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-rw-r--r--libcrystfel/src/hdf5-file.c551
1 files changed, 459 insertions, 92 deletions
diff --git a/libcrystfel/src/hdf5-file.c b/libcrystfel/src/hdf5-file.c
index 1ee61245..3f90117d 100644
--- a/libcrystfel/src/hdf5-file.c
+++ b/libcrystfel/src/hdf5-file.c
@@ -41,6 +41,46 @@
#include "utils.h"
+struct hdf5_write_location {
+
+ char *location;
+ int n_panels;
+ int *panel_idxs;
+
+ int max_ss;
+ int max_fs;
+
+};
+
+
+int split_group_and_object(char* path, char** group, char** object)
+{
+ char *sep;
+ char *store;
+
+ sep = path;
+ store = sep;
+ sep = strpbrk(sep + 1, "/");
+ if ( sep != NULL ) {
+ while ( 1 ) {
+ store = sep;
+ sep = strpbrk(sep + 1, "/");
+ if ( sep == NULL ) {
+ break;
+ }
+ }
+ }
+ if ( store == path ) {
+ *group = NULL;
+ *object = strdup(path);
+ } else {
+ *group = strndup(path, store - path);
+ *object = strdup(store+1);
+ }
+ return 0;
+};
+
+
struct hdfile {
const char *path; /* Current data path */
@@ -73,7 +113,6 @@ struct hdfile *hdfile_open(const char *filename)
}
f->data_open = 0;
-
return f;
}
@@ -229,7 +268,7 @@ void hdfile_close(struct hdfile *f)
/* Deprecated */
int hdf5_write(const char *filename, const void *data,
- int width, int height, int type)
+ int width, int height, int type)
{
hid_t fh, gh, sh, dh; /* File, group, dataspace and data handles */
hid_t ph; /* Property list */
@@ -288,15 +327,23 @@ int hdf5_write(const char *filename, const void *data,
}
-int hdf5_write_image(const char *filename, struct image *image)
+int hdf5_write_image(const char *filename, struct image *image, char *element)
{
- hid_t fh, gh, sh, dh; /* File, group, dataspace and data handles */
- hid_t ph; /* Property list */
- herr_t r;
- hsize_t size[2];
double lambda, eV;
double *arr;
- int i;
+ hsize_t size1d[1];
+ herr_t r;
+ hid_t fh, gh, sh, dh; /* File, group, dataspace and data handles */
+ int i, pi, li;
+ char * default_location;
+ struct hdf5_write_location *locations;
+ struct hdf5_write_location *new_location;
+ int num_locations;
+
+ if ( image->det == NULL ) {
+ ERROR("Geometry not available\n");
+ return 1;
+ }
fh = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
if ( fh < 0 ) {
@@ -304,56 +351,258 @@ int hdf5_write_image(const char *filename, struct image *image)
return 1;
}
- gh = H5Gcreate2(fh, "data", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
- if ( gh < 0 ) {
- ERROR("Couldn't create group\n");
- H5Fclose(fh);
+ if ( element != NULL) {
+ default_location = strdup(element);
+ } else {
+ default_location = strdup("/data/data");
+ }
+
+ locations = malloc(sizeof(struct hdf5_write_location));
+ if ( locations == NULL ) {
+ ERROR("Couldn't create write location list for file: %s\n",
+ filename);
return 1;
}
+ locations[0].max_ss = 0;
+ locations[0].max_fs = 0;
+ if ( image->det->panels[0].data_from != NULL ) {
+ locations[0].location = image->det->panels[0].data_from;
+ } else {
+ locations[0].location = default_location;
+ }
+ locations[0].panel_idxs = NULL;
+ locations[0].n_panels = 0;
+ num_locations = 1;
- /* Note the "swap" here, according to section 3.2.5,
- * "C versus Fortran Dataspaces", of the HDF5 user's guide. */
- size[0] = image->height;
- size[1] = image->width;
- sh = H5Screate_simple(2, size, NULL);
+ for ( pi=0; pi<image->det->n_panels; pi++ ) {
- /* Set compression */
- ph = H5Pcreate(H5P_DATASET_CREATE);
- H5Pset_chunk(ph, 2, size);
- H5Pset_deflate(ph, 3);
+ struct panel p;
+ int li;
+ int panel_processed;
+ char *p_location;
+
+ p = image->det->panels[pi];
+
+ if ( p.data_from == NULL ) {
+ p_location = default_location;
+ } else {
+ p_location = p.data_from;
+ }
+
+ panel_processed = 0;
+
+ for ( li=0; li<num_locations; li++ ) {
+
+ if ( strcmp(p_location, locations[li].location) == 0 ) {
+
+ int *new_panel_idxs;
+
+ new_panel_idxs = realloc(locations[li].panel_idxs,
+ (locations[li].n_panels+1)*sizeof(int));
+ if ( new_panel_idxs == NULL ) {
+ ERROR("Error while managing write location list for file: %s\n",
+ filename);
+ return 1;
+ }
+ locations[li].panel_idxs = new_panel_idxs;
+ locations[li].panel_idxs[locations[li].n_panels] = pi;
+ locations[li].n_panels += 1;
+ if ( p.orig_max_fs > locations[li].max_fs ) {
+ locations[li].max_fs = p.orig_max_fs;
+ }
+ if ( p.orig_max_ss > locations[li].max_ss ) {
+ locations[li].max_ss = p.orig_max_ss;
+ }
+ panel_processed = 1;
+ }
+ }
+
+ if ( panel_processed == 0) {
+
+ struct hdf5_write_location * new_locations;
+ new_locations = realloc(locations,
+ (num_locations+1)*sizeof(struct hdf5_write_location));
+ if ( new_locations == NULL ) {
+ ERROR("Error while managing write location list for file: %s\n",
+ filename);
+ return 1;
+ }
+ locations = new_locations;
+ new_location = &locations[num_locations];
+ new_location = malloc(sizeof(struct hdf5_write_location));
+ if ( new_location == NULL ) {
+ ERROR("Error while managing write location list for file: %s\n",
+ filename);
+ return 1;
+ }
+ locations[num_locations].max_ss = p.orig_max_ss;
+ locations[num_locations].max_fs = p.orig_max_fs;
+ locations[num_locations].location = p_location;
+ locations[num_locations].panel_idxs = malloc(sizeof(int));
+ if ( locations[num_locations].panel_idxs == NULL ) {
+ ERROR("Error while managing write location list for file: %s\n",
+ filename);
+ return 1;
+ }
+ locations[num_locations].panel_idxs[0] = pi;
+ locations[num_locations].n_panels = 1;
+
+ num_locations += 1;
+ }
- dh = H5Dcreate2(gh, "data", H5T_NATIVE_FLOAT, sh,
- H5P_DEFAULT, ph, H5P_DEFAULT);
- if ( dh < 0 ) {
- ERROR("Couldn't create dataset\n");
- H5Fclose(fh);
- return 1;
}
- /* Muppet check */
- H5Sget_simple_extent_dims(sh, size, NULL);
+ for ( li=0; li<num_locations; li++ ) {
- r = H5Dwrite(dh, H5T_NATIVE_FLOAT, H5S_ALL,
- H5S_ALL, H5P_DEFAULT, image->data);
- if ( r < 0 ) {
- ERROR("Couldn't write data\n");
+ hid_t ph, gph;
+ hid_t dh_dataspace;
+ hsize_t size[2];
+
+ char *path, *group = NULL, *object = NULL;
+ int fail;
+
+ path = locations[li].location;
+ fail = split_group_and_object(path, &group, &object);
+ if ( fail ) {
+ ERROR("Error while determining write locations for file: %s\n",
+ filename);
+ return 1;
+ }
+
+
+ gph = H5Pcreate(H5P_LINK_CREATE);
+ H5Pset_create_intermediate_group(gph, 1);
+
+ if ( group != NULL ) {
+ fail = H5Gget_objinfo (fh, group, 0, NULL);
+ if ( fail ) {
+
+ gh = H5Gcreate2(fh, group, gph, H5P_DEFAULT, H5P_DEFAULT);
+ if ( gh < 0 ) {
+ ERROR("Couldn't create group\n");
+ H5Fclose(fh);
+ return 1;
+ }
+ } else {
+ gh = H5Gopen2(fh, group, H5P_DEFAULT);
+ }
+
+ } else {
+ gh = -1;
+ }
+
+ /* Note the "swap" here, according to section 3.2.5,
+ * "C versus Fortran Dataspaces", of the HDF5 user's guide. */
+ size[0] = locations[li].max_ss+1;
+ size[1] = locations[li].max_fs+1;
+ sh = H5Screate_simple(2, size, NULL);
+
+ /* Set compression */
+ ph = H5Pcreate(H5P_DATASET_CREATE);
+ H5Pset_chunk(ph, 2, size);
+ H5Pset_deflate(ph, 3);
+
+ if ( group != NULL ) {
+ dh = H5Dcreate2(gh, object, H5T_NATIVE_FLOAT, sh,
+ H5P_DEFAULT, ph, H5P_DEFAULT);
+ } else {
+ dh = H5Dcreate2(fh, object, H5T_NATIVE_FLOAT, sh,
+ H5P_DEFAULT, ph, H5P_DEFAULT);
+ }
+
+ if ( dh < 0 ) {
+ ERROR("Couldn't create dataset\n");
+ H5Fclose(fh);
+ return 1;
+ }
+
+ /* Muppet check */
+ H5Sget_simple_extent_dims(sh, size, NULL);
+
+ for ( pi=0; pi<locations[li].n_panels; pi ++ ) {
+
+ hsize_t f_offset[2], f_count[2];
+ hsize_t m_offset[2], m_count[2];
+ hsize_t dimsm[2];
+ hid_t memspace;
+ struct panel p;
+ int check;
+
+ p = image->det->panels[locations[li].panel_idxs[pi]];
+
+ f_offset[0] = p.orig_min_ss;
+ f_offset[1] = p.orig_min_fs;
+ f_count[0] = p.orig_max_ss - p.orig_min_ss +1;
+ f_count[1] = p.orig_max_fs - p.orig_min_fs +1;
+
+ dh_dataspace = H5Dget_space(dh);
+ check = H5Sselect_hyperslab(dh_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(group);
+ free(object);
+ H5Pclose(ph);
+ H5Pclose(gph);
+ H5Dclose(dh);
+ H5Sclose(dh_dataspace);
+ H5Sclose(sh);
+ if ( gh != -1 ) H5Gclose(gh);
+ H5Fclose(fh);
+ return 1;
+ }
+
+ m_offset[0] = p.min_ss;
+ m_offset[1] = p.min_fs;
+ m_count[0] = p.max_ss - p.min_ss +1;
+ m_count[1] = p.max_fs - p.min_fs +1;
+ dimsm[0] = image->height;
+ dimsm[1] = image->width;
+ memspace = H5Screate_simple(2, dimsm, NULL);
+ check = H5Sselect_hyperslab(memspace, H5S_SELECT_SET,
+ m_offset, NULL, m_count, NULL);
+
+ r = H5Dwrite(dh, H5T_NATIVE_FLOAT, memspace,
+ dh_dataspace, H5P_DEFAULT, image->data);
+ if ( r < 0 ) {
+ ERROR("Couldn't write data\n");
+ free(group);
+ free(object);
+ H5Pclose(ph);
+ H5Pclose(gph);
+ H5Dclose(dh);
+ H5Sclose(dh_dataspace);
+ H5Sclose(sh);
+ H5Sclose(memspace);
+ if ( gh != -1 ) H5Gclose(gh);
+ H5Fclose(fh);
+ return 1;
+ }
+
+ H5Sclose(dh_dataspace);
+ H5Sclose(memspace);
+ }
+
+ free(group);
+ free(object);
+ H5Pclose(ph);
+ H5Pclose(gph);
+ H5Sclose(sh);
H5Dclose(dh);
- H5Fclose(fh);
- return 1;
- }
- H5Dclose(dh);
+ if ( gh != -1 ) H5Gclose(gh);
- H5Gclose(gh);
+ }
gh = H5Gcreate2(fh, "LCLS", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if ( gh < 0 ) {
- printf("Couldn't create group\n");
+ ERROR("Couldn't create group\n");
H5Fclose(fh);
return 1;
}
- size[0] = 1;
- sh = H5Screate_simple(1, size, NULL);
+ size1d[0] = 1;
+ sh = H5Screate_simple(1, size1d, NULL);
dh = H5Dcreate2(gh, "photon_energy_eV", H5T_NATIVE_DOUBLE, sh,
H5P_DEFAULT, H5S_ALL, H5P_DEFAULT);
@@ -395,8 +644,8 @@ int hdf5_write_image(const char *filename, struct image *image)
arr[i] = 1.0e10/image->spectrum[i].k;
}
- size[0] = image->spectrum_size;
- sh = H5Screate_simple(1, size, NULL);
+ size1d[0] = image->spectrum_size;
+ sh = H5Screate_simple(1, size1d, NULL);
dh = H5Dcreate2(gh, "spectrum_wavelengths_A", H5T_NATIVE_DOUBLE,
sh, H5P_DEFAULT, H5S_ALL, H5P_DEFAULT);
@@ -423,8 +672,8 @@ int hdf5_write_image(const char *filename, struct image *image)
H5Dclose(dh);
free(arr);
- size[0] = 1;
- sh = H5Screate_simple(1, size, NULL);
+ size1d[0] = 1;
+ sh = H5Screate_simple(1, size1d, NULL);
dh = H5Dcreate2(gh, "number_of_samples", H5T_NATIVE_INT, sh,
H5P_DEFAULT, H5S_ALL, H5P_DEFAULT);
@@ -440,10 +689,12 @@ int hdf5_write_image(const char *filename, struct image *image)
}
H5Gclose(gh);
-
- H5Pclose(ph);
-
H5Fclose(fh);
+ free(default_location);
+ for ( li=0; li<num_locations; li ++ ) {
+ free(locations[li].panel_idxs);
+ }
+ free(locations);
return 0;
}
@@ -582,7 +833,6 @@ static int unpack_panels(struct image *image, struct detector *det)
if ( flags & image->det->mask_bad ) bad = 1;
}
-
image->bad[pi][fs+p->w*ss] = bad;
}
@@ -594,72 +844,189 @@ static int unpack_panels(struct image *image, struct detector *det)
}
-int hdf5_read(struct hdfile *f, struct image *image, int satcorr)
+int hdf5_read(struct hdfile *f, struct image *image, const char* element, int satcorr)
{
herr_t r;
float *buf;
uint16_t *flags;
- hid_t mask_dh;
-
- /* Note the "swap" here, according to section 3.2.5,
- * "C versus Fortran Dataspaces", of the HDF5 user's guide. */
- image->width = f->ny;
- image->height = f->nx;
-
- buf = malloc(sizeof(float)*f->nx*f->ny);
+ 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 = NULL;
- r = H5Dread(f->dh, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL,
- H5P_DEFAULT, buf);
- if ( r < 0 ) {
- ERROR("Couldn't read data\n");
- free(buf);
+ if ( image->det == NULL ) {
+ ERROR("Geometry not available\n");
return 1;
}
- image->data = buf;
- if ( (image->det != NULL) && (image->det->mask != NULL) ) {
+ p_w = image->det->panels[0].w;
+ sum_p_h = 0;
- mask_dh = H5Dopen2(f->fh, image->det->mask, H5P_DEFAULT);
- if ( mask_dh <= 0 ) {
- ERROR("Couldn't open flags\n");
- image->flags = NULL;
- } else {
- flags = malloc(sizeof(uint16_t)*f->nx*f->ny);
- r = H5Dread(mask_dh, H5T_NATIVE_UINT16, H5S_ALL, H5S_ALL,
- H5P_DEFAULT, flags);
- if ( r < 0 ) {
- ERROR("Couldn't read flags\n");
- free(flags);
- image->flags = NULL;
- } else {
- image->flags = flags;
- }
- H5Dclose(mask_dh);
+ for ( pi=0; pi<image->det->n_panels; pi++ ) {
+
+ if ( image->det->panels[pi].w != p_w ) {
+ ERROR("Panels have different width. Not supported yet\n");
+ return 1;
}
+ if ( image->det->panels[pi].mask != NULL ) mask_is_present = 1;
+
+ sum_p_h += image->det->panels[pi].h;
+
}
- if ( satcorr ) debodge_saturation(f, image);
+ buf = malloc(sizeof(float)*p_w*sum_p_h);
+ if ( mask_is_present ) {
+ flags = calloc(p_w*sum_p_h,sizeof(uint16_t));
+ }
+ image->width = p_w;
+ image->height = sum_p_h;
+
+ 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++ ) {
+
+ int data_width, data_height;
+ hsize_t f_offset[2], f_count[2];
+ hsize_t m_offset[2], m_count[2];
+ hsize_t dimsm[2];
+ herr_t check;
+ hid_t dataspace, memspace, mask_dataspace;
+ int fail;
- if ( image->det != NULL ) {
+ struct panel *p;
+ p=&image->det->panels[pi];
+
+ if ( p->orig_min_fs == -1 ) p->orig_min_fs = p->min_fs;
+ if ( p->orig_max_fs == -1 ) p->orig_max_fs = p->max_fs;
+ if ( p->orig_min_ss == -1 ) p->orig_min_ss = p->min_ss;
+ if ( p->orig_max_ss == -1 ) p->orig_max_ss = p->max_ss;
+
+ if ( p->data_from != NULL ) {
+ fail = hdfile_set_image(f, p->data_from);
+ } else if ( element != NULL ) {
+ fail = hdfile_set_image(f, element);
+ } else {
+ fail = hdfile_set_first_image(f,"/");
+ }
+ if ( fail ) {
+ ERROR("Couldn't select path for panel %s\n",
+ p->name);
+ return 1;
+ }
- if ( (image->width != image->det->max_fs + 1 )
- || (image->height != image->det->max_ss + 1))
+ data_width = f->ny;
+ data_height = f->nx;
+ if ( (data_width < p->w )
+ || (data_height < p->h) )
{
- ERROR("Image size doesn't match geometry size"
- " - rejecting image.\n");
- ERROR("Image size: %i,%i. Geometry size: %i,%i\n",
- image->width, image->height,
- image->det->max_fs + 1, image->det->max_ss + 1);
+ ERROR("Data size doesn't match panel geometry size"
+ " - rejecting image.\n");
+ ERROR("Panel name: %s. Data size: %i,%i. Geometry size: %i,%i\n",
+ p->name, data_width, data_height,
+ p->w, p->h);
return 1;
}
- fill_in_values(image->det, f);
+ f_offset[0] = p->orig_min_ss;
+ f_offset[1] = p->orig_min_fs;
+ f_count[0] = p->orig_max_ss - p->orig_min_ss +1;
+ f_count[1] = p->orig_max_fs - p->orig_min_fs +1;
+ dataspace = H5Dget_space(f->dh);
+ 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(buf);
+ return 1;
+ }
- unpack_panels(image, image->det);
+ m_offset[0] = curr_ss;
+ m_offset[1] = 0;
+ m_count[0] = p->orig_max_ss - p->orig_min_ss +1;
+ m_count[1] = m_max_fs - m_min_fs +1;
+ 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",
+ p->name);
+ free(buf);
+ return 1;
+ }
+ r = H5Dread(f->dh, H5T_NATIVE_FLOAT, memspace, dataspace,
+ H5P_DEFAULT, buf);
+ if ( r < 0 ) {
+ ERROR("Couldn't read data for panel %s\n",
+ p->name);
+ free(buf);
+ return 1;
+ }
+ H5Dclose(f->dh);
+ f->data_open = 0;
+ H5Sclose(dataspace);
+ H5Sclose(memspace);
+
+ if ( p->mask != NULL ) {
+ 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(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;
+ }
+ H5Dclose(mask_dataspace);
+ H5Dclose(mask_dh);
+ }
+
+ }
+
+ p->min_fs = m_min_fs;
+ p->max_fs = m_max_fs;
+ p->min_ss = curr_ss;
+ p->max_ss = curr_ss + p->h-1;
+ curr_ss += p->h;
+ }
+
+ 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);
+
+ unpack_panels(image, image->det);
+
if ( image->beam != NULL ) {
fill_in_beam_parameters(image->beam, f);
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-18 02:35:17 +0000