diff options
| -rw-r--r-- | libcrystfel/src/hdf5-file.c | 181 |
1 files changed, 79 insertions, 102 deletions
diff --git a/libcrystfel/src/hdf5-file.c b/libcrystfel/src/hdf5-file.c index 1852f2d5..02cb66ee 100644 --- a/libcrystfel/src/hdf5-file.c +++ b/libcrystfel/src/hdf5-file.c @@ -986,19 +986,82 @@ int hdf5_read(struct hdfile *f, struct image *image, const char *element, } +static void load_mask(struct hdfile *f, struct event *ev, char *mask, + const char *pname, struct image *image, + size_t p_w, size_t sum_p_h, + hsize_t *f_offset, hsize_t *f_count, + hsize_t *m_offset, hsize_t *m_count) +{ + hid_t mask_dataspace, mask_dh; + int exists; + int check, r; + hid_t memspace; + hsize_t dimsm[2]; + + if ( ev != NULL ) { + mask = retrieve_full_path(ev, mask); + } + + exists = check_path_existence(f->fh, mask); + if ( !exists ) { + ERROR("Cannot find flags for panel %s\n", pname); + goto err; + } + + mask_dh = H5Dopen2(f->fh, mask, H5P_DEFAULT); + if ( mask_dh <= 0 ) { + ERROR("Couldn't open flags for panel %s\n", pname); + goto err; + } + + mask_dataspace = H5Dget_space(mask_dh); + check = H5Sselect_hyperslab(mask_dataspace, H5S_SELECT_SET, + f_offset, NULL, f_count, NULL); + if ( check < 0 ) { + ERROR("Error selecting mask dataspace for panel %s\n", pname); + goto err; + } + + dimsm[0] = sum_p_h; + dimsm[1] = p_w; + memspace = H5Screate_simple(2, dimsm, NULL); + check = H5Sselect_hyperslab(memspace, H5S_SELECT_SET, + m_offset, NULL, m_count, NULL); + if ( check < 0 ) { + ERROR("Error selecting memory dataspace for panel %s\n", pname); + goto err; + } + + r = H5Dread(mask_dh, H5T_NATIVE_UINT16, memspace, + mask_dataspace, H5P_DEFAULT, image->flags); + if ( r < 0 ) { + ERROR("Couldn't read flags for panel %s\n", pname); + goto err; + } + + H5Sclose(mask_dataspace); + H5Dclose(mask_dh); + if ( ev != NULL ) free(mask); + + return; + +err: + if ( ev != NULL ) free(mask); + free(image->flags); + image->flags = NULL; + return; +} + + int hdf5_read2(struct hdfile *f, struct image *image, struct event *ev, int satcorr) { herr_t r; float *buf; - uint16_t *flags; int sum_p_h; int p_w; int m_min_fs, curr_ss, m_max_fs; - int mask_is_present; - int no_mask_loaded; int pi; - hid_t mask_dh = 0; if ( image->det == NULL ) { ERROR("Geometry not available\n"); @@ -1015,23 +1078,27 @@ int hdf5_read2(struct hdfile *f, struct image *image, struct event *ev, return 1; } - if ( image->det->panels[pi].mask != NULL ) mask_is_present = 1; - sum_p_h += image->det->panels[pi].h; } buf = malloc(sizeof(float)*p_w*sum_p_h); - if ( mask_is_present ) { - flags = calloc(p_w*sum_p_h,sizeof(uint16_t)); + if ( buf == NULL ) { + ERROR("Failed to allocate memory for image\n"); + return 1; } image->width = p_w; image->height = sum_p_h; + image->flags = calloc(p_w*sum_p_h,sizeof(uint16_t)); + if ( image->flags == NULL ) { + ERROR("Failed to allocate memory for flags\n"); + return 1; + } + m_min_fs = 0; m_max_fs = p_w-1; curr_ss = 0; - no_mask_loaded = 1; for ( pi=0; pi<image->det->n_panels; pi++ ) { @@ -1042,7 +1109,7 @@ int hdf5_read2(struct hdfile *f, struct image *image, struct event *ev, hsize_t m_offset[2], m_count[2]; hsize_t dimsm[2]; herr_t check; - hid_t dataspace, memspace, mask_dataspace; + hid_t dataspace, memspace; int fail; struct panel *p; @@ -1170,92 +1237,8 @@ int hdf5_read2(struct hdfile *f, struct image *image, struct event *ev, H5Sclose(memspace); if ( p->mask != NULL ) { - - if ( ev != NULL ) { - - int exists; - char *mask_full_path; - - mask_full_path = retrieve_full_path(ev, p->mask); - - exists = check_path_existence(f->fh, - mask_full_path); - if ( !exists ) { - ERROR("Cannot find flags for panel %s\n", - p->name); - return 1; - } - - mask_dh = H5Dopen2(f->fh, mask_full_path, - H5P_DEFAULT); - - if ( mask_dh <= 0 ) { - ERROR("Couldn't open flags for panel %s\n", - p->name); - image->flags = NULL; - } else { - - mask_dataspace = H5Dget_space(mask_dh); - check = H5Sselect_hyperslab(mask_dataspace, H5S_SELECT_SET, - f_offset, NULL, f_count, NULL); - if ( check < 0 ) { - ERROR("Error selecting mask dataspace for panel %s\n", - p->name); - } - r = H5Dread(mask_dh, H5T_NATIVE_UINT16, memspace, - mask_dataspace, H5P_DEFAULT, flags); - if ( r < 0 ) { - ERROR("Couldn't read flags for panel %s\n", - p->name); - } else { - no_mask_loaded = 0; - } - - H5Sclose(mask_dataspace); - H5Dclose(mask_dh); - - } - - } else { - - int exists; - exists = check_path_existence(f->fh, p->mask); - if ( !exists ) { - ERROR("Cannot find flags for panel %s\n", - p->name); - return 1; - } - - mask_dh = H5Dopen2(f->fh, p->mask, H5P_DEFAULT); - if ( mask_dh <= 0 ) { - ERROR("Couldn't open flags for panel %s\n", - p->name); - image->flags = NULL; - } else { - - mask_dataspace = H5Dget_space(mask_dh); - check = H5Sselect_hyperslab(mask_dataspace, H5S_SELECT_SET, - f_offset, NULL, f_count, NULL); - if ( check < 0 ) { - ERROR("Error selecting mask dataspace for panel %s\n", - p->name); - } - r = H5Dread(mask_dh, H5T_NATIVE_UINT16, memspace, - mask_dataspace, H5P_DEFAULT, flags); - if ( r < 0 ) { - ERROR("Couldn't read flags for panel %s\n", - p->name); - } else { - no_mask_loaded = 0; - } - - H5Sclose(mask_dataspace); - H5Dclose(mask_dh); - - } - - } - + load_mask(f, ev, p->mask, p->name, image, p_w, sum_p_h, + f_offset, f_count, m_offset, m_count); } p->min_fs = m_min_fs; @@ -1271,12 +1254,6 @@ int hdf5_read2(struct hdfile *f, struct image *image, struct event *ev, image->data = buf; - if ( no_mask_loaded ) { - free(flags); - } else { - image->flags = flags; - } - if ( satcorr ) debodge_saturation(f, image); fill_in_values(image->det, f, ev); |