char* ossimHdf4SubDataset::getTileBuf(const ossimIrect& rect, ossim_uint32 band)
{
// bool status = false;
int32 start[H4_MAX_NC_DIMS], edges[H4_MAX_NC_DIMS];
if (m_rank == 3)
{
start[0] = band;
start[1] = rect.ul().y;
start[2] = rect.ul().x;
edges[0] = 1;
edges[1] = rect.height();
edges[2] = rect.width();
}
else if (m_rank == 2)
{
start[0] = rect.ul().y;
start[1] = rect.ul().x;
edges[0] = rect.height();
edges[1] = rect.width();
}
int32 numValues = rect.width() * rect.height();
ossim_int32 size = getDataTypeSize(m_dataType);
char* data = new char[size * numValues];
// intn statusSd = SDreaddata(m_sds_id, start, NULL, edges, (VOIDP)data);
SDreaddata(m_sds_id, start, NULL, edges, (VOIDP)data);
return data;
}
void
hdf_get_sds(
char *filename,
char *sds_name,
int *start,
int *stride,
int *edge,
void *data, /* area for input data */
int *status) /* see above */
{
int32 edge32[MAX_VAR_DIMS];
int32 i;
char name[MAX_NC_NAME];
int32 natts; /* # attributes */
int32 number_type; /* HDF type */
int32 rank;
int s; /* error status */
int32 sd_id; /* file handle */
int32 sds_id; /* SDS handle */
int32 sds_index; /* SDS index */
int32 shape32[MAX_VAR_DIMS];
int32 start32[MAX_VAR_DIMS];
int32 stride32[MAX_VAR_DIMS];
sd_id = SDstart(filename, DFACC_RDONLY);
CHECK(sd_id >= 0, 1);
sds_index = SDnametoindex(sd_id, sds_name);
CHECK(sds_index >= 0, 2);
sds_id = SDselect(sd_id, sds_index);
CHECK(sds_id >= 0, 3);
s = SDgetinfo(sds_id, name, &rank, shape32, &number_type, &natts);
CHECK(s == SUCCEED, 4);
for (i = 0; i < rank; i++) {
start32[i] = start[i];
stride32[i] = stride[i];
edge32[i] = edge[i];
}
s = SDreaddata(sds_id, start32, stride32, edge32, data);
CHECK(s == SUCCEED, 5);
s = SDend(sd_id);
CHECK(s == SUCCEED, 6);
*status = 0;
}
void
RemapHDF4::getDepthSlice(int slc,
uchar *slice)
{
int nbytes = m_width*m_height*m_bytesPerVoxel;
int32 start[2], edges[2];
start[0] = start[1] = 0;
edges[0] = m_width;
edges[1] = m_height;
int32 sd_id = SDstart(m_imageList[slc].toAscii().data(),
DFACC_READ);
int32 sds_id = SDselect(sd_id, m_Index);
int status = SDreaddata(sds_id,
start, NULL, edges,
(VOIDP)slice);
status = SDendaccess(sds_id);
status = SDend(sd_id);
}
/* Read current scan line for all bands to be processed.
Returns 0 if no errors, non-zero otherwise. */
int read_scan(int iscan, SDS sds[Nitems])
{
int ib;
for (ib = 0; ib < Nitems; ib++) {
if (sds[ib].id == -1) continue;
switch (sds[ib].rank) {
case 2: sds[ib].start[0] = iscan * sds[ib].rowsperscan; break;
case 3: sds[ib].start[1] = iscan * sds[ib].rowsperscan; break;
}
if (SDreaddata(sds[ib].id, sds[ib].start, NULL, sds[ib].edges,
sds[ib].data) == -1) {
fprintf(stderr, " Can't read scan %d of SDS \"%s\"\n", iscan, sds[ib].name);
return 1;
}
}
return 0;
}
/* Retrieve the variable values. Return success (0) if the
* variable values were obtained sucessfully, otherwise this
* function returns the failure status (-1).
*/
int cuvarget_hdf(CuFile* file, int varid, const long start[], const long count[], void* values){
int32 sds_id, i, ndims;
int32 *startvalues, *edges, natts;
int32 dim_sizes[H4_MAX_VAR_DIMS];
char name[H4_MAX_NC_NAME+1];
hdf_type dtype;
/* Get the identifier for the data set. */
sds_id = SDselect(file->internid1, varid);
/* Get the number of dimensions. */
if (SDgetinfo(sds_id, name, &ndims, dim_sizes, &dtype, &natts) == -1) {
cuerrorreport_hdf();
return (-1);
}
/* Define dimension size */
startvalues = (int32 *)malloc((ndims)*sizeof(int32));
edges = (int32 *)malloc((ndims)*sizeof(int32));
for (i = 0; i < ndims; ++i) {
startvalues[i] = start[i];
edges[i] = count[i];
}
/* Read the data array. */
if (SDreaddata(sds_id, startvalues, NULL, edges, (VOIDP)values) == -1) {
cuerrorreport_hdf();
return (-1);
}
free ((char *) startvalues);
free ((char *) edges);
/* Return success ( 0 ). */
return (CU_SUCCESS);
}
static void *var_readv(SDSVarInfo *var, void **bufp, int *index)
{
int32 start[H4_MAX_VAR_DIMS], count[H4_MAX_VAR_DIMS];
size_t bufsize = sds_type_size(var->type);
for (int i = 0; i < var->ndims; i++) {
if (index[i] < 0) {
start[i] = 0;
count[i] = (int32)var->dims[i]->size;
} else {
start[i] = (int32)index[i];
count[i] = 1;
}
bufsize *= (size_t)count[i];
}
H4Buffer *buf = prep_read_buffer(var, bufp);
h4buffer_ensure(buf, bufsize);
int status = SDreaddata(buf->sds_id, start, NULL, count, buf->data);
CHECK_HDF_ERROR(var->sds->path, status);
return buf->data;
}
static intn test_dim1_SDS2(void)
{
char sds_name[20];
float32 sds1_data[] = {0.1, 2.3, 4.5, 6.7, 8.9};
float32 sds2_data[2][3] = {{0.1, 2.3, 4.5}, {4.5, 6.7, 8.9}};
int32 dimsize[1], dimsize2[2];
int32 sds1_id, sds2_id, file_id, dim_id, index;
int32 start=0, stride=1, stat;
int32 start2[2]={0,0}, stride2[2]={1,1};
int32 scale1 [5] = {101,102,103,104,105}, scale1_out[5];
int32 num_type, array_rank, attributes;
int32 n_datasets, n_file_attrs, n_local_attrs;
float32 out_data2[2][3];
intn datanum, ranknum, status =0, i, idx, idx1, idx2;
intn num_errs = 0; /* number of errors so far */
file_id = SDstart(FILE2, DFACC_CREATE);
CHECK(file_id, FAIL, "SDstart");
dimsize[0] = 5;
dimsize2[0] = 2;
dimsize2[1] = 3;
sds1_id = SDcreate(file_id, VAR1_NAME, DFNT_FLOAT32, 1, dimsize);
CHECK(sds1_id, FAIL, "SDcreate");
/* Set the dimension name to be the same as the next dataset (not
created yet) */
dim_id = SDgetdimid(sds1_id, 0);
CHECK(dim_id, FAIL, "SDgetdimid");
status = SDsetdimname(dim_id, VAR2_NAME);
CHECK(status, FAIL, "SDsetdimname");
/* Get file info and verify that there is 1 dataset in the file */
status = SDfileinfo(file_id, &n_datasets, &n_file_attrs);
CHECK(status, FAIL, "SDfileinfo");
VERIFY(n_datasets, 1, "SDfileinfo");
/* Create and write data to the second dataset VAR2_NAME */
sds2_id = SDcreate(file_id, VAR2_NAME, DFNT_FLOAT32, 2, dimsize2);
CHECK(sds2_id, FAIL, "SDcreate");
stat = SDwritedata(sds2_id, start2, stride2, dimsize2, sds2_data);
CHECK(status, FAIL, "SDwritedata");
status = SDendaccess(sds2_id);
CHECK(status, FAIL, "SDendaccess");
/* Get file info and verify that there are 2 datasets in the file. */
status = SDfileinfo(file_id, &n_datasets, &n_file_attrs);
CHECK(status, FAIL, "SDfileinfo");
VERIFY(n_datasets, 2, "SDfileinfo");
/* Write values to the dimension VAR2_NAME (same name as VAR2_NAME) */
status = SDsetdimscale (dim_id, dimsize[0], DFNT_INT32, scale1);
CHECK(status, FAIL, "SDsetdimscale");
/* Get file info and verify that there are 3 datasets in the file:
2 SDS and 1 coordinate variable */
status = SDfileinfo(file_id, &n_datasets, &n_file_attrs);
CHECK(status, FAIL, "SDfileinfo");
VERIFY(n_datasets, 3, "SDfileinfo");
/* Close dataset and file */
status = SDendaccess(sds1_id);
CHECK(status, FAIL, "SDendaccess");
status = SDend(file_id);
CHECK(status, FAIL, "SDend");
/* Open the file again to check its data */
file_id = SDstart(FILE2, DFACC_RDWR);
CHECK(file_id, FAIL, "SDstart");
/* Verify dimension scale of the first dimension of SDS VAR1_NAME */
/* Get access to dataset VAR1_NAME */
index = SDnametoindex(file_id, VAR1_NAME);
CHECK(index, FAIL, "SDnametoindex");
sds1_id = SDselect(file_id, index);
CHECK(sds1_id, FAIL, "SDselect");
/* Get access to its first dimension */
dim_id = SDgetdimid(sds1_id, 0);
CHECK(dim_id, FAIL, "SDgetdimid");
/* Get dimension scale and verify the values */
status = SDgetdimscale (dim_id, scale1_out);
CHECK(status, FAIL, "SDgetdimscale");
for (idx = 0; idx < dimsize[0]; idx++)
if (scale1_out[idx] != scale1[idx])
{
fprintf(stderr, "Read value (%d) differs from written (%d) at [%d]\n", scale1_out[idx], scale1[idx], idx);
num_errs++;
}
/* End verifying dimension scale */
/* Verify dimension scale of the first dimension of SDS VAR1_NAME */
/* Get access to dataset VAR2_NAME */
index = SDnametoindex(file_id, VAR2_NAME);
CHECK(index, FAIL, "SDnametoindex");
sds2_id = SDselect(file_id, index);
CHECK(sds2_id, FAIL, "SDselect");
/* Get dataset's info and verify them */
status = SDgetinfo(sds2_id, sds_name, &array_rank, dimsize2,
&num_type, &n_local_attrs);
CHECK(status, FAIL, "SDgetinfo");
VERIFY(array_rank, 2, "SDfileinfo");
VERIFY(num_type, DFNT_FLOAT32, "SDfileinfo");
VERIFY(n_local_attrs, 0, "SDfileinfo");
/* Read and verify the dataset's data */
status = SDreaddata (sds2_id, start2, NULL, dimsize2, &out_data2);
CHECK(status, FAIL, "SDreaddata");
for (idx1 = 0; idx1 < dimsize2[0]; idx1++)
for (idx2 = 0; idx2 < dimsize2[1]; idx2++)
{
if (out_data2[idx1][idx2] != sds2_data[idx1][idx2])
{
fprintf(stderr, "Read value (%f) differs from written (%f) at [%d][%d]\n", out_data2[idx1][idx2], sds2_data[idx1][idx2], idx1, idx2);
num_errs++;
}
}
/* Verify again that the number of datasets in the file is 3, 2 SDSs and
1 coordinate variable */
status = SDfileinfo(file_id, &n_datasets, &n_file_attrs);
CHECK(status, FAIL, "SDfileinfo");
VERIFY(n_datasets, 3, "SDfileinfo");
status = SDendaccess(sds1_id);
CHECK(status, FAIL, "SDendaccess");
status = SDendaccess(sds2_id);
CHECK(status, FAIL, "SDendaccess");
status = SDend(file_id);
CHECK(status, FAIL, "SDend");
/* Return the number of errors that's been kept track of so far */
return num_errs;
} /* test_dim1_SDS2 */
void
RemapHDF4::generateHistogram()
{
float rSize = m_rawMax-m_rawMin;
QProgressDialog progress("Generating Histogram",
"Cancel",
0, 100,
0);
progress.setMinimumDuration(0);
int nX, nY, nZ;
nX = m_depth;
nY = m_width;
nZ = m_height;
int nbytes = nY*nZ*m_bytesPerVoxel;
uchar *tmp = new uchar[nbytes];
m_histogram.clear();
if (m_voxelType == _UChar ||
m_voxelType == _Char ||
m_voxelType == _UShort ||
m_voxelType == _Short)
{
for(uint i=0; i<rSize+1; i++)
m_histogram.append(0);
}
else
{
for(uint i=0; i<65536; i++)
m_histogram.append(0);
}
int histogramSize = m_histogram.size()-1;
int32 start[2], edges[2];
start[0] = start[1] = 0;
edges[0] = m_width;
edges[1] = m_height;
for(uint i=0; i<nX; i++)
{
progress.setValue((int)(100.0*(float)i/(float)nX));
qApp->processEvents();
int32 sd_id = SDstart(m_imageList[i].toAscii().data(),
DFACC_READ);
int32 sds_id = SDselect(sd_id, m_Index);
int status = SDreaddata(sds_id,
start, NULL, edges,
(VOIDP)tmp);
status = SDendaccess(sds_id);
status = SDend(sd_id);
if (m_voxelType == _UChar)
{
uchar *ptr = tmp;
GENHISTOGRAM();
}
else if (m_voxelType == _Char)
{
char *ptr = (char*) tmp;
GENHISTOGRAM();
}
if (m_voxelType == _UShort)
{
ushort *ptr = (ushort*) tmp;
GENHISTOGRAM();
}
else if (m_voxelType == _Short)
{
short *ptr = (short*) tmp;
GENHISTOGRAM();
}
else if (m_voxelType == _Int)
{
int *ptr = (int*) tmp;
GENHISTOGRAM();
}
else if (m_voxelType == _Float)
{
float *ptr = (float*) tmp;
GENHISTOGRAM();
}
}
delete [] tmp;
while(m_histogram.last() == 0)
m_histogram.removeLast();
while(m_histogram.first() == 0)
m_histogram.removeFirst();
progress.setValue(100);
qApp->processEvents();
}
int main(int ac, char **av)
{
char input_file_path[256], output_file_path[256];
char hdf4sds_name[256], hdf4sds_attr_name[256];
char hdf4sds_str_attr_buff[256];
int hdf4sd_id, hdf4access_mode, hdf4status, hdf4n_datasets, hdf4n_file_attrs,
hdf4sds_id, hdf4sds_index, hdf4sds_rank, hdf4sds_data_type,
hdf4sds_n_attrs, hdf4sds_attr_data_type, hdf4sds_attr_n_values,
hdf4sds_num_elements;
int hdf4sds_dim_sizes[8], hdf4sds_read_start[8], hdf4sds_read_stride[8];
float *hdf4sds_flt_buff;
hid_t hdf5file_id, hdf5dataset_id, hdf5space_id, hdf5attr_id,
hdf5attr_space_id, hdf5str_type;
herr_t hdf5status;
hsize_t hdf5dataset_dims[8], hdf5attr_size;
/* Get input file name from the command line, and create output file name */
if (ac < 2) {
fprintf(stderr, "Usage is: hdf4tohdf5 inputfile outputfile\n");
fprintf(stderr, "If no output file is given, inputfile.h5 will be produced.\n");
return 1;
}
strcpy(input_file_path, av[1]);
if (ac > 2) {
strcpy(output_file_path, av[2]);
} else {
strcpy(output_file_path, input_file_path);
strcat(output_file_path, ".h5");
}
/* Open hdf4 file */
hdf4access_mode = DFACC_READ;
hdf4sd_id = SDstart(input_file_path, hdf4access_mode);
hdf4status = SDfileinfo(hdf4sd_id, &hdf4n_datasets, &hdf4n_file_attrs);
if (hdf4status == FAIL) {
fprintf(stderr, "Reading hdf4 file failed. Returning.\n");
return 1;
}
#ifdef DEBUG
printf("Id: %i, Datasets: %i, File_attrs: %i\n", hdf4sd_id, hdf4n_datasets,
hdf4n_file_attrs);
#endif
/* Open hdf5 file */
hdf5file_id = H5Fcreate(output_file_path, H5F_ACC_TRUNC, H5P_DEFAULT,
H5P_DEFAULT);
if (hdf5file_id < 0) {
fprintf(stderr, "Failed to open HDF5 file %s for writing.\n",
output_file_path);
return 1;
}
/* Loop through datasets */
for(hdf4sds_index = 0; hdf4sds_index < hdf4n_datasets; hdf4sds_index++) {
hdf4sds_id = SDselect(hdf4sd_id, hdf4sds_index);
hdf4status = SDgetinfo(hdf4sds_id, hdf4sds_name, &hdf4sds_rank,
hdf4sds_dim_sizes, &hdf4sds_data_type,
&hdf4sds_n_attrs);
#ifdef DEBUG
printf("\nsds_id: %i, sds_name: %s, sds_rank: %i, sds_data_type: %i,\nn_attrs_: %i, dim_sizes: %i %i %i\n", hdf4sds_id, hdf4sds_name, hdf4sds_rank, hdf4sds_data_type, hdf4sds_n_attrs, hdf4sds_dim_sizes[0], hdf4sds_dim_sizes[1], hdf4sds_dim_sizes[2]);
#endif
/* Get data from SDS into buffer */
hdf4sds_num_elements = hdf4sds_dim_sizes[0];
hdf4sds_read_start[0] = 0;
hdf4sds_read_stride[0] = 1;
if (hdf4sds_rank > 1){
for(int i=1; i < hdf4sds_rank; i++) {
hdf4sds_num_elements = hdf4sds_num_elements*hdf4sds_dim_sizes[i];
hdf4sds_read_start[i] = 0;
hdf4sds_read_stride[i] = 1;
}
}
#ifdef DEBUG
printf("Total number of elements for this sds: %i\n",
hdf4sds_num_elements);
#endif
/* Allocate the buffer to read in the data */
hdf4sds_flt_buff = malloc((sizeof (float))*hdf4sds_num_elements);
hdf4status = SDreaddata(hdf4sds_id, hdf4sds_read_start,
hdf4sds_read_stride, hdf4sds_dim_sizes,
(VOIDP)hdf4sds_flt_buff);
/* Have all of the data from the hdf4 file,
now need to load it into hdf5 */
for (int i=0; i < hdf4sds_rank; i++) {
hdf5dataset_dims[i] = (hsize_t)hdf4sds_dim_sizes[i];
}
hdf5space_id = H5Screate_simple(hdf4sds_rank, hdf5dataset_dims,
hdf5dataset_dims);
if (hdf4sds_data_type == 5) { //Floats
hdf5dataset_id = H5Dcreate(hdf5file_id, hdf4sds_name, H5T_IEEE_F32LE,
hdf5space_id, H5P_DEFAULT);
hdf5status = H5Dwrite(hdf5dataset_id, H5T_IEEE_F32LE, H5S_ALL, H5S_ALL,
H5P_DEFAULT, hdf4sds_flt_buff);
/* We've finished reading in the data. Free the hdf4 data buffer. */
free(hdf4sds_flt_buff);
/*Assign the HDF5 attributes */
for(int i=0; i < hdf4sds_n_attrs; i++) {
hdf4status = SDattrinfo(hdf4sds_id, i, hdf4sds_attr_name,
&hdf4sds_attr_data_type, &hdf4sds_attr_n_values);
#ifdef DEBUG
printf("Attribute %i: Name = %s, Data type = %i, N_values = %i\n",
i, hdf4sds_attr_name, hdf4sds_attr_data_type,
hdf4sds_attr_n_values);
#endif
if(hdf4sds_attr_data_type == 4) { /* Read the string attributes */
hdf4status = SDreadattr(hdf4sds_id, i, (VOIDP)hdf4sds_str_attr_buff);
hdf4sds_str_attr_buff[hdf4sds_attr_n_values]='\0';
#ifdef DEBUG
printf("Value: %s\n", hdf4sds_str_attr_buff);
#endif
hdf5attr_size = (hsize_t)hdf4sds_attr_n_values;
hdf5attr_space_id = H5Screate(H5S_SCALAR);
hdf5str_type = H5Tcopy(H5T_C_S1);
hdf5status = H5Tset_size(hdf5str_type,
(size_t)hdf4sds_attr_n_values);
hdf5attr_id = H5Acreate(hdf5dataset_id, hdf4sds_attr_name,
hdf5str_type, hdf5attr_space_id,
H5P_DEFAULT);
hdf5status = H5Awrite(hdf5attr_id, hdf5str_type,
hdf4sds_str_attr_buff);
hdf5status = H5Aclose(hdf5attr_id);
}
}
hdf5status = H5Dclose(hdf5dataset_id);
}
hdf5status = H5Sclose(hdf5space_id);
hdf4status = SDendaccess(hdf4sds_id);
}
/* Close access to hdf4 file */
hdf4status = SDend(hdf4sd_id);
/* Close access to HDF5 file */
hdf5status = H5Fclose(hdf5file_id);
return 0;
}
void
RemapHDF4::findMinMax()
{
QProgressDialog progress("Finding Min and Max",
"Cancel",
0, 100,
0);
progress.setMinimumDuration(0);
int nX, nY, nZ;
nX = m_depth;
nY = m_width;
nZ = m_height;
int nbytes = nY*nZ*m_bytesPerVoxel;
uchar *tmp = new uchar[nbytes];
m_rawMin = 10000000;
m_rawMax = -10000000;
int32 start[2], edges[2];
start[0] = start[1] = 0;
edges[0] = m_width;
edges[1] = m_height;
for(uint i=0; i<m_depth; i++)
{
progress.setValue((int)(100.0*(float)i/(float)nX));
qApp->processEvents();
int32 sd_id = SDstart(m_imageList[i].toAscii().data(),
DFACC_READ);
int32 sds_id = SDselect(sd_id, m_Index);
int status = SDreaddata(sds_id,
start, NULL, edges,
(void*)tmp);
status = SDendaccess(sds_id);
status = SDend(sd_id);
if (m_voxelType == _UChar)
{
uchar *ptr = tmp;
FINDMINMAX();
}
else if (m_voxelType == _Char)
{
char *ptr = (char*) tmp;
FINDMINMAX();
}
if (m_voxelType == _UShort)
{
ushort *ptr = (ushort*) tmp;
FINDMINMAX();
}
else if (m_voxelType == _Short)
{
short *ptr = (short*) tmp;
FINDMINMAX();
}
else if (m_voxelType == _Int)
{
int *ptr = (int*) tmp;
FINDMINMAX();
}
else if (m_voxelType == _Float)
{
float *ptr = (float*) tmp;
FINDMINMAX();
}
}
delete [] tmp;
progress.setValue(100);
qApp->processEvents();
}
/* Test SDSs with unlimited dimensions. This routine creates SDSs with
unlimited dimensions, writes data to it, and checks the sizes returned
by SDgetdatasize
*/
static intn test_extend_SDSs(int32 fid)
{
int32 sds_id, sds_index;
int32 dimsize[2], start[2], edges[2];
int32 dimsize1[1], start1[1], edges1[1];
int32 data[Y_LENGTH][X_LENGTH];
float fdata[Y_LENGTH];
int32 output[Y_LENGTH][X_LENGTH];
intn status;
int i, j;
int num_errs = 0; /* number of errors so far */
/* Initialize data for the dataset */
for (j = 0; j < Y_LENGTH; j++) {
for (i = 0; i < X_LENGTH; i++)
data[j][i] = (i + j) + 1;
}
/* Create a 2x2 dataset called "EmptyDataset" */
dimsize[0] = SD_UNLIMITED;
dimsize[1] = X_LENGTH;
sds_id = SDcreate(fid, "AppendableDataset 1", DFNT_INT32, 2, dimsize);
CHECK(sds_id, FAIL, "test_extend_SDSs: SDcreate 'AppendableDataset 1'");
/* Write the stored data to the dataset */
start[0] = start[1] = 0;
edges[0] = Y_LENGTH;
edges[1] = X_LENGTH;
status = SDwritedata(sds_id, start, NULL, edges, (VOIDP)data);
CHECK(sds_id, FAIL, "test_extend_SDSs: SDwritedata");
/* Check data. */
HDmemset(&output, 0, sizeof(output));
status = SDreaddata(sds_id, start, NULL, edges, (VOIDP)output);
CHECK(sds_id, FAIL, "test_extend_SDSs: SDreaddata");
/* Initialize data for the dataset */
for (j = 0; j < Y_LENGTH; j++)
for (i = 0; i < X_LENGTH; i++)
if (output[j][i] != data[j][i])
fprintf(stderr, "Read value (%d) differs from written (%d) at [%d,%d]\n", output[j][i], data[j][i], j, i);
/* Close this SDS */
status = SDendaccess(sds_id);
CHECK(status, FAIL, "test_extend_SDSs: SDendaccess");
/* Check that this SDS is empty */
check_datasizes(fid, "AppendableDataset 1", Y_LENGTH*X_LENGTH*SIZE_INT32, Y_LENGTH*X_LENGTH*SIZE_INT32, &num_errs);
/* Create another dataset with 1 unlimited dimension */
sds_id = SDcreate(fid, "AppendableDataset 2", DFNT_FLOAT64, 1, dimsize);
CHECK(sds_id, FAIL, "test_extend_SDSs: SDcreate 'AppendableDataset 2'");
/* Define the location and size of the data to be written to the dataset */
start1[0] = 0;
edges1[0] = Y_LENGTH;
/* Write the stored data to the dataset */
status = SDwritedata(sds_id, start1, NULL, edges1, (VOIDP)fdata);
CHECK(sds_id, FAIL, "test_extend_SDSs: SDwritedata");
/* Close this SDS */
status = SDendaccess(sds_id);
CHECK(status, FAIL, "test_extend_SDSs: SDendaccess");
/* Check the size of the data of this SDS */
check_datasizes(fid, "AppendableDataset 2", Y_LENGTH*SIZE_FLOAT64, Y_LENGTH*SIZE_FLOAT64, &num_errs);
/* Return the number of errors that's been kept track of so far */
return num_errs;
} /* test_extend_SDSs */
static intn test_szip_chunk_3d()
{
/************************* Variable declaration **************************/
int32 sd_id, sds_id0, sds_id, sds_index;
intn status;
int32 dim_sizes[3];
HDF_CHUNK_DEF c_def; /* Chunking definitions */
HDF_CHUNK_DEF c_def_out; /* Chunking definitions */
int32 c_flags, c_flags_out;
int32 start[3], edges[3];
int16 fill_value = 0; /* Fill value */
comp_coder_t comp_type; /* to retrieve compression type into */
comp_info cinfo; /* compression information structure */
int num_errs = 0; /* number of errors so far */
int i,j,k;
for (i = 0; i < SDS_DIM0; i++) {
for (j = 0; j < SDS_DIM1; j++) {
for (k = 0; k < SDS_DIM2; k++) {
out_data[i][j][k] = i*100+j*10+k;
}}}
/* Initialize chunk lengths. */
c_def.comp.chunk_lengths[0] = CHK_DIM0;
c_def.comp.chunk_lengths[1] = CHK_DIM1;
c_def.comp.chunk_lengths[2] = CHK_DIM2;
/* Create the file and initialize SD interface. */
sd_id = SDstart (FILE_NAME_3D, DFACC_CREATE);
CHECK(sd_id, FAIL, "SDstart");
/* Create SDS_DIM0xSDS_DIM1 SDS. */
dim_sizes[0] = SDS_DIM0;
dim_sizes[1] = SDS_DIM1;
dim_sizes[2] = SDS_DIM2;
sds_id = SDcreate (sd_id, SDS_NAME_CH3D, DFNT_INT16, RANK_CH3, dim_sizes);
CHECK(sds_id, FAIL, "SDcreate:Failed to create a data set for chunking/szip compression testing");
/* Create a similar SDS and will make it chunked, but will not
write data to it */
sds_id0 = SDcreate (sd_id, SDS_NAME_CH0, DFNT_INT16, RANK_CH3, dim_sizes);
CHECK(sds_id0, FAIL, "SDcreate:Failed to create a data set for chunking/szip compression testing");
/* Fill the SDS array with the fill value. */
status = SDsetfillvalue (sds_id, (VOIDP)&fill_value);
CHECK(status, FAIL, "SDsetfillvalue");
/* Set parameters for Chunking/SZIP */
c_def.comp.comp_type = COMP_CODE_SZIP;
c_def.comp.cinfo.szip.pixels_per_block = 2;
c_def.comp.cinfo.szip.options_mask = SZ_EC_OPTION_MASK;
c_def.comp.cinfo.szip.options_mask |= SZ_MSB_OPTION_MASK;
c_def.comp.cinfo.szip.bits_per_pixel = 2;
c_def.comp.cinfo.szip.pixels = 16;
c_def.comp.cinfo.szip.pixels_per_scanline = 2;
c_flags = HDF_CHUNK | HDF_COMP;
status = SDsetchunk (sds_id0, c_def, c_flags);
status = SDsetchunk (sds_id, c_def, c_flags);
CHECK(status, FAIL, "SDsetchunk");
start[0] = 0;
start[1] = 0;
start[2] = 0;
edges[0] = SDS_DIM0;
edges[1] = SDS_DIM1;
edges[2] = SDS_DIM2;
status = SDwritedata (sds_id, start, NULL, edges, (VOIDP) out_data);
CHECK(status, FAIL, "SDwritedata");
HDmemset(&c_def_out, 0, sizeof(HDF_CHUNK_DEF));
c_flags_out = 0;
status = SDgetchunkinfo(sds_id0, &c_def_out, &c_flags_out);
CHECK(status, FAIL, "SDgetchunkinfo");
VERIFY(c_flags_out, c_flags, "SDgetchunkinfo");
VERIFY(c_def_out.comp.comp_type, COMP_CODE_SZIP, "SDgetchunkinfo");
HDmemset(&c_def_out, 0, sizeof(HDF_CHUNK_DEF));
c_flags_out = 0;
status = SDgetchunkinfo(sds_id, &c_def_out, &c_flags_out);
CHECK(status, FAIL, "SDgetchunkinfo");
VERIFY(c_flags_out, c_flags, "SDgetchunkinfo");
VERIFY(c_def_out.comp.comp_type, COMP_CODE_SZIP, "SDgetchunkinfo");
/* Terminate access to the data sets. */
status = SDendaccess (sds_id0);
CHECK(status, FAIL, "SDendaccess");
status = SDendaccess (sds_id);
CHECK(status, FAIL, "SDendaccess");
/* Terminate access to the SD interface and close the file. */
status = SDend (sd_id);
CHECK(status, FAIL, "SDend");
/*
* Verify the compressed data
*/
/* Reopen the file and access the first data set. */
sd_id = SDstart (FILE_NAME_3D, DFACC_READ);
sds_index = 0;
sds_id = SDselect (sd_id, sds_index);
CHECK(sds_id, FAIL, "SDselect:Failed to select a data set for chunking/szip compression testing");
/* Retrieve compression information about the dataset */
comp_type = COMP_CODE_INVALID; /* reset variables before retrieving info */
HDmemset(&cinfo, 0, sizeof(cinfo)) ;
status = SDgetcompinfo(sds_id, &comp_type, &cinfo);
CHECK(status, FAIL, "SDgetcompinfo");
VERIFY(comp_type, COMP_CODE_SZIP, "SDgetcompinfo");
/* Retrieve compression method alone from the dataset */
comp_type = COMP_CODE_INVALID; /* reset variables before retrieving info */
status = SDgetcomptype(sds_id, &comp_type);
CHECK(status, FAIL, "SDgetcomptype");
VERIFY(comp_type, COMP_CODE_SZIP, "SDgetcomptype");
start[0] = 0;
start[1] = 0;
start[2] = 0;
edges[0] = SDS_DIM0;
edges[1] = SDS_DIM1;
edges[2] = SDS_DIM2;
status = SDreaddata (sds_id, start, NULL, edges, (VOIDP)all_data);
CHECK(status, FAIL, "SDreaddata");
for (i = 0; i < SDS_DIM0; i++) {
for (j = 0; j < SDS_DIM1; j++) {
for (k = 0; k < SDS_DIM2; k++) {
if (out_data[i][j][k] != all_data[i][j][k])
{
fprintf(stderr,"Bogus val in loc [%d][%d][%d] want %ld got %ld\n", i, j,k, out_data[i][j][k], all_data[i][j][k]);
num_errs++;
}
}
}
}
/* Terminate access to the data set. */
status = SDendaccess (sds_id);
CHECK(status, FAIL, "SDendaccess");
/* Terminate access to the SD interface and close the file. */
status = SDend (sd_id);
CHECK(status, FAIL, "SDend");
/* Return the number of errors that's been kept track of so far */
return num_errs;
} /* test_szip_chunk_3D */
QImage
RemapHDF4::getHeightSliceImage(int slc)
{
if (m_image)
delete [] m_image;
m_image = new uchar[m_depth*m_width];
int nbytes = m_depth*m_width*m_bytesPerVoxel;
uchar *tmp = new uchar[nbytes];
uchar *hdftmp = new uchar[m_width*m_bytesPerVoxel];
int32 start[2], edges[2];
start[0] = slc;
start[1] = 0;
edges[0] = m_width;
edges[1] = 1;
for(uint i=0; i<m_depth; i++)
{
int32 sd_id = SDstart(m_imageList[i].toAscii().data(),
DFACC_READ);
int32 sds_id = SDselect(sd_id, m_Index);
int status = SDreaddata(sds_id,
start, NULL, edges,
(VOIDP)hdftmp);
status = SDendaccess(sds_id);
status = SDend(sd_id);
for(uint j=0; j<m_width; j++)
tmp[i*m_width+j] = hdftmp[j];
}
int rawSize = m_rawMap.size()-1;
for(uint i=0; i<m_depth*m_width; i++)
{
int idx = m_rawMap.size()-1;
float frc = 0;
float v;
if (m_voxelType == _UChar)
v = ((uchar *)tmp)[i];
else if (m_voxelType == _Char)
v = ((char *)tmp)[i];
else if (m_voxelType == _UShort)
v = ((ushort *)tmp)[i];
else if (m_voxelType == _Short)
v = ((short *)tmp)[i];
else if (m_voxelType == _Int)
v = ((int *)tmp)[i];
else if (m_voxelType == _Float)
v = ((float *)tmp)[i];
if (v < m_rawMap[0])
{
idx = 0;
frc = 0;
}
else if (v > m_rawMap[rawSize])
{
idx = rawSize-1;
frc = 1;
}
else
{
for(uint m=0; m<rawSize; m++)
{
if (v >= m_rawMap[m] &&
v <= m_rawMap[m+1])
{
idx = m;
frc = ((float)v-(float)m_rawMap[m])/
((float)m_rawMap[m+1]-(float)m_rawMap[m]);
}
}
}
uchar pv = m_pvlMap[idx] + frc*(m_pvlMap[idx+1]-m_pvlMap[idx]);
m_image[i] = pv;
}
QImage img = QImage(m_image, m_width, m_depth, m_width, QImage::Format_Indexed8);
delete [] tmp;
return img;
}
static intn test_szip_SDSfl64bit()
{
/************************* Variable declaration **************************/
int32 sd_id, sds_id;
intn status;
int32 dim_sizes[2], array_rank, num_type, attributes;
char name[H4_MAX_NC_NAME];
comp_info c_info;
int32 start[2], edges[2];
float64 fill_value = 0; /* Fill value */
int i,j;
int num_errs = 0; /* number of errors so far */
float64 out_data[LENGTH][WIDTH];
float64 in_data[LENGTH][WIDTH]={
100.0,100.0,200.0,200.0,300.0,400.0,
100.0,100.0,200.0,200.0,300.0,400.0,
100.0,100.0,200.0,200.0,300.0,400.0,
300.0,300.0, 0.0,400.0,300.0,400.0,
300.0,300.0, 0.0,400.0,300.0,400.0,
300.0,300.0, 0.0,400.0,300.0,400.0,
0.0, 0.0,600.0,600.0,300.0,400.0,
500.0,500.0,600.0,600.0,300.0,400.0,
0.0, 0.0,600.0,600.0,300.0,400.0};
/********************* End of variable declaration ***********************/
/* Create the file and initialize SD interface */
sd_id = SDstart (FILE_NAMEfl64, DFACC_CREATE);
CHECK(sd_id, FAIL, "SDstart");
/* Create the SDS */
dim_sizes[0] = LENGTH;
dim_sizes[1] = WIDTH;
sds_id = SDcreate (sd_id, SDS_NAME, DFNT_FLOAT64, RANK, dim_sizes);
CHECK(sds_id, FAIL, "SDcreate:Failed to create a data set for szip compression testing");
/* Define the location, pattern, and size of the data set */
for (i = 0; i < RANK; i++) {
start[i] = 0;
edges[i] = dim_sizes[i];
}
/* Fill the SDS array with the fill value */
status = SDsetfillvalue (sds_id, (VOIDP)&fill_value);
CHECK(status, FAIL, "SDsetfillvalue");
/* Initialization for SZIP */
c_info.szip.pixels_per_block = 2;
c_info.szip.options_mask = SZ_EC_OPTION_MASK;
c_info.szip.options_mask |= SZ_RAW_OPTION_MASK;
c_info.szip.bits_per_pixel = 0;
c_info.szip.pixels = 0;
c_info.szip.pixels_per_scanline = 0;
/* Set the compression */
status = SDsetcompress (sds_id, COMP_CODE_SZIP, &c_info);
CHECK(status, FAIL, "SDsetcompress");
/* Write data to the SDS */
status = SDwritedata(sds_id, start, NULL, edges, (VOIDP)in_data);
CHECK(status, FAIL, "SDwritedata");
/* Terminate access to the data set */
status = SDendaccess (sds_id);
CHECK(status, FAIL, "SDendaccess");
/* Terminate access to the SD interface and close the file to
flush the compressed info to the file */
status = SDend (sd_id);
CHECK(status, FAIL, "SDend");
/*
* Verify the compressed data
*/
/* Reopen the file and select the first SDS */
sd_id = SDstart (FILE_NAMEfl64, DFACC_READ);
CHECK(sd_id, FAIL, "SDstart");
sds_id = SDselect (sd_id, 0);
CHECK(sds_id, FAIL, "SDselect:Failed to select a data set for szip compression testing");
/* Retrieve information of the data set */
status = SDgetinfo(sds_id, name, &array_rank, dim_sizes, &num_type, &attributes);
CHECK(status, FAIL, "SDgetinfo");
/* Wipe out the output buffer */
HDmemset(&out_data, 0, sizeof(out_data));
/* Read the data set */
start[0] = 0;
start[1] = 0;
edges[0] = LENGTH;
edges[1] = WIDTH;
status = SDreaddata (sds_id, start, NULL, edges, (VOIDP)out_data);
CHECK(status, FAIL, "SDreaddata");
/* Compare read data against input data */
for (j=0; j<LENGTH; j++)
{
for (i=0; i<WIDTH; i++)
if (out_data[j][i] != in_data[j][i])
{
fprintf(stderr,"Bogus val in loc [%d][%d] in compressed dset, want %ld got %ld\n", j, i, (long)in_data[j][i], (long)out_data[j][i]);
num_errs++;
}
}
/* Terminate access to the data set */
status = SDendaccess (sds_id);
CHECK(status, FAIL, "SDendaccess");
/* Terminate access to the SD interface and close the file */
status = SDend (sd_id);
CHECK(status, FAIL, "SDend");
/* Return the number of errors that's been kept track of so far */
return num_errs;
} /* test_szip_SDSfl64bit */
static intn test_dim1_SDS1(void)
{
char sds_name[20];
float32 sds1_data[] = {0.1, 2.3, 4.5, 6.7, 8.9};
float32 out_data[5];
int32 dimsize[1];
int32 sds_id, file_id, dim_id, index;
int32 start=0, stride=1;
int32 scale1 [5] = {101,102,103,104,105}, scale1_out[5];
int32 num_type, array_rank, count;
int32 n_datasets, n_file_attrs, n_local_attrs, n_vars = 0;
intn datanum, ranknum, status =0, i, idx, idx1, idx2;
hdf_varlist_t* var_list;
intn is_coord = FALSE;
char attr_name[H4_MAX_NC_NAME], attr_values[80];
intn num_errs = 0; /* number of errors so far */
file_id = SDstart(FILE1, DFACC_CREATE);
CHECK(file_id, FAIL, "SDstart");
/* Create a one-dim dataset named VAR1_NAME, of type DFNT_FLOAT32. */
dimsize[0] = 5;
sds_id = SDcreate(file_id, VAR1_NAME, DFNT_FLOAT32, 1, dimsize);
CHECK(sds_id, FAIL, "SDcreate");
/* Set the dimension name to be the same as its dataset. */
dim_id = SDgetdimid(sds_id, 0);
CHECK(dim_id, FAIL, "SDgetdimid");
status = SDsetdimname(dim_id, VAR1_NAME);
/* status = SDsetdimname(dim_id, VAR1_NAME);
*/
CHECK(status, FAIL, "SDsetdimname");
/* Get file info and verify that there is 1 dataset in the file. */
status = SDfileinfo(file_id, &n_datasets, &n_file_attrs);
CHECK(status, FAIL, "SDfileinfo");
VERIFY(n_datasets, 1, "SDfileinfo");
/* Set an attribute to dimension VAR1_NAME. */
status = SDsetattr(dim_id, ATTR1_NAME, DFNT_CHAR8, ATTR1_LEN, ATTR1_VAL);
CHECK(status, FAIL, "SDsetattr");
/* Set an attribute to dataset VAR1_NAME. */
status = SDsetattr(sds_id, ATTR2_NAME, DFNT_CHAR8, ATTR2_LEN, ATTR2_VAL);
CHECK(status, FAIL, "SDsetattr");
/* Get file info and verify that there are 2 datasets in the file:
1 SDS and 1 coordinate variable (because of SDsetattr dim) */
status = SDfileinfo(file_id, &n_datasets, &n_file_attrs);
CHECK(status, FAIL, "SDfileinfo");
VERIFY(n_datasets, 2, "SDfileinfo");
/* Write data to the SDS */
status = SDwritedata(sds_id, &start, &stride, dimsize, (VOIDP)sds1_data);
CHECK(status, FAIL, "SDwritedata");
/* Close dataset and file. */
status = SDendaccess(sds_id);
CHECK(status, FAIL, "SDendaccess");
status = SDend(file_id);
CHECK(status, FAIL, "SDend");
/* Open the file again to check its data */
file_id = SDstart(FILE1, DFACC_RDWR);
CHECK(file_id, FAIL, "SDstart");
/* Check variable type and attributes of each element in the file */
/* Get the number of variables of name VAR1_NAME */
status = SDgetnumvars_byname(file_id, VAR1_NAME, &n_vars);
if (n_vars == 1)
{
/* Get index of dataset VAR1_NAME */
index = SDnametoindex(file_id, VAR1_NAME);
CHECK(index, FAIL, "SDnametoindex");
}
else
{
/* Get the list of all variables of named VAR1_NAME */
var_list = (hdf_varlist_t *)HDmalloc(n_vars * sizeof(hdf_varlist_t));
status = SDnametoindices(file_id, VAR1_NAME, var_list);
/* In this case, the first variable is a dataset */
for (idx = 0; idx < n_vars; idx++)
{
if (var_list[idx].var_type == IS_SDSVAR)
{
index = var_list[idx].var_index;
VERIFY(index, 0, "SDnametoindices");
}
}
}
sds_id = SDselect(file_id, index);
CHECK(sds_id, FAIL, "SDselect");
/* Verify that this variable is a dataset. */
is_coord = SDiscoordvar(sds_id);
VERIFY(is_coord, FALSE, "SDiscoordvar");
/* Read and verify the information of the SDS' first attribute. */
status = SDattrinfo(sds_id, 0, attr_name, &num_type, &count);
CHECK(status, FAIL, "SDattrinfo");
VERIFY(count, ATTR2_LEN, "SDattrinfo");
VERIFY(HDstrncmp(attr_name, ATTR2_NAME, 14), 0, "SDattrinfo");
/* Read and verify the values of the SDS' first attribute. */
status = SDreadattr(sds_id, 0, attr_values);
CHECK(status, FAIL, "SDreadattr");
if (HDstrncmp(attr_values, ATTR2_VAL, ATTR2_LEN) != 0)
{
fprintf(stderr, "Unmatched attribute values for SDS %s: is <%s>, should be <%s>\n", VAR1_NAME, attr_values, ATTR2_VAL);
num_errs++;
}
/* Get access to the SDS' first dimension. */
dim_id = SDgetdimid(sds_id, 0);
CHECK(dim_id, FAIL, "SDgetdimid");
/* Read and verify the information of the dimension's first attribute. */
status = SDattrinfo(dim_id, 0, attr_name, &num_type, &count);
CHECK(status, FAIL, "SDattrinfo");
VERIFY(count, 19, "SDattrinfo");
VERIFY(HDstrncmp(attr_name, ATTR1_NAME, 21), 0, "SDattrinfo");
/* Read and verify the values of the dimension's first attribute. */
status = SDreadattr(dim_id, 0, attr_values);
CHECK(status, FAIL, "SDreadattr");
if (HDstrncmp(attr_values, ATTR1_VAL, ATTR1_LEN) != 0)
{
fprintf(stderr, "Unmatched attribute values for dimension %s: is <%s>, should be <%s>\n", VAR1_NAME, attr_values, ATTR1_VAL);
num_errs++;
}
/* Verify again that the number of datasets in the file is 2, 1 SDS and
1 coordinate variable */
status = SDfileinfo(file_id, &n_datasets, &n_file_attrs);
CHECK(status, FAIL, "SDfileinfo");
VERIFY(n_datasets, 2, "SDfileinfo");
VERIFY(n_file_attrs, 0, "SDfileinfo");
/* Read and verify the dataset's data */
status = SDreaddata (sds_id, &start, NULL, dimsize, &out_data);
CHECK(status, FAIL, "SDreaddata");
for (idx1 = 0; idx1 < dimsize[0]; idx1++)
if (out_data[idx1] != sds1_data[idx1])
{
fprintf(stderr, "Read value (%f) differs from written (%f) at [%d]\n", out_data[idx1], sds1_data[idx1], idx1);
num_errs++;
}
/* Close dataset and file. */
status = SDendaccess(sds_id);
CHECK(status, FAIL, "SDendaccess");
status = SDend(file_id);
CHECK(status, FAIL, "SDend");
/* Return the number of errors that's been kept track of so far */
return num_errs;
} /* test_dim1_SDS1 */
QPair<QVariant, QVariant>
RemapHDF4::rawValue(int d, int w, int h)
{
QPair<QVariant, QVariant> pair;
if (d < 0 || d >= m_depth ||
w < 0 || w >= m_width ||
h < 0 || h >= m_height)
{
pair.first = QVariant("OutOfBounds");
pair.second = QVariant("OutOfBounds");
return pair;
}
uchar *hdftmp = new uchar[m_bytesPerVoxel];
int32 start[2], edges[2];
start[0] = w;
start[1] = h;
edges[0] = 1;
edges[1] = 1;
int32 sd_id = SDstart(m_imageList[d].toAscii().data(),
DFACC_READ);
int32 sds_id = SDselect(sd_id, m_Index);
int status = SDreaddata(sds_id,
start, NULL, edges,
(VOIDP)hdftmp);
if (status == -1)
QMessageBox::information(0, "error", "Cannot read");
status = SDendaccess(sds_id);
status = SDend(sd_id);
QVariant v;
if (m_voxelType == _UChar)
{
uchar *aptr = (uchar*) hdftmp;
uchar a = *aptr;
v = QVariant((uint)a);
}
else if (m_voxelType == _Char)
{
char *aptr = (char*) hdftmp;
char a = *aptr;
v = QVariant((int)a);
}
else if (m_voxelType == _UShort)
{
ushort *aptr = (ushort*) hdftmp;
ushort a = *aptr;
v = QVariant((uint)a);
}
else if (m_voxelType == _Short)
{
short *aptr = (short*) hdftmp;
short a = *aptr;
v = QVariant((int)a);
}
else if (m_voxelType == _Int)
{
int *aptr = (int*) hdftmp;
int a = *aptr;
v = QVariant((int)a);
}
else if (m_voxelType == _Float)
{
float *aptr = (float*) hdftmp;
double a = *aptr;
v = QVariant((double)a);
}
int rawSize = m_rawMap.size()-1;
int idx = rawSize;
float frc = 0;
float val;
if (v.type() == QVariant::UInt)
val = v.toUInt();
else if (v.type() == QVariant::Int)
val = v.toInt();
else if (v.type() == QVariant::Double)
val = v.toDouble();
if (val <= m_rawMap[0])
{
idx = 0;
frc = 0;
}
else if (val >= m_rawMap[rawSize])
{
idx = rawSize-1;
frc = 1;
}
else
{
for(uint m=0; m<rawSize; m++)
{
if (val >= m_rawMap[m] &&
val <= m_rawMap[m+1])
{
idx = m;
frc = ((float)val-(float)m_rawMap[m])/
((float)m_rawMap[m+1]-(float)m_rawMap[m]);
}
}
}
uchar pv = m_pvlMap[idx] + frc*(m_pvlMap[idx+1]-m_pvlMap[idx]);
pair.first = v;
pair.second = QVariant((uint)pv);
return pair;
}
void ossimHdfGridModel::setGridNodes(ossimDblGrid& grid, int32 sds_id, const ossimIpt& spacing)
{
int x=0, y=0;
ossim_uint32 index = 0;
if (m_isHdf4)
{
int32 dim_sizes[MAX_VAR_DIMS];
int32 rank, data_type, n_attrs;
char name[MAX_NC_NAME];
int32 status = SDgetinfo(sds_id, name, &rank, dim_sizes, &data_type, &n_attrs);
if (status == -1)
return;
int32 origin[2] = {0, 0};
int32 num_rows = dim_sizes[0];
int32 num_cols = dim_sizes[1];
ossimDpt grid_origin(0,0); // The grid as used in base class, has UV-space always at 0,0 origin
ossimIpt grid_size (num_cols, num_rows);
ossimDpt dspacing (spacing);
grid.initialize(grid_size, grid_origin, dspacing);
float32* values = new float32 [num_rows * num_cols];
intn statusN = SDreaddata(sds_id, origin, NULL, dim_sizes, (VOIDP)values);
if (statusN > -1)
{
for (y = 0; y < num_rows; y++)
{
for (x = 0; x < num_cols; x++)
{
grid.setNode(x, y, values[index++]);
}
}
}
delete values;
}
else
{
hsize_t dims_out[2]; //dataset dimensions
hid_t datatype = H5Dget_type(sds_id);
hid_t dataspace = H5Dget_space(sds_id); //dataspace handle
int rank = H5Sget_simple_extent_ndims(dataspace);
if (rank == 2)
{
herr_t status_n = H5Sget_simple_extent_dims(dataspace, dims_out, NULL);
ossim_int32 latGridRows = dims_out[0];
ossim_int32 lonGridCols = dims_out[1];
ossim_int32 cols = spacing.x;
ossim_int32 rows = spacing.y;
ossim_int32 spacingX = 0;
ossim_int32 spacingY = 0;
if (rows % latGridRows == 0 && cols % lonGridCols == 0)
{
spacingY = rows/latGridRows; //line increment step
spacingX = cols/lonGridCols; //pixel increment step
}
ossimIpt gridSpacing(spacingX, spacingY);
ossimDpt grid_origin(0,0); // The grid as used in base class, has UV-space always at 0,0 origin
ossimIpt grid_size (cols, rows);
ossimDpt dspacing (gridSpacing);
grid.initialize(grid_size, grid_origin, dspacing);
if( H5Tequal(H5T_NATIVE_FLOAT, datatype))
{
ossim_float32* data_out = new ossim_float32[dims_out[0] * dims_out[1]];
herr_t status = H5Dread(sds_id, datatype, dataspace, dataspace,
H5P_DEFAULT, data_out);
index = 0;
for (y = 0; y < rows; y++)
{
for (x = 0; x < cols; x++)
{
index = x + y * cols;
grid.setNode(x, y, data_out[index]);
}
}
delete[] data_out;
}
else if( H5Tequal(H5T_NATIVE_DOUBLE, datatype))
{
ossim_float64* data_out = new ossim_float64[dims_out[0] * dims_out[1]];
herr_t status = H5Dread(sds_id, datatype, dataspace, dataspace,
H5P_DEFAULT, data_out);
index = 0;
for (y = 0; y < rows; y++)
{
for (x = 0; x < cols; x++)
{
index = x + y * cols;
grid.setNode(x, y, data_out[index]);
}
}
delete[] data_out;
}
}
H5Tclose(datatype);
H5Sclose(dataspace);
}
}
void
RemapHDF4::saveTrimmed(QString trimFile,
int dmin, int dmax,
int wmin, int wmax,
int hmin, int hmax)
{
QProgressDialog progress("Saving trimmed volume",
"Cancel",
0, 100,
0);
progress.setMinimumDuration(0);
int nX, nY, nZ;
nX = m_depth;
nY = m_width;
nZ = m_height;
int mX, mY, mZ;
mX = dmax-dmin+1;
mY = wmax-wmin+1;
mZ = hmax-hmin+1;
int nbytes = m_height*m_width*m_bytesPerVoxel;
uchar *tmp = new uchar[nbytes];
uchar vt;
if (m_voxelType == _UChar) vt = 0; // unsigned byte
if (m_voxelType == _Char) vt = 1; // signed byte
if (m_voxelType == _UShort) vt = 2; // unsigned short
if (m_voxelType == _Short) vt = 3; // signed short
if (m_voxelType == _Int) vt = 4; // int
if (m_voxelType == _Float) vt = 8; // float
QFile fout(trimFile);
fout.open(QFile::WriteOnly);
fout.write((char*)&vt, 1);
fout.write((char*)&mX, 4);
fout.write((char*)&mY, 4);
fout.write((char*)&mZ, 4);
int32 start[2], edges[2];
start[0] = 0;
start[1] = 0;
edges[0] = m_width;
edges[1] = m_height;
for(uint i=dmin; i<=dmax; i++)
{
int32 sd_id = SDstart(m_imageList[i].toAscii().data(),
DFACC_READ);
int32 sds_id = SDselect(sd_id, m_Index);
int status = SDreaddata(sds_id,
start, NULL, edges,
(VOIDP)tmp);
status = SDendaccess(sds_id);
status = SDend(sd_id);
for(uint j=wmin; j<=wmax; j++)
{
memcpy(tmp+(j-wmin)*mZ*m_bytesPerVoxel,
tmp+(j*nZ + hmin)*m_bytesPerVoxel,
mZ*m_bytesPerVoxel);
}
fout.write((char*)tmp, mY*mZ*m_bytesPerVoxel);
progress.setValue((int)(100*(float)(i-dmin)/(float)mX));
qApp->processEvents();
}
fout.close();
delete [] tmp;
m_headerBytes = 13; // to be used for applyMapping function
}
/********************************************************************
Name: test_getszipdata() - verifies that SZIP compressed data can be read
when either SZIP library encoder or only decoder is present
Description:
This test function opens the existing file "sds_szipped.dat" that
contains a dataset with SZIP compression and verifies that the SZIP
compressed data can be read with or without the encoder as long as
the szlib is available.
The input file, sds_szipped.dat, is generated by the program
mfhdf/libsrc/gen_sds_szipped.c
Return value:
The number of errors occurred in this routine.
BMR - Oct 10, 2008
*********************************************************************/
#ifdef H4_HAVE_LIBSZ /* needed to read data, either decoder or encoder */
static intn test_getszipdata()
{
/************************* Variable declaration **************************/
int32 sd_id, sds_id;
intn status;
int32 dim_sizes[2], array_rank, num_type, attributes;
char name[H4_MAX_NC_NAME];
comp_info c_info;
int32 start[2], edges[2];
int16 fill_value = 0; /* Fill value */
int i,j;
int num_errs = 0; /* number of errors so far */
int32 out_data[SZ_LENGTH][SZ_WIDTH];
char testfile[512] = "";
char *basename = "sds_szipped.dat";
/* data to compare against read data from sds_szipped.dat */
int32 in_data[SZ_LENGTH][SZ_WIDTH]={
100,100,200,200,300,
0, 0, 0, 0, 0,
100,100,200,200,300,
400,300,200,100,0,
300,300, 0,400,300,
300,300, 0,400,300,
300,300, 0,400,300,
0, 0,600,600,300,
500,500,600,600,300,
0, 0,600,600,300,
0, 0,600,600,300,
0, 0,600,600,300,
0, 0,600,600,300,
500,500,600,600,300,
500,500,600,600,300,
500,500,600,600,300 };
/********************* End of variable declaration ***********************/
/* Make the name for the test file */
make_datafilename(basename, testfile, sizeof(testfile));
/* Open the file */
sd_id = SDstart (testfile, DFACC_READ);
CHECK(sd_id, FAIL, "SDstart");
/* Get the first SDS */
sds_id = SDselect (sd_id, 0);
CHECK(sds_id, FAIL, "SDselect:Failed to select a data set for szip compression testing");
/* Retrieve information of the data set */
status = SDgetinfo(sds_id, name, &array_rank, dim_sizes, &num_type, &attributes);
CHECK(status, FAIL, "SDgetinfo");
/* Prepare for reading */
start[0] = 0;
start[1] = 0;
edges[0] = dim_sizes[0];
edges[1] = dim_sizes[1];
/* Wipe out the output buffer */
HDmemset(&out_data, 0, sizeof(out_data));
/* Read the data set */
status = SDreaddata (sds_id, start, NULL, edges, (VOIDP)out_data);
CHECK(status, FAIL, "SDreaddata");
/* Compare read data against input data */
for (j=0; j<SZ_LENGTH; j++)
{
for (i=0; i<SZ_WIDTH; i++)
if (out_data[j][i] != in_data[j][i])
{
fprintf(stderr,"This one: Bogus val in loc [%d][%d] in compressed dset, want %ld got %ld\n", j, i, (long)in_data[j][i], (long)out_data[j][i]);
num_errs++;
}
}
/* Terminate access to the data set */
status = SDendaccess (sds_id);
CHECK(status, FAIL, "SDendaccess");
/* Terminate access to the SD interface and close the file */
status = SDend (sd_id);
CHECK(status, FAIL, "SDend");
/* Return the number of errors that's been kept track of so far */
return num_errs;
} /* test_getszipdata */
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;
}
static intn test_szip_chunk()
{
/************************* Variable declaration **************************/
int32 sd_id, sds_id, sds_index;
intn status;
int32 flag, maxcache, new_maxcache;
int32 dim_sizes[2], origin[2];
HDF_CHUNK_DEF c_def; /* Chunking definitions */
HDF_CHUNK_DEF c_def_out; /* Chunking definitions */
int32 c_flags, c_flags_out;
int32 all_data[LENGTH_CH][WIDTH_CH];
int32 start[2], edges[2];
int32 comp_size=0, uncomp_size=0;
int32 chunk_out[CLENGTH][CWIDTH];
int32 row[CWIDTH] = { 5, 5 };
int32 column[CLENGTH] = { 4, 4, 4 };
int32 fill_value = 0; /* Fill value */
comp_coder_t comp_type; /* to retrieve compression type into */
comp_info cinfo; /* compression information structure */
int num_errs = 0; /* number of errors so far */
int i,j;
/*
* Define all chunks. Note that chunks 4 & 5 are not used to write,
* only to verify the read data. The 'row' and 'column' are used
* to write in the place of these chunks.
*/
int32 chunk1[CLENGTH][CWIDTH] = { 1, 1,
1, 1,
1, 1 };
int32 chunk2[CLENGTH][CWIDTH] = { 2, 2,
2, 2,
2, 2 };
int32 chunk3[CLENGTH][CWIDTH] = { 3, 3,
3, 3,
3, 3 };
int32 chunk4[CLENGTH][CWIDTH] = { 0, 4,
0, 4,
0, 4 };
int32 chunk5[CLENGTH][CWIDTH] = { 0, 0,
5, 5,
0, 0 };
int32 chunk6[CLENGTH][CWIDTH] = { 6, 6,
6, 6,
6, 6 };
/* Initialize chunk lengths. */
c_def.comp.chunk_lengths[0] = CLENGTH;
c_def.comp.chunk_lengths[1] = CWIDTH;
/* Create the file and initialize SD interface. */
sd_id = SDstart (FILE_NAME, DFACC_CREATE);
CHECK(sd_id, FAIL, "SDstart");
/* Create LENGTH_CHxWIDTH_CH SDS. */
dim_sizes[0] = LENGTH_CH;
dim_sizes[1] = WIDTH_CH;
sds_id = SDcreate (sd_id, SDS_NAME_CH,DFNT_INT32, RANK_CH, dim_sizes);
CHECK(sds_id, FAIL, "SDcreate:Failed to create a data set for chunking/szip compression testing");
/* Fill the SDS array with the fill value. */
status = SDsetfillvalue (sds_id, (VOIDP)&fill_value);
CHECK(status, FAIL, "SDsetfillvalue");
/* Set parameters for Chunking/SZIP */
c_def.comp.comp_type = COMP_CODE_SZIP;
c_def.comp.cinfo.szip.pixels_per_block = 2;
c_def.comp.cinfo.szip.options_mask = SZ_EC_OPTION_MASK;
c_def.comp.cinfo.szip.options_mask |= SZ_MSB_OPTION_MASK;
c_def.comp.cinfo.szip.bits_per_pixel = 0;
c_def.comp.cinfo.szip.pixels = 0;
c_def.comp.cinfo.szip.pixels_per_scanline = 0;
c_flags = HDF_CHUNK | HDF_COMP;
status = SDsetchunk (sds_id, c_def, c_flags);
CHECK(status, FAIL, "SDsetchunk");
/* Set chunk cache to hold maximum of 3 chunks. */
maxcache = 3;
flag = 0;
new_maxcache = SDsetchunkcache (sds_id, maxcache, flag);
CHECK(new_maxcache, FAIL, "SDsetchunkcache");
HDmemset(&c_def_out, 0, sizeof(HDF_CHUNK_DEF));
c_flags_out = 0;
status = SDgetchunkinfo(sds_id, &c_def_out, &c_flags_out);
CHECK(status, FAIL, "SDgetchunkinfo");
VERIFY(c_flags_out, c_flags, "SDgetchunkinfo");
VERIFY(c_def_out.comp.comp_type, COMP_CODE_SZIP, "SDgetchunkinfo");
/*
* Write chunks using SDwritechunk function. Chunks can be written
* in any order.
*/
/* Write the chunk with the coordinates (0,0). */
origin[0] = 0;
origin[1] = 0;
status = SDwritechunk (sds_id, origin, (VOIDP) chunk1);
CHECK(status, FAIL, "SDwritechunk");
/* Write the chunk with the coordinates (1,0). */
origin[0] = 1;
origin[1] = 0;
status = SDwritechunk (sds_id, origin, (VOIDP) chunk3);
CHECK(status, FAIL, "SDwritechunk");
/* Write the chunk with the coordinates (0,1). */
origin[0] = 0;
origin[1] = 1;
status = SDwritechunk (sds_id, origin, (VOIDP) chunk2);
CHECK(status, FAIL, "SDwritechunk");
/* Write chunk with the coordinates (1,2) using SDwritedata function. */
start[0] = 6;
start[1] = 2;
edges[0] = 3;
edges[1] = 2;
status = SDwritedata (sds_id, start, NULL, edges, (VOIDP) chunk6);
CHECK(status, FAIL, "SDwritedata");
/* Fill second column in the chunk with the coordinates (1,1) using
* SDwritedata function. */
start[0] = 3;
start[1] = 3;
edges[0] = 3;
edges[1] = 1;
status = SDwritedata (sds_id, start, NULL, edges, (VOIDP) column);
CHECK(status, FAIL, "SDwritedata");
/* Fill second row in the chunk with the coordinates (0,2) using
* SDwritedata function. */
start[0] = 7;
start[1] = 0;
edges[0] = 1;
edges[1] = 2;
status = SDwritedata (sds_id, start, NULL, edges, (VOIDP) row);
CHECK(status, FAIL, "SDwritedata");
/* Terminate access to the data set. */
status = SDendaccess (sds_id);
CHECK(status, FAIL, "SDendaccess");
/* Terminate access to the SD interface and close the file. */
status = SDend (sd_id);
CHECK(status, FAIL, "SDend");
/*
* Verify the compressed data
*/
/* Reopen the file and access the first data set. */
sd_id = SDstart (FILE_NAME, DFACC_READ);
sds_index = 0;
sds_id = SDselect (sd_id, sds_index);
CHECK(sds_id, FAIL, "SDselect:Failed to select a data set for chunking/szip compression testing");
/* Retrieve compression information about the dataset */
comp_type = COMP_CODE_INVALID; /* reset variables before retrieving info */
HDmemset(&cinfo, 0, sizeof(cinfo)) ;
status = SDgetcompinfo(sds_id, &comp_type, &cinfo);
CHECK(status, FAIL, "SDgetcompinfo");
VERIFY(comp_type, COMP_CODE_SZIP, "SDgetcompinfo");
/* Retrieve compression method alone from the dataset */
comp_type = COMP_CODE_INVALID; /* reset variables before retrieving info */
status = SDgetcomptype(sds_id, &comp_type);
CHECK(status, FAIL, "SDgetcomptype");
VERIFY(comp_type, COMP_CODE_SZIP, "SDgetcomptype");
/* Read the entire data set using SDreaddata function. */
start[0] = 0;
start[1] = 0;
edges[0] = LENGTH_CH;
edges[1] = WIDTH_CH;
status = SDreaddata (sds_id, start, NULL, edges, (VOIDP)all_data);
CHECK(status, FAIL, "SDreaddata");
/*
* This is how the entire array should look like:
*
* 1 1 2 2
* 1 1 2 2
* 1 1 2 2
* 3 3 0 4
* 3 3 0 4
* 3 3 0 4
* 0 0 6 6
* 5 5 6 6
* 0 0 6 6
*/
/* Read chunk #4 with the coordinates (1,1) and verify it. */
origin[0] = 1;
origin[1] = 1;
status = SDreadchunk (sds_id, origin, chunk_out);
CHECK(status, FAIL, "SDreadchunk");
for (j=0; j<CLENGTH; j++)
{
for (i=0; i<CWIDTH; i++)
{
if (chunk_out[j][i] != chunk4[j][i])
{
fprintf(stderr,"Bogus val in loc [%d][%d] in chunk #4, want %ld got %ld\n", j, i, chunk4[j][i], chunk_out[j][i]);
num_errs++;
}
}
}
/*
* Read chunk #5 with the coordinates (2,0) and verify it.
*/
origin[0] = 2;
origin[1] = 0;
status = SDreadchunk (sds_id, origin, chunk_out);
CHECK(status, FAIL, "SDreadchunk");
for (j=0; j<CLENGTH; j++)
{
for (i=0; i<CWIDTH; i++)
if (chunk_out[j][i] != chunk5[j][i])
{
fprintf(stderr,"Bogus val in loc [%d][%d] in chunk #5, want %ld got %ld\n", j, i, chunk5[j][i], chunk_out[j][i]);
num_errs++;
}
}
/* Get the data sizes */
status = SDgetdatasize(sds_id, &comp_size, &uncomp_size);
CHECK(status, FAIL, "test_chkcmp_SDSs: SDgetdatasize");
/* Terminate access to the data set. */
status = SDendaccess (sds_id);
CHECK(status, FAIL, "SDendaccess");
/* Terminate access to the SD interface and close the file. */
status = SDend (sd_id);
CHECK(status, FAIL, "SDend");
/* Return the number of errors that's been kept track of so far */
return num_errs;
} /* test_szip_chunk */
static int read_partial_array(const coda_cursor *cursor, long offset, long length, void *dst)
{
int32 start[MAX_HDF4_VAR_DIMS];
int32 stride[MAX_HDF4_VAR_DIMS];
int32 edge[MAX_HDF4_VAR_DIMS];
long i;
switch (((coda_hdf4_type *)cursor->stack[cursor->n - 1].type)->tag)
{
case tag_hdf4_basic_type_array:
coda_set_error(CODA_ERROR_INVALID_ARGUMENT, "partial array reading is not supported for HDF4 attributes");
return -1;
case tag_hdf4_GRImage:
{
coda_hdf4_GRImage *type;
type = (coda_hdf4_GRImage *)cursor->stack[cursor->n - 1].type;
stride[0] = 1;
stride[1] = 1;
if (length < type->dim_sizes[1])
{
start[0] = offset / type->dim_sizes[1];
start[1] = offset % type->dim_sizes[1];
edge[0] = 1;
edge[1] = length;
if (start[1] + edge[1] > type->dim_sizes[1])
{
coda_set_error(CODA_ERROR_INVALID_ARGUMENT, "partial array reading for HDF4 GRImage requires "
"offset (%ld) and length (%ld) to represent a hyperslab (range [%ld,%ld] "
"exceeds length of dimension #1 (%ld)))", offset, length, (long)start[1],
(long)start[1] + edge[1] - 1, type->dim_sizes[1]);
return -1;
}
}
else
{
if (length % type->dim_sizes[1] != 0)
{
coda_set_error(CODA_ERROR_INVALID_ARGUMENT, "partial array reading for HDF4 GRImage requires "
"length (%ld) to be a multiple of the subdimension size (%ld)", length,
type->dim_sizes[1]);
return -1;
}
if (offset % type->dim_sizes[1] != 0)
{
coda_set_error(CODA_ERROR_INVALID_ARGUMENT, "partial array reading for HDF4 GRImage requires "
" offset (%ld) to be a multiple of the subdimension size (%ld)", offset,
type->dim_sizes[1]);
return -1;
}
start[0] = offset / type->dim_sizes[1];
start[1] = 0;
edge[0] = length / type->dim_sizes[1];
edge[1] = type->dim_sizes[1];
if (start[0] + edge[0] > type->dim_sizes[0])
{
coda_set_error(CODA_ERROR_INVALID_ARGUMENT, "partial array reading for HDF4 GRImage requires "
"offset (%ld) and length (%ld) to represent a hyperslab (range [%ld,%ld] "
"exceeds length of dimension #0 (%ld)))", offset, length, (long)start[0],
(long)start[0] + edge[0] - 1, type->dim_sizes[0]);
return -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;
long block_size = 1;
type = (coda_hdf4_SDS *)cursor->stack[cursor->n - 1].type;
/* determine hyperslab start/edge */
if (type->rank == 0)
{
coda_set_error(CODA_ERROR_INVALID_ARGUMENT, "partial array reading not allowed for zero "
"dimensional HDF4 SDS");
return -1;
}
for (i = type->rank - 1; i >= 0; i--)
{
if (length <= block_size * type->dimsizes[i])
{
if (length % block_size != 0)
{
coda_set_error(CODA_ERROR_INVALID_ARGUMENT, "partial array reading for HDF4 SDS requires "
"length (%ld) to be a multiple of the subdimension size (%ld)", length,
block_size);
return -1;
}
start[i] = (offset / block_size) % type->dimsizes[i];
edge[i] = length / block_size;
break;
}
start[i] = 0;
edge[i] = type->dimsizes[i];
block_size *= type->dimsizes[i];
}
if (offset % block_size != 0)
{
coda_set_error(CODA_ERROR_INVALID_ARGUMENT, "partial array reading for HDF4 SDS requires offset "
"(%ld) to be a multiple of the subdimension size (%ld)", offset, block_size);
return -1;
}
if (start[i] + edge[i] > type->dimsizes[i])
{
coda_set_error(CODA_ERROR_INVALID_ARGUMENT, "partial array reading for HDF4 SDS requires offset "
"(%ld) and length (%ld) to represent a hyperslab (range [%ld,%ld] exceeds length "
"of dimension #%d (%ld)))", offset, length, (long)start[i],
(long)start[i] + edge[i] - 1, i, type->dimsizes[i]);
return -1;
}
while (i > 0)
{
block_size *= type->dimsizes[i];
i--;
start[i] = (offset / block_size) % 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_set_error(CODA_ERROR_INVALID_ARGUMENT, "partial array reading is not supported for HDF4 Vdata");
return -1;
default:
assert(0);
exit(1);
}
return 0;
}
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;
}
Databox *ReadSDS(char *filename, int ds_num,
double default_value)
{
Databox *v;
int32 dim[MAX_VAR_DIMS];
int32 edges[3];
int32 start[3];
int i;
int z;
int32 type;
char name[MAX_NC_NAME];
int32 sd_id;
int32 sds_id;
int32 rank, nt, nattrs;
int nx, ny, nz;
int m;
double *double_ptr;
sd_id = SDstart(filename, DFACC_RDONLY);
sds_id = SDselect(sd_id, ds_num);
SDgetinfo(sds_id, name, &rank, dim, &type, &nattrs);
start[0] = start[1] = start[2] = 0;
/* create the new databox structure */
if((v = NewDatabox(dim[2], dim[1], dim[0], 0, 0, 0, 0, 0, 0, default_value)) == NULL)
return((Databox *)NULL);
double_ptr = DataboxCoeffs(v);
edges[0] = 1;
edges[1] = DataboxNy(v);
edges[2] = DataboxNx(v);
switch (type) {
case DFNT_FLOAT32 :
{
float32 *convert_ptr, *data;
if( (data = convert_ptr = (float32 *)malloc(dim[1]*dim[2] *
sizeof(float32))) == NULL)
{
exit(1);
}
for(z=0; z < dim[0]; z++)
{
start[0] = z;
SDreaddata(sds_id, start, NULL, edges, data);
convert_ptr = data;
for(i=dim[1]*dim[2]; i--;)
*double_ptr++ = *convert_ptr++;
}
free(data);
break;
};
case DFNT_FLOAT64 :
{
float64 *convert_ptr, *data;
if( (data = convert_ptr = (float64 *)malloc(dim[1]*dim[2] *
sizeof(float64))) == NULL)
{
exit(1);
}
for(z=0; z < dim[0]; z++)
{
start[0] = z;
SDreaddata(sds_id, start, NULL, edges, data);
convert_ptr = data;
for(i=dim[1]*dim[2]; i--;)
*double_ptr++ = *convert_ptr++;
}
free(data);
break;
};
case DFNT_INT8 :
{
int8 *convert_ptr, *data;
if( (data = convert_ptr = (int8 *)malloc(dim[1]*dim[2] *
sizeof(int8))) == NULL)
{
exit(1);
}
for(z=0; z < dim[0]; z++)
{
start[0] = z;
SDreaddata(sds_id, start, NULL, edges, data);
convert_ptr = data;
for(i=dim[1]*dim[2]; i--;)
*double_ptr++ = *convert_ptr++;
}
free(data);
break;
};
case DFNT_UINT8 :
{
uint8 *convert_ptr, *data;
if( (data = convert_ptr = (uint8 *)malloc(dim[1]*dim[2] *
sizeof(uint8))) == NULL)
{
exit(1);
}
for(z=0; z < dim[0]; z++)
{
start[0] = z;
SDreaddata(sds_id, start, NULL, edges, data);
convert_ptr = data;
for(i=dim[1]*dim[2]; i--;)
*double_ptr++ = *convert_ptr++;
}
free(data);
break;
};
case DFNT_INT16 :
{
int16 *convert_ptr, *data;
if( (data = convert_ptr = (int16 *)malloc(dim[1]*dim[2] *
sizeof(int16))) == NULL)
{
exit(1);
}
for(z=0; z < dim[0]; z++)
{
start[0] = z;
SDreaddata(sds_id, start, NULL, edges, data);
convert_ptr = data;
for(i=dim[1]*dim[2]; i--;)
*double_ptr++ = *convert_ptr++;
}
free(data);
break;
};
case DFNT_UINT16 :
{
uint16 *convert_ptr, *data;
if( (data = convert_ptr = (uint16 *)malloc(dim[1]*dim[2] *
sizeof(uint16))) == NULL)
{
exit(1);
}
for(z=0; z < dim[0]; z++)
{
start[0] = z;
SDreaddata(sds_id, start, NULL, edges, data);
convert_ptr = data;
for(i=dim[1]*dim[2]; i--;)
*double_ptr++ = *convert_ptr++;
}
free(data);
break;
};
case DFNT_INT32 :
{
int32 *convert_ptr, *data;
if( (data = convert_ptr = (int32 *)malloc(dim[1]*dim[2] *
sizeof(int32))) == NULL)
{
exit(1);
}
for(z=0; z < dim[0]; z++)
{
start[0] = z;
SDreaddata(sds_id, start, NULL, edges, data);
convert_ptr = data;
for(i=dim[1]*dim[2]; i--;)
*double_ptr++ = *convert_ptr++;
}
free(data);
break;
};
case DFNT_UINT32 :
{
uint32 *convert_ptr, *data;
if( (data = convert_ptr = (uint32 *)malloc(dim[1]*dim[2] *
sizeof(uint32))) == NULL)
{
exit(1);
}
for(z=0; z < dim[0]; z++)
{
start[0] = z;
SDreaddata(sds_id, start, NULL, edges, data);
convert_ptr = data;
for(i=dim[1]*dim[2]; i--;)
*double_ptr++ = *convert_ptr++;
}
free(data);
break;
};
}
SDendaccess(sds_id);
SDend(sd_id);
return v;
}
int main(int argc, char *argv[])
{
char *MOD021KMfile, *MOD02HKMfile, *MOD02QKMfile;
char *filename; /* output file */
FILE *fp;
int outfile_exists;
char *ancpath;
SDS sds[Nitems], outsds[Nbands], dem, height;
int32 MOD02QKMfile_id, MOD02HKMfile_id, MOD021KMfile_id;
int32 sd_id, attr_index, count, num_type;
int ib, j, iscan, Nscans, irow, jcol, idx, crsidx;
int nbands;
char *SDSlocatorQKM[Nitems] = {"EV_250_RefSB", "EV_250_RefSB",
"EV_500_RefSB", "EV_500_RefSB", "EV_500_RefSB",
"EV_500_RefSB", "EV_500_RefSB","EV_1KM_RefSB", "EV_1KM_RefSB",
"EV_1KM_RefSB", "EV_1KM_RefSB", "EV_1KM_RefSB", "EV_1KM_RefSB",
"EV_1KM_RefSB", "EV_1KM_RefSB", "EV_1KM_RefSB", "SolarZenith",
"SensorZenith", "SolarAzimuth", "SensorAzimuth", "Longitude",
"Latitude"};
char *SDSlocatorHKM[Nitems] = {"EV_500_RefSB",
"EV_500_RefSB", "EV_500_RefSB", "EV_500_RefSB",
"EV_500_RefSB", "EV_500_RefSB", "EV_500_RefSB",
"Reflectance_Img_I1","Reflectance_Img_I2","Reflectance_Img_I3",
"EV_1KM_RefSB","EV_1KM_RefSB","EV_1KM_RefSB", "EV_1KM_RefSB",
"EV_1KM_RefSB", "EV_1KM_RefSB","SolZenAng_Mod",
"SenZenAng_Mod", "SolAziAng_Mod", "SenAziAng_Mod", "Longitude",
"Latitude" };
char *SDSlocator1KM[Nitems] = {"Reflectance_Mod_M5",
"Reflectance_Mod_M7", "Reflectance_Mod_M3",
"Reflectance_Mod_M4", "Reflectance_Mod_M8",
"Reflectance_Mod_M10", "Reflectance_Mod_M11",
"EV_1KM_RefSB", "EV_1KM_RefSB", "EV_1KM_RefSB", "EV_1KM_RefSB",
"EV_1KM_RefSB", "EV_1KM_RefSB",
"EV_1KM_RefSB", "EV_1KM_RefSB", "EV_1KM_RefSB", "SolZenAng_Mod",
"SenZenAng_Mod", "SolAziAng_Mod", "SenAziAng_Mod", "Longitude",
"Latitude"};
char indexlocator[Nitems] = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 5, 7,
9, 10, 0, 0, 0, 0, 0, 0};
char numtypelocator[Nitems] = {DFNT_UINT16, DFNT_UINT16, DFNT_UINT16,
DFNT_UINT16, DFNT_UINT16, DFNT_UINT16, DFNT_UINT16,
DFNT_UINT16, DFNT_UINT16, DFNT_UINT16, DFNT_UINT16,
DFNT_UINT16, DFNT_UINT16, DFNT_UINT16, DFNT_UINT16,
DFNT_UINT16,DFNT_FLOAT32 ,DFNT_FLOAT32 ,DFNT_FLOAT32 ,DFNT_FLOAT32 ,
DFNT_FLOAT32, DFNT_FLOAT32};
uint16 *l1bdata[Nbands];
float32 *sola, *solz, *sena, *senz, *solzfill;
float32 *lon, *lat, *lonfill, *latfill;
char *attr_name;
float64 scale_factor[Nitems], add_offset[Nitems];
unsigned char process[Nbands];
float refl, *mus, muv, phi;
float *rhoray, *sphalb, *TtotraytH2O, *tOG;
int aggfactor, crsrow1, crsrow2, crscol1, crscol2;
int crsidx11, crsidx12, crsidx21, crsidx22;
float mus0, mus11, mus12, mus21, mus22;
float fractrow, fractcol, t, u;
float rhoray0, rhoray11, rhoray12, rhoray21, rhoray22;
float sphalb0, sphalb11, sphalb12, sphalb21, sphalb22;
float reflmin=REFLMIN, reflmax=REFLMAX, maxsolz=MAXSOLZ;
int bad;
int write_mode = DFACC_CREATE;
int st;
size_t nbytes;
int ftype;
extern char *optarg;
extern int optind, opterr;
int option_index = 0;
static int verbose, overwrite;
static int gzip, append;
static int output500m, output1km;
static int sealevel, TOA, nearest;
char dummy[H4_MAX_NC_NAME];
enum{OPT_BANDS = 1, OPT_RANGE, OPT_OUTFILE, OPT_MAXSOLZ};
static struct option long_options[] = {
{"1km", no_argument, &output1km, 1},
{"500m", no_argument, &output500m, 1},
{"append", no_argument, &append, 1},
{"bands", required_argument, (int *) NULL, OPT_BANDS},
{"gzip", no_argument, &gzip, 1},
{"maxsolz", required_argument, (int *) NULL, OPT_MAXSOLZ},
{"nearest", no_argument, &nearest, 1},
{"of", required_argument, (int *) NULL, OPT_OUTFILE},
{"overwrite", no_argument, &overwrite, 1},
{"range", required_argument, (int *) NULL, OPT_RANGE},
{"sealevel", no_argument, &sealevel, 1},
{"toa", no_argument, &TOA, 1},
{"verbose", no_argument, &verbose, 1},
{(char *) NULL, 0, (int *) NULL, 0}
};
int c;
static char dem_filename_buff[MAXNAMELENGTH];
MOD021KMfile = MOD02HKMfile = MOD02QKMfile = (char *) NULL;
filename = (char *) NULL;
for (ib = 0; ib < Nbands; ib++) process[ib] = FALSE;
/* default settings */
output500m = output1km = 0;
append = gzip = nearest = sealevel = TOA = verbose = overwrite = 0;
while ((c = getopt_long(argc, argv, "", long_options,
&option_index)) >= 0) {
switch (c) {
case 0:
/* do nothing for options which will have a
flag set automatically by getopt_long() */
break;
case OPT_BANDS:
if (parse_bands(optarg, process)) {
fputs("Invalid band(s) specified.\n",
stderr);
exit(1);
}
break;
case OPT_RANGE:
if (sscanf(optarg, "%g,%g", &reflmin, &reflmax) != 2) {
fputs("Error parsing reflectance range.\n", stderr);
exit(1);
}
if ( range_check(reflmin, 0.0F, 1.0F) ||
range_check(reflmax, 0.0F, 1.0F) ||
(reflmin >= reflmax) ) {
fputs("Invalid reflectance range.\n", stderr);
exit(1);
}
printf("Output reflectance range [%.3f,%.3f] requested.\n",
reflmin, reflmax);
break;
case OPT_MAXSOLZ:
maxsolz = (float) atof(optarg);
if (range_check(maxsolz, 0.0F, 90.0F)) {
fputs("Invalid max. solar zenith angle.\n", stderr);
exit(1);
}
break;
case OPT_OUTFILE:
filename = optarg;
break;
default:
usage();
exit(1);
}
}
if (append) write_mode = DFACC_RDWR;
/* at least one input file must follow */
if (optind >= argc) {
usage();
exit(1);
}
/* check for conflicting options */
if (overwrite && append) {
fputs("Options --overwrite and --append are mutually exclusive.\n",
stderr);
exit(1);
}
if (sealevel && TOA) {
fputs("Options --sealevel and --toa are mutually exclusive.\n",
stderr);
exit(1);
}
#ifdef DEBUG
printf("append = %d\n", append);
if (filename) printf("output filename = %s\n", filename);
printf("output1km = %d\n", (int) output1km);
printf("output500m = %d\n", (int) output500m);
printf("gzip = %d\n", gzip);
printf("nearest = %d\n", nearest);
printf("sealevel = %d\n", sealevel);
printf("TOA = %d\n", TOA);
printf("Max. solar zenith angle: %g degrees\n", maxsolz);
if (filename) printf("Output file: %s.", filename);
#endif
if (verbose) puts("Verbose mode requested.");
if (overwrite) puts("Overwriting existing output file.");
if (gzip) puts("Gzip compression requested.");
if (sealevel) puts("Sea-level atmospheric correction requested. Terrain height ignored.");
if (TOA) puts("Top-of-the-atmosphere reflectance requested. No atmospheric correction.");
if (output1km) puts("1km-resolution output requested.");
if (nearest) puts("Interpolation disabled.");
/* parse input file names */
for (j = optind; j < argc; j++) {
ftype = input_file_type(argv[j]);
switch (ftype) {
case INPUT_1KM:
MOD021KMfile = argv[j];
break;
case INPUT_500M:
MOD02HKMfile = argv[j];
break;
case INPUT_250M:
MOD02QKMfile = argv[j];
break;
default:
fprintf(stderr,
"Unrecognized input file \"%s\".\n",
argv[j]);
MOD021KMfile = argv[j];
/* exit(1); I commented that*/
break;
}
}
if (verbose && MOD021KMfile)
printf("Input geolocation file: %s\n", MOD021KMfile);
/* output file name is mandatory */
if (!filename) {
fputs("Missing output file name.\n", stderr);
exit(1);
}
#ifdef DEBUG
if (MOD021KMfile) printf("MOD/MYD021KMfile = %s\n", MOD021KMfile);
if (MOD02HKMfile) printf("MOD/MYD02HKMfile = %s\n", MOD02HKMfile);
if (MOD02QKMfile) printf("MOD/MYD02QKMfile = %s\n", MOD02QKMfile);
#endif
/*
1KM file is mandatory for angles.
HKM file is mandatory unless 1-km output is requested.
QKM file is mandatory unless 500-m or 1-km output is requested.
*/
/* if ( (!MOD021KMfile) ||
(!MOD02HKMfile && !output1km) ||
(!MOD02QKMfile && !output500m && !output1km) ) {
fputs("Invalid combination of input files.\n", stderr);
exit(1);
}
commented that too Eric*/
/* count number of bands to process */
for (ib = nbands = 0; ib < Nbands; ib++) if (process[ib]) nbands++;
if (nbands < 1) {
process[BAND1] = process[BAND3] = process[BAND4] = TRUE;
if (verbose)
puts("No band(s) specified. Default is bands 1, 3, and 4.");
}
/* open input files */
if ( MOD02QKMfile && (!output500m) &&
!output1km &&
(MOD02QKMfile_id = SDstart(MOD02QKMfile, DFACC_READ)) == -1 ) {
fprintf(stderr, "Cannot open input file %s.\n", MOD02QKMfile);
exit(1);
}
if ( MOD02HKMfile && (!output1km) &&
(MOD02HKMfile_id = SDstart(MOD02HKMfile, DFACC_READ)) == -1 ) {
fprintf(stderr, "Cannot open input file %s.\n", MOD02HKMfile);
exit(1);
}
if ( MOD021KMfile &&
(MOD021KMfile_id = SDstart(MOD021KMfile, DFACC_READ)) == -1 ) {
fprintf(stderr, "Cannot open input file %s.\n", MOD021KMfile);
exit(1);
}
if (!sealevel && !TOA) {
dem.filename = dem_filename_buff;
if ((ancpath = getenv("ANCPATH")) == NULL)
sprintf(dem.filename, "%s/%s", ANCPATH, DEMFILENAME);
else
sprintf(dem.filename, "%s/%s", ancpath, DEMFILENAME);
if ( (dem.file_id = SDstart(dem.filename, DFACC_READ)) == -1 ) {
fprintf(stderr, "Cannot open file %s.\n", dem.filename);
exit(1);
}
}
if ( (fp = fopen(filename, "r")) ) {
(void) fclose(fp);
outfile_exists = 1;
}
else
outfile_exists = 0;
if ((write_mode == DFACC_CREATE) && !overwrite && outfile_exists) {
fprintf(stderr, "File \"%s\" already exits.\n", filename);
exit(1);
}
if (output500m) {
sds[BAND10].file_id =sds[BAND8].file_id = sds[BAND9].file_id = MOD02HKMfile_id;
sds[BAND10].filename =sds[BAND8].filename = sds[BAND9].filename = MOD02HKMfile;
}
else {
if (output1km) {
sds[BAND1].file_id = sds[BAND2].file_id = MOD021KMfile_id;
sds[BAND1].filename = sds[BAND2].filename = MOD021KMfile;
}
else {
sds[BAND1].file_id = sds[BAND2].file_id = MOD02QKMfile_id;
sds[BAND1].filename = sds[BAND2].filename = MOD02QKMfile;
}
}
if (output1km) {
sds[BAND3].file_id = sds[BAND4].file_id =
sds[BAND5].file_id = sds[BAND6].file_id =
sds[BAND7].file_id = MOD021KMfile_id;
sds[BAND3].filename = sds[BAND4].filename =
sds[BAND5].filename = sds[BAND6].filename =
sds[BAND7].filename = MOD021KMfile;
}
else {
sds[BAND3].file_id = sds[BAND4].file_id =
sds[BAND5].file_id = sds[BAND6].file_id =
sds[BAND7].file_id = MOD02HKMfile_id;
sds[BAND3].filename = sds[BAND4].filename =
sds[BAND5].filename = sds[BAND6].filename =
sds[BAND7].filename = MOD02HKMfile;
}
sds[SOLZ].file_id = sds[SOLA].file_id =
sds[SENZ].file_id = sds[SENA].file_id = sds[LON].file_id =
sds[LAT].file_id = MOD021KMfile_id;
sds[SOLZ].filename = sds[SOLA].filename =
sds[SENZ].filename = sds[SENA].filename = sds[LON].filename =
sds[LAT].filename = MOD021KMfile;
sds[BAND11].file_id =
sds[BAND12].file_id = sds[BAND13].file_id =
sds[BAND14].file_id = sds[BAND15].file_id =
sds[BAND16].file_id = MOD021KMfile_id;
sds[BAND11].filename =
sds[BAND12].filename = sds[BAND13].filename =
sds[BAND14].filename = sds[BAND15].filename =
sds[BAND16].filename = MOD021KMfile;
for (ib=0; ib < Nitems; ib++) {
/* initializing these fields will simplify releasing memory later */
sds[ib].data = sds[ib].fillvalue = (void *) NULL;
if ( ib < Nbands &&
! process[ib] ) {
sds[ib].id = -1;
continue;
}
if (output500m)
sds[ib].name = SDSlocatorHKM[ib];
else if (output1km)
sds[ib].name = SDSlocator1KM[ib];
else
sds[ib].name = SDSlocatorQKM[ib];
if ( (sds[ib].index = SDnametoindex(sds[ib].file_id, sds[ib].name)) == -1 ) {
fprintf(stderr, "Cannot find SDS %s in file %s.\n", sds[ib].name, sds[ib].filename);
continue;
}
if ( (sds[ib].id = SDselect(sds[ib].file_id, sds[ib].index)) == -1 ) {
fprintf(stderr, "Cannot select SDS no. %d\n", sds[ib].index);
if (ib < Nbands)
process[ib] = FALSE;
continue;
}
/*
Original code passed sds[ib].name as destination for SDS name in call to SDgetinfo().
This was causing a core dump, apparently because SDgetinfo() writes some additional
characters beyond the terminating null at the end of the SDS name, so I replaced
the argument with a dummy character array.
*/
if (SDgetinfo(sds[ib].id, dummy, &sds[ib].rank, sds[ib].dim_sizes, &sds[ib].num_type, &sds[ib].n_attr) == -1) {
fprintf(stderr, "Can't get info from SDS \"%s\" in file %s.\n", sds[ib].name, sds[ib].filename);
SDendaccess(sds[ib].id);
sds[ib].id = -1;
if (ib < Nbands)
process[ib] = FALSE;
continue;
}
sds[ib].factor = 1;
if (ib < 5 ) sds[ib].factor = 2.441742e-05;
attr_name = "scale_factor";
printf("band %d \n",ib);
if ( (attr_index = SDfindattr(sds[ib].id, attr_name)) != -1 &&
SDattrinfo(sds[ib].id, attr_index, dummy, &num_type, &count) != -1 &&
SDreadattr(sds[ib].id, attr_index, scale_factor) != -1 )
sds[ib].factor = ((float32 *)scale_factor)[indexlocator[ib]];
else {
attr_name = "Scale";
if ((attr_index = SDfindattr(sds[ib].id, attr_name)) != -1 &&
SDattrinfo(sds[ib].id, attr_index, dummy, &num_type, &count) != -1 &&
SDreadattr(sds[ib].id, attr_index, scale_factor) != -1 )
sds[ib].factor = *scale_factor;
}
sds[ib].offset = 0;
attr_name = "reflectance_offsets";
if ( (attr_index = SDfindattr(sds[ib].id, attr_name)) != -1 &&
SDattrinfo(sds[ib].id, attr_index, dummy, &num_type, &count) != -1 &&
SDreadattr(sds[ib].id, attr_index, add_offset) != -1 )
sds[ib].offset = ((float32 *)add_offset)[indexlocator[ib]];
else {
attr_name = "add_offset";
if ( (attr_index = SDfindattr(sds[ib].id, attr_name)) != -1 &&
SDattrinfo(sds[ib].id, attr_index, dummy, &num_type, &count) != -1 &&
SDreadattr(sds[ib].id, attr_index, add_offset) != -1 )
sds[ib].offset = *add_offset;
}
sds[ib].fillvalue = (void *) malloc(1 * DFKNTsize(sds[ib].num_type));
if ( SDgetfillvalue(sds[ib].id, sds[ib].fillvalue) != 0 ) {
fprintf(stderr, "Cannot read fill value of SDS \"%s\".\n", sds[ib].name);
/* exit(1); commmented that*/
}
switch (sds[ib].rank) {
case 2:
sds[ib].Nl = sds[ib].dim_sizes[0];
sds[ib].Np = sds[ib].dim_sizes[1];
sds[ib].rowsperscan = (int)(NUM1KMROWPERSCAN * sds[ib].Np / (float)NUM1KMCOLPERSCAN + 0.5);
sds[ib].start[1] = 0;
sds[ib].edges[0] = sds[ib].rowsperscan;
sds[ib].edges[1] = sds[ib].Np;
break;
case 3:
sds[ib].Nl = sds[ib].dim_sizes[1];
sds[ib].Np = sds[ib].dim_sizes[2];
sds[ib].rowsperscan = (int)(NUM1KMROWPERSCAN * sds[ib].Np / (float)NUM1KMCOLPERSCAN + 0.5);
sds[ib].start[0] = indexlocator[ib];
sds[ib].start[2] = 0;
sds[ib].edges[0] = 1;
sds[ib].edges[1] = sds[ib].rowsperscan;
sds[ib].edges[2] = sds[ib].Np;
break;
default:
fprintf(stderr, "SDS rank must be 2 or 3.\n");
continue;
}
if (verbose)
printf("SDS \"%s\": %dx%d scale factor: %g offset: %g\n", sds[ib].name, sds[ib].Np, sds[ib].Nl, sds[ib].factor, sds[ib].offset);
if (sds[ib].num_type != numtypelocator[ib]) {
fprintf(stderr, "SDS \"%s\" has not the expected data type.\n", sds[ib].name);
exit(-1);
}
sds[ib].data = malloc(sds[ib].Np * sds[ib].rowsperscan * DFKNTsize(sds[ib].num_type));
if (!sds[ib].data) {
(void) fputs("Error allocating memory.\n", stderr);
exit(1);
}
}
if (sealevel || TOA) {
dem.id = -1;
dem.Nl = dem.Np = 0;
}
else {
/* dem.name = strdup(DEMSDSNAME); */
dem.name = DEMSDSNAME;
if ( (dem.index = SDnametoindex(dem.file_id, dem.name)) == -1 ) {
fprintf(stderr, "Cannot find SDS %s in file %s.\n", dem.name, dem.filename);
exit(1);
}
if ( (dem.id = SDselect(dem.file_id, dem.index)) == -1 ) {
fprintf(stderr, "Cannot select SDS no. %d\n", dem.index);
exit(1);
}
if (SDgetinfo(dem.id, dummy, &dem.rank, dem.dim_sizes, &dem.num_type, &dem.n_attr) == -1) {
fprintf(stderr, "Can't get info from SDS \"%s\" in file %s.\n", dem.name, dem.filename);
SDendaccess(dem.id);
exit(1);
}
dem.Nl = dem.dim_sizes[0];
dem.Np = dem.dim_sizes[1];
dem.rowsperscan = (int)(NUM1KMROWPERSCAN * dem.Np / (float)NUM1KMCOLPERSCAN + 0.5);
}
if ( sds[SOLZ].id == -1 ||
sds[SOLA].id == -1 ||
sds[SENZ].id == -1 ||
sds[SENA].id == -1 ||
sds[LON].id == -1 ||
sds[LAT].id == -1 ||
((dem.id == -1) && !sealevel && !TOA) ) {
fprintf(stderr, "Solar and Sensor angles and DEM are necessary to process granule.\n");
exit(1);
}
if ( sds[REFSDS].Np != sds[SOLZ].Np ||
sds[REFSDS].Np != sds[SOLA].Np ||
sds[REFSDS].Np != sds[SENZ].Np ||
sds[REFSDS].Np != sds[SENA].Np ||
sds[REFSDS].Np != sds[LON].Np ||
sds[REFSDS].Np != sds[LAT].Np ) {
fprintf(stderr, "Solar and Sensor angles must have identical dimensions.\n");
exit(1);
}
ib = 0;
while (sds[ib].id == -1) ib++;
if (ib >= Nbands) {
fprintf(stderr, "No L1B SDS can be read successfully.\n");
exit(1);
}
Nscans = sds[ib].Nl / sds[ib].rowsperscan;
/* finally, open output file */
if ( (sd_id = SDstart(filename, write_mode)) == -1 ) {
fprintf(stderr, "Cannot open output file %s.\n", filename);
exit(1);
}
if (!append) {
if (write_global_attributes(sd_id, MOD021KMfile, MOD02HKMfile,
MOD02QKMfile, maxsolz, sealevel, TOA, nearest)) {
fputs("Error writing global attributes.\n", stderr);
exit(1);
}
}
/* create output SDSs and set SDS-specific attributes and dimension names */
if (init_output_sds(sd_id, process, outsds, sds, gzip, verbose)) exit(1);
mus = (float *) malloc(sds[REFSDS].rowsperscan * sds[REFSDS].Np * sizeof(float));
height.data = (int16 *) malloc(sds[REFSDS].rowsperscan * sds[REFSDS].Np * sizeof(int16));
if (!mus || !height.data) {
(void) fputs("Error allocating memory.\n", stderr);
exit(1);
}
if (sealevel || TOA)
dem.data = (void *) NULL;
else {
dem.data = (int16 *) malloc(dem.Nl * dem.Np * sizeof(int16));
if (!dem.data) {
(void) fputs("Error allocating memory.\n", stderr);
exit(1);
}
}
if (!TOA) {
nbytes = Nbands * sds[REFSDS].rowsperscan * sds[REFSDS].Np * sizeof(float);
rhoray = (float *) malloc(nbytes);
sphalb = (float *) malloc(nbytes);
TtotraytH2O = (float *) malloc(nbytes);
tOG = (float *) malloc(nbytes);
if (!rhoray || !sphalb || !TtotraytH2O || !tOG) {
(void) fputs("Error allocating memory.\n", stderr);
exit(1);
}
}
solz = sds[SOLZ].data;
sola = sds[SOLA].data;
senz = sds[SENZ].data;
sena = sds[SENA].data;
solzfill = sds[SOLZ].fillvalue;
lon = sds[LON].data;
lat = sds[LAT].data;
lonfill = sds[LON].fillvalue;
latfill = sds[LAT].fillvalue;
for (ib = 0; ib < Nbands; ib++) l1bdata[ib] = sds[ib].data;
/* don't need DEM if --sealevel or --toa specified */
if (!sealevel && !TOA) {
dem.start[0] = 0;
dem.start[1] = 0;
dem.edges[0] = dem.Nl;
dem.edges[1] = dem.Np;
if (SDreaddata(dem.id, dem.start, NULL, dem.edges, dem.data) == -1) {
fprintf(stderr, " Can't read DEM SDS \"%s\"\n", dem.name);
exit(-1);
}
(void) SDendaccess(dem.id);
(void) SDend(dem.file_id);
}
/* loop over each MODIS scan */
for (iscan = 0; iscan < Nscans; iscan++) {
if ((iscan % NUM1KMROWPERSCAN == 0) && verbose)
printf("Processing scan %d...\n", iscan);
/* Fill scan buffer for each band to be processed.
Exit scan loop if error occurred while reading. */
if (read_scan(iscan, sds)) break;
for (idx = 0; idx < sds[REFSDS].rowsperscan*sds[REFSDS].Np; idx++) {
if (solz[idx] * sds[SOLZ].factor >= maxsolz)
solz[idx] = *solzfill;
if (!sealevel &&
(lon[idx] == *lonfill || lat[idx] == *latfill))
solz[idx] = *solzfill;
if (solz[idx] != *solzfill) {
mus[idx] = cos(solz[idx] * sds[SOLZ].factor * DEG2RAD);
if (sealevel || TOA)
((int16 *)height.data)[idx] = 0;
else
((int16 *)height.data)[idx] =
(int16) interp_dem(lat[idx],
lon[idx], &dem);
}
}
if (!TOA) {
for (irow=0; irow<sds[REFSDS].rowsperscan; irow++) {
for (jcol=0; jcol<sds[REFSDS].Np; jcol++) {
idx = irow * sds[REFSDS].Np + jcol;
if (solz[idx] == *solzfill) continue;
phi = sola[idx] * sds[SOLA].factor - sena[idx] * sds[SENA].factor;
muv = cos(senz[idx] * sds[SENZ].factor * DEG2RAD);
if ( getatmvariables(mus[idx], muv, phi, ((int16 *)height.data)[idx],
process,
&sphalb[idx * Nbands], &rhoray[idx * Nbands],
&TtotraytH2O[idx * Nbands], &tOG[idx * Nbands]) == -1 )
solz[idx] = *solzfill;
/* printf(" some data %f %f %f %f %f \n",senz[idx],phi,mus[idx],rhoray[idx * Nbands],tOG[idx * Nbands]);*/
}
}
}
for (ib=0; ib<Nbands; ib++) {
if (! process[ib]) continue;
aggfactor = outsds[ib].rowsperscan / sds[REFSDS].rowsperscan;
for (irow=0; irow<outsds[ib].rowsperscan; irow++) {
if (!nearest) {
fractrow = (float)irow / aggfactor - 0.5; /* We want fractrow integer on coarse pixel center */
crsrow1 = floor(fractrow);
crsrow2 = crsrow1 + 1;
if (crsrow1 < 0) crsrow1 = crsrow2 + 1;
if (crsrow2 > sds[REFSDS].rowsperscan - 1) crsrow2 = crsrow1 - 1;
t = (fractrow - crsrow1) / (crsrow2 - crsrow1);
}
for (jcol=0; jcol<outsds[ib].Np; jcol++) {
idx = irow * outsds[ib].Np + jcol;
crsidx = (int)(irow / aggfactor) * sds[REFSDS].Np + (int)(jcol / aggfactor);
if ( solz[crsidx] == *solzfill || /* Bad geolocation or night pixel */
l1bdata[ib][idx] >= 65528 ) { /* VIIRS SDR is read as uint16, fills start at 65528 */
if (l1bdata[ib][idx] == (65536 + MISSING))
((int16 *)outsds[ib].data)[idx] = 32768 + MISSING;
else
((int16 *)outsds[ib].data)[idx] = *(int16 *)outsds[ib].fillvalue;
continue;
}
if (nearest) {
mus0 = mus[crsidx];
if (! TOA) {
rhoray0 = rhoray[crsidx * Nbands + ib];
sphalb0 = sphalb[crsidx * Nbands + ib];
if ( sphalb0 <= 0.0F ) { /* Atm variables not computed successfully in this band */
((int16 *)outsds[ib].data)[idx] = *(int16 *)outsds[ib].fillvalue;
continue;
}
}
}
else {
fractcol = ((float) jcol) / aggfactor - 0.5F; /* We want fractcol integer on coarse pixel center */
crscol1 = (int) floor(fractcol);
crscol2 = crscol1 + 1;
if (crscol1 < 0) crscol1 = crscol2 + 1;
if (crscol2 > sds[REFSDS].Np - 1) crscol2 = crscol1 - 1;
u = (fractcol - crscol1) / (crscol2 - crscol1); /* We want u=0 on coarse pixel center */
crsidx11 = crsrow1 * sds[REFSDS].Np + crscol1;
crsidx12 = crsrow1 * sds[REFSDS].Np + crscol2;
crsidx21 = crsrow2 * sds[REFSDS].Np + crscol1;
crsidx22 = crsrow2 * sds[REFSDS].Np + crscol2;
/* mus0 = t * u * mus[crsidx22] + (1.0F - t) * u * mus[crsidx12] + t * (1.0F - u) * mus[crsidx21] + (1.0F - t) * (1.0F - u) * mus[crsidx11];
bad = (solz[crsidx11] == *solzfill) ||
(solz[crsidx12] == *solzfill) ||
(solz[crsidx21] == *solzfill) ||
(solz[crsidx22] == *solzfill);
commented by eric to handle the viirs fill value hardcoding */
bad = (solz[crsidx11] <-900.) ||
(solz[crsidx12] <-900.) ||
(solz[crsidx21] <-900.) ||
(solz[crsidx22] <-900.);
if (bad) {
((int16 *)outsds[ib].data)[idx] = *(int16 *)outsds[ib].fillvalue;
continue;
}
if (! TOA) {
rhoray11 = rhoray[crsidx11 * Nbands + ib];
rhoray12 = rhoray[crsidx12 * Nbands + ib];
rhoray21 = rhoray[crsidx21 * Nbands + ib];
rhoray22 = rhoray[crsidx22 * Nbands + ib];
rhoray0 = t * u * rhoray22 + (1.0F - t) * u * rhoray12 + t * (1.0F - u) * rhoray21 + (1.0F - t) * (1.0F - u) * rhoray11;
sphalb11 = sphalb[crsidx11 * Nbands + ib];
sphalb12 = sphalb[crsidx12 * Nbands + ib];
sphalb21 = sphalb[crsidx21 * Nbands + ib];
sphalb22 = sphalb[crsidx22 * Nbands + ib];
bad = (sphalb11 <= 0.0F) ||
(sphalb12 <= 0.0F) ||
(sphalb21 <= 0.0F) ||
(sphalb22 <= 0.0F);
if (bad) {
((int16 *)outsds[ib].data)[idx] = *(int16 *)outsds[ib].fillvalue;
continue;
}
sphalb0 = t * u * sphalb22 + (1.0F - t) * u * sphalb12 + t * (1.0F - u) * sphalb21 + (1.0F - t) * (1.0F - u) * sphalb11;
}
}
/* TOA reflectance */
/*printf(" mus0 is %f\n",mus0);*/
refl = (l1bdata[ib][idx] - sds[ib].offset) * sds[ib].factor /*/ mus0 commented by Eric who suspected something*/;
/* corrected reflectance */
if (!TOA)
refl = correctedrefl(refl, TtotraytH2O[crsidx * Nbands + ib],
tOG[crsidx * Nbands + ib], rhoray0, sphalb0);
/* reflectance bounds checking */
if (refl > reflmax) refl = reflmax;
if (refl < reflmin) refl = reflmin;
((int16 *)outsds[ib].data)[idx] = (int16) (refl / outsds[ib].factor + 0.5);
}
}
}
/* write current scan line for all processed bands */
if (write_scan(iscan, process, outsds)) {
fprintf(stderr, "Cannot write scan %d of SDS %s\n",
iscan, outsds[ib].name);
exit(1);
}
} /* end of scan loop */
for (ib = 0; ib < Nitems; ib++)
if (sds[ib].id != -1) SDendaccess(sds[ib].id);
for (ib = 0; ib < Nbands; ib++)
if (process[ib]) SDendaccess(outsds[ib].id);
SDend(MOD02QKMfile_id);
SDend(MOD02HKMfile_id);
SDend(MOD021KMfile_id);
SDend(sd_id);
/* ----- free memory ----- */
for (ib = 0; ib < Nitems; ib++) {
if (sds[ib].fillvalue) free(sds[ib].fillvalue);
if (sds[ib].data) free(sds[ib].data);
}
free(height.data);
free(mus);
if (!TOA) {
free(tOG);
free(TtotraytH2O);
free(sphalb);
free(rhoray);
}
/* not allocated if --sealevel specified */
if (dem.data) free(dem.data);
return 0;
}
void
RemapHDF4::findMinMaxandGenerateHistogram()
{
QProgressDialog progress("Generating Histogram",
"Cancel",
0, 100,
0);
progress.setMinimumDuration(0);
float rSize;
float rMin;
m_histogram.clear();
if (m_voxelType == _UChar ||
m_voxelType == _Char)
{
if (m_voxelType == _UChar) rMin = 0;
if (m_voxelType == _Char) rMin = -127;
rSize = 255;
for(uint i=0; i<256; i++)
m_histogram.append(0);
}
else if (m_voxelType == _UShort ||
m_voxelType == _Short)
{
if (m_voxelType == _UShort) rMin = 0;
if (m_voxelType == _Short) rMin = -32767;
rSize = 65536;
for(uint i=0; i<65536; i++)
m_histogram.append(0);
}
else
{
QMessageBox::information(0, "Error", "Why am i here ???");
return;
}
int nX, nY, nZ;
nX = m_depth;
nY = m_width;
nZ = m_height;
int nbytes = nY*nZ*m_bytesPerVoxel;
uchar *tmp = new uchar[nbytes];
int32 start[2], edges[2];
start[0] = start[1] = 0;
edges[0] = m_width;
edges[1] = m_height;
for(uint i=0; i<m_depth; i++)
{
progress.setValue((int)(100.0*(float)i/(float)m_depth));
qApp->processEvents();
int32 sd_id = SDstart(m_imageList[i].toAscii().data(),
DFACC_READ);
int32 sds_id = SDselect(sd_id, m_Index);
int status = SDreaddata(sds_id,
start, NULL, edges,
(VOIDP)tmp);
status = SDendaccess(sds_id);
status = SDend(sd_id);
if (m_voxelType == _UChar)
{
uchar *ptr = tmp;
MINMAXANDHISTOGRAM();
}
else if (m_voxelType == _Char)
{
char *ptr = (char*) tmp;
MINMAXANDHISTOGRAM();
}
if (m_voxelType == _UShort)
{
ushort *ptr = (ushort*) tmp;
MINMAXANDHISTOGRAM();
}
else if (m_voxelType == _Short)
{
short *ptr = (short*) tmp;
MINMAXANDHISTOGRAM();
}
else if (m_voxelType == _Int)
{
int *ptr = (int*) tmp;
MINMAXANDHISTOGRAM();
}
else if (m_voxelType == _Float)
{
float *ptr = (float*) tmp;
MINMAXANDHISTOGRAM();
}
}
delete [] tmp;
while(m_histogram.last() == 0)
m_histogram.removeLast();
while(m_histogram.first() == 0)
m_histogram.removeFirst();
progress.setValue(100);
qApp->processEvents();
}
