static int read_basic_type(const coda_cursor *cursor, void *dst)
{
int32 start[MAX_HDF4_VAR_DIMS];
int32 stride[MAX_HDF4_VAR_DIMS];
int32 edge[MAX_HDF4_VAR_DIMS];
long index;
long i;
index = cursor->stack[cursor->n - 1].index;
assert(cursor->n > 1);
switch (((coda_hdf4_type *)cursor->stack[cursor->n - 2].type)->tag)
{
case tag_hdf4_basic_type_array:
{
coda_cursor array_cursor;
char *buffer;
int native_type_size;
long num_elements;
/* we first read the whole array and then return only the requested element */
array_cursor = *cursor;
array_cursor.n--;
if (coda_cursor_get_num_elements(&array_cursor, &num_elements) != 0)
{
return -1;
}
assert(index < num_elements);
native_type_size =
get_native_type_size(((coda_hdf4_type *)cursor->stack[cursor->n - 1].type)->definition->read_type);
buffer = malloc(num_elements * native_type_size);
if (buffer == NULL)
{
coda_set_error(CODA_ERROR_OUT_OF_MEMORY, "out of memory (could not allocate %lu bytes) (%s:%u)",
(long)(num_elements * native_type_size), __FILE__, __LINE__);
return -1;
}
if (read_attribute(&array_cursor, buffer, -1) != 0)
{
free(buffer);
return -1;
}
memcpy(dst, &buffer[index * native_type_size], native_type_size);
free(buffer);
}
break;
case tag_hdf4_attributes:
case tag_hdf4_file_attributes:
if (read_attribute(cursor, dst, -1) != 0)
{
return -1;
}
break;
case tag_hdf4_GRImage:
{
coda_hdf4_GRImage *type;
stride[0] = 1;
stride[1] = 1;
edge[0] = 1;
edge[1] = 1;
type = (coda_hdf4_GRImage *)cursor->stack[cursor->n - 2].type;
if (type->ncomp != 1)
{
uint8 *buffer;
int component_size;
int component_index;
component_size = get_native_type_size(type->basic_type->definition->read_type);
/* HDF4 does not allow reading a single component of a GRImage, so we have to first read all
* components and then return only the data item that was requested */
buffer = malloc(component_size * type->ncomp);
if (buffer == NULL)
{
coda_set_error(CODA_ERROR_OUT_OF_MEMORY, "out of memory (could not allocate %lu bytes) (%s:%u)",
(long)(component_size * type->ncomp), __FILE__, __LINE__);
return -1;
}
component_index = index % type->ncomp;
index /= type->ncomp;
/* For GRImage data the first dimension is the fastest running */
start[0] = index % type->dim_sizes[0];
start[1] = index / type->dim_sizes[0];
if (GRreadimage(type->ri_id, start, stride, edge, buffer) != 0)
{
coda_set_error(CODA_ERROR_HDF4, NULL);
free(buffer);
return -1;
}
memcpy(dst, &buffer[component_index * component_size], component_size);
free(buffer);
}
else
{
/* For GRImage data the first dimension is the fastest running */
start[0] = index % type->dim_sizes[0];
start[1] = index / type->dim_sizes[0];
if (GRreadimage(type->ri_id, start, stride, edge, dst) != 0)
{
coda_set_error(CODA_ERROR_HDF4, NULL);
return -1;
}
}
}
break;
case tag_hdf4_SDS:
{
coda_hdf4_SDS *type;
type = (coda_hdf4_SDS *)cursor->stack[cursor->n - 2].type;
if (type->rank == 0)
{
start[0] = 0;
edge[1] = 1;
}
else
{
for (i = type->rank - 1; i >= 0; i--)
{
start[i] = index % type->dimsizes[i];
index /= type->dimsizes[i];
edge[i] = 1;
}
}
if (SDreaddata(type->sds_id, start, NULL, edge, dst) != 0)
{
coda_set_error(CODA_ERROR_HDF4, NULL);
return -1;
}
}
break;
case tag_hdf4_Vdata_field:
{
coda_hdf4_Vdata *type;
coda_hdf4_Vdata_field *field_type;
int record_pos;
int order_pos;
assert(cursor->n > 2);
type = (coda_hdf4_Vdata *)cursor->stack[cursor->n - 3].type;
field_type = (coda_hdf4_Vdata_field *)cursor->stack[cursor->n - 2].type;
order_pos = index % field_type->order;
record_pos = index / field_type->order;
if (VSseek(type->vdata_id, record_pos) < 0)
{
coda_set_error(CODA_ERROR_HDF4, NULL);
return -1;
}
if (VSsetfields(type->vdata_id, field_type->field_name) != 0)
{
coda_set_error(CODA_ERROR_HDF4, NULL);
return -1;
}
if (field_type->order > 1)
{
/* HDF4 does not allow reading part of a vdata field, so we have to first read the full field and
* then return only the data item that was requested */
uint8 *buffer;
int element_size;
int size;
size = VSsizeof(type->vdata_id, field_type->field_name);
if (size < 0)
{
coda_set_error(CODA_ERROR_HDF4, NULL);
return -1;
}
buffer = malloc(size);
if (buffer == NULL)
{
coda_set_error(CODA_ERROR_OUT_OF_MEMORY, "out of memory (could not allocate %lu bytes) (%s:%u)",
(long)size, __FILE__, __LINE__);
return -1;
}
if (VSread(type->vdata_id, buffer, 1, FULL_INTERLACE) < 0)
{
coda_set_error(CODA_ERROR_HDF4, NULL);
free(buffer);
return -1;
}
/* the size of a field element is the field size divided by the order of the field */
element_size = size / field_type->order;
memcpy(dst, &buffer[order_pos * element_size], element_size);
free(buffer);
}
else
{
if (VSread(type->vdata_id, (uint8 *)dst, 1, FULL_INTERLACE) < 0)
{
coda_set_error(CODA_ERROR_HDF4, NULL);
return -1;
}
}
}
break;
default:
assert(0);
exit(1);
}
return 0;
}
//// [[Rcpp::export]]
int binlist(int x) {
int numbins = 0, *binnums = NULL;
int i;
int file_id,vdata_ref, vdata_id,numrecs,pvd_id;
char PARAM[] = "chlor_a";
initbin();
/* Open the HDF file. */
file_id = Hopen("S1998001.L3b_DAY_CHL.main", DFACC_READ, 0);
if(file_id == FAIL){
fprintf(stderr,"-E- %s line %d: Hopen(%s,DFACC_READ,0) failed.\n",
__FILE__,__LINE__,"S1998001.L3b_DAY_CHL.main");
return(EXIT_FAILURE);
}
/* Initialize the Vdata interface. */
if(Vstart(file_id) == FAIL){
fprintf(stderr,"-E- %s line %d: Vstart(%d) failed.\n",
__FILE__,__LINE__,file_id);
return(EXIT_FAILURE);
}
/* Open the "BinList" Vdata. */
vdata_ref = VSfind(file_id,"BinList");
if(vdata_ref == FAIL){
fprintf(stderr,"-E- %s line %d: VSfind(%d,\"BinList\") failed.\n",
__FILE__,__LINE__,file_id);
return(EXIT_FAILURE);
}
vdata_id = VSattach(file_id, vdata_ref, "r");
if(vdata_id == FAIL){
fprintf(stderr,"-E- %s line %d: VSattach(%d,%d,\"r\") failed.\n",
__FILE__,__LINE__,file_id,vdata_ref);
return(EXIT_FAILURE);
}
/* Find out how many bins are stored in this file. */
numrecs = VSelts(vdata_id);
if(numrecs == FAIL){
fprintf(stderr,"-E- %s line %d: VSelts(%d) failed.\n",
__FILE__,__LINE__,vdata_id);
return(EXIT_FAILURE);
}
// this doesn't seem to be necessary?
/* Set up to read the fields in the BinList Vdata records. */
// if(VSsetfields(vdata_id,BLIST_FIELDS) == FAIL){
// fprintf(stderr,"-E- %s line %d: VSsetfields(%d,%s) failed.\n",
// __FILE__,__LINE__,vdata_id,BLIST_FIELDS);
// return(EXIT_FAILURE);
// }
/* Open the parameter-specific Vdata. */
vdata_ref = VSfind(file_id,PARAM);
if(vdata_ref == 0){
fprintf(stderr,"-E- %s line %d: VSfind(%d,\"%s\") failed.\n",
__FILE__,__LINE__,file_id,PARAM);
return(EXIT_FAILURE);
}
pvd_id = VSattach(file_id, vdata_ref, "r");
if(pvd_id == FAIL){
fprintf(stderr,"-E- %s line %d: VSattach(%d,%d,\"r\") failed.\n",
__FILE__,__LINE__,file_id,vdata_ref);
return(EXIT_FAILURE);
}
/* Set up to read the fields in the parameter-specific Vdata records. */
{
int len;
len = 2*strlen(PARAM) + strlen("_sum,") + strlen("_sum_sq") + 1;
param_fields = (char *)malloc(len);
if(param_fields == NULL){
fprintf(stderr,"-E- %s line %d: Memory allocation failed.\n",
__FILE__,__LINE__);
return(EXIT_FAILURE);
}
strcpy(param_fields,PARAM);
strcat(param_fields,"_sum,");
strcat(param_fields,PARAM);
strcat(param_fields,"_sum_sq");
}
if(VSsetfields(pvd_id,param_fields) == FAIL){
fprintf(stderr,"-E- %s line %d: VSsetfields(%d,%s) failed.\n",
__FILE__,__LINE__,pvd_id,param_fields);
return(EXIT_FAILURE);
}
printf(param_fields);
printf("\n");
/* Output a header record to identify the fields written out below. */
printf("%80s%15.15s %15.15s\n"," ",PARAM,PARAM);
printf(" bin centerlat centerlon");
printf(" north south west east");
printf(" n N sum_obs sum_squared_obs weight");
printf(" time_trend_bits l2_flag_bits sel\n");
printf("------- --------- ----------");
printf(" --------- --------- ---------- ----------");
printf(" ---- --- --------------- --------------- ---------------");
printf(" ---------------- -------------------------------- ---\n");
// for(i = 0; i < numbins; i++){
for(i = 0; i < 10; i++){
int recno;
// recno = binsearch(binnums[i],vdata_id,numrecs);
recno = i;
if(recno >= 0){
double n,s,w,e,clat,clon;
/*
Read the sum and sum-of-squares for the
the specified parameter for this bin.
*/
if(VSseek(pvd_id,recno) == FAIL){
fprintf(stderr,"-E- %s line %d: VSseek(%d,%d) failed.\n",
__FILE__,__LINE__,pvd_id,recno);
return(EXIT_FAILURE);
}
if(VSread(pvd_id,paramrec,1,FULL_INTERLACE) != 1){
fprintf(stderr,"-E- %s line %d: ",__FILE__,__LINE__);
fprintf(stderr,"VSread(%d,paramrec,1,FULL_INTERLACE) failed.\n",
pvd_id);
return(EXIT_FAILURE);
}
/*
VSfpack() sets the global sum and sum_sq variables
via the paramptrs pointer array.
*/
if(
VSfpack(
pvd_id,_HDF_VSUNPACK,param_fields,paramrec,PREC_SIZE,1,NULL,paramptrs
)
== FAIL){
fprintf(stderr,"-E- %s line %d: ",__FILE__,__LINE__);
fprintf(stderr,"VSfpack(%d, ...) failed.\n", pvd_id);
return(EXIT_FAILURE);
}
/* Get the geographical coordinates associated with this bin. */
// bin2latlon(binnums[i],&clat,&clon);
// bin2bounds(binnums[i],&n,&s,&w,&e);
/* Output the results. */
// printf("%7d %9.5f %10.5f %9.5f %9.5f %10.5f %10.5f ",
// binnums[i],clat,clon,n,s,w,e);
// printf("%4d %3d ",nobs,nscenes);
// printf("% .8e % .8e % .8e ",sum,sum_sq,weights);
printf("% .8e % .8e % .8e ",sum,sum_sq,0.0);
// printf("%.16s %.32s ",bitstr16(time_rec),bitstr32(flags_set));
// printf("%3d",sel_cat);
printf("\n");
}
}
if(VSdetach(pvd_id) == FAIL){
fprintf(stderr,"-E- %s line %d: VSdetach(%d) failed.\n",
__FILE__,__LINE__,pvd_id);
return(EXIT_FAILURE);
}
if(VSdetach(vdata_id) == FAIL){
fprintf(stderr,"-E- %s line %d: VSdetach(%d) failed.\n",
__FILE__,__LINE__,vdata_id);
return(EXIT_FAILURE);
}
if(Vend(file_id) == FAIL){
fprintf(stderr,"-E- %s line %d: Vend(%d) failed.\n",
__FILE__,__LINE__,file_id);
return(EXIT_FAILURE);
}
if(Hclose(file_id) == FAIL){
fprintf(stderr,"-E- %s line %d: Hclose(%d) failed.\n",
__FILE__,__LINE__,file_id);
return(EXIT_FAILURE);
}
free(param_fields);
free(binnums);
return 2;
}
static int read_array(const coda_cursor *cursor, void *dst)
{
int32 start[MAX_HDF4_VAR_DIMS];
int32 stride[MAX_HDF4_VAR_DIMS];
int32 edge[MAX_HDF4_VAR_DIMS];
long num_elements;
long i;
if (coda_hdf4_cursor_get_num_elements(cursor, &num_elements) != 0)
{
return -1;
}
if (num_elements <= 0)
{
/* no data to be read */
return 0;
}
switch (((coda_hdf4_type *)cursor->stack[cursor->n - 1].type)->tag)
{
case tag_hdf4_basic_type_array:
if (read_attribute(cursor, dst, -1) != 0)
{
return -1;
}
break;
case tag_hdf4_GRImage:
{
coda_hdf4_GRImage *type;
type = (coda_hdf4_GRImage *)cursor->stack[cursor->n - 1].type;
start[0] = 0;
start[1] = 0;
stride[0] = 1;
stride[1] = 1;
edge[0] = type->dim_sizes[0];
edge[1] = type->dim_sizes[1];
if (GRreadimage(type->ri_id, start, stride, edge, dst) != 0)
{
coda_set_error(CODA_ERROR_HDF4, NULL);
return -1;
}
}
break;
case tag_hdf4_SDS:
{
coda_hdf4_SDS *type;
type = (coda_hdf4_SDS *)cursor->stack[cursor->n - 1].type;
if (type->rank == 0)
{
start[0] = 0;
edge[0] = 1;
}
else
{
for (i = 0; i < type->rank; i++)
{
start[i] = 0;
edge[i] = type->dimsizes[i];
}
}
if (SDreaddata(type->sds_id, start, NULL, edge, dst) != 0)
{
coda_set_error(CODA_ERROR_HDF4, NULL);
return -1;
}
}
break;
case tag_hdf4_Vdata_field:
{
coda_hdf4_Vdata *type;
coda_hdf4_Vdata_field *field_type;
assert(cursor->n > 1);
type = (coda_hdf4_Vdata *)cursor->stack[cursor->n - 2].type;
field_type = (coda_hdf4_Vdata_field *)cursor->stack[cursor->n - 1].type;
if (VSseek(type->vdata_id, 0) < 0)
{
coda_set_error(CODA_ERROR_HDF4, NULL);
return -1;
}
if (VSsetfields(type->vdata_id, field_type->field_name) != 0)
{
coda_set_error(CODA_ERROR_HDF4, NULL);
return -1;
}
if (VSread(type->vdata_id, (uint8 *)dst, field_type->num_records, FULL_INTERLACE) < 0)
{
coda_set_error(CODA_ERROR_HDF4, NULL);
return -1;
}
}
break;
default:
assert(0);
exit(1);
}
return 0;
}
int main( )
{
/************************* Variable declaration **************************/
intn status_n; /* returned status for functions returning an intn */
int32 status_32, /* returned status for functions returning an int32 */
file_id, vgroup_id, vgroup_ref, vdata_id, vdata_ref,
num_of_records, num_of_vals_per_rec, record_pos,
obj_index, /* index of an object within a vgroup */
num_of_pairs, /* number of tag/ref number pairs, i.e., objects */
obj_tag, obj_ref, /* tag/ref number of an HDF object */
vgroup_pos = 0; /* position of a vgroup in the file */
float32 databuf[N_RECORDS][N_VALS_PER_REC];
int16 rec_num;
/********************** End of variable declaration ***********************/
char FIELDNAME_LIST[MAX_FIELDNAME_LIST_LENGTH];
memset(FIELDNAME_LIST, 0x00, MAX_FIELDNAME_LIST_LENGTH);
int i;
for (i = 0; i < N_VALS_PER_REC; i++) {
char buffer[256];
if (i == 0) {
sprintf(buffer, "%d", i);
} else {
sprintf(buffer, " %d", i);
}
strcat(FIELDNAME_LIST, buffer);
}
file_id = Hopen (FILE_NAME, DFACC_READ, 0);
status_n = Vstart (file_id);
vgroup_ref = -1;
vgroup_ref = Vgetid (file_id, vgroup_ref);
if (vgroup_ref == -1) exit(1);
vgroup_ref = Vgetid (file_id, vgroup_ref);
if (vgroup_ref == -1) exit(1);
vgroup_id = Vattach (file_id, vgroup_ref, "r");
num_of_pairs = Vntagrefs (vgroup_id);
if (num_of_pairs > 0)
{
printf ("\nVgroup #%d contains:\n", vgroup_pos);
for (obj_index = 0; obj_index < num_of_pairs; obj_index++)
{
status_n = Vgettagref (vgroup_id, obj_index, &obj_tag, &obj_ref);
printf ("tag = %d, ref = %d", obj_tag, obj_ref);
if (Visvg (vgroup_id, obj_ref))
printf (" <-- is a vgroup\n");
else if (Visvs (vgroup_id, obj_ref)) {
printf (" <-- is a vdata\n");
vdata_ref = VSfind (file_id, VDATA_NAME);
vdata_id = VSattach (file_id, vdata_ref, "r");
status_n = VSsetfields (vdata_id, FIELDNAME_LIST);
record_pos = VSseek (vdata_id, RECORD_INDEX);
num_of_records =
VSread (vdata_id, (uint8 *)databuf, N_RECORDS, FULL_INTERLACE);
for (rec_num = 0; rec_num < num_of_records; rec_num++)
{
for (num_of_vals_per_rec = 0; num_of_vals_per_rec < N_VALS_PER_REC; num_of_vals_per_rec++) {
printf ("%6.2f\n", databuf[rec_num][num_of_vals_per_rec]);
}
}
}
else {
printf (" <-- neither vdata nor vgroup\n");
}
} /* for */
} /* if */
else
printf ("Vgroup #%d contains no HDF objects\n", vgroup_pos);
/*
* Terminate access to the current vgroup.
*/
status_32 = Vdetach (vgroup_id);
/*
* Move to the next vgroup position.
*/
vgroup_pos++;
/*
* Terminate access to the V interface and close the file.
*/
status_n = Vend (file_id);
status_n = Hclose (file_id);
return 0;
}
