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-rw-r--r--libcrystfel/src/image.c286
1 files changed, 283 insertions, 3 deletions
diff --git a/libcrystfel/src/image.c b/libcrystfel/src/image.c
index c808e55c..971fe0ee 100644
--- a/libcrystfel/src/image.c
+++ b/libcrystfel/src/image.c
@@ -2055,11 +2055,291 @@ void image_free(struct image *image)
}
+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 *get_peaks_cxi_dtempl(const DataTemplate *dtempl,
- const char *filename,
- const char *event,
- int half_pixel_shift)
+ 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;
+ }
+
+ 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;
+ }
+
+ 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];
+
+ pn = data_template_find_panel(dtempl, fs, ss);
+ if ( pn < -1 ) {
+ ERROR("Peak not in panel!\n");
+ continue;
+ }
+
+ /* Convert coordinates to panel-relative */
+ data_template_file_to_panel_coords(dtempl, &fs, &ss);
+
+ image_add_feature(features, fs, ss, pn,
+ NULL, val, NULL);
+
+ }
+
return NULL;
}
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-19 01:14:38 +0000