Fixed handling of string attributes. These are treated as HDF5 native strings

now rather than arrays of chars.


git-svn-id: http://svn.cactuscode.org/arrangements/CactusExternal/FlexIO/trunk@51 21a6bef8-4479-4f54-8f8d-0db94a2919ef

1 files changed, 74 insertions, 52 deletions

diff --git a/src/H5IO.cc b/src/H5IO.cc
index 009bdbd..d5d8795 100644
--- a/src/H5IO.cc
+++ b/src/H5IO.cc
@@ -37,14 +37,14 @@ hid_t H5IO::DataType2H5(IObase::DataType nt){
   }
 }
 
-IObase::DataType H5IO::H5DataType2DataType(hid_t nt){ 
+IObase::DataType H5IO::H5DataType2DataType(hid_t nt){
   H5T_class_t typeclass;
   size_t typesize;
-  
+
   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);
@@ -98,7 +98,7 @@ IObase::DataType H5IO::H5DataType2DataType(hid_t nt){
   case H5T_OPAQUE:
     puts("Cannot convert type Opaque");
     break;
-  case H5T_COMPOUND: 
+  case H5T_COMPOUND:
   default:
     puts("Cannot convert type Unknown");
     break;
@@ -136,7 +136,7 @@ IObase::DataType H5IO::H52DataType(hid_t &nt){
   fprintf(stderr,"H5IO::H52DataType(): Don't recognize type %d\n",(int)nt);
   return Error;
 }
-#endif 
+#endif
 int H5IO::createdataspace(int rank,CONST int *dims){
   if(dataspacevalid && rankf==(hsize_t) rank){
     // lets compare dims
@@ -170,8 +170,8 @@ int H5IO::createdatatype(IObase::DataType dt){
 
 int H5IO::selectdataset(int i){
   // printf("datasetvalid=%u i=%d index=%d nitems=%d\n",datasetvalid,i,index,nitems);
- 
-  if(index==i && datasetvalid) 
+
+  if(index==i && datasetvalid)
     return index;
   index=i;
   if(index>=nitems) index=nitems-1;
@@ -201,22 +201,22 @@ int H5IO::selectdataset(int i){
 }
 
 herr_t H5IOcounter(hid_t group_id,
-	       const char *member_name, 
+	       const char *member_name,
 		      void *operator_data){
   int *count = (int*)operator_data;
   /* typedef struct H5G_stat_t {
     unsigned long fileno[2];
-    unsigned long objno[2]; 
-    unsigned nlink; 
-    int type; 
-    time_t mtime; 
+    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, 
+  if(H5Gget_objinfo(group_id,
 		 member_name,
-		 1 /* follow links */, 
+		 1 /* follow links */,
 		    &objinfo)<0) {
     //fprintf(stderr,"\tcounter: Bad Info [%s] count=%u\n",member_name,*count);
     return 0; // error (probably bad symlink)
@@ -236,18 +236,18 @@ struct H5IO_getname_t {
   char *name;
 };
 herr_t H5IOgetname(hid_t group_id,
-			  const char *member_name, 
+			  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, 
+  if(H5Gget_objinfo(group_id,
 		    member_name,
-		    1 /* follow links */, 
+		    1 /* follow links */,
 		    &objinfo)<0) return 0; // error (probably bad symlink)
   // only count objects that are datasets (not subgroups)
-  if(objinfo.type!=H5G_DATASET) 
+  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);
@@ -402,7 +402,7 @@ int H5IO::write(IObase::DataType typeID,int rank,CONST int *dims,const void *dat
 //}
 
 int H5IO::readInfo(char *name,IObase::DataType &typeID,int &rank,int *dims,int maxdims){
-  
+
   // name shouls be attribute "long_name");
   if(hasread){
     //printf("hasread=1, so get next dataset index %u\n",index+1);
@@ -494,7 +494,7 @@ int H5IO::readAnnotation(int number,char *annotation,int maxlen){
 #endif
   if(maxlen>30)
     sprintf(annotation,"not-implemented");
-  else if(annotation) 
+  else if(annotation)
     *annotation=0;
   return 1;
 }
@@ -505,7 +505,7 @@ int H5IO::nAnnotations(){
   select(index);
   int32 ref=SDidtoref(sid);
   if(DFANgetlablen(filename,DFTAG_NDG,ref)<=0) return 0; // no labels found
-  return 1; // always 1 annotation per object limit for H5 is appears 
+  return 1; // always 1 annotation per object limit for H5 is appears
 #endif
   return 0;
 }
@@ -515,13 +515,26 @@ int H5IO::writeAttribute(CONST char *name,IObase::DataType typeID,Long length,co
   selectdataset(index); // make sure it is selected
   //printf("\tindex=%u\n",index);
   // create a datashape
-  hsize_t     dimsa[2]={0,0};
-  dimsa[0]=length;
-  hid_t shape = H5Screate_simple(1, dimsa, NULL);
-  hid_t attrib = H5Acreate(dataset,name,DataType2H5(typeID),shape,H5P_DEFAULT);
-  H5Awrite(attrib, DataType2H5(typeID), data);
+  hid_t datatype = DataType2H5(typeID);
+  int is_string = datatype == H5T_NATIVE_CHAR;
+  if (is_string)
+  {
+    datatype = H5Tcopy (H5T_C_S1);
+    // we want the string length (without the trailing '\0')
+    H5Tset_size (datatype, length - 1);
+    length = 1;
+  }
+  hsize_t dimsa = length;
+  hid_t shape = dimsa > 1 ? H5Screate_simple (1, &dimsa, NULL) :
+                            H5Screate (H5S_SCALAR);
+  hid_t attrib = H5Acreate(dataset,name,datatype,shape,H5P_DEFAULT);
+  H5Awrite(attrib, datatype, data);
   H5Aclose(attrib);
   H5Sclose(shape);
+  if (is_string)
+  {
+    H5Tclose (datatype);
+  }
   return 1;
 }
 
@@ -531,18 +544,21 @@ int H5IO::readAttributeInfo(int number,char *name,IObase::DataType &typeID,Long
   hid_t atype = H5Aget_type(attrib);
   hid_t ashape = H5Aget_space(attrib);
   H5Aget_name(attrib,maxnamelen,name);
-  /* hsize_t ranka = */ H5Sget_simple_extent_ndims(ashape);
-  // rank should always be 1;
-  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
-  
+  // rank should always be 0 for scalars and 1 for arrays;
+  hsize_t arank = H5Sget_simple_extent_ndims(ashape);
+  hsize_t adims;
+  if ((arank != 0 && arank != 1) ||
+      H5Sget_simple_extent_dims (ashape, &adims, NULL) < 0)
+  {
+    return (0);
+  }
+  typeID = H5DataType2DataType(atype);
+  nelem = arank ? adims : 1; // single-dimensional array for attributes
+  if (H5Tget_class (atype) == H5T_STRING)
+  { 
+    nelem = H5Tget_size(atype);
+  }
+
   H5Tclose(atype);
   H5Sclose(ashape);
   H5Aclose(attrib);
@@ -554,11 +570,11 @@ struct H5IOatt_name2index_t {
   int count;
 };
 herr_t H5IOattr_name2index(hid_t group_id,
-			   const char *member_name, 
+			   const char *member_name,
 			   void *operator_data){
   H5IOatt_name2index_t *s=(H5IOatt_name2index_t*)operator_data;
   s->count++;
-  if(!strcmp(member_name,s->name)) 
+  if(!strcmp(member_name,s->name))
     return s->count;
   else{
     return 0;
@@ -566,7 +582,7 @@ herr_t H5IOattr_name2index(hid_t group_id,
 }
 
 herr_t H5IOattr_count(hid_t group_id,
-			   const char *member_name, 
+			   const char *member_name,
 			   void *operator_data){
   // cycle through all attribs as a dummy counter
   int *count = (int *)operator_data;
@@ -586,15 +602,21 @@ int H5IO::readAttributeInfo(CONST char *name,IObase::DataType &typeID,Long &nele
   hid_t attrib = H5Aopen_name(dataset,name);
   hid_t atype = H5Aget_type(attrib);
   hid_t ashape = H5Aget_space(attrib);
-  /* hsize_t ranka = */ H5Sget_simple_extent_ndims(ashape);
-  // rank should always be 1;
-  hsize_t dimsa[5];
-  H5Sget_simple_extent_dims(ashape,dimsa,NULL);
+  // rank should always be 0 for scalars and 1 for arrays;
+  hsize_t arank = H5Sget_simple_extent_ndims(ashape);
+  hsize_t adims;
+  if ((arank != 0 && arank != 1) ||
+      H5Sget_simple_extent_dims (ashape, &adims, NULL) < 0)
+  {
+    return (0);
+  }
   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
-  
+  nelem = arank ? adims : 1; // single-dimensional array for attributes
+  if (H5Tget_class (atype) == H5T_STRING)
+  {
+    nelem = H5Tget_size(atype);
+  }
+
   H5Tclose(atype);
   H5Sclose(ashape);
   H5Aclose(attrib);
@@ -627,7 +649,7 @@ int H5IO::reserveChunk(IObase::DataType typeID,int rank,CONST int *dims){
   create(rank,dims,typeID);
   current_rank=rank;
   return 1;
-#endif 
+#endif
   return 1;
 }
 
@@ -675,7 +697,7 @@ Long8 f_h5_open (char *file,char *accessname,int flen,int alen){
     return 0;
   }
   IObase *fid=new H5IO(file,mode);
-  if(fid->isValid()) 
+  if(fid->isValid())
     return (Long8)fid;
   else
     delete fid; // file open failed
@@ -706,7 +728,7 @@ IOFile H5IOopen (char *file,char *accessname){
     mode=IObase::Read;
   else if(*accessname=='a')
     mode=IObase::Append;
-  else if(!strcmp(accessname,"write") || 
+  else if(!strcmp(accessname,"write") ||
 	  !strcmp(accessname,"create") ||
 	  !strcmp(accessname,"wb"))
     mode = IObase::Write;