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-rw-r--r--libcrystfel/src/detector.c72
-rw-r--r--libcrystfel/src/detector.h8
-rw-r--r--libcrystfel/src/hdf5-file.c551
-rw-r--r--libcrystfel/src/hdf5-file.h4
-rw-r--r--src/dw-hdfsee.c28
-rw-r--r--src/partial_sim.c2
-rw-r--r--src/pattern_sim.c2
-rw-r--r--src/process_image.c24
8 files changed, 541 insertions, 150 deletions
diff --git a/libcrystfel/src/detector.c b/libcrystfel/src/detector.c
index 537f1f30..4681ab28 100644
--- a/libcrystfel/src/detector.c
+++ b/libcrystfel/src/detector.c
@@ -496,6 +496,16 @@ static struct panel *new_panel(struct detector *det, const char *name)
new->clen_from = strdup(new->clen_from);
}
+ /* Create a new copy of the data location if needed */
+ if ( new->data_from != NULL ) {
+ new->data_from = strdup(new->data_from);
+ }
+
+ /* Create a new copy of the bad pixel mask location */
+ if ( new->mask != NULL ) {
+ new->mask = strdup(new->data_from);
+ }
+
return new;
}
@@ -666,6 +676,20 @@ static int parse_field_for_panel(struct panel *panel, const char *key,
panel->clen_from = NULL;
}
+ } else if ( strcmp(key, "data_from") == 0 ) {
+ if ( strncmp(val,"/",1) != 0 ) {
+ ERROR("Invalid data location '%s'\n", val);
+ reject = -1;
+ }
+ panel->data_from = strdup(val);
+
+ } else if ( strcmp(key, "mask") == 0 ) {
+ if ( strncmp(val,"/",1) != 0 ) {
+ ERROR("Invalid mask location '%s'\n", val);
+ reject = -1;
+ }
+ panel->mask = strdup(val);
+
} else if ( strcmp(key, "coffset") == 0) {
panel->coffset = atof(val);
} else if ( strcmp(key, "res") == 0 ) {
@@ -751,11 +775,7 @@ static int parse_field_bad(struct badregion *panel, const char *key,
static void parse_toplevel(struct detector *det, const char *key,
const char *val)
{
- if ( strcmp(key, "mask") == 0 ) {
-
- det->mask = strdup(val);
-
- } else if ( strcmp(key, "mask_bad") == 0 ) {
+ if ( strcmp(key, "mask_bad") == 0 ) {
char *end;
double v = strtod(val, &end);
@@ -864,7 +884,6 @@ struct detector *get_detector_geometry(const char *filename)
det->bad = NULL;
det->mask_good = 0;
det->mask_bad = 0;
- det->mask = NULL;
det->n_rigid_groups = 0;
det->rigid_groups = NULL;
@@ -873,6 +892,10 @@ struct detector *get_detector_geometry(const char *filename)
det->defaults.min_ss = -1;
det->defaults.max_fs = -1;
det->defaults.max_ss = -1;
+ det->defaults.orig_min_fs = -1;
+ det->defaults.orig_min_ss = -1;
+ det->defaults.orig_max_fs = -1;
+ det->defaults.orig_max_ss = -1;
det->defaults.cnx = NAN;
det->defaults.cny = NAN;
det->defaults.clen = -1.0;
@@ -887,6 +910,8 @@ struct detector *get_detector_geometry(const char *filename)
det->defaults.rigid_group = NULL;
det->defaults.adu_per_eV = NAN;
det->defaults.max_adu = +INFINITY;
+ det->defaults.mask = NULL;
+ det->defaults.data_from = NULL;
strncpy(det->defaults.name, "", 1023);
do {
@@ -1075,6 +1100,8 @@ out:
det->max_ss = max_ss;
free(det->defaults.clen_from);
+ free(det->defaults.data_from);
+ free(det->defaults.mask);
/* Calculate matrix inverses and other stuff */
for ( i=0; i<det->n_panels; i++ ) {
@@ -1130,7 +1157,6 @@ void free_detector_geometry(struct detector *det)
free(det->panels);
free(det->bad);
- free(det->mask);
free(det);
}
@@ -1143,12 +1169,6 @@ struct detector *copy_geom(const struct detector *in)
out = malloc(sizeof(struct detector));
memcpy(out, in, sizeof(struct detector));
- if ( in->mask != NULL ) {
- out->mask = strdup(in->mask);
- } else {
- out->mask = NULL; /* = in->mask */
- }
-
out->panels = malloc(out->n_panels * sizeof(struct panel));
memcpy(out->panels, in->panels, out->n_panels * sizeof(struct panel));
@@ -1170,6 +1190,18 @@ struct detector *copy_geom(const struct detector *in)
p->clen_from = strdup(p->clen_from);
}
+ if ( p->data_from != NULL ) {
+ /* Make a copy of the data_from fields unique to this
+ * copy of the structure. */
+ p->clen_from = strdup(p->clen_from);
+ }
+
+ if ( p->clen_from != NULL ) {
+ /* Make a copy of the mask fields unique to this
+ * copy of the structure. */
+ p->clen_from = strdup(p->clen_from);
+ }
+
}
for ( i=0; i<in->n_panels; i++ ) {
@@ -1206,6 +1238,10 @@ struct detector *simple_geometry(const struct image *image)
geom->panels[0].cny = -image->height / 2.0;
geom->panels[0].rigid_group = NULL;
geom->panels[0].max_adu = INFINITY;
+ geom->panels[0].orig_min_fs = -1;
+ geom->panels[0].orig_max_fs = -1;
+ geom->panels[0].orig_min_ss = -1;
+ geom->panels[0].orig_max_ss = -1;
geom->panels[0].fsx = 1;
geom->panels[0].fsy = 0;
@@ -1400,6 +1436,16 @@ int write_detector_geometry(const char *filename, struct detector *det)
p->name, p->rigid_group->name);
}
+ if ( p->data_from != NULL ) {
+ fprintf(fh, "%s/data_from = %s\n",
+ p->name, p->data_from);
+ }
+
+ if ( p->mask != NULL ) {
+ fprintf(fh, "%s/mask = %s\n",
+ p->name, p->mask);
+ }
+
}
fclose(fh);
diff --git a/libcrystfel/src/detector.h b/libcrystfel/src/detector.h
index 157c2edf..fcd44ed2 100644
--- a/libcrystfel/src/detector.h
+++ b/libcrystfel/src/detector.h
@@ -80,12 +80,14 @@ struct panel
double coffset;
double clen; /* Camera length in metres */
char *clen_from;
+ char *mask;
double res; /* Resolution in pixels per metre */
char badrow; /* 'x' or 'y' */
int no_index; /* Don't index peaks in this panel if non-zero */
struct rigid_group *rigid_group; /* Rigid group */
double adu_per_eV; /* Number of ADU per eV */
double max_adu; /* Treat pixel as unreliable if higher than this */
+ char *data_from;
double fsx;
double fsy;
@@ -97,6 +99,11 @@ struct panel
double xss;
double yss;
+ int orig_min_fs;
+ int orig_max_fs;
+ int orig_min_ss;
+ int orig_max_ss;
+
int w; /* Width, calculated as max_fs-min_fs+1 */
int h; /* Height, calculated as max_ss-min_ss+1 */
};
@@ -132,7 +139,6 @@ struct detector
struct badregion *bad;
int n_bad;
- char *mask;
unsigned int mask_bad;
unsigned int mask_good;
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);
diff --git a/libcrystfel/src/hdf5-file.h b/libcrystfel/src/hdf5-file.h
index aca00692..1cac71a5 100644
--- a/libcrystfel/src/hdf5-file.h
+++ b/libcrystfel/src/hdf5-file.h
@@ -48,9 +48,9 @@ extern "C" {
extern int hdf5_write(const char *filename, const void *data,
int width, int height, int type);
-extern int hdf5_write_image(const char *filename, struct image *image);
+extern int hdf5_write_image(const char *filename, struct image *image, char *element);
-extern int hdf5_read(struct hdfile *f, struct image *image, int satcorr);
+extern int hdf5_read(struct hdfile *f, struct image *image, const char *element, int satcorr);
extern struct hdfile *hdfile_open(const char *filename);
extern int hdfile_set_image(struct hdfile *f, const char *path);
diff --git a/src/dw-hdfsee.c b/src/dw-hdfsee.c
index 93bedf7f..3a2d24d2 100644
--- a/src/dw-hdfsee.c
+++ b/src/dw-hdfsee.c
@@ -1862,8 +1862,8 @@ static gint displaywindow_newhdf(GtkMenuItem *item, struct newhdf *nh)
a = gtk_check_menu_item_get_active(GTK_CHECK_MENU_ITEM(nh->widget));
if ( !a ) return 0;
- hdfile_set_image(nh->dw->hdfile, nh->name);
- hdf5_read(nh->dw->hdfile, nh->dw->image, 0);
+ hdf5_read(nh->dw->hdfile, nh->dw->image, nh->name, 0);
+
// /* Check that the geometry still fits */
// if ( !geometry_fits(nh->dw->image, nh->dw->simple_geom) ) {
// int using = 0;
@@ -1991,10 +1991,8 @@ static GtkWidget *displaywindow_addhdfgroup(struct hdfile *hdfile,
gtk_menu_shell_append(GTK_MENU_SHELL(mss), ss);
gtk_menu_item_set_submenu(GTK_MENU_ITEM(item),
mss);
-
}
-
}
gtk_menu_shell_append(GTK_MENU_SHELL(ms), item);
@@ -2500,6 +2498,7 @@ DisplayWindow *displaywindow_open(const char *filename, const char *peaks,
DisplayWindow *dw;
char *title;
GtkWidget *vbox;
+ int check;
dw = calloc(1, sizeof(DisplayWindow));
if ( dw == NULL ) return NULL;
@@ -2541,6 +2540,10 @@ DisplayWindow *displaywindow_open(const char *filename, const char *peaks,
dw->image->det = det_geom;
+ /* TODO: Move the opening of the file in hd5_read.
+ * Currently not possible because the file handle
+ * must be stored in dw */
+
/* Open the file, if any */
if ( filename != NULL ) {
@@ -2549,19 +2552,10 @@ DisplayWindow *displaywindow_open(const char *filename, const char *peaks,
free(dw);
return NULL;
} else {
- int fail = -1;
-
- if ( element == NULL ) {
- fail = hdfile_set_first_image(dw->hdfile, "/");
- } else {
- fail = hdfile_set_image(dw->hdfile, element);
- }
-
- if ( !fail ) {
- dw->image->filename = strdup(filename);
- hdf5_read(dw->hdfile, dw->image, 0);
- } else {
- ERROR("Couldn't select path\n");
+ dw->image->filename = strdup(filename);
+ check = hdf5_read(dw->hdfile, dw->image, element, 0);
+ if (check) {
+ ERROR("Couldn't load file\n");
free(dw);
return NULL;
}
diff --git a/src/partial_sim.c b/src/partial_sim.c
index ebff2e20..9c876c27 100644
--- a/src/partial_sim.c
+++ b/src/partial_sim.c
@@ -204,7 +204,7 @@ static void draw_and_write_image(struct image *image, RefList *reflections,
image->data[i] += poisson_noise(rng, background);
}
- hdf5_write_image(image->filename, image);
+ hdf5_write_image(image->filename, image, NULL);
free(image->data);
}
diff --git a/src/pattern_sim.c b/src/pattern_sim.c
index fca12bab..361a3bcd 100644
--- a/src/pattern_sim.c
+++ b/src/pattern_sim.c
@@ -750,7 +750,7 @@ int main(int argc, char *argv[])
number++;
/* Write the output file */
- hdf5_write_image(filename, &image);
+ hdf5_write_image(filename, &image, NULL);
}
diff --git a/src/process_image.c b/src/process_image.c
index 96752832..1e2c7077 100644
--- a/src/process_image.c
+++ b/src/process_image.c
@@ -76,29 +76,7 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
hdfile = hdfile_open(image.filename);
if ( hdfile == NULL ) return;
- if ( iargs->element != NULL ) {
-
- int r;
- r = hdfile_set_image(hdfile, iargs->element);
- if ( r ) {
- ERROR("Couldn't select path '%s'\n", iargs->element);
- hdfile_close(hdfile);
- return;
- }
-
- } else {
-
- int r;
- r = hdfile_set_first_image(hdfile, "/");
- if ( r ) {
- ERROR("Couldn't select first path\n");
- hdfile_close(hdfile);
- return;
- }
-
- }
-
- check = hdf5_read(hdfile, &image, 1);
+ check = hdf5_read(hdfile, &image, iargs->element, 1);
if ( check ) {
hdfile_close(hdfile);
return;
generated by cgit v1.2.3 (git 2.25.1) at 2024-08-05 17:46:57 +0000