diff options
| -rw-r--r-- | libcrystfel/src/hdf5-file.c | 69 |
1 files changed, 65 insertions, 4 deletions
diff --git a/libcrystfel/src/hdf5-file.c b/libcrystfel/src/hdf5-file.c index a7430fb2..36ded323 100644 --- a/libcrystfel/src/hdf5-file.c +++ b/libcrystfel/src/hdf5-file.c @@ -2041,6 +2041,56 @@ void copy_hdf5_fields(struct hdfile *f, const struct copy_hdf5_field *copyme, } +static int make_dataspaces(hid_t dh, struct event *ev, hid_t *memspace, + hid_t *filespace) +{ + hsize_t *f_offset, *f_count; + hsize_t *m_offset, *m_count; + hid_t sh, mh; + int ndims; + int i; + + /* Check that there are at least as many dim entries as dimensions */ + sh = H5Dget_space(dh); + ndims = H5Sget_simple_extent_ndims(sh); + if ( ndims > ev->dim_length ) { + return 1; + } + + /* Now set up arrays of offsets and counts in files and memory */ + f_offset = malloc(sizeof(hsize_t)*ndims); + f_count = malloc(sizeof(hsize_t)*ndims); + m_offset = malloc(sizeof(hsize_t)*ndims); + m_count = malloc(sizeof(hsize_t)*ndims); + if ( (f_offset == NULL) || (f_count == NULL) + || (m_offset == NULL) || (m_count == NULL) ) return 1; + + for ( i=0; i<ev->dim_length; i++ ) { + f_offset[i] = ev->dim_entries[i]; + f_count[i] = 1; + m_offset[i] = 0; + m_count[i] = 1; + } + + if ( H5Sselect_hyperslab(sh, H5S_SELECT_SET, + f_offset, NULL, f_count, NULL) ) return 1; + + free(f_offset); + free(f_count); + + mh = H5Screate_simple(ndims, m_count, NULL); + if ( H5Sselect_hyperslab(mh, H5S_SELECT_SET, + m_offset, NULL, m_count, NULL) ) return 1; + free(m_offset); + free(m_count); + + *memspace = mh; + *filespace = sh; + + return 0; +} + + char *hdfile_get_string_value(struct hdfile *f, const char *name, struct event *ev) { @@ -2077,22 +2127,33 @@ char *hdfile_get_string_value(struct hdfile *f, const char *name, H5Tclose(type); free(subst_name); return "WTF?"; - } + } else if ( v > 0 ) { - if ( v && (v>0) ) { + hid_t memspace, filespace; - r = H5Dread(dh, type, H5S_ALL, H5S_ALL, + if ( make_dataspaces(dh, ev, &memspace, &filespace) ) { + H5Tclose(type); + free(subst_name); + return strdup("[couldn't make dataspaces]"); + } + + r = H5Dread(dh, type, memspace, filespace, H5P_DEFAULT, &tmp); if ( r < 0 ) { H5Tclose(type); free(subst_name); - return NULL; + return strdup("[couldn't read vlen string]"); } + H5Sclose(memspace); + H5Sclose(filespace); + return tmp; } else { + /* v == 0 */ + size = H5Tget_size(type); tmp = malloc(size+1); |