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-rw-r--r--libcrystfel/src/image-hdf5.c1223
1 files changed, 1223 insertions, 0 deletions
diff --git a/libcrystfel/src/image-hdf5.c b/libcrystfel/src/image-hdf5.c
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+++ b/libcrystfel/src/image-hdf5.c
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+/*
+ * image-hdf5.c
+ *
+ * Image loading, HDF5 parts
+ *
+ * Copyright © 2012-2020 Deutsches Elektronen-Synchrotron DESY,
+ * a research centre of the Helmholtz Association.
+ *
+ * Authors:
+ * 2020 Thomas White <taw@physics.org>
+ *
+ * This file is part of CrystFEL.
+ *
+ * CrystFEL is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * CrystFEL is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with CrystFEL. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+#include <config.h>
+
+#include <stdlib.h>
+#include <assert.h>
+#include <math.h>
+#include <stdio.h>
+#include <hdf5.h>
+#include <unistd.h>
+
+#include "image.h"
+#include "utils.h"
+#include "events.h"
+#include "detgeom.h"
+
+#include "datatemplate.h"
+#include "datatemplate_priv.h"
+
+
+static int load_hdf5_hyperslab(struct panel_template *p,
+ const char *filename,
+ const char *event,
+ void **pdata,
+ hid_t el_type, size_t el_size,
+ int skip_placeholders_ok,
+ const char *path_spec)
+{
+ struct event *ev;
+ hid_t fh;
+ herr_t r;
+ hsize_t *f_offset, *f_count;
+ hid_t dh;
+ int hsi;
+ herr_t check;
+ hid_t dataspace, memspace;
+ hsize_t dims[2];
+ char *panel_full_path;
+ void *data;
+ int ndims, dpos;
+ int skip_placeholders = 0;
+
+ if ( access(filename, R_OK) == -1 ) {
+ ERROR("File does not exist or cannot be read: %s\n",
+ filename);
+ return 1;
+ }
+
+ fh = H5Fopen(filename, H5F_ACC_RDONLY, H5P_DEFAULT);
+ if ( fh < 0 ) {
+ ERROR("Couldn't open file: %s\n", filename);
+ return 1;
+ }
+
+ ev = get_event_from_event_string(event);
+ if ( (ev == NULL) && (event != NULL) ) {
+ ERROR("Invalid event identifier '%s'\n", event);
+ H5Fclose(fh);
+ return 1;
+ }
+
+ panel_full_path = retrieve_full_path(ev, path_spec);
+
+ if ( !check_path_existence(fh, panel_full_path) ) {
+ ERROR("Cannot find data for panel %s (%s)\n",
+ p->name, panel_full_path);
+ free_event(ev);
+ H5Fclose(fh);
+ return 1;
+ }
+
+ dh = H5Dopen2(fh, panel_full_path, H5P_DEFAULT);
+ if ( dh < 0 ) {
+ ERROR("Cannot open data for panel %s (%s)\n",
+ p->name, panel_full_path);
+ free(panel_full_path);
+ free_event(ev);
+ H5Fclose(fh);
+ return 1;
+ }
+
+ free(panel_full_path);
+
+ /* Set up dataspace for file
+ * (determine where to read the data from) */
+ dataspace = H5Dget_space(dh);
+ ndims = H5Sget_simple_extent_ndims(dataspace);
+ if ( ndims < 0 ) {
+ ERROR("Failed to get number of dimensions for panel %s\n",
+ p->name);
+ free_event(ev);
+ H5Fclose(fh);
+ return 1;
+ }
+
+ if ( ndims != p->dim_structure->num_dims ) {
+ /* Dimensionality doesn't match */
+ int n_nonplaceholder = 0;
+ for ( hsi=0; hsi<p->dim_structure->num_dims; hsi++ ) {
+ if ( p->dim_structure->dims[hsi] != HYSL_PLACEHOLDER ) {
+ n_nonplaceholder++;
+ }
+ }
+
+ /* If the dimensions match after excluding
+ * placeholders, it's OK - probably a static mask
+ * in a multi-event file. */
+ if ( ndims == n_nonplaceholder ) {
+ skip_placeholders = 1;
+ }
+ }
+
+ f_offset = malloc(ndims*sizeof(hsize_t));
+ f_count = malloc(ndims*sizeof(hsize_t));
+ if ( (f_offset == NULL) || (f_count == NULL ) ) {
+ ERROR("Failed to allocate offset or count.\n");
+ free_event(ev);
+ H5Fclose(fh);
+ return 1;
+ }
+
+ dpos = 0;
+ for ( hsi=0; hsi<p->dim_structure->num_dims; hsi++ ) {
+
+ switch ( p->dim_structure->dims[hsi] ) {
+
+ case HYSL_FS:
+ f_offset[dpos] = p->orig_min_fs;
+ f_count[dpos] = p->orig_max_fs - p->orig_min_fs+1;
+ dpos++;
+ break;
+
+ case HYSL_SS:
+ f_offset[dpos] = p->orig_min_ss;
+ f_count[dpos] = p->orig_max_ss - p->orig_min_ss+1;
+ dpos++;
+ break;
+
+ case HYSL_PLACEHOLDER:
+ if ( !skip_placeholders ) {
+ f_offset[dpos] = ev->dim_entries[0];
+ f_count[dpos] = 1;
+ dpos++;
+ }
+ break;
+
+ default:
+ f_offset[dpos] = p->dim_structure->dims[hsi];
+ f_count[dpos] = 1;
+ dpos++;
+ break;
+
+ }
+
+ }
+
+ check = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET,
+ f_offset, NULL, f_count, NULL);
+ if ( check < 0 ) {
+ ERROR("Error selecting file dataspace for panel %s\n",
+ p->name);
+ free(f_offset);
+ free(f_count);
+ free_event(ev);
+ H5Fclose(fh);
+ return 1;
+ }
+
+ dims[0] = p->orig_max_ss - p->orig_min_ss + 1;
+ dims[1] = p->orig_max_fs - p->orig_min_fs + 1;
+ memspace = H5Screate_simple(2, dims, NULL);
+
+ data = malloc(dims[0]*dims[1]*el_size);
+ if ( data == NULL ) {
+ ERROR("Failed to allocate panel %s\n", p->name);
+ free(f_offset);
+ free(f_count);
+ free_event(ev);
+ H5Fclose(fh);
+ return 1;
+ }
+
+ r = H5Dread(dh, el_type, memspace, dataspace,
+ H5P_DEFAULT, data);
+ if ( r < 0 ) {
+ ERROR("Couldn't read data for panel %s\n",
+ p->name);
+ free(f_offset);
+ free(f_count);
+ free(data);
+ free_event(ev);
+ H5Fclose(fh);
+ return 1;
+ }
+
+ H5Dclose(dh);
+ H5Sclose(dataspace);
+ free(f_offset);
+ free(f_count);
+ free_event(ev);
+ H5Fclose(fh);
+
+ *pdata = data;
+ return 0;
+}
+
+
+struct image *image_hdf5_read(DataTemplate *dtempl,
+ const char *filename, const char *event)
+{
+ struct image *image;
+ int i;
+
+ image = image_new();
+ if ( image == NULL ) {
+ ERROR("Couldn't allocate image structure.\n");
+ return NULL;
+ }
+
+ image->dp = malloc(dtempl->n_panels*sizeof(float *));
+ if ( image->dp == NULL ) {
+ ERROR("Failed to allocate data array.\n");
+ image_free(image);
+ return NULL;
+ }
+
+ /* Set all pointers to NULL for easier clean-up */
+ for ( i=0; i<dtempl->n_panels; i++ ) image->dp[i] = NULL;
+
+ for ( i=0; i<dtempl->n_panels; i++ ) {
+ if ( load_hdf5_hyperslab(&dtempl->panels[i], filename,
+ event, (void *)&image->dp[i],
+ H5T_NATIVE_FLOAT,
+ sizeof(float), 0,
+ dtempl->panels[i].data) )
+ {
+ ERROR("Failed to load panel data\n");
+ image_free(image);
+ return NULL;
+ }
+ }
+
+ image->filename = strdup(filename);
+ image->ev = safe_strdup(event);
+
+ return image;
+}
+
+
+int image_hdf5_read_mask(struct panel_template *p,
+ const char *filename, const char *event,
+ int *bad, int mask_good, int mask_bad)
+{
+ int p_w, p_h;
+ int *mask = NULL;
+ long unsigned int j;
+
+ p_w = p->orig_max_fs - p->orig_min_fs + 1;
+ p_h = p->orig_max_ss - p->orig_min_ss + 1;
+
+ if ( load_hdf5_hyperslab(p, filename, event,
+ (void *)&mask, H5T_NATIVE_INT,
+ sizeof(int), 1, p->mask) )
+ {
+ ERROR("Failed to load mask data\n");
+ free(mask);
+ return 1;
+ }
+
+ for ( j=0; j<p_w*p_h; j++ ) {
+
+ /* Bad if it's missing any of the "good" bits */
+ if ( (mask[j] & mask_good) != mask_good ) bad[j] = 1;
+
+ /* Bad if it has any of the "bad" bits. */
+ if ( mask[j] & mask_bad ) bad[j] = 1;
+
+ }
+
+ free(mask);
+ return 0;
+}
+
+
+double image_hdf5_get_value(const char *name, const char *filename,
+ const char *event)
+{
+ hid_t dh;
+ hid_t type;
+ hid_t class;
+ hid_t sh;
+ hid_t ms;
+ hsize_t *f_offset = NULL;
+ hsize_t *f_count = NULL;
+ hsize_t m_offset[1];
+ hsize_t m_count[1];
+ hsize_t msdims[1];
+ hsize_t size[64];
+ herr_t r;
+ herr_t check;
+ int check_pe;
+ int dim_flag;
+ int ndims;
+ int i;
+ char *subst_name = NULL;
+ struct event *ev;
+ hid_t fh;
+ double val;
+
+ if ( access(filename, R_OK) == -1 ) {
+ ERROR("File does not exist or cannot be read: %s\n", filename);
+ return NAN;
+ }
+
+ fh = H5Fopen(filename, H5F_ACC_RDONLY, H5P_DEFAULT);
+ if ( fh < 0 ) {
+ ERROR("Couldn't open file: %s\n", filename);
+ return NAN;
+ }
+ ev = get_event_from_event_string(event);
+ if ( (ev == NULL) && (event != NULL) ) {
+ ERROR("Invalid event identifier '%s'\n", event);
+ H5Fclose(fh);
+ return NAN;
+ }
+
+ subst_name = retrieve_full_path(ev, name);
+
+ check_pe = check_path_existence(fh, subst_name);
+ if ( check_pe == 0 ) {
+ ERROR("No such event-based numeric field '%s'\n", subst_name);
+ return NAN;
+ }
+
+ dh = H5Dopen2(fh, subst_name, H5P_DEFAULT);
+ type = H5Dget_type(dh);
+ class = H5Tget_class(type);
+
+ if ( (class != H5T_FLOAT) && (class != H5T_INTEGER) ) {
+ ERROR("Not a floating point or integer value.\n");
+ H5Tclose(type);
+ H5Dclose(dh);
+ return NAN;
+ }
+
+ /* Get the dimensionality. We have to cope with scalars expressed as
+ * arrays with all dimensions 1, as well as zero-d arrays. */
+ sh = H5Dget_space(dh);
+ ndims = H5Sget_simple_extent_ndims(sh);
+ if ( ndims > 64 ) {
+ ERROR("Too many dimensions for numeric value\n");
+ H5Tclose(type);
+ H5Dclose(dh);
+ return NAN;
+ }
+ H5Sget_simple_extent_dims(sh, size, NULL);
+
+ m_offset[0] = 0;
+ m_count[0] = 1;
+ msdims[0] = 1;
+ ms = H5Screate_simple(1,msdims,NULL);
+
+ /* Check that the size in all dimensions is 1
+ * or that one of the dimensions has the same
+ * size as the hyperplane events */
+
+ dim_flag = 0;
+
+ for ( i=0; i<ndims; i++ ) {
+ if ( size[i] == 1 ) continue;
+ if ( ( i==0 ) && (ev != NULL) && (size[i] > ev->dim_entries[0]) ) {
+ dim_flag = 1;
+ } else {
+ H5Tclose(type);
+ H5Dclose(dh);
+ return NAN;
+ }
+ }
+
+ if ( dim_flag == 0 ) {
+
+ if ( H5Dread(dh, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL,
+ H5P_DEFAULT, &val) < 0 )
+ {
+ ERROR("Couldn't read value.\n");
+ H5Tclose(type);
+ H5Dclose(dh);
+ return NAN;
+ }
+
+ } else {
+
+ f_offset = malloc(ndims*sizeof(hsize_t));
+ f_count = malloc(ndims*sizeof(hsize_t));
+
+ for ( i=0; i<ndims; i++ ) {
+
+ if ( i == 0 ) {
+ f_offset[i] = ev->dim_entries[0];
+ f_count[i] = 1;
+ } else {
+ f_offset[i] = 0;
+ f_count[i] = 0;
+ }
+
+ }
+
+ check = H5Sselect_hyperslab(sh, H5S_SELECT_SET,
+ f_offset, NULL, f_count, NULL);
+ if ( check <0 ) {
+ ERROR("Error selecting dataspace for float value");
+ free(f_offset);
+ free(f_count);
+ return NAN;
+ }
+
+ ms = H5Screate_simple(1,msdims,NULL);
+ check = H5Sselect_hyperslab(ms, H5S_SELECT_SET,
+ m_offset, NULL, m_count, NULL);
+ if ( check < 0 ) {
+ ERROR("Error selecting memory dataspace for float value");
+ free(f_offset);
+ free(f_count);
+ return NAN;
+ }
+
+ r = H5Dread(dh, H5T_NATIVE_DOUBLE, ms, sh, H5P_DEFAULT, &val);
+ if ( r < 0 ) {
+ ERROR("Couldn't read value.\n");
+ H5Tclose(type);
+ H5Dclose(dh);
+ return NAN;
+ }
+
+ }
+
+ free_event(ev);
+ free(subst_name);
+ H5Fclose(fh);
+
+ return val;
+}
+
+
+static int read_peak_count(hid_t fh, char *path, int line,
+ int *num_peaks)
+{
+
+ hid_t dh, sh, mh;
+ hsize_t size[1];
+ hsize_t max_size[1];
+ hsize_t offset[1], count[1];
+ hsize_t m_offset[1], m_count[1], dimmh[1];
+ int tw, r;
+
+ dh = H5Dopen2(fh, path, H5P_DEFAULT);
+ if ( dh < 0 ) {
+ ERROR("Data block %s not found.\n", path);
+ return 1;
+ }
+
+ sh = H5Dget_space(dh);
+ if ( sh < 0 ) {
+ H5Dclose(dh);
+ ERROR("Couldn't get dataspace for data.\n");
+ return 1;
+ }
+
+ if ( H5Sget_simple_extent_ndims(sh) != 1 ) {
+ ERROR("Data block %s has the wrong dimensionality (%i).\n",
+ path, H5Sget_simple_extent_ndims(sh));
+ H5Sclose(sh);
+ H5Dclose(dh);
+ return 1;
+ }
+
+ H5Sget_simple_extent_dims(sh, size, max_size);
+
+ tw = size[0];
+
+ if ( line > tw-1 ) {
+ H5Sclose(sh);
+ H5Dclose(dh);
+ ERROR("Data block %s does not contain data for required event.\n",
+ path);
+ return 1;
+ }
+
+ offset[0] = line;
+ count[0] = 1;
+
+ r = H5Sselect_hyperslab(sh, H5S_SELECT_SET,
+ offset, NULL, count, NULL);
+ if ( r < 0 ) {
+ ERROR("Error selecting file dataspace "
+ "for data block %s\n", path);
+ H5Dclose(dh);
+ H5Sclose(sh);
+ return 1;
+ }
+
+ m_offset[0] = 0;
+ m_count[0] = 1;
+ dimmh[0] = 1;
+ mh = H5Screate_simple(1, dimmh, NULL);
+ r = H5Sselect_hyperslab(mh, H5S_SELECT_SET,
+ m_offset, NULL, m_count, NULL);
+ if ( r < 0 ) {
+ ERROR("Error selecting memory dataspace "
+ "for data block %s\n", path);
+ H5Dclose(dh);
+ H5Sclose(sh);
+ H5Sclose(mh);
+ return 1;
+ }
+
+ r = H5Dread(dh, H5T_NATIVE_INT, mh,
+ sh, H5P_DEFAULT, num_peaks);
+ if ( r < 0 ) {
+ ERROR("Couldn't read data for block %s, line %i\n", path, line);
+ H5Dclose(dh);
+ H5Sclose(sh);
+ H5Sclose(mh);
+ return 1;
+ }
+
+ H5Dclose(dh);
+ H5Sclose(sh);
+ H5Sclose(mh);
+ return 0;
+}
+
+
+static float *read_hdf5_data(hid_t fh, char *path, int line)
+{
+
+ hid_t dh, sh, mh;
+ hsize_t size[2];
+ hsize_t max_size[2];
+ hsize_t offset[2], count[2];
+ hsize_t m_offset[2], m_count[2], dimmh[2];
+ float *buf;
+ int tw, r;
+
+ dh = H5Dopen2(fh, path, H5P_DEFAULT);
+ if ( dh < 0 ) {
+ ERROR("Data block (%s) not found.\n", path);
+ return NULL;
+ }
+
+ sh = H5Dget_space(dh);
+ if ( sh < 0 ) {
+ H5Dclose(dh);
+ ERROR("Couldn't get dataspace for data.\n");
+ return NULL;
+ }
+
+ if ( H5Sget_simple_extent_ndims(sh) != 2 ) {
+ ERROR("Data block %s has the wrong dimensionality (%i).\n",
+ path, H5Sget_simple_extent_ndims(sh));
+ H5Sclose(sh);
+ H5Dclose(dh);
+ return NULL;
+ }
+
+ H5Sget_simple_extent_dims(sh, size, max_size);
+
+ tw = size[0];
+ if ( line> tw-1 ) {
+ H5Sclose(sh);
+ H5Dclose(dh);
+ ERROR("Data block %s does not contain data for required event.\n",
+ path);
+ return NULL;
+ }
+
+ offset[0] = line;
+ offset[1] = 0;
+ count[0] = 1;
+ count[1] = size[1];
+
+ r = H5Sselect_hyperslab(sh, H5S_SELECT_SET, offset, NULL, count, NULL);
+ if ( r < 0 ) {
+ ERROR("Error selecting file dataspace "
+ "for data block %s\n", path);
+ H5Dclose(dh);
+ H5Sclose(sh);
+ return NULL;
+ }
+
+ m_offset[0] = 0;
+ m_offset[1] = 0;
+ m_count[0] = 1;
+ m_count[1] = size[1];
+ dimmh[0] = 1;
+ dimmh[1] = size[1];
+
+ mh = H5Screate_simple(2, dimmh, NULL);
+ r = H5Sselect_hyperslab(mh, H5S_SELECT_SET,
+ m_offset, NULL, m_count, NULL);
+ if ( r < 0 ) {
+ ERROR("Error selecting memory dataspace "
+ "for data block %s\n", path);
+ H5Dclose(dh);
+ H5Sclose(sh);
+ H5Sclose(mh);
+ return NULL;
+ }
+
+ buf = malloc(size[1]*sizeof(float));
+ if ( buf == NULL ) return NULL;
+ r = H5Dread(dh, H5T_NATIVE_FLOAT, mh, sh, H5P_DEFAULT, buf);
+ if ( r < 0 ) {
+ ERROR("Couldn't read data for block %s, line %i\n", path, line);
+ H5Dclose(dh);
+ H5Sclose(sh);
+ H5Sclose(mh);
+ return NULL;
+ }
+
+ H5Dclose(dh);
+ H5Sclose(sh);
+ H5Sclose(mh);
+ return buf;
+}
+
+
+ImageFeatureList *image_hdf5_read_peaks_cxi(const DataTemplate *dtempl,
+ const char *filename,
+ const char *event,
+ int half_pixel_shift)
+{
+ ImageFeatureList *features;
+ hid_t fh;
+ char path_n[1024];
+ char path_x[1024];
+ char path_y[1024];
+ char path_i[1024];
+ int r;
+ int pk;
+ struct event *ev;
+ char *subst_name;
+
+ int line = 0;
+ int num_peaks;
+
+ float *buf_x;
+ float *buf_y;
+ float *buf_i;
+
+ double peak_offset = half_pixel_shift ? 0.5 : 0.0;
+
+ if ( access(filename, R_OK) == -1 ) {
+ ERROR("File does not exist or cannot be read: %s\n",
+ filename);
+ return NULL;
+ }
+
+ fh = H5Fopen(filename, H5F_ACC_RDONLY, H5P_DEFAULT);
+ if ( fh < 0 ) {
+ ERROR("Couldn't open file: %s\n", filename);
+ return NULL;
+ }
+
+ ev = get_event_from_event_string(event);
+ if ( (ev == NULL) && (event != NULL) ) {
+ ERROR("Invalid event identifier '%s'\n", event);
+ H5Fclose(fh);
+ return NULL;
+ }
+
+ if ( ev->dim_entries == NULL ) {
+ ERROR("CXI format peak list format selected,"
+ "but file has no event structure");
+ return NULL;
+ }
+ line = ev->dim_entries[0];
+
+ subst_name = retrieve_full_path(ev, dtempl->peak_list);
+ free_event(ev);
+ if ( subst_name == NULL ) {
+ ERROR("Invalid peak path %s\n", subst_name);
+ H5Fclose(fh);
+ return NULL;
+ }
+
+ if ( check_path_existence(fh, subst_name) == 0 ) {
+ ERROR("Peak path not found: %s:%s",
+ filename, subst_name);
+ free(subst_name);
+ H5Fclose(fh);
+ return NULL;
+ }
+
+ snprintf(path_n, 1024, "%s/nPeaks", subst_name);
+ snprintf(path_x, 1024, "%s/peakXPosRaw", subst_name);
+ snprintf(path_y, 1024, "%s/peakYPosRaw", subst_name);
+ snprintf(path_i, 1024, "%s/peakTotalIntensity", subst_name);
+
+ r = read_peak_count(fh, path_n, line, &num_peaks);
+ if ( r != 0 ) return NULL;
+
+ buf_x = read_hdf5_data(fh, path_x, line);
+ if ( r != 0 ) return NULL;
+
+ buf_y = read_hdf5_data(fh, path_y, line);
+ if ( r != 0 ) return NULL;
+
+ buf_i = read_hdf5_data(fh, path_i, line);
+ if ( r != 0 ) return NULL;
+
+ features = image_feature_list_new();
+
+ for ( pk=0; pk<num_peaks; pk++ ) {
+
+ float fs, ss, val;
+ int pn;
+
+ fs = buf_x[pk] + peak_offset;
+ ss = buf_y[pk] + peak_offset;
+ val = buf_i[pk];
+
+ if ( data_template_file_to_panel_coords(dtempl,
+ &fs, &ss,
+ &pn) )
+ {
+ ERROR("Failed to convert %i,%i to "
+ "panel-relative coordinates\n", fs, ss);
+ } else {
+ image_add_feature(features, fs, ss, pn,
+ NULL, val, NULL);
+ }
+
+ }
+
+ return features;
+}
+
+
+ImageFeatureList *image_hdf5_read_peaks_hdf5(const DataTemplate *dtempl,
+ const char *filename,
+ const char *event,
+ int half_pixel_shift)
+{
+ hid_t fh, dh, sh;
+ hsize_t size[2];
+ hsize_t max_size[2];
+ int i;
+ float *buf;
+ herr_t r;
+ int tw;
+ struct event *ev;
+ char *subst_name;
+ ImageFeatureList *features;
+ double peak_offset = half_pixel_shift ? 0.5 : 0.0;
+
+ if ( access(filename, R_OK) == -1 ) {
+ ERROR("File does not exist or cannot be read: %s\n",
+ filename);
+ return NULL;
+ }
+
+ fh = H5Fopen(filename, H5F_ACC_RDONLY, H5P_DEFAULT);
+ if ( fh < 0 ) {
+ ERROR("Couldn't open file: %s\n", filename);
+ return NULL;
+ }
+
+ ev = get_event_from_event_string(event);
+ if ( (ev == NULL) && (event != NULL) ) {
+ ERROR("Invalid event identifier '%s'\n", event);
+ H5Fclose(fh);
+ return NULL;
+ }
+
+ subst_name = retrieve_full_path(ev, dtempl->peak_list);
+ free_event(ev);
+ if ( subst_name == NULL ) {
+ ERROR("Invalid peak path %s\n", subst_name);
+ free_event(ev);
+ H5Fclose(fh);
+ return NULL;
+ }
+
+ if ( check_path_existence(fh, subst_name) == 0 ) {
+ ERROR("Peak path not found: %s:%s",
+ filename, subst_name);
+ free(subst_name);
+ H5Fclose(fh);
+ return NULL;
+ }
+
+ dh = H5Dopen2(fh, subst_name, H5P_DEFAULT);
+ free(subst_name);
+ if ( dh < 0 ) {
+ ERROR("Peak list (%s) not found.\n", subst_name);
+ H5Fclose(fh);
+ return NULL;
+ }
+
+ sh = H5Dget_space(dh);
+ if ( sh < 0 ) {
+ ERROR("Couldn't get dataspace for peak list.\n");
+ H5Dclose(dh);
+ H5Fclose(fh);
+ return NULL;
+ }
+
+ if ( H5Sget_simple_extent_ndims(sh) != 2 ) {
+ ERROR("Peak list has the wrong dimensionality (%i).\n",
+ H5Sget_simple_extent_ndims(sh));
+ H5Sclose(sh);
+ H5Dclose(dh);
+ H5Fclose(fh);
+ return NULL;
+ }
+
+ H5Sget_simple_extent_dims(sh, size, max_size);
+ H5Sclose(sh);
+
+ tw = size[1];
+ if ( (tw != 3) && (tw != 4) ) {
+ ERROR("Peak list has the wrong dimensions.\n");
+ H5Dclose(dh);
+ H5Fclose(fh);
+ return NULL;
+ }
+
+ buf = malloc(sizeof(float)*size[0]*size[1]);
+ if ( buf == NULL ) {
+ ERROR("Couldn't reserve memory for the peak list.\n");
+ H5Dclose(dh);
+ H5Fclose(fh);
+ return NULL;
+ }
+ r = H5Dread(dh, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL,
+ H5P_DEFAULT, buf);
+ if ( r < 0 ) {
+ ERROR("Couldn't read peak list.\n");
+ H5Dclose(dh);
+ H5Fclose(fh);
+ return NULL;
+ }
+
+ features = image_feature_list_new();
+ if ( features == NULL ) {
+ ERROR("Failed to allocate peak list\n");
+ H5Dclose(dh);
+ H5Fclose(fh);
+ return NULL;
+ }
+
+ for ( i=0; i<size[0]; i++ ) {
+
+ float fs, ss, val;
+ int pn;
+
+ fs = buf[tw*i+0] + peak_offset;
+ ss = buf[tw*i+1] + peak_offset;
+ val = buf[tw*i+2];
+
+ if ( data_template_file_to_panel_coords(dtempl,
+ &fs, &ss,
+ &pn) )
+ {
+ ERROR("Failed to convert %i,%i to "
+ "panel-relative coordinates\n", fs, ss);
+ } else {
+ image_add_feature(features, fs, ss, pn,
+ NULL, val, NULL);
+ }
+
+ }
+
+ free(buf);
+ H5Dclose(dh);
+ H5Fclose(fh);
+
+ return features;
+}
+
+
+struct parse_params {
+ hid_t fh;
+ int path_dim;
+ const char *path;
+ struct event *curr_event;
+ struct event_list *ev_list;
+ int top_level;
+};
+
+
+static herr_t parse_file_event_structure(hid_t loc_id, char *name,
+ const H5L_info_t *info,
+ struct parse_params *pp)
+
+{
+ char *substituted_path;
+ char *ph_loc;
+ char *truncated_path;
+ htri_t check;
+ herr_t herrt_iterate, herrt_info;
+ struct H5O_info_t object_info;
+
+ if ( !pp->top_level ) {
+
+ int fail_push;
+
+ fail_push = push_path_entry_to_event(pp->curr_event, name);
+ if ( fail_push ) {
+ return -1;
+ }
+
+ substituted_path = event_path_placeholder_subst(name, pp->path);
+
+ } else {
+ substituted_path = strdup(pp->path);
+ }
+
+ if ( pp->top_level == 1 ) {
+ pp->top_level = 0;
+ }
+
+ truncated_path = strdup(substituted_path);
+ ph_loc = strstr(substituted_path,"%");
+ if ( ph_loc != NULL) {
+ truncated_path[ph_loc-substituted_path] = '\0';
+ }
+
+ herrt_iterate = 0;
+ herrt_info = 0;
+
+ check = check_path_existence(pp->fh, truncated_path);
+ if ( check == 0 ) {
+ pop_path_entry_from_event(pp->curr_event);
+ return 0;
+ } else {
+
+ herrt_info = H5Oget_info_by_name(pp->fh, truncated_path,
+ &object_info, H5P_DEFAULT);
+ if ( herrt_info < 0 ) {
+ free(truncated_path);
+ free(substituted_path);
+ return -1;
+ }
+
+ if ( pp->curr_event->path_length == pp->path_dim
+ && object_info.type == H5O_TYPE_DATASET )
+ {
+
+ int fail_append;
+
+ fail_append = append_event_to_event_list(pp->ev_list,
+ pp->curr_event);
+ if ( fail_append ) {
+ free(truncated_path);
+ free(substituted_path);
+ return -1;
+ }
+
+ pop_path_entry_from_event(pp->curr_event);
+ return 0;
+
+ } else {
+
+ pp->path = substituted_path;
+
+ if ( object_info.type == H5O_TYPE_GROUP ) {
+
+ herrt_iterate = H5Literate_by_name(pp->fh,
+ truncated_path, H5_INDEX_NAME,
+ H5_ITER_NATIVE, NULL,
+ (H5L_iterate_t)parse_file_event_structure,
+ (void *)pp, H5P_DEFAULT);
+ }
+ }
+ }
+
+ pop_path_entry_from_event(pp->curr_event);
+
+ free(truncated_path);
+ free(substituted_path);
+
+ return herrt_iterate;
+}
+
+
+static int fill_paths(hid_t fh, const DataTemplate *dtempl, int pi,
+ struct event_list *master_el)
+{
+ struct parse_params pparams;
+ struct event *empty_event;
+ struct event_list *panel_ev_list;
+ int ei;
+ int check;
+
+ empty_event = initialize_event();
+ panel_ev_list = initialize_event_list();
+ if ( (empty_event == NULL) || (panel_ev_list == NULL) )
+ {
+ ERROR("Failed to allocate memory for event list.\n");
+ return 1;
+ }
+
+ pparams.path = dtempl->panels[pi].data;
+ pparams.fh = fh;
+ pparams.path_dim = dtempl->path_dim;
+ pparams.curr_event = empty_event;
+ pparams.top_level = 1;
+ pparams.ev_list = panel_ev_list;
+
+ check = parse_file_event_structure(fh, NULL, NULL, &pparams);
+ if ( check < 0 ) {
+ free_event(empty_event);
+ free_event_list(panel_ev_list);
+ return 1;
+ }
+
+ for ( ei=0; ei<panel_ev_list->num_events; ei++ ) {
+
+ int fail_add;
+
+ fail_add = add_non_existing_event_to_event_list(master_el,
+ panel_ev_list->events[ei]);
+ if ( fail_add ) {
+ free_event(empty_event);
+ free_event_list(panel_ev_list);
+ return 1;
+ }
+
+ }
+
+ free_event(empty_event);
+ free_event_list(panel_ev_list);
+
+ return 0;
+}
+
+
+static int check_dims(hid_t fh, struct panel_template *p,
+ struct event *ev,
+ struct event_list *events, int *global_path_dim)
+{
+ char *full_panel_path;
+ hid_t dh;
+ hid_t sh;
+ int dims;
+ hsize_t *size;
+ hsize_t *max_size;
+ int hsdi;
+ int panel_path_dim = 0;
+ struct dim_structure *panel_dim_structure;
+
+ /* Get the full path for this panel in this event */
+ full_panel_path = retrieve_full_path(ev, p->data);
+
+ dh = H5Dopen2(fh, full_panel_path, H5P_DEFAULT);
+ if ( dh < 0 ) {
+ ERROR("Error opening '%s'\n", full_panel_path);
+ ERROR("Failed to enumerate events. "
+ "Check your geometry file.\n");
+ return 1;
+ }
+
+ sh = H5Dget_space(dh);
+ dims = H5Sget_simple_extent_ndims(sh);
+ size = malloc(dims*sizeof(hsize_t));
+ max_size = malloc(dims*sizeof(hsize_t));
+ if ( (size==NULL) || (max_size==NULL) ) {
+ ERROR("Failed to allocate memory for dimensions\n");
+ return 1;
+ }
+
+ dims = H5Sget_simple_extent_dims(sh, size, max_size);
+
+ panel_dim_structure = p->dim_structure;
+ for ( hsdi=0; hsdi<panel_dim_structure->num_dims; hsdi++ ) {
+ if ( panel_dim_structure->dims[hsdi] == HYSL_PLACEHOLDER ) {
+ panel_path_dim = size[hsdi];
+ break;
+ }
+ }
+
+ if ( *global_path_dim == -1 ) {
+
+ *global_path_dim = panel_path_dim;
+
+ } else if ( panel_path_dim != *global_path_dim ) {
+
+ ERROR("All panels must have the same number of frames\n");
+ ERROR("Panel %s has %i frames in one dimension, but the first "
+ "panel has %i.\n",
+ p->name, panel_path_dim, *global_path_dim);
+ free(size);
+ free(max_size);
+ return 1;
+ }
+
+ H5Sclose(sh);
+ H5Dclose(dh);
+
+ return 0;
+}
+
+
+struct event_list *image_hdf5_expand_frames(const DataTemplate *dtempl,
+ const char *filename)
+{
+ struct event_list *master_el;
+ hid_t fh;
+
+ fh = H5Fopen(filename, H5F_ACC_RDONLY, H5P_DEFAULT);
+ if ( fh < 0 ) {
+ ERROR("Couldn't open file '%s'\n", filename);
+ return NULL;
+ }
+
+ master_el = initialize_event_list();
+ if ( master_el == NULL ) {
+ ERROR("Failed to allocate event list.\n");
+ H5Fclose(fh);
+ return NULL;
+ }
+
+ /* First expand any placeholders in the HDF5 paths */
+ if ( dtempl->path_dim != 0 ) {
+ int pi;
+ for ( pi=0; pi<dtempl->n_panels; pi++ ) {
+ if ( fill_paths(fh, dtempl, pi, master_el) ) {
+ ERROR("Failed to enumerate paths.\n");
+ H5Fclose(fh);
+ return NULL;
+ }
+ }
+ }
+
+ /* Now enumerate the placeholder dimensions */
+ if ( dtempl->dim_dim > 0 ) {
+
+ struct event_list *master_el_with_dims;
+ int evi;
+
+ /* If there were no HDF5 path placeholders, add a dummy event */
+ if ( master_el->num_events == 0 ) {
+ struct event *empty_ev;
+ empty_ev = initialize_event();
+ append_event_to_event_list(master_el, empty_ev);
+ free(empty_ev);
+ }
+
+ master_el_with_dims = initialize_event_list();
+
+ /* For each event so far, expand the dimensions */
+ for ( evi=0; evi<master_el->num_events; evi++ ) {
+
+ int pi;
+ int global_path_dim = -1;
+ int mlwd;
+
+ /* Check the dimensionality of each panel */
+ for ( pi=0; pi<dtempl->n_panels; pi++ ) {
+ if ( check_dims(fh, &dtempl->panels[pi],
+ master_el->events[evi],
+ master_el_with_dims,
+ &global_path_dim) )
+ {
+ ERROR("Failed to enumerate dims.\n");
+ H5Fclose(fh);
+ return NULL;
+ }
+ }
+
+ /* Add this dimensionality to all events */
+ for ( mlwd=0; mlwd<global_path_dim; mlwd++ ) {
+
+ struct event *mlwd_ev;
+
+ mlwd_ev = copy_event(master_el->events[evi]);
+ push_dim_entry_to_event(mlwd_ev, mlwd);
+ append_event_to_event_list(master_el_with_dims,
+ mlwd_ev);
+ free_event(mlwd_ev);
+ }
+
+ }
+
+ free_event_list(master_el);
+ H5Fclose(fh);
+ return master_el_with_dims;
+
+ } else {
+
+ H5Fclose(fh);
+ return master_el;
+
+ }
+}
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-17 08:31:01 +0000