   nitems = count; // just for internal bookkeeping
   return count;
 }
@@ -442,7 +478,9 @@ int H5IO::readAnnotationInfo(int number,int &length){
   length=(int)DFANgetlablen(filename,DFTAG_NDG,ref);
   return length;
 #endif
-  return 1;
+  //  sprintf(annotation,"not-implemented");
+  length=0;
+  return 0;
 }
 
 int H5IO::readAnnotation(int number,char *annotation,int maxlen){
@@ -454,6 +492,10 @@ int H5IO::readAnnotation(int number,char *annotation,int maxlen){
   int32 ref=SDidtoref(sid);
   return (int)DFANgetlabel(filename,DFTAG_NDG,ref,annotation,maxlen);
 #endif
+  if(maxlen>30)
+    sprintf(annotation,"not-implemented");
+  else if(annotation) 
+    *annotation=0;
   return 1;
 }
 
@@ -465,7 +507,7 @@ int H5IO::nAnnotations(){
   if(DFANgetlablen(filename,DFTAG_NDG,ref)<=0) return 0; // no labels found
   return 1; // always 1 annotation per object limit for H5 is appears 
 #endif
-  return 1;
+  return 0;
 }
 
 int H5IO::writeAttribute(CONST char *name,IObase::DataType typeID,Long length,const void *data){
@@ -491,9 +533,14 @@ int H5IO::readAttributeInfo(int number,char *name,IObase::DataType &typeID,Long
   H5Aget_name(attrib,maxnamelen,name);
   /* hsize_t ranka = */ H5Sget_simple_extent_ndims(ashape);
   // rank should always be 1;
-  hsize_t dimsa[5];
-  H5Sget_simple_extent_dims(ashape,dimsa,NULL);
-  typeID = H5DataType2DataType(atype);
+  hsize_t dimsa[5]={0,0,0,0,0},ndimsa=0,npointsa;
+  if(H5Sget_simple_extent_dims(ashape,dimsa,NULL)<0) dimsa[0]=0;
+  ndimsa=H5Sget_simple_extent_ndims(ashape);
+  npointsa=H5Sget_simple_extent_npoints(ashape);
+  // fprintf(stderr,"dimsa[0]=%d ndimsa=%d npoints=%u\n",dimsa[0],ndimsa,npointsa);
+  typeID = H5DataType2DataType(atype);  
+  if(typeID==Char8 && dimsa[0]==0) // special case for strings
+    dimsa[0]  = H5Tget_size(atype);
   nelem = dimsa[0]; // single-dimensional array for attributes
   
   H5Tclose(atype);
@@ -544,6 +591,8 @@ int H5IO::readAttributeInfo(CONST char *name,IObase::DataType &typeID,Long &nele
   hsize_t dimsa[5];
   H5Sget_simple_extent_dims(ashape,dimsa,NULL);
   typeID = H5DataType2DataType(atype);
+  if(typeID==Char8 && dimsa[0]==0) // special case for strings
+    dimsa[0]  = H5Tget_size(atype);
   nelem = dimsa[0]; // single-dimensional array for attributes
   
   H5Tclose(atype);
@@ -557,7 +606,7 @@ int H5IO::readAttribute(int number,void *data){
   selectdataset(index); // just to be sure we've got data
   hid_t attrib = H5Aopen_idx(dataset,number);
   hid_t atype = H5Aget_type(attrib);
-  H5Aread(attrib,DataType2H5(H5DataType2DataType(atype)),data);
+  H5Aread(attrib,atype /*DataType2H5(H5DataType2DataType(atype))*/ ,data);
   H5Tclose(atype);
   H5Aclose(attrib);
   return 1;
diff --git a/src/IEEEIO.cc b/src/IEEEIO.cc
index a71e381..c36751e 100644
--- a/src/IEEEIO.cc
+++ b/src/IEEEIO.cc
@@ -5,7 +5,7 @@
 
 #ifdef WIN32
 // Are we Microsoft VC++ 5.0 or 6.0?
-#if defined(_MSC_VER) && ( (_MSC_VER == 1100) || (_MSC_VER == 1200) ) // yes we are
+#if defined(_MSC_VER) && ( (_MSC_VER == 1100) || (_MSC_VER == 1200) || (_MSC_VER == 1300)) // yes we are
 #include <fcntl.h>
 #ifdef  O_RDONLY
 #undef  O_RDONLY
@@ -1374,19 +1374,44 @@ Long8 f_ieee_open (char *file,char *accessname,int flen,int alen){
   return 0;
 }
 
+/*
+ Fortran passes strings without 0-bytes.
+ C requires a 0-byte at the end of a string.
+ We may not modify the passed string, because it
+ might reside in a read only text segment, thus
+ we need a local copy to append a 0-byte.
+ Performance is not an issue here, because file access
+ is much slower than this little memory shifting anyway.
+ */
+
 Long8 f_ieee_openr(char *filename,int namelen){
-  filename[namelen]='\0';
-  return (Long8)(new IEEEIO(filename,IObase::Read));
+
+char*fn = new char[namelen+1]; 
+  strncpy(fn, filename, namelen);
+  fn[namelen]='\0';
+Long8 ID =  (Long8)(new IEEEIO(filename,IObase::Read)); 
+    delete fn; 
+    return ID;
 }
 
 Long8 f_ieee_openw(char *filename,int namelen){
-  filename[namelen]='\0';
-  return (Long8)(new IEEEIO(filename,IObase::Write));
+
+char*fn = new char[namelen+1]; 
+  strncpy(fn, filename, namelen);
+  fn[namelen]='\0';
+Long8 ID = (Long8)(new IEEEIO(filename,IObase::Write));
+    delete fn; 
+    return ID;
 }
 
 Long8 f_ieee_opena(char *filename,int namelen){
-  filename[namelen]='\0';
-  return (Long8)(new IEEEIO(filename,IObase::Append));
+
+char*fn = new char[namelen+1]; 
+  strncpy(fn, filename, namelen);
+  fn[namelen]='\0';
+Long8 ID = (Long8)(new IEEEIO(filename,IObase::Append));
+    delete fn; 
+    return ID;
 }
 
 void ieee_bufon(Long8 *fileID,int bufsize){
diff --git a/src/IO.cc b/src/IO.cc
index c0860c1..622f2cd 100644
--- a/src/IO.cc
+++ b/src/IO.cc
@@ -126,8 +126,19 @@ int f_io_seek(Long8 *deviceID,int *dataset_index){
 //--------------Annotations
 int f_io_writenote(Long8 *deviceID,char *annotation,int size){
   IObase *dev=(IObase*)(*deviceID);
+#if 0
   annotation[size]='\0'; // Yeah! its unsafe I know..!! (but it works!)
   return dev->writeAnnotation(annotation);
+#else 
+  // well, the problem is that it does not work if the annotation 
+  // string resides in a readonly text segment... (Werner)
+char*ann = new char[size+1]; 
+	strncpy(ann, annotation, size); 
+	ann[size] = '\0';
+int i = dev->writeAnnotation(ann); 
+     delete ann;
+     return i;
+#endif
 }
 
 int f_io_readnote(Long8 *deviceID,int *idx,char *annotation,int maxsize){ 
@@ -149,10 +160,25 @@ int f_io_numnote(Long8 *deviceID){
 int f_io_writeatt(Long8 *deviceID,char *name,
 		 int *datatype,Long *nelements,const void *data,int namesize){
   IObase *dev=(IObase*)(*deviceID);
+#if 0
   name[namesize]='\0'; // cap name (to be certain).. unsafe but it works
   // should copy into a flexarray which will be destroyed on return
   IObase::DataType typeID = IObase::Int2DataType(*datatype);
   return dev->writeAttribute(name,typeID,*nelements,data);
+
+#else 
+  // well, the problem is that it does not work if the annotation 
+  // string resides in a readonly text segment... (Werner)
+char*tmp = new char[namesize+1]; 
+	strncpy(tmp, name, namesize); 
+	tmp[namesize] = '\0';
+  IObase::DataType typeID = IObase::Int2DataType(*datatype);
+int i =  dev->writeAttribute(tmp,typeID,*nelements,data);
+     delete tmp;
+     return i;
+#endif
+
+
 }
 
 int f_io_attinfo(Long8 *deviceID,char *name,