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modified reading of NX_class attribute - to accommodate both

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DATATYPE  H5T_STRING {
      STRSIZE 14;
      STRPAD H5T_STR_NULLTERM;
      CSET H5T_CSET_ASCII;
      CTYPE H5T_C_S1;
   }

and

   DATATYPE  H5T_STRING {
      STRSIZE H5T_VARIABLE;
      STRPAD H5T_STR_NULLTERM;
      CSET H5T_CSET_UTF8;
      CTYPE H5T_C_S1;
   }
This commit is contained in:
Clemens Vonrhein
2024-12-17 09:59:55 +00:00
parent 4cf18ceff4
commit d7801cdb54
1 changed files with 36 additions and 61 deletions
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src/file.c
+36 -61
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@@ -578,28 +578,28 @@ int get_dectris_eiger_pixel_mask(const struct ds_desc_t *desc, int *buffer) {
int n_filters = H5Pget_nfilters(dcpl);
H5Z_filter_t filter_id;
if (n_filters>0) {
unsigned int flags;
size_t nelmts = 1;
unsigned int values_out[1] = {99};
char filter_name[80];
filter_id = H5Pget_filter(dcpl, (unsigned) 0, &flags, &nelmts, values_out, sizeof(filter_name), filter_name, NULL);
if (filter_id>=0) {
fprintf(stderr," filter name =\"%s\"\n",filter_name);
}
unsigned int flags;
size_t nelmts = 1;
unsigned int values_out[1] = {99};
char filter_name[80];
filter_id = H5Pget_filter(dcpl, (unsigned) 0, &flags, &nelmts, values_out, sizeof(filter_name), filter_name, NULL);
if (filter_id>=0) {
fprintf(stderr," filter name =\"%s\"\n",filter_name);
}
}
err = H5Dread(ds_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, buffer);
if (err < 0) {
if (n_filters>0) {
ERROR_JUMP(-1, close_dataset, "Error reading detectorSpecific/pixel_mask with filter(s)");
}
else {
ERROR_JUMP(-1, close_dataset, "Error reading detectorSpecific/pixel_mask");
}
if (n_filters>0) {
ERROR_JUMP(-1, close_dataset, "Error reading detectorSpecific/pixel_mask with filter(s)");
}
else {
ERROR_JUMP(-1, close_dataset, "Error reading detectorSpecific/pixel_mask");
}
}
if (H5Zfilter_avail(BS_H5_FILTER_ID)) {
fprintf(stderr," bitshuffle filter is available now since H5Dread (of pixel-mask) triggered loading of the filter.\n");
fprintf(stderr," bitshuffle filter is available now since H5Dread (of pixel-mask) triggered loading of the filter.\n");
}
close_dataset:
@@ -630,9 +630,9 @@ herr_t det_visit_callback(hid_t root_id, const char *name,
/* check for an "NX_class" attribute */
{
int str_size = 0;
void *buffer = NULL;
hid_t a_id, t_id, mt_id;
char* buffer = (char*)malloc(1);
buffer[0] = '\0';
hid_t a_id, t_id;
if (H5Aexists(g_id, "NX_class") <= 0) {
/* not an error - just close group and allow continuation */
retval = 0;
@@ -652,70 +652,45 @@ herr_t det_visit_callback(hid_t root_id, const char *name,
if (t_id < 0) {
ERROR_JUMP(-1, close_attr, "Error getting datatype");
}
if (H5Tis_variable_str(t_id) > 0) {
str_size = -1;
buffer = malloc(sizeof(char *));
} else {
str_size = H5Tget_size(t_id);
buffer = malloc(str_size + 1);
H5A_info_t a_info;
herr_t err = H5Aget_info(a_id, &a_info);
if (err<0) {
ERROR_JUMP(-1, close_type,
"Unable to get attribute info for NX_class");
}
else {
if (a_info.cset != H5T_CSET_ASCII && a_info.cset != H5T_CSET_UTF8) {
fprintf(stderr," %s : NX_class attribute info cset = unknown with size %d\n",name,(int) a_info.data_size);
}
}
buffer = (char *)malloc(sizeof(char)*(H5Tget_size(t_id)+1));
if (!buffer) {
ERROR_JUMP(-1, close_type, "Error allocating string buffer");
}
mt_id = H5Tcopy(H5T_C_S1);
if (mt_id < 0) {
ERROR_JUMP(-1, free_buffer, "Error creating HDF5 String datatype");
}
// set the target string type to be one longer than the recorded string
// in keeping with the malloc'd buffer - if this is already a null
// terminated string then we will just have two nulls, if it is not
// then we won't clobber the last char in the buffer with a null in the
// H5Aread call
if (H5Tset_size(mt_id, str_size == -1 ? H5T_VARIABLE : str_size + 1) < 0) {
char message[64];
sprintf(message, "Error setting string datatype to size %d", str_size);
ERROR_JUMP(-1, close_mtype, message);
}
if (H5Aread(a_id, mt_id, buffer) < 0) {
if (H5Aread(a_id, t_id, buffer) < 0) {
char message[256];
sprintf(
message,
"H5OVisit callback: Error reading NX_class attribute on group %.128s",
name);
ERROR_JUMP(-1, close_mtype, message);
ERROR_JUMP(-1, free_buffer, message);
}
/* at least one file has been seen where the NX_class attribute was not null
* terminated and extraneous bytes where being read by strcmp - set the end
* byte to null
*/
if (str_size > 0)
((char *)buffer)[str_size] = '\0';
/* test for NXdata or NXdetector */
{
char *nxclass = str_size > 0 ? (char *)buffer : *((char **)buffer);
if (strcmp("NXdata", nxclass) == 0) {
if (strcmp("NXdata", buffer) == 0) {
hid_t out_id = H5Gopen(root_id, name, H5P_DEFAULT);
output_data->nxdata = out_id;
} else if (strcmp("NXdetector", nxclass) == 0) {
}
else if (strcmp("NXdetector", buffer) == 0) {
hid_t out_id = H5Gopen(root_id, name, H5P_DEFAULT);
output_data->nxdetector = out_id;
}
}
if (str_size == -1) {
hsize_t dims[1] = {1};
hid_t s_id = H5Screate_simple(1, dims, NULL);
H5Sselect_all(s_id);
H5Dvlen_reclaim(mt_id, s_id, H5P_DEFAULT, buffer);
H5Sclose(s_id);
}
close_mtype:
H5Tclose(mt_id);
free_buffer:
free(buffer);
close_type: