Creating your own HDF5 product

The following discussion assumes the use of a UNIX operating system.

When creating your own HDF5 product, there are two header files that should be included, read_vhlhdf.h and write_vhlhdf.h.

When compiling a binary, there are three libraries that must be linked in; these are libhlhdf.a, libhdf5.a and libz.a. It is also possible to link the shared library libhdf5.so instead of libhdf5.a.

The HL-HDF package was installed with a hldef.mk file that can be included in your own Makefile in order to get the correct paths to both the zlib and the hdf5 library. It also contains information on which C-compiler the HL-HDF package was compiled with and some other goodies.

A simple Makefile could look like this:

include /usr/local/hlhdf/mkf/hldef.mk

HLHDF_INCDIR = -I/usr/local/hlhdf/include
HLHDF_LIBDIR = -L/usr/local/hlhdf/lib

CFLAGS = $(OPTS) $(DEFS) -I. $(ZLIB_INCDIR) $(HDF5_INCDIR) \
         $(HLHDF_INCDIR)

LDFLAGS = -L. $(ZLIB_LIBDIR) $(HDF5_LIBDIR) $(HLHDF_LIBDIR)

LIBS = -lhlhdf -lhdf5 -lz -lm

TARGET=myTestProgram
SOURCES=test_program.c
OBJECTS=$(SOURCES:.c=.o)

all: $(TARGET)

$(TARGET): $(OBJECTS)
           $(CC) -o $@ $(LDFLAGS) $(OBJECTS) $(LIBS)

clean:
           @\rm -f *.o *~ so_locations core

distclean: clean
           @\rm -f $(TARGET)

distribution:
           @echo "Would bring the latest revision upto date"

install:
           @$(HL_INSTALL) -f -o -C $(TARGET) ${MY_BIN_PATH}/$(TARGET)

Now, when the Makefile has been created, it might be a good idea to write your own HDF5 product. The following example will create a dataset with a two-dimensional array of integers, and two attributes connected to this dataset. It will also create a group containing one attribute.

#include <read_vhlhdf.h>
#include <write_vhlhdf.h>

int main(int argc, char** argv)
{
  HL_NodeList* aList=NULL;
  HL_Node* aNode=NULL;
  int* anArray=NULL;
  int anIntValue;
  float aFloatValue;
  hsize_t dims[]={10,10};
  int npts=100;
  int i;

  initHlHdf();  /* Initialize the HL-HDF library */
  debugHlHdf(2); /* Activate debugging */

  if(!(aList = newHL_NodeList())) {
    fprintf(stderr,"Failed to allocate nodelist");
    goto fail;
  }

  if(!(anArray = malloc(sizeof(int)*npts))) {
    fprintf(stderr,"Failed to allocate memory for array.");
    goto fail;
  }
  for(i=0;i<npts;i++)
    anArray[i]=i;

  addNode(aList,(aNode = newHL_Group("/group1")));
  addNode(aList,(aNode = newHL_Attribute("/group1/attribute1")));
  anIntValue=10;
  setScalarValue(aNode,sizeof(anIntValue),(unsigned char*)&anIntValue,"int",-1);

  addNode(aList,(aNode = newHL_Dataset("/dataset1")));
  setArrayValue(aNode,sizeof(int),2,dims,(unsigned char*)anArray,"int",-1);

  addNode(aList,(aNode = newHL_Attribute("/dataset1/attribute2")));
  anIntValue=20;
  setScalarValue(aNode,sizeof(anIntValue),(unsigned char*)&anIntValue,"int",-1);

  addNode(aList,(aNode = newHL_Attribute("/dataset1/attribute3")));
  aFloatValue=99.99;
  setScalarValue(aNode,sizeof(aFloatValue),(unsigned char*)&aFloatValue,
                 "float",-1);

  strcpy(aList->filename,"written_hdffile.hdf");
  writeNodeList(aList,6);

  freeHL_NodeList(aList);
  exit(0);
  return 0; /* Won't come here */
 fail:
  freeHL_NodeList(aList);
  exit(1);
  return 1; /* Won't come here */
}

When you have created your own HDF5 product, it might be a good idea to create some code for reading this file and checking its contents.

#include <read_vhlhdf.h>
#include <write_vhlhdf.h>

int main(int argc, char** argv)
{
  HL_NodeList* aList=NULL;
  HL_Node* aNode=NULL;
  int* anArray=NULL;
  int anIntValue;
  float aFloatValue;
  int npts;
  int i;

  initHlHdf();  /* Initialize the HL-HDF library */
  debugHlHdf(2); /* Activate debugging */

  if(!(aList = readHL_NodeList("written_hdffile.hdf"))) {
    fprintf(stderr,"Failed to read nodelist\n");
    goto fail;
  }

  selectAllNodes(aList);  /* Select everything for retrival */

  fetchMarkedNodes(aList);

  if((aNode = getNode(aList,"/group1")))
    printf("%s exists\n",aNode->name);

  if((aNode = getNode(aList,"/group1/attribute1"))) {
    memcpy(&anIntValue,aNode->data,aNode->dSize);
    printf("%s exists and have value %d\n",aNode->name,anIntValue);
  }

  if((aNode = getNode(aList,"/dataset1"))) {
    anArray = (int*)aNode->data;
    npts = 1;
    for(i=0;i<aNode->ndims;i++)
      npts*=aNode->dims[i];
    printf("%s exists and has the values:\n",aNode->name);
    for(i=0;i<npts;i++) {
      printf("%d ", anArray[i]);
      if((i%aNode->dims[0])==0) {
        printf("\n");
      }
    }
    printf("\n");
  }

  if((aNode = getNode(aList,"/dataset1/attribute2"))) {
    memcpy(&anIntValue,aNode->data,aNode->dSize);
    printf("%s exists and have the value %d\n",aNode->name,anIntValue);
  }

  if((aNode = getNode(aList,"/dataset1/attribute3"))) {
    memcpy(&aFloatValue,aNode->data,aNode->dSize);
    printf("%s exists and have the value %f\n",aNode->name,aFloatValue);
  }
  freeHL_NodeList(aList);
  exit(0);
  return 0; /* Never reached */
 fail:
  freeHL_NodeList(aList);
  exit(1);
  return 1; /* Never reached */
}