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-rw-r--r--libcrystfel/src/detector.c499
-rw-r--r--libcrystfel/src/detector.h113
-rw-r--r--libcrystfel/src/reax.c2
-rw-r--r--src/dw-hdfsee.c37
-rw-r--r--src/dw-hdfsee.h7
-rw-r--r--src/hdfsee.c15
6 files changed, 561 insertions, 112 deletions
diff --git a/libcrystfel/src/detector.c b/libcrystfel/src/detector.c
index f5f6bb57..ecb0ea99 100644
--- a/libcrystfel/src/detector.c
+++ b/libcrystfel/src/detector.c
@@ -59,6 +59,19 @@
*/
+
+struct rg_definition {
+ char *name;
+ char *pns;
+};
+
+
+struct rgc_definition {
+ char *name;
+ char *rgs;
+};
+
+
static int atob(const char *a)
{
if ( strcasecmp(a, "true") == 0 ) return 1;
@@ -203,6 +216,57 @@ static int dir_conv(const char *a, double *sx, double *sy)
}
+static int count_trailing_spaces(const char *string) {
+
+ int i;
+
+ for ( i=0; i<strlen(string); i++ ) {
+ if ( !isspace(string[i]) ) {
+ return i;
+ }
+ }
+
+ return -1;
+}
+
+
+static void build_output_line (const char *line, char *new_line,
+ const char *string_to_write)
+{
+ int nsp, i, w, ww;
+ int trailsp;
+ int n_bits;
+ char **bits;
+
+ n_bits = assplode(line, "=", &bits, ASSPLODE_NONE);
+ trailsp = count_trailing_spaces(bits[1]);
+
+ strcat(new_line, bits[0]);
+ strcat(new_line, "=");
+
+ for ( nsp=0; nsp < trailsp; nsp++ ) {
+ strcat(new_line, " ");
+ }
+ strcat(new_line, string_to_write);
+
+ for ( w=0; w<strlen(line); w++ ) {
+ if ( strncmp(&line[w],";",1) == 0 ) {
+ for ( ww=w-1; ww>=0; ww-- ) {
+ if ( !isspace(line[ww])) {
+ strcat(new_line, &line[ww]);
+ break;
+ }
+ }
+ break;
+ }
+ }
+ if ( w == strlen(line) ) strcat(new_line, "\n");
+
+ for ( i=0; i<n_bits; i++) free(bits[i]);
+ free(bits);
+}
+
+
struct rvec get_q_for_panel(struct panel *p, double fs, double ss,
double *ttp, double k)
{
@@ -509,6 +573,52 @@ void fill_in_values(struct detector *det, struct hdfile *f, struct event* ev)
}
+int panel_is_in_rigid_group(const struct rigid_group *rg, struct panel *p)
+{
+ int i;
+
+ for ( i=0; i<rg->n_panels; i++ ) {
+ if ( rg->panels[i] == p ) {
+ return 1;
+ }
+ }
+
+ return 0;
+}
+
+
+int rigid_group_is_in_collection(struct rg_collection *c,
+ struct rigid_group *rg)
+{
+ int i;
+
+ for ( i=0; i<c->n_rigid_groups; i++ ) {
+ if ( c->rigid_groups[i] == rg ) {
+ return 1;
+ }
+ }
+
+ return 0;
+}
+
+
+struct rg_collection *find_rigid_group_collection_by_name(struct detector *det,
+ const char *name)
+{
+ int i;
+
+ for ( i=0; i<det->n_rg_collections; i++ ) {
+ if ( strcmp(det->rigid_group_collections[i]->name,
+ name) == 0 ) {
+ return det->rigid_group_collections[i];
+ }
+ }
+
+ return NULL;
+
+}
+
+
static struct panel *new_panel(struct detector *det, const char *name)
{
struct panel *new;
@@ -643,6 +753,41 @@ static struct rigid_group *find_or_add_rg(struct detector *det,
}
+static struct rg_collection *find_or_add_rg_coll(struct detector *det,
+ const char *name)
+{
+ int i;
+ struct rg_collection **new;
+ struct rg_collection *rgc;
+
+ for ( i=0; i<det->n_rg_collections; i++ ) {
+
+ if ( strcmp(det->rigid_group_collections[i]->name, name) == 0 ) {
+ return det->rigid_group_collections[i];
+ }
+
+ }
+
+ new = realloc(det->rigid_group_collections,
+ (1+det->n_rg_collections)*
+ sizeof(struct rg_collection *));
+ if ( new == NULL ) return NULL;
+
+ det->rigid_group_collections = new;
+
+ rgc = malloc(sizeof(struct rg_collection));
+ if ( rgc == NULL ) return NULL;
+
+ det->rigid_group_collections[det->n_rg_collections++] = rgc;
+
+ rgc->name = strdup(name);
+ rgc->rigid_groups = NULL;
+ rgc->n_rigid_groups = 0;
+
+ return rgc;
+}
+
+
static void add_to_rigid_group(struct rigid_group *rg, struct panel *p)
{
struct panel **pn;
@@ -653,12 +798,27 @@ static void add_to_rigid_group(struct rigid_group *rg, struct panel *p)
return;
}
- assert(p->rigid_group == rg);
rg->panels = pn;
rg->panels[rg->n_panels++] = p;
}
+static void add_to_rigid_group_coll(struct rg_collection *rgc,
+ struct rigid_group *rg)
+{
+ struct rigid_group **r;
+
+ r = realloc(rgc->rigid_groups, (1+rgc->n_rigid_groups)*
+ sizeof(struct rigid_group *));
+ if ( r == NULL ) {
+ ERROR("Couldn't add rigid group to collection.\n");
+ return;
+ }
+
+ rgc->rigid_groups = r;
+ rgc->rigid_groups[rgc->n_rigid_groups++] = rg;
+}
+
static void rigid_groups_free(struct detector *det)
{
int i;
@@ -672,19 +832,33 @@ static void rigid_groups_free(struct detector *det)
free(det->rigid_groups);
}
-
-static void fix_up_rigid_groups(struct detector *det)
+static void rigid_groups_collection_free(struct detector *det)
{
int i;
- for ( i=0; i<det->n_panels; i++ ) {
+ if ( det->rigid_group_collections == NULL ) return;
+ for ( i=0; i<det->n_rg_collections; i++ ) {
+ free(det->rigid_group_collections[i]->name);
+ free(det->rigid_group_collections[i]->rigid_groups);
+ free(det->rigid_group_collections[i]);
+ }
+ free(det->rigid_group_collections);
+}
- struct panel *p = &det->panels[i];
- if ( p->rigid_group != NULL ) {
- add_to_rigid_group(p->rigid_group, p);
- }
+static struct rigid_group *find_rigid_group_by_name(struct detector *det,
+ char *name)
+{
+ int i;
+
+ for ( i=0; i<det->n_rigid_groups; i++ ) {
+ if ( strcmp(det->rigid_groups[i]->name, name) == 0 ) {
+ return det->rigid_groups[i];
+ }
}
+
+ return NULL;
+
}
@@ -708,7 +882,7 @@ static int parse_field_for_panel(struct panel *panel, const char *key,
} else if ( strcmp(key, "adu_per_eV") == 0 ) {
panel->adu_per_eV = atof(val);
} else if ( strcmp(key, "rigid_group") == 0 ) {
- panel->rigid_group = find_or_add_rg(det, val);
+ add_to_rigid_group(find_or_add_rg(det, val), panel);
} else if ( strcmp(key, "clen") == 0 ) {
char *end;
@@ -824,8 +998,12 @@ static int parse_field_bad(struct badregion *panel, const char *key,
static void parse_toplevel(struct detector *det, struct beam_params *beam,
- const char *key, const char *val)
+ const char *key, const char *val,
+ struct rg_definition ***rg_defl,
+ struct rgc_definition ***rgc_defl, int *n_rg_defs,
+ int *n_rgc_defs)
{
+
if ( strcmp(key, "mask_bad") == 0 ) {
char *end;
@@ -860,6 +1038,33 @@ static void parse_toplevel(struct detector *det, struct beam_params *beam,
if ( beam != NULL ) {
beam->photon_energy_scale = atof(val);
}
+ } else if (strncmp(key, "rigid_group", 11) == 0 &&
+ strncmp(key, "rigid_group_collection", 22) != 0 ) {
+
+ struct rg_definition **new;
+
+ new = realloc(*rg_defl,
+ ((*n_rg_defs)+1)*sizeof(struct rg_definition*));
+ *rg_defl = new;
+
+ (*rg_defl)[*n_rg_defs] = malloc(sizeof(struct rg_definition));
+ (*rg_defl)[*n_rg_defs]->name = strdup(key+12);
+ (*rg_defl)[*n_rg_defs]->pns = strdup(val);
+ *n_rg_defs = *n_rg_defs+1;
+
+ } else if ( strncmp(key, "rigid_group_collection", 22) == 0 ) {
+
+ struct rgc_definition **new;
+
+ new = realloc(*rgc_defl, ((*n_rgc_defs)+1)*
+ sizeof(struct rgc_definition*));
+ *rgc_defl = new;
+
+ (*rgc_defl)[*n_rgc_defs] =
+ malloc(sizeof(struct rgc_definition));
+ (*rgc_defl)[*n_rgc_defs]->name = strdup(key+23);
+ (*rgc_defl)[*n_rgc_defs]->rgs = strdup(val);
+ *n_rgc_defs = *n_rgc_defs+1;
} else if ( parse_field_for_panel(&det->defaults, key, val, det) ) {
ERROR("Unrecognised top level field '%s'\n", key);
@@ -933,6 +1138,7 @@ struct detector *get_detector_geometry(const char *filename,
char *rval;
char **bits;
int i;
+ int rgi, rgci;
int reject = 0;
int path_dim;
int dim_dim;
@@ -940,6 +1146,10 @@ struct detector *get_detector_geometry(const char *filename,
int x, y, max_fs, max_ss;
int dim_reject = 0;
int dim_dim_reject = 0;
+ struct rg_definition **rg_defl = NULL;
+ struct rgc_definition **rgc_defl = NULL;
+ int n_rg_definitions = 0;
+ int n_rgc_definitions = 0;
fh = fopen(filename, "r");
if ( fh == NULL ) return NULL;
@@ -966,6 +1176,8 @@ struct detector *get_detector_geometry(const char *filename,
det->rigid_groups = NULL;
det->path_dim = 0;
det->dim_dim = 0;
+ det->n_rg_collections = 0;
+ det->rigid_group_collections = NULL;
/* The default defaults... */
det->defaults.min_fs = -1;
@@ -987,7 +1199,6 @@ struct detector *get_detector_geometry(const char *filename,
det->defaults.fsy = 0.0;
det->defaults.ssx = 0.0;
det->defaults.ssy = 1.0;
- det->defaults.rigid_group = NULL;
det->defaults.adu_per_eV = NAN;
det->defaults.max_adu = +INFINITY;
det->defaults.mask = NULL;
@@ -1034,7 +1245,9 @@ struct detector *get_detector_geometry(const char *filename,
if ( n2 < 2 ) {
/* This was a top-level option, not handled above. */
- parse_toplevel(det, beam, bits[0], bits[2]);
+ parse_toplevel(det, beam, bits[0], bits[2], &rg_defl,
+ &rgc_defl, &n_rg_definitions,
+ &n_rgc_definitions);
for ( i=0; i<n1; i++ ) free(bits[i]);
free(bits);
for ( i=0; i<n2; i++ ) free(path[i]);
@@ -1338,6 +1551,90 @@ out:
free(det->defaults.data);
free(det->defaults.mask);
+ for ( rgi=0; rgi<n_rg_definitions; rgi++) {
+
+ int pi, n1;
+ struct rigid_group *rigidgroup = NULL;
+
+ rigidgroup = find_or_add_rg(det, rg_defl[rgi]->name);
+
+ n1 = assplode(rg_defl[rgi]->pns, ",", &bits, ASSPLODE_NONE);
+
+ for ( pi=0; pi<n1; pi++ ) {
+
+ struct panel *p;
+
+ p = find_panel_by_name(det, bits[pi]);
+ if ( p == NULL ) {
+ ERROR("Cannot add panel to rigid group\n");
+ ERROR("Panel not found: %s\n", bits[pi]);
+ }
+ add_to_rigid_group(rigidgroup, p);
+ free(bits[pi]);
+ }
+ free(bits);
+ free(rg_defl[rgi]->name);
+ free(rg_defl[rgi]->pns);
+ free(rg_defl[rgi]);
+ }
+ free(rg_defl);
+
+ for ( rgci=0; rgci<n_rgc_definitions; rgci++) {
+
+ int rgi, n2;
+ struct rg_collection *rgcollection = NULL;
+
+ rgcollection = find_or_add_rg_coll(det, rgc_defl[rgci]->name);
+
+ n2 = assplode(rgc_defl[rgci]->rgs, ",", &bits, ASSPLODE_NONE);
+
+ for ( rgi=0; rgi<n2; rgi++ ) {
+
+ struct rigid_group *r;
+
+ r = find_rigid_group_by_name(det, bits[rgi]);
+ if ( r == NULL ) {
+ ERROR("Cannot add rigid group to collection\n");
+ ERROR("Rigid groups not found: %s\n", bits[rgi]);
+ }
+ add_to_rigid_group_coll(rgcollection, r);
+ free(bits[rgi]);
+ }
+ free(rgc_defl[rgci]->name);
+ free(rgc_defl[rgci]->rgs);
+ free(rgc_defl[rgci]);
+ }
+ free(rgc_defl);
+
+ if ( n_rg_definitions == 0) {
+
+ int pi;
+
+ for ( pi=0; pi<det->n_panels; pi++ ) {
+
+ struct rigid_group *rigidgroup = NULL;
+
+ rigidgroup = find_or_add_rg(det, det->panels[pi].name);
+ add_to_rigid_group(rigidgroup, &det->panels[pi]);
+
+ }
+ }
+
+ if ( n_rgc_definitions == 0) {
+
+ int rgi;
+ struct rg_collection *rgcollection = NULL;
+
+ rgcollection = find_or_add_rg_coll(det, "default");
+
+ for ( rgi=0; rgi<det->n_rigid_groups; rgi++ ) {
+
+ add_to_rigid_group_coll(rgcollection,
+ det->rigid_groups[rgi]);
+
+ }
+ }
+
/* Calculate matrix inverses and other stuff */
for ( i=0; i<det->n_panels; i++ ) {
@@ -1348,7 +1645,6 @@ out:
if ( p->fsx*p->ssy == p->ssx*p->fsy ) {
ERROR("Panel %i transformation singular.\n", i);
- reject = 1;
}
d = (double)p->fsx*p->ssy - p->ssx*p->fsy;
@@ -1360,15 +1656,9 @@ out:
p->w = p->max_fs - p->min_fs + 1;
p->h = p->max_ss - p->min_ss + 1;
- if ( p->rigid_group == NULL ) {
- p->rigid_group = find_or_add_rg(det, p->name);
- }
-
}
- /* Fix up rigid group panel pointers now that the panels and RGs have
- * stopped being realloc()ed */
- fix_up_rigid_groups(det);
+
find_min_max_d(det);
@@ -1385,6 +1675,7 @@ void free_detector_geometry(struct detector *det)
int i;
rigid_groups_free(det);
+ rigid_groups_collection_free(det);
for ( i=0; i<det->n_panels; i++ ) {
free(det->panels[i].clen_from);
@@ -1460,16 +1751,34 @@ struct detector *copy_geom(const struct detector *in)
for ( i=0; i<in->n_panels; i++ ) {
- struct rigid_group *rg;
+ int rgi;
- rg = in->panels[i].rigid_group;
- if ( rg == NULL ) continue;
-
- out->panels[i].rigid_group = find_or_add_rg(out, rg->name);
+ for ( rgi=0; rgi<in->n_rigid_groups; rgi++ ) {
+ if ( panel_is_in_rigid_group(in->rigid_groups[rgi],
+ &in->panels[i])) {
+ add_to_rigid_group(find_or_add_rg(out,
+ in->rigid_groups[rgi]->name),
+ &out->panels[i]);
+ }
+ }
}
- fix_up_rigid_groups(out);
+ for ( i=0; i<in->n_rigid_groups; i++ ) {
+
+ int rgci;
+
+ for ( rgci=0; rgci<in->n_rg_collections; rgci++ ) {
+ if ( rigid_group_is_in_collection(
+ in->rigid_group_collections[rgci],
+ in->rigid_groups[i]) )
+ {
+ add_to_rigid_group_coll(find_or_add_rg_coll(out,
+ in->rigid_group_collections[rgci]->name),
+ out->rigid_groups[i]);
+ }
+ }
+ }
return out;
}
@@ -1494,7 +1803,6 @@ struct detector *simple_geometry(const struct image *image)
geom->panels[0].orig_max_ss = image->height-1;
geom->panels[0].cnx = -image->width / 2.0;
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;
@@ -1642,7 +1950,9 @@ void get_pixel_extents(struct detector *det,
int write_detector_geometry(const char *geometry_filename,
- const char *output_filename, struct detector *det)
+ const char *output_filename, struct detector *det,
+ const char *additional_comment,
+ int write_panel_coffset)
{
FILE *ifh;
FILE *fh;
@@ -1655,53 +1965,142 @@ int write_detector_geometry(const char *geometry_filename,
if ( ifh == NULL ) return 1;
fh = fopen(output_filename, "w");
- if ( fh == NULL ) return 1;
+ if ( fh == NULL ) {
+ fclose(fh);
+ return 1;
+ }
+
+ if ( additional_comment != NULL ) {
+
+ char additional_comment_tmp[1024];
+
+ strcpy(additional_comment_tmp, "; ");
+ strncat(additional_comment_tmp, additional_comment, 1021);
+ strcat(additional_comment_tmp, "\n");
+ if ( strlen(additional_comment) > 1021 ) {
+ strncpy(&additional_comment_tmp[1023], "\0", 1);
+ }
+ fputs(additional_comment_tmp, fh);
+ }
+ if ( write_panel_coffset ) {
+
+ char new_line[1024];
+ strcpy(new_line,"; Optimized panel offsets can be found at the "
+ "end of the file\n");
+ fputs(new_line, fh);
+
+ }
do {
char *rval;
char line[1024];
+ char new_line[1024];
+ char string_to_write[512];
+
int n_bits;
char **bits;
+
int i;
struct panel *p;
+ strcpy(new_line,"\0");
+ strcpy(string_to_write,"\0");
+
rval = fgets(line, 1023, ifh);
if ( rval == NULL ) break;
- n_bits = assplode(line, "/", &bits, ASSPLODE_NONE);
+ n_bits = assplode(line, "/=", &bits, ASSPLODE_NONE);
- if ( n_bits < 2 || n_bits > 2 ) {
- for ( i=0; i<n_bits; i++ ) free(bits[i]);
- fputs(line, fh);
+ if ( n_bits != 3 ) {
+ if ( strstr(bits[0], "coffset" ) != NULL &&
+ write_panel_coffset ) {
+ continue;
+ } else {
+ fputs(line, fh);
+ }
} else {
+
p = find_panel_by_name(det, bits[0]);
- if ( strncmp(bits[1], "fs = ", 5) == 0) {
- fprintf(fh, "%s/fs = %+fx %+fy\n",
- p->name, p->fsx, p->fsy);
+ if ( p != NULL ) {
+
+ if(strstr(bits[1], "fs") != NULL &&
+ strstr(bits[1], "min_fs") == NULL &&
+ strstr(bits[1], "max_fs") == NULL) {
+
+ sprintf(string_to_write, "%+fx %+fy",
+ p->fsx, p->fsy);
+ build_output_line(line, new_line,
+ string_to_write);
+ fputs(new_line, fh);
+ continue;
+
+ } else if ( strstr(bits[1], "ss") != NULL &&
+ strstr(bits[1], "min_ss") == NULL &&
+ strstr(bits[1], "max_ss") == NULL) {
+
+ sprintf(string_to_write, "%+fx %+fy",
+ p->ssx, p->ssy);
+ build_output_line(line, new_line,
+ string_to_write);
+ fputs(new_line, fh);
+ continue;
+
+ } else if ( strstr(bits[1], "corner_x") != NULL) {
+
+ sprintf(string_to_write, "%g",
+ p->cnx);
+ build_output_line(line, new_line,
+ string_to_write);
+ fputs(new_line, fh);
+ continue;
+
+ } else if ( strstr(bits[1], "corner_y") != NULL) {
+
+ sprintf(string_to_write, "%g",
+ p->cny);
+ build_output_line(line, new_line,
+ string_to_write);
+ fputs(new_line, fh);
+ continue;
+
+ } else if ( strstr(bits[1], "coffset") != NULL) {
+
+ if ( write_panel_coffset ) {
+ continue;
+ } else {
+ fputs(line, fh);
+ continue;
+ }
+
+ } else {
+ fputs(line, fh);
+ }
+ } else {
+ fputs(line, fh);
+ }
+ }
- } else if ( strncmp(bits[1], "ss = ", 5) == 0) {
- fprintf(fh, "%s/ss = %+fx %+fy\n",
- p->name, p->ssx, p->ssy);
+ for ( i=0; i<n_bits; i++ ) free(bits[i]);
- } else if ( strncmp(bits[1], "corner_x = ", 11) == 0) {
- fprintf(fh, "%s/corner_x = %g\n",
- p->name, p->cnx);
+ } while ( 1 );
- } else if ( strncmp(bits[1], "corner_y = ", 11) == 0) {
- fprintf(fh, "%s/corner_y = %g\n",
- p->name, p->cny);
+ if ( write_panel_coffset ) {
- } else {
- fputs(line, fh);
- }
+ int pi;
+ char new_line[1024];
- for ( i=0; i<n_bits; i++ ) free(bits[i]);
+ strcpy(new_line, "\n");
+ fputs(new_line, fh);
+ for ( pi=0; pi<det->n_panels; pi++ ) {
+ sprintf(new_line, "%s/coffset = %f\n",
+ det->panels[pi].name, det->panels[pi].coffset);
+ fputs(new_line, fh);
}
+ }
- } while ( 1 );
fclose(ifh);
fclose(fh);
diff --git a/libcrystfel/src/detector.h b/libcrystfel/src/detector.h
index f43df2cc..87fcc890 100644
--- a/libcrystfel/src/detector.h
+++ b/libcrystfel/src/detector.h
@@ -71,52 +71,61 @@ struct rigid_group
};
-struct panel
+struct rg_collection
{
- char name[1024]; /* Name for this panel */
+ char *name;
+ struct rigid_group **rigid_groups;
+ int n_rigid_groups;
+};
- /* Position of panel in the data block in memory (see below) */
- int min_fs; /* Smallest FS value considered to be in the panel */
- int max_fs; /* Largest FS value considered to be in this panel */
- int min_ss; /* ... and so on */
- int max_ss;
- double cnx; /* Location of corner (min_fs,min_ss) in pixels */
- double cny;
- 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;
-
- struct dim_structure *dim_structure;
-
- double fsx;
- double fsy;
- double ssx;
- double ssy;
-
- double xfs;
- double yfs;
- double xss;
- double yss;
-
- /* Position of the panel in the data block in the file. The panels may
- * get moved around when the file is loaded (see hdf5_read2()),
- * especially if the panels come from different HDF5 elements. */
- 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 */
+struct panel
+{
+
+ char name[1024]; /* Name for this panel */
+
+ /* Position of panel in the data block in memory (see below) */
+ int min_fs; /* Smallest FS value considered to be in the panel */
+ int max_fs; /* Largest FS value considered to be in this panel */
+ int min_ss; /* ... and so on */
+ int max_ss;
+
+ double cnx; /* Location of corner (min_fs,min_ss) in pixels */
+ double cny;
+ 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;
+
+ struct dim_structure *dim_structure;
+
+ double fsx;
+ double fsy;
+ double ssx;
+ double ssy;
+
+ double xfs;
+ double yfs;
+ double xss;
+ double yss;
+
+ /* Position of the panel in the data block in the file. The panels may
+ * get moved around when the file is loaded (see hdf5_read2()),
+ * especially if the panels come from different HDF5 elements. */
+ 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 */
};
@@ -156,6 +165,9 @@ struct detector
struct rigid_group **rigid_groups;
int n_rigid_groups;
+ struct rg_collection **rigid_group_collections;
+ int n_rg_collections;
+
/* Location of the pixel furthest away from the beam position, which
* will have the largest value of 2theta regardless of camera length
* and wavelength */
@@ -207,6 +219,12 @@ extern void get_pixel_extents(struct detector *det,
extern void fill_in_values(struct detector *det, struct hdfile *f,
struct event* ev);
+extern int panel_is_in_rigid_group(const struct rigid_group *rg,
+ struct panel *p);
+
+extern int rigid_group_is_in_collection(struct rg_collection *c,
+ struct rigid_group *rg);
+
extern struct detector *copy_geom(const struct detector *in);
extern int reverse_2d_mapping(double x, double y, double *pfs, double *pss,
@@ -218,10 +236,11 @@ extern double smallest_q(struct image *image);
extern struct panel *find_panel_by_name(struct detector *det, const char *name);
-extern int write_detector_geometry(const char* geometry_filename,
+extern int write_detector_geometry(const char *geometry_filename,
const char *output_filename,
- struct detector *det);
-
+ struct detector *det,
+ const char *additional_comment,
+ int write_panel_coffset);
extern void mark_resolution_range_as_bad(struct image *image,
double min, double max);
@@ -229,6 +248,8 @@ extern void mark_resolution_range_as_bad(struct image *image,
extern int single_panel_data_source (struct detector *det, const char *element);
+struct rg_collection *find_rigid_group_collection_by_name(struct detector *det,
+ const char *name);
#ifdef __cplusplus
}
diff --git a/libcrystfel/src/reax.c b/libcrystfel/src/reax.c
index 770084e1..e2dd249a 100644
--- a/libcrystfel/src/reax.c
+++ b/libcrystfel/src/reax.c
@@ -155,7 +155,7 @@ static void fill_and_transform(struct dvec *dir, ImageFeatureList *flist,
p = find_panel(det, f->fs, f->ss);
assert(p != NULL);
- if ( p->rigid_group != rg ) continue;
+ if ( !panel_is_in_rigid_group(rg, p) ) continue;
}
diff --git a/src/dw-hdfsee.c b/src/dw-hdfsee.c
index ea15077f..287c7349 100644
--- a/src/dw-hdfsee.c
+++ b/src/dw-hdfsee.c
@@ -1208,7 +1208,8 @@ static int save_geometry_file(DisplayWindow *dw)
gtk_dialog_run(GTK_DIALOG(d));
output_filename = gtk_file_chooser_get_filename(GTK_FILE_CHOOSER (d));
w = write_detector_geometry(dw->geom_filename, output_filename,
- dw->image->det);
+ dw->image->det, "Manually optimized with "
+ "hdfsee", 0);
if ( w != 0 ) {
ERROR("Error saving geometry!\n");
}
@@ -1261,7 +1262,7 @@ static gint displaywindow_set_calibmode(GtkWidget *d, DisplayWindow *dw)
if ( (dw->calib_mode_curr_rg == NULL)
&& (dw->calib_mode_curr_p == NULL) )
{
- dw->calib_mode_curr_rg = dw->image->det->rigid_groups[0];
+ dw->calib_mode_curr_rg = dw->rg_coll->rigid_groups[0];
dw->calib_mode_curr_p = dw->calib_mode_curr_rg->panels[0];
}
@@ -2118,8 +2119,8 @@ static int curr_rg_pointer_index(DisplayWindow *dw)
{
int r;
- for ( r=0; r<dw->image->det->n_rigid_groups; ++r) {
- if ( dw->image->det->rigid_groups[r] == dw->calib_mode_curr_rg ) {
+ for ( r=0; r<dw->rg_coll->n_rigid_groups; ++r) {
+ if ( dw->rg_coll->rigid_groups[r] == dw->calib_mode_curr_rg ) {
return r;
}
}
@@ -2146,22 +2147,22 @@ static int curr_p_pointer_index(DisplayWindow *dw)
static void select_next_group(DisplayWindow *dw, int num_rg)
{
- if ( dw->calib_mode_curr_rg == dw->image->det->rigid_groups[num_rg-1] ) {
- dw->calib_mode_curr_rg = dw->image->det->rigid_groups[0];
+ if ( dw->calib_mode_curr_rg == dw->rg_coll->rigid_groups[num_rg-1] ) {
+ dw->calib_mode_curr_rg = dw->rg_coll->rigid_groups[0];
} else {
dw->calib_mode_curr_rg =
- dw->image->det->rigid_groups[curr_rg_pointer_index(dw)+1];
+ dw->rg_coll->rigid_groups[curr_rg_pointer_index(dw)+1];
}
}
static void select_prev_group(DisplayWindow *dw, int num_rg)
{
- if ( dw->calib_mode_curr_rg == dw->image->det->rigid_groups[0] ) {
- dw->calib_mode_curr_rg = dw->image->det->rigid_groups[num_rg-1];
+ if ( dw->calib_mode_curr_rg == dw->rg_coll->rigid_groups[0] ) {
+ dw->calib_mode_curr_rg = dw->rg_coll->rigid_groups[num_rg-1];
} else {
dw->calib_mode_curr_rg =
- dw->image->det->rigid_groups[curr_rg_pointer_index(dw)-1];
+ dw->rg_coll->rigid_groups[curr_rg_pointer_index(dw)-1];
}
}
@@ -2471,6 +2472,7 @@ DisplayWindow *displaywindow_open(char *filename, char *geom_filename,
const char *element, const char *event,
struct detector *det_geom,
struct beam_params *beam,
+ const char* rgcoll_name,
int show_rings, double *ring_radii,
int n_rings, double ring_size,
int median_filter)
@@ -2643,7 +2645,20 @@ DisplayWindow *displaywindow_open(char *filename, char *geom_filename,
gtk_widget_set_sensitive(GTK_WIDGET(w), FALSE);
}
- ww = gtk_ui_manager_get_widget(dw->ui, "/ui/displaywindow/events");
+ if ( rgcoll_name != NULL ) {
+
+ dw->rg_coll = find_rigid_group_collection_by_name(dw->image->det,
+ rgcoll_name);
+
+ if ( dw->rg_coll == NULL ) {
+ ERROR("Cannot find rigid group collection: %s\n",
+ rgcoll_name);
+ return NULL;
+ }
+ }
+
+ ww = gtk_ui_manager_get_widget(dw->ui,
+ "/ui/displaywindow/events");
if ( dw->image->det == dw->simple_geom || dw->multi_event == 0) {
gtk_widget_set_sensitive(GTK_WIDGET(ww), FALSE);
diff --git a/src/dw-hdfsee.h b/src/dw-hdfsee.h
index 7d3232d7..39b82250 100644
--- a/src/dw-hdfsee.h
+++ b/src/dw-hdfsee.h
@@ -121,8 +121,9 @@ typedef struct {
int n_rings;
CalibMode calib_mode;
- struct rigid_group *calib_mode_curr_rg;
- struct panel *calib_mode_curr_p;
+ struct rg_collection *rg_coll;
+ struct rigid_group *calib_mode_curr_rg;
+ struct panel *calib_mode_curr_p;
int calib_mode_show_focus;
GtkWidget *statusbar;
@@ -147,7 +148,7 @@ extern DisplayWindow *displaywindow_open(char *filename, char *geom_filename,
const char *event,
struct detector *det_geom,
struct beam_params *beam,
- int show_rings,
+ const char *rgcoll_name, int show_rings,
double *ring_radii, int n_rings,
double ring_size, int median_filter);
diff --git a/src/hdfsee.c b/src/hdfsee.c
index b9394d33..c5557c38 100644
--- a/src/hdfsee.c
+++ b/src/hdfsee.c
@@ -82,6 +82,8 @@ static void show_help(const char *s)
" -g, --geometry=<filename> Use geometry from file for display.\n"
" (When this option is used, the value of\n"
" of the -e parameter is ignored)"
+" -m, --beam=<filename> Get beam parameters from <filename>.\n"
+" -o, --rigid-groups=<coll> Use rigid group collection <coll>.\n"
"\n");
}
@@ -128,6 +130,7 @@ int main(int argc, char *argv[])
char *cscale = NULL;
char *element = NULL;
char *event = NULL;
+ char *rgcoll_name = NULL;
double ring_size = 5.0;
char *reslist = NULL;
double ring_radii[128];
@@ -154,6 +157,7 @@ int main(int argc, char *argv[])
{"median-filter", 1, NULL, 3},
{"calibration-mode", 0, &config_calibmode, 1},
{"event", 1, NULL, 5},
+ {"rigid-groups", 1, NULL, 'o'},
{0, 0, NULL, 0}
};
@@ -171,7 +175,7 @@ int main(int argc, char *argv[])
gtk_init(&argc, &argv);
/* Short options */
- while ((c = getopt_long(argc, argv, "hp:b:i:c:e:g:2:r:m:",
+ while ((c = getopt_long(argc, argv, "hp:b:i:c:e:g:2:r:m:o:",
longopts, NULL)) != -1) {
char *test;
@@ -227,6 +231,10 @@ int main(int argc, char *argv[])
beam = &cbeam;
break;
+ case 'o' :
+ rgcoll_name = strdup(optarg);
+ break;
+
case 2 :
ring_size = strtod(optarg, &test);
if ( test == optarg ) {
@@ -292,6 +300,10 @@ int main(int argc, char *argv[])
return 1;
}
+ if (rgcoll_name == NULL) {
+ rgcoll_name = strdup("default");
+ }
+
if ( cscale == NULL ) cscale = strdup("colour");
if ( strcmp(cscale, "mono") == 0 ) {
colscale = SCALE_MONO;
@@ -315,6 +327,7 @@ int main(int argc, char *argv[])
config_calibmode,
colscale, element,
event, det_geom, beam,
+ rgcoll_name,
config_showrings,
ring_radii,
n_rings,
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-16 20:31:45 +0000