aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
Diffstat
-rw-r--r--libcrystfel/src/datatemplate.c165
-rw-r--r--libcrystfel/src/datatemplate.h8
-rw-r--r--src/make_pixelmap.c133
3 files changed, 239 insertions, 67 deletions
diff --git a/libcrystfel/src/datatemplate.c b/libcrystfel/src/datatemplate.c
index f996c99b..2593a7f9 100644
--- a/libcrystfel/src/datatemplate.c
+++ b/libcrystfel/src/datatemplate.c
@@ -1309,3 +1309,168 @@ void data_template_add_copy_header(DataTemplate *dt,
/* FIXME: Add "header" to list of things to copy */
STATUS("Adding %s\n", header);
}
+
+
+/* If possible, i.e. if there are no references to image headers in
+ * 'dt', generate a detgeom structure from it.
+ *
+ * NB This is probably not the function you're looking for!
+ * The detgeom structure should normally come from loading an image,
+ * reading a stream or similar. This function should only be used
+ * when there is really no data involved, e.g. in make_pixelmap.
+ */
+struct detgeom *data_template_to_detgeom(const DataTemplate *dt)
+{
+ struct detgeom *detgeom;
+ int i;
+
+ if ( dt == NULL ) return NULL;
+
+ detgeom = malloc(sizeof(struct detgeom));
+ if ( detgeom == NULL ) return;
+
+ detgeom->panels = malloc(dt->n_panels*sizeof(struct detgeom_panel));
+ if ( detgeom->panels == NULL ) return;
+
+ detgeom->n_panels = dt->n_panels;
+
+ for ( i=0; i<dt->n_panels; i++ ) {
+
+ detgeom->panels[i].name = safe_strdup(dt->panels[i].name);
+
+ detgeom->panels[i].pixel_pitch = dt->panels[i].pixel_pitch;
+
+ /* NB cnx,cny are in pixels, cnz is in m */
+ detgeom->panels[i].cnx = dt->panels[i].cnx;
+ detgeom->panels[i].cny = dt->panels[i].cny;
+ detgeom->panels[i].cnz = get_length(image, dt->panels[i].cnz_from);
+
+ /* Apply offset (in m) and then convert cnz from
+ * m to pixels */
+ detgeom->panels[i].cnz += dt->panels[i].cnz_offset;
+ detgeom->panels[i].cnz /= detgeom->panels[i].pixel_pitch;
+
+ detgeom->panels[i].max_adu = dt->panels[i].max_adu;
+ detgeom->panels[i].adu_per_photon = 1.0; /* FIXME ! */
+
+ detgeom->panels[i].w = dt->panels[i].orig_max_fs
+ - dt->panels[i].orig_min_fs + 1;
+ detgeom->panels[i].h = dt->panels[i].orig_max_ss
+ - dt->panels[i].orig_min_ss + 1;
+
+ detgeom->panels[i].fsx = dt->panels[i].fsx;
+ detgeom->panels[i].fsy = dt->panels[i].fsy;
+ detgeom->panels[i].fsz = dt->panels[i].fsz;
+ detgeom->panels[i].ssx = dt->panels[i].ssx;
+ detgeom->panels[i].ssy = dt->panels[i].ssy;
+ detgeom->panels[i].ssz = dt->panels[i].ssz;
+
+ }
+
+ return detgeom;
+}
+
+
+int data_template_get_slab_extents(const DataTemplate *dt,
+ int *pw, int *ph)
+{
+ int w, h;
+ char *data_from;
+
+ data_from = dt->panels[0].data;
+
+ w = 0; h = 0;
+ for ( i=0; i<dt->n_panels; i++ ) {
+
+ struct panel_template *p = &dt->panels[i];
+
+ if ( strcmp(data_from, p->data) != 0 ) {
+ /* Not slabby */
+ return 1;
+ }
+
+ if ( p->dim_structure != NULL ) {
+ int j;
+ for ( j=0; j<p->dim_structure->ndims; j++ ) {
+ if ( p->dim_structure->dims[j] == HYSL_PLACEHOLDER ) {
+ /* Not slabby */
+ return 1;
+ }
+ }
+ }
+
+ if ( p->file_max_fs > w ) {
+ w = p->file_max_fs;
+ }
+ if ( p->file_max_ss > h ) {
+ h = p->file_max_ss;
+ }
+ }
+
+ /* Inclusive -> exclusive */
+ *pw = w + 1;
+ *ph = h + 1;
+ return 0;
+}
+
+
+/* Return non-zero if pixel fs,ss on panel p is in a bad region
+ * as specified in the geometry file (regions only, not including
+ * masks, NaN/inf, no_index etc */
+int data_template_in_bad_region(DataTemplate *dtempl,
+ int pn, double fs, double ss)
+{
+ double rx, ry;
+ double xs, ys;
+ int i;
+ struct panel_template *p;
+
+ if ( p >= dtempl->n_panels ) {
+ ERROR("Panel index out of range\n");
+ return 0;
+ }
+ p = dtempl->panels[pn];
+
+ /* Convert xs and ys, which are in fast scan/slow scan coordinates,
+ * to x and y */
+ xs = fs*p->fsx + ss*p->ssx;
+ ys = fs*p->fsy + ss*p->ssy;
+
+ rx = xs + p->cnx;
+ ry = ys + p->cny;
+
+ for ( i=0; i<dtempl->n_bad; i++ ) {
+
+ struct dt_badregion *b = &dtempl->bad[i];
+
+ if ( (b->panel != NULL)
+ && (strcmp(b->panel, p->name) != 0) ) continue;
+
+ if ( b->is_fsss ) {
+
+ int nfs, nss;
+
+ /* fs/ss bad regions are specified according
+ * to the original coordinates */
+ nfs = fs + p->orig_min_fs;
+ nss = ss + p->orig_min_ss;
+
+ if ( nfs < b->min_fs ) continue;
+ if ( nfs > b->max_fs ) continue;
+ if ( nss < b->min_ss ) continue;
+ if ( nss > b->max_ss ) continue;
+
+ } else {
+
+ if ( rx < b->min_x ) continue;
+ if ( rx > b->max_x ) continue;
+ if ( ry < b->min_y ) continue;
+ if ( ry > b->max_y ) continue;
+
+ }
+
+ return 1;
+ }
+
+ return 0;
+}
diff --git a/libcrystfel/src/datatemplate.h b/libcrystfel/src/datatemplate.h
index fd99d5f0..9cb60bf1 100644
--- a/libcrystfel/src/datatemplate.h
+++ b/libcrystfel/src/datatemplate.h
@@ -33,6 +33,7 @@
#include <config.h>
#endif
+#include "detgeom.h"
/**
* \file datatemplate.h
@@ -67,6 +68,13 @@ extern int data_template_panel_to_file_coords(const DataTemplate *dt,
extern void data_template_add_copy_header(DataTemplate *dt,
const char *header);
+extern struct detgeom *data_template_to_detgeom(const DataTemplate *dt);
+
+extern int data_template_get_slab_extents(const DataTemplate *dt, int *pw, int *ph);
+
+extern int data_template_in_bad_region(DataTemplate *dtempl,
+ int pn, double fs, double ss);
+
#ifdef __cplusplus
}
#endif
diff --git a/src/make_pixelmap.c b/src/make_pixelmap.c
index 1a1ed5f3..eedcb439 100644
--- a/src/make_pixelmap.c
+++ b/src/make_pixelmap.c
@@ -7,7 +7,7 @@
* a research centre of the Helmholtz Association.
*
* Authors:
- * 2012-2018 Thomas White <taw@physics.org>
+ * 2012-2020 Thomas White <taw@physics.org>
* 2016-2016 Omri Mor <omor1@asu.edu>
*
* This file is part of CrystFEL.
@@ -41,8 +41,11 @@
#include <unistd.h>
#include <getopt.h>
#include <assert.h>
+#include <hdf5.h>
-#include "detector.h"
+#include "utils.h"
+#include "datatemplate.h"
+#include "detgeom.h"
static void show_help(const char *s)
@@ -126,7 +129,7 @@ static void create_scalar(hid_t gh, const char *name, float val)
static void write_pixelmap_hdf5(const char *filename,
float *x, float *y, float *z,
- int width, int height, float res, float coffset)
+ int width, int height, float res)
{
hid_t fh;
@@ -141,7 +144,6 @@ static void write_pixelmap_hdf5(const char *filename,
create_array(fh, "z", z, H5T_NATIVE_FLOAT, width, height);
create_scalar(fh, "res", res);
- create_scalar(fh, "coffset", coffset);
H5Fclose(fh);
}
@@ -171,12 +173,12 @@ int main(int argc, char *argv[])
int c;
char *input_file = NULL;
char *output_file = NULL;
- struct detector *det = NULL;
+ DataTemplate *dtempl;
+ struct detgeom *detgeom;
int fs, ss, w, h;
float *x, *y, *z;
uint16_t *b;
- int i;
- float res, coffset;
+ float res;
int badmap = 0;
int good_pixel_val = 1;
int bad_pixel_val = 0;
@@ -248,24 +250,28 @@ int main(int argc, char *argv[])
}
/* Load geometry */
- det = get_detector_geometry(input_file, NULL);
- if ( det == NULL ) {
- ERROR("Failed to read geometry from '%s'\n", input_file);
+ dtempl = data_template_new_from_file(input_file);
+ if ( dtempl == NULL ) {
+ ERROR("Failed to read geometry from '%s'\n",
+ input_file);
return 1;
}
free(input_file);
+ detgeom = data_template_to_detgeom(dtempl);
+ if ( detgeom == NULL ) {
+ ERROR("Could not make detector structure.\n");
+ ERROR("Geometry file must not contain references to "
+ "image header values\n");
+ return 1;
+ }
+
/* Determine max orig fs and ss */
- w = 0; h = 0;
- for ( i=0; i<det->n_panels; i++ ) {
- if ( det->panels[i].orig_max_fs > w ) {
- w = det->panels[i].orig_max_fs;
- }
- if ( det->panels[i].orig_max_ss > h ) {
- h = det->panels[i].orig_max_ss;
- }
+ if ( data_template_get_slab_extents(dtempl, &w, &h) ) {
+ ERROR("Pixel map can only be created if all panels "
+ "have their data in one \"slab\".\n");
+ return 1;
}
- w += 1; h += 1; /* Inclusive -> Exclusive */
STATUS("Data slab size: %i x %i\n", w, h);
x = malloc(w*h*sizeof(float));
@@ -277,66 +283,59 @@ int main(int argc, char *argv[])
return 1;
}
+ /* For every pixel in the slab ... */
for ( ss=0; ss<h; ss++ ) {
- for ( fs=0; fs<w; fs++ ) {
-
- double rx, ry;
- struct panel *p;
- double xs, ys;
- double cfs, css;
- int nfs, nss;
-
- p = find_orig_panel(det, fs, ss);
-
- /* Add half a pixel to fs and ss to get the fs,ss
- * coordinates of the CENTRE of the pixel */
- cfs = fs + 0.5;
- css = ss + 0.5;
- xs = (cfs - p->orig_min_fs)*p->fsx
- + (css - p->orig_min_ss)*p->ssx;
- ys = (cfs - p->orig_min_fs)*p->fsy
- + (css - p->orig_min_ss)*p->ssy;
-
- rx = (xs + p->cnx) / p->res;
- ry = (ys + p->cny) / p->res;
-
- x[fs + w*ss] = rx;
- y[fs + w*ss] = ry;
- z[fs + w*ss] = 0.0; /* FIXME */
-
- nfs = fs - p->orig_min_fs;
- nss = ss - p->orig_min_ss;
- if ( in_bad_region(det, p, nfs, nss) ) {
- b[fs + w*ss] = bad_pixel_val;
- } else {
- b[fs + w*ss] = good_pixel_val;
- }
+ for ( fs=0; fs<w; fs++ ) {
+
+ double rx, ry;
+ double xs, ys;
+ float cfs, css;
+ int pn;
+ struct detgeom_panel *p;
+
+ /* Add half a pixel to fs and ss to get the fs,ss
+ * coordinates of the CENTRE of the pixel */
+ cfs = fs + 0.5;
+ css = ss + 0.5;
+
+ if ( data_template_file_to_panel_coords(dtempl,
+ &cfs, &css,
+ &pn) )
+ {
+ ERROR("Couldn't convert coordinates\n");
+ return 1;
+ }
+ p = &detgeom->panels[pn];
+
+ xs = cfs*p->fsx + css*p->ssx;
+ ys = cfs*p->fsy + css*p->ssy;
+
+ rx = (xs + p->cnx) * p->pixel_pitch;
+ ry = (ys + p->cny) * p->pixel_pitch;
+
+ x[fs + w*ss] = rx;
+ y[fs + w*ss] = ry;
+ z[fs + w*ss] = 0.0; /* 2D part only */
+
+ if ( data_template_in_bad_region(dtempl, pn, cfs, css) ) {
+ b[fs + w*ss] = bad_pixel_val;
+ } else {
+ b[fs + w*ss] = good_pixel_val;
}
- progress_bar(ss, h, "Converting");
}
- STATUS("\n");
-
- res = det->defaults.res;
- /* use the res of the first panel if not in global definitions
- * assumes one of these exist */
- if ( res == -1.0 ) {
- res = det->panels[0].res;
}
- coffset = det->defaults.coffset;
- /* use the coffset of the first panel if not in global definitions
- * assumes one of these exist*/
- if ( coffset == 0.0 ) {
- coffset = det->panels[0].coffset;
- }
+ res = 1.0 / detgeom->panels[0].pixel_pitch;
if ( badmap ) {
write_badmap_hdf5(output_file, b, w, h);
} else {
- write_pixelmap_hdf5(output_file, x, y, z, w, h, res, coffset);
+ write_pixelmap_hdf5(output_file, x, y, z, w, h, res);
}
+ data_template_free(dtempl);
+
return 0;
}
generated by cgit v1.2.3 (git 2.25.1) at 2024-10-25 09:22:14 +0000