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-rw-r--r--libcrystfel/src/events.h2
-rw-r--r--libcrystfel/src/hdf5-file.c390
-rw-r--r--libcrystfel/src/hdf5-file.h3
-rw-r--r--src/indexamajig.c5
-rw-r--r--src/process_image.c8
-rw-r--r--src/process_image.h1
6 files changed, 359 insertions, 50 deletions
diff --git a/libcrystfel/src/events.h b/libcrystfel/src/events.h
index ee47c5a5..3dfaf0ec 100644
--- a/libcrystfel/src/events.h
+++ b/libcrystfel/src/events.h
@@ -33,8 +33,6 @@
#ifndef EVENTS_H
#define EVENTS_H
-#include "detector.h"
-
struct event
{
char **path_entries;
diff --git a/libcrystfel/src/hdf5-file.c b/libcrystfel/src/hdf5-file.c
index fceff0e7..923d27ca 100644
--- a/libcrystfel/src/hdf5-file.c
+++ b/libcrystfel/src/hdf5-file.c
@@ -192,32 +192,35 @@ int hdfile_set_image(struct hdfile *f, const char *path,
}
-int get_peaks(struct image *image, struct hdfile *f, const char *p)
+static int read_peak_count(struct hdfile *f, char *path, int line,
+ int *num_peaks)
{
- hid_t dh, sh;
- hsize_t size[2];
- hsize_t max_size[2];
- int i;
- float *buf;
- herr_t r;
- int tw;
- dh = H5Dopen2(f->fh, p, H5P_DEFAULT);
+ 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(f->fh, path, H5P_DEFAULT);
if ( dh < 0 ) {
- ERROR("Peak list (%s) not found.\n", p);
+ 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 peak list.\n");
+ ERROR("Couldn't get dataspace for data.\n");
return 1;
}
- if ( H5Sget_simple_extent_ndims(sh) != 2 ) {
- ERROR("Peak list has the wrong dimensionality (%i).\n",
- H5Sget_simple_extent_ndims(sh));
+ 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;
@@ -225,57 +228,362 @@ int get_peaks(struct image *image, struct hdfile *f, const char *p)
H5Sget_simple_extent_dims(sh, size, max_size);
- tw = size[1];
- if ( (tw != 3) && (tw != 4) ) {
+ tw = size[0];
+
+ if ( line > tw-1 ) {
H5Sclose(sh);
H5Dclose(dh);
- ERROR("Peak list has the wrong dimensions.\n");
+ ERROR("Data block %s does not contain data for required event.\n",
+ path);
return 1;
}
- buf = malloc(sizeof(float)*size[0]*size[1]);
- if ( buf == NULL ) {
+ 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);
- ERROR("Couldn't reserve memory for the peak list.\n");
+ H5Sclose(sh);
+ H5Sclose(mh);
return 1;
}
- r = H5Dread(dh, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
+
+ r = H5Dread(dh, H5T_NATIVE_INT, mh,
+ sh, H5P_DEFAULT, num_peaks);
if ( r < 0 ) {
- ERROR("Couldn't read peak list.\n");
- free(buf);
+ ERROR("Couldn't read data for block %s, line %i\n", path, line);
+ H5Dclose(dh);
+ H5Sclose(sh);
+ H5Sclose(mh);
return 1;
}
- if ( image->features != NULL ) {
- image_feature_list_free(image->features);
+ H5Dclose(dh);
+ H5Sclose(sh);
+ H5Sclose(mh);
+ return 0;
+}
+
+
+
+static int read_hdf5_data_into_buffer(struct hdfile *f, char *path, int line,
+ float *buff)
+{
+
+ 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];
+
+ int tw, r;
+
+ dh = H5Dopen2(f->fh, path, H5P_DEFAULT);
+ if ( dh < 0 ) {
+ ERROR("Data block (%s) not found.\n", path);
+ return 1;
}
- image->features = image_feature_list_new();
- for ( i=0; i<size[0]; i++ ) {
+ sh = H5Dget_space(dh);
+ if ( sh < 0 ) {
+ H5Dclose(dh);
+ ERROR("Couldn't get dataspace for data.\n");
+ return 1;
+ }
- float fs, ss, val;
- struct panel *p;
+ 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 1;
+ }
- fs = buf[tw*i+0];
- ss = buf[tw*i+1];
- val = buf[tw*i+2];
+ H5Sget_simple_extent_dims(sh, size, max_size);
- p = find_orig_panel(image->det, fs, ss);
- if ( p == NULL ) continue;
- if ( p->no_index ) continue;
+ 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;
+ }
- /* Convert coordinates to match rearranged panels in memory */
- fs = fs - p->orig_min_fs + p->min_fs;
- ss = ss - p->orig_min_ss + p->min_ss;
+ offset[0] = line;
+ offset[1] = 0;
+ count[0] = 1;
+ count[1] = 4096;
- image_add_feature(image->features, fs, ss, image, val, NULL);
+ 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_offset[1] = 0;
+ m_count[0] = 1;
+ m_count[1] = 4096;
+ dimmh[0] = 1;
+ dimmh[1] = 4096;
+
+ 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 1;
+ }
+
+ r = H5Dread(dh, H5T_NATIVE_FLOAT, mh,
+ sh, H5P_DEFAULT, buff);
+ if ( r < 0 ) {
+ ERROR("Couldn't read data for block %s, line %i\n", path, line);
+ H5Dclose(dh);
+ H5Sclose(sh);
+ H5Sclose(mh);
+ return 1;
}
- free(buf);
- H5Sclose(sh);
H5Dclose(dh);
+ H5Sclose(sh);
+ H5Sclose(mh);
+ return 0;
+}
+
+
+int get_peaks(struct image *image, struct hdfile *f, const char *p,
+ int cxidb_format, struct filename_plus_event *fpe)
+{
+
+ if ( cxidb_format ) {
+
+ char *path_n;
+ char *path_x;
+ char *path_y;
+ char *path_i;
+ int r;
+ int pk;
+
+ int line = 0;
+ int num_peaks;
+
+ float buf_x[4096];
+ float buf_y[4096];
+ float buf_i[4096];
+
+ path_n=malloc((strlen(p)+strlen("/nPeaks")+1)*sizeof(char));
+ path_x=malloc((strlen(p)+strlen("/peakXPosRaw")+1)*sizeof(char));
+ path_y=malloc((strlen(p)+strlen("/peakYPosRaw")+1)*sizeof(char));
+ path_i=malloc((strlen(p)+strlen("/peakIntensity")+1)*sizeof(char));
+
+ if ( fpe != NULL && fpe->ev != NULL && fpe->ev->dim_entries != NULL ) {
+ line = fpe->ev->dim_entries[0];
+ } else {
+ ERROR("CXIDB peak list format selected,"
+ "but file has no event structure");
+ free(path_n);
+ free(path_x);
+ free(path_y);
+ free(path_i);
+ return 1;
+ }
+
+
+ strncpy(path_n, p, strlen(p));
+ strncpy(&path_n[strlen(p)], "/nPeaks\0",
+ strlen("/nPeaks\0"));
+
+ r = read_peak_count(f, path_n, line, &num_peaks);
+ if ( r != 0) {
+ free(path_n);
+ free(path_x);
+ free(path_y);
+ free(path_i);
+ return 1;
+ }
+
+ strncpy(path_x, p, strlen(p));
+ strncpy(&path_x[strlen(p)], "/peakXPosRaw\0",
+ strlen("/peakXPosRaw\0"));
+ r = read_hdf5_data_into_buffer(f, path_x, line, buf_x);
+ if ( r != 0) {
+ free(path_n);
+ free(path_x);
+ free(path_y);
+ free(path_i);
+ return 1;
+ }
+
+ strncpy(path_y, p, strlen(p));
+ strncpy(&path_y[strlen(p)], "/peakYPosRaw\0",
+ strlen("/peakYPosRaw\0"));
+ r = read_hdf5_data_into_buffer(f, path_y, line, buf_y);
+ if ( r != 0) {
+ free(path_n);
+ free(path_x);
+ free(path_y);
+ free(path_i);
+ return 1;
+ }
+
+ strncpy(path_i, p, strlen(p));
+ strncpy(&path_i[strlen(p)], "/peakIntensity\0",
+ strlen("/peakIntensity\0"));
+ r = read_hdf5_data_into_buffer(f, path_i, line, buf_i);
+ if ( r != 0) {
+ free(path_n);
+ free(path_x);
+ free(path_y);
+ free(path_i);
+ return 1;
+ }
+
+
+ if ( image->features != NULL ) {
+ image_feature_list_free(image->features);
+ }
+ image->features = image_feature_list_new();
+
+ for ( pk=0; pk<num_peaks; pk++ ) {
+
+ float fs, ss, val;
+ struct panel *p;
+
+ fs = buf_x[pk];
+ ss = buf_y[pk];
+ val = buf_i[pk];
+
+ p = find_orig_panel(image->det, fs, ss);
+ if ( p == NULL ) continue;
+ if ( p->no_index ) continue;
+
+ /* Convert coordinates to match rearranged panels in memory */
+ fs = fs - p->orig_min_fs + p->min_fs;
+ ss = ss - p->orig_min_ss + p->min_ss;
+
+ image_add_feature(image->features, fs, ss, image, val, NULL);
+
+ }
+
+ free(path_n);
+ free(path_x);
+ free(path_y);
+ free(path_i);
+
+ } else {
+
+ hid_t dh, sh;
+ hsize_t size[2];
+ hsize_t max_size[2];
+ int i;
+ float *buf;
+ herr_t r;
+ int tw;
+
+ dh = H5Dopen2(f->fh, p, H5P_DEFAULT);
+ if ( dh < 0 ) {
+ ERROR("Peak list (%s) not found.\n", p);
+ return 1;
+ }
+
+ sh = H5Dget_space(dh);
+ if ( sh < 0 ) {
+ H5Dclose(dh);
+ ERROR("Couldn't get dataspace for peak list.\n");
+ return 1;
+ }
+
+ 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);
+ return 1;
+ }
+
+ H5Sget_simple_extent_dims(sh, size, max_size);
+
+ tw = size[1];
+ if ( (tw != 3) && (tw != 4) ) {
+ H5Sclose(sh);
+ H5Dclose(dh);
+ ERROR("Peak list has the wrong dimensions.\n");
+ return 1;
+ }
+
+ buf = malloc(sizeof(float)*size[0]*size[1]);
+ if ( buf == NULL ) {
+ H5Sclose(sh);
+ H5Dclose(dh);
+ ERROR("Couldn't reserve memory for the peak list.\n");
+ return 1;
+ }
+ r = H5Dread(dh, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
+ if ( r < 0 ) {
+ ERROR("Couldn't read peak list.\n");
+ free(buf);
+ return 1;
+ }
+
+ if ( image->features != NULL ) {
+ image_feature_list_free(image->features);
+ }
+ image->features = image_feature_list_new();
+
+ for ( i=0; i<size[0]; i++ ) {
+
+ float fs, ss, val;
+ struct panel *p;
+
+ fs = buf[tw*i+0];
+ ss = buf[tw*i+1];
+ val = buf[tw*i+2];
+
+ p = find_orig_panel(image->det, fs, ss);
+ if ( p == NULL ) continue;
+ if ( p->no_index ) continue;
+
+ /* Convert coordinates to match rearranged panels in memory */
+ fs = fs - p->orig_min_fs + p->min_fs;
+ ss = ss - p->orig_min_ss + p->min_ss;
+
+ image_add_feature(image->features, fs, ss, image, val, NULL);
+
+ }
+
+ free(buf);
+ H5Sclose(sh);
+ H5Dclose(dh);
+
+ }
return 0;
}
diff --git a/libcrystfel/src/hdf5-file.h b/libcrystfel/src/hdf5-file.h
index 336684a5..93ef1d95 100644
--- a/libcrystfel/src/hdf5-file.h
+++ b/libcrystfel/src/hdf5-file.h
@@ -79,7 +79,8 @@ extern void hdfile_close(struct hdfile *f);
extern int hdfile_is_scalar(struct hdfile *f, const char *name, int verbose);
char *hdfile_get_string_value(struct hdfile *f, const char *name,
struct event* ev);
-extern int get_peaks(struct image *image, struct hdfile *f, const char *p);
+extern int get_peaks(struct image *image, struct hdfile *f, const char *p,
+ int cxidb_format, struct filename_plus_event *fpe);
extern double get_value(struct hdfile *f, const char *name);
extern double get_ev_based_value(struct hdfile *f, const char *name,
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 80894804..6aeaaad5 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -99,6 +99,9 @@ static void show_help(const char *s)
" hdf5 : Get from a table in HDF5 file.\n"
" --hdf5-peaks=<p> Find peaks table in HDF5 file here.\n"
" Default: /processing/hitfinder/peakinfo\n"
+" --cxidb-hdf5-peaks Peaks in the HDF5 file are in CXIDB format.\n"
+" Only used in conjunction with the --hdf5-peaks,\n"
+" ignored otherwise."
" --integration=<meth> Perform final pattern integration using <meth>.\n"
"\n\n"
"For more control over the process, you might need:\n\n"
@@ -216,6 +219,7 @@ int main(int argc, char *argv[])
iargs.beam = &beam;
iargs.element = NULL;
iargs.hdf5_peak_path = strdup("/processing/hitfinder/peakinfo");
+ iargs.cxidb_hdf5_peaks = 0;
iargs.copyme = NULL;
iargs.pk_inn = -1.0;
iargs.pk_mid = -1.0;
@@ -265,6 +269,7 @@ int main(int argc, char *argv[])
{"no-use-saturated", 0, &iargs.use_saturated, 0},
{"no-revalidate", 0, &iargs.no_revalidate, 1},
{"check-hdf5-snr", 0, &iargs.check_hdf5_snr, 1},
+ {"cxidb-hdf5-peaks", 0, &iargs.cxidb_hdf5_peaks, 1},
/* Long-only options which don't actually do anything */
{"no-sat-corr", 0, &iargs.satcorr, 0},
diff --git a/src/process_image.c b/src/process_image.c
index 41810e12..57bc9e3c 100644
--- a/src/process_image.c
+++ b/src/process_image.c
@@ -179,12 +179,8 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
case PEAK_HDF5:
/* Get peaks from HDF5 */
- if ( !single_panel_data_source(iargs->det, iargs->element) ) {
- ERROR("Peaks from HDF5 file not supported with "
- "multiple panel data sources.\n");
- }
-
- if ( get_peaks(&image, hdfile, iargs->hdf5_peak_path) ) {
+ if ( get_peaks(&image, hdfile, iargs->hdf5_peak_path,
+ iargs->cxidb_hdf5_peaks, pargs->filename_p_e) ) {
ERROR("Failed to get peaks from HDF5 file.\n");
}
if ( !iargs->no_revalidate ) {
diff --git a/src/process_image.h b/src/process_image.h
index 5d9f2c27..891553e6 100644
--- a/src/process_image.h
+++ b/src/process_image.h
@@ -64,6 +64,7 @@ struct index_args
struct beam_params *beam;
char *element;
char *hdf5_peak_path;
+ int cxidb_hdf5_peaks;
float pk_inn;
float pk_mid;
float pk_out;
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-09 02:46:56 +0000