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-rw-r--r--src/detector.c1234
1 files changed, 0 insertions, 1234 deletions
diff --git a/src/detector.c b/src/detector.c
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--- a/src/detector.c
+++ /dev/null
@@ -1,1234 +0,0 @@
-/*
- * detector.c
- *
- * Detector properties
- *
- * (c) 2006-2011 Thomas White <taw@physics.org>
- * (c) 2011 Rick Kirian <rkirian@asu.edu>
- *
- * Part of CrystFEL - crystallography with a FEL
- *
- */
-
-
-#include <stdlib.h>
-#include <math.h>
-#include <stdio.h>
-#include <string.h>
-#include <assert.h>
-#include <ctype.h>
-
-#include "image.h"
-#include "utils.h"
-#include "diffraction.h"
-#include "detector.h"
-#include "beam-parameters.h"
-#include "hdf5-file.h"
-
-
-/**
- * SECTION:detector
- * @short_description: Detector geometry
- * @title: Detector
- * @section_id:
- * @see_also:
- * @include: "detector.h"
- * @Image:
- *
- * This structure represents the detector geometry
- */
-
-
-static int atob(const char *a)
-{
- if ( strcasecmp(a, "true") == 0 ) return 1;
- if ( strcasecmp(a, "false") == 0 ) return 0;
- return atoi(a);
-}
-
-
-static int assplode_algebraic(const char *a_orig, char ***pbits)
-{
- int len, i;
- int nexp;
- char **bits;
- char *a;
- int idx, istr;
-
- len = strlen(a_orig);
-
- /* Add plus at start if no sign there already */
- if ( (a_orig[0] != '+') && (a_orig[0] != '-') ) {
- len += 1;
- a = malloc(len+1);
- snprintf(a, len+1, "+%s", a_orig);
- a[len] = '\0';
-
- } else {
- a = strdup(a_orig);
- }
-
- /* Count the expressions */
- nexp = 0;
- for ( i=0; i<len; i++ ) {
- if ( (a[i] == '+') || (a[i] == '-') ) nexp++;
- }
-
- bits = calloc(nexp, sizeof(char *));
-
- /* Break the string up */
- idx = -1;
- istr = 0;
- assert((a[0] == '+') || (a[0] == '-'));
- for ( i=0; i<len; i++ ) {
-
- char ch;
-
- ch = a[i];
-
- if ( (ch == '+') || (ch == '-') ) {
- if ( idx >= 0 ) bits[idx][istr] = '\0';
- idx++;
- bits[idx] = malloc(len+1);
- istr = 0;
- }
-
- if ( !isdigit(ch) && (ch != '.') && (ch != 'x') && (ch != 'y')
- && (ch != '+') && (ch != '-') )
- {
- ERROR("Invalid character '%C' found.\n", ch);
- return 0;
- }
-
- assert(idx >= 0);
- bits[idx][istr++] = ch;
-
- }
- if ( idx >= 0 ) bits[idx][istr] = '\0';
-
- *pbits = bits;
- free(a);
-
- return nexp;
-}
-
-
-/* Parses the scan directions (accounting for possible rotation)
- * Assumes all white spaces have been already removed */
-static int dir_conv(const char *a, double *sx, double *sy)
-{
- int n;
- char **bits;
- int i;
-
- *sx = 0.0; *sy = 0.0;
-
- n = assplode_algebraic(a, &bits);
-
- if ( n == 0 ) {
- ERROR("Invalid direction '%s'\n", a);
- return 1;
- }
-
- for ( i=0; i<n; i++ ) {
-
- int len;
- double val;
- char axis;
- int j;
-
- len = strlen(bits[i]);
- assert(len != 0);
- axis = bits[i][len-1];
- if ( (axis != 'x') && (axis != 'y') ) {
- ERROR("Invalid symbol '%C' - must be x or y.\n", axis);
- return 1;
- }
-
- /* Chop off the symbol now it's dealt with */
- bits[i][len-1] = '\0';
-
- /* Check for anything that isn't part of a number */
- for ( j=0; j<strlen(bits[i]); j++ ) {
- if ( isdigit(bits[i][j]) ) continue;
- if ( bits[i][j] == '+' ) continue;
- if ( bits[i][j] == '-' ) continue;
- if ( bits[i][j] == '.' ) continue;
- ERROR("Invalid coefficient '%s'\n", bits[i]);
- }
-
- if ( strlen(bits[i]) == 0 ) {
- val = 1.0;
- } else {
- val = atof(bits[i]);
- }
- if ( strlen(bits[i]) == 1 ) {
- if ( bits[i][0] == '+' ) val = 1.0;
- if ( bits[i][0] == '-' ) val = -1.0;
- }
- if ( axis == 'x' ) {
- *sx += val;
- } else if ( axis == 'y' ) {
- *sy += val;
- }
-
- free(bits[i]);
-
- }
- free(bits);
-
- //STATUS("'%s' -> %5.2fx + %5.2fy\n", a, *sx, *sy);
-
- return 0;
-}
-
-
-struct rvec get_q_for_panel(struct panel *p, double fs, double ss,
- double *ttp, double k)
-{
- struct rvec q;
- double twotheta, r, az;
- double rx, ry;
- double xs, ys;
-
- /* 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) / p->res;
- ry = (ys + p->cny) / p->res;
-
- /* Calculate q-vector for this sub-pixel */
- r = sqrt(pow(rx, 2.0) + pow(ry, 2.0));
-
- twotheta = atan2(r, p->clen);
- az = atan2(ry, rx);
- if ( ttp != NULL ) *ttp = twotheta;
-
- q.u = k * sin(twotheta)*cos(az);
- q.v = k * sin(twotheta)*sin(az);
- q.w = k * (cos(twotheta) - 1.0);
-
- return q;
-}
-
-
-struct rvec get_q(struct image *image, double fs, double ss,
- double *ttp, double k)
-{
- struct panel *p;
- const unsigned int fsi = fs;
- const unsigned int ssi = ss; /* Explicit rounding */
-
- /* Determine which panel to use */
- p = find_panel(image->det, fsi, ssi);
- assert(p != NULL);
-
- return get_q_for_panel(p, fs-(double)p->min_fs, ss-(double)p->min_ss,
- ttp, k);
-}
-
-
-int in_bad_region(struct detector *det, double fs, double ss)
-{
- double rx, ry;
- struct panel *p;
- double xs, ys;
- int i;
-
- /* Determine which panel to use */
- p = find_panel(det, fs, ss);
-
- /* No panel found -> definitely bad! */
- if ( p == NULL ) return 1;
-
- /* Convert xs and ys, which are in fast scan/slow scan coordinates,
- * to x and y */
- xs = (fs-(double)p->min_fs)*p->fsx + (ss-(double)p->min_ss)*p->ssx;
- ys = (fs-(double)p->min_fs)*p->fsy + (ss-(double)p->min_ss)*p->ssy;
-
- rx = xs + p->cnx;
- ry = ys + p->cny;
-
- for ( i=0; i<det->n_bad; i++ ) {
- struct badregion *b = &det->bad[i];
- 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;
-}
-
-
-double get_tt(struct image *image, double fs, double ss)
-{
- double r, rx, ry;
- struct panel *p;
- double xs, ys;
-
- p = find_panel(image->det, fs, ss);
-
- /* Convert xs and ys, which are in fast scan/slow scan coordinates,
- * to x and y */
- xs = (fs-p->min_fs)*p->fsx + (ss-p->min_ss)*p->ssx;
- ys = (fs-p->min_fs)*p->fsy + (ss-p->min_ss)*p->ssy;
-
- rx = (xs + p->cnx) / p->res;
- ry = (ys + p->cny) / p->res;
-
- r = sqrt(pow(rx, 2.0) + pow(ry, 2.0));
-
- return atan2(r, p->clen);
-}
-
-
-void record_image(struct image *image, int do_poisson)
-{
- int x, y;
- double total_energy, energy_density;
- double ph_per_e;
- double area;
- double max_tt = 0.0;
- int n_inf1 = 0;
- int n_neg1 = 0;
- int n_nan1 = 0;
- int n_inf2 = 0;
- int n_neg2 = 0;
- int n_nan2 = 0;
-
- /* How many photons are scattered per electron? */
- area = M_PI*pow(image->beam->beam_radius, 2.0);
- total_energy = image->beam->fluence * ph_lambda_to_en(image->lambda);
- energy_density = total_energy / area;
- ph_per_e = (image->beam->fluence /area) * pow(THOMSON_LENGTH, 2.0);
- STATUS("Fluence = %8.2e photons, "
- "Energy density = %5.3f kJ/cm^2, "
- "Total energy = %5.3f microJ\n",
- image->beam->fluence, energy_density/1e7, total_energy*1e6);
-
- for ( x=0; x<image->width; x++ ) {
- for ( y=0; y<image->height; y++ ) {
-
- double counts;
- double cf;
- double intensity, sa;
- double pix_area, Lsq;
- double xs, ys, rx, ry;
- double dsq, proj_area;
- struct panel *p;
-
- intensity = (double)image->data[x + image->width*y];
- if ( isinf(intensity) ) n_inf1++;
- if ( intensity < 0.0 ) n_neg1++;
- if ( isnan(intensity) ) n_nan1++;
-
- p = find_panel(image->det, x, y);
-
- /* Area of one pixel */
- pix_area = pow(1.0/p->res, 2.0);
- Lsq = pow(p->clen, 2.0);
-
- /* Area of pixel as seen from crystal (approximate) */
- proj_area = pix_area * cos(image->twotheta[x + image->width*y]);
-
- /* Calculate distance from crystal to pixel */
- xs = (x-p->min_fs)*p->fsx + (y-p->min_ss)*p->ssx;
- ys = (x-p->min_fs)*p->fsy + (y-p->min_ss)*p->ssy;
- rx = (xs + p->cnx) / p->res;
- ry = (ys + p->cny) / p->res;
- dsq = sqrt(pow(rx, 2.0) + pow(ry, 2.0));
-
- /* Projected area of pixel divided by distance squared */
- sa = proj_area / (dsq + Lsq);
-
- if ( do_poisson ) {
- counts = poisson_noise(intensity * ph_per_e
- * sa * image->beam->dqe );
- } else {
- cf = intensity * ph_per_e * sa * image->beam->dqe;
- counts = cf;
- }
-
- image->data[x + image->width*y] = counts
- * image->beam->adu_per_photon;
-
- /* Sanity checks */
- if ( isinf(image->data[x+image->width*y]) ) n_inf2++;
- if ( isnan(image->data[x+image->width*y]) ) n_nan2++;
- if ( image->data[x+image->width*y] < 0.0 ) n_neg2++;
-
- if ( image->twotheta[x + image->width*y] > max_tt ) {
- max_tt = image->twotheta[x + image->width*y];
- }
-
- }
- progress_bar(x, image->width-1, "Post-processing");
- }
-
- STATUS("Max 2theta = %.2f deg, min d = %.2f nm\n",
- rad2deg(max_tt), (image->lambda/(2.0*sin(max_tt/2.0)))/1e-9);
-
- double tt_side = image->twotheta[(image->width/2)+image->width*0];
- STATUS("At middle of bottom edge: %.2f deg, min d = %.2f nm\n",
- rad2deg(tt_side), (image->lambda/(2.0*sin(tt_side/2.0)))/1e-9);
-
- tt_side = image->twotheta[0+image->width*(image->height/2)];
- STATUS("At middle of left edge: %.2f deg, min d = %.2f nm\n",
- rad2deg(tt_side), (image->lambda/(2.0*sin(tt_side/2.0)))/1e-9);
-
- STATUS("Halve the d values to get the voxel size for a synthesis.\n");
-
- if ( n_neg1 + n_inf1 + n_nan1 + n_neg2 + n_inf2 + n_nan2 ) {
- ERROR("WARNING: The raw calculation produced %i negative"
- " values, %i infinities and %i NaNs.\n",
- n_neg1, n_inf1, n_nan1);
- ERROR("WARNING: After processing, there were %i negative"
- " values, %i infinities and %i NaNs.\n",
- n_neg2, n_inf2, n_nan2);
- }
-}
-
-
-struct panel *find_panel(struct detector *det, double fs, double ss)
-{
- int p;
-
- for ( p=0; p<det->n_panels; p++ ) {
- if ( (fs >= det->panels[p].min_fs)
- && (fs <= det->panels[p].max_fs)
- && (ss >= det->panels[p].min_ss)
- && (ss <= det->panels[p].max_ss) ) {
- return &det->panels[p];
- }
- }
-
- return NULL;
-}
-
-
-int find_panel_number(struct detector *det, int fs, int ss)
-{
- int p;
-
- for ( p=0; p<det->n_panels; p++ ) {
- if ( (fs >= det->panels[p].min_fs)
- && (fs <= det->panels[p].max_fs)
- && (ss >= det->panels[p].min_ss)
- && (ss <= det->panels[p].max_ss) ) return p;
- }
-
- return -1;
-}
-
-
-void fill_in_values(struct detector *det, struct hdfile *f)
-{
- int i;
-
- for ( i=0; i<det->n_panels; i++ ) {
-
- struct panel *p = &det->panels[i];
-
- if ( p->clen_from != NULL ) {
- p->clen = get_value(f, p->clen_from) * 1.0e-3;
- free(p->clen_from);
- p->clen_from = NULL;
- }
-
- p->clen += p->coffset;
-
- }
-}
-
-
-static struct panel *new_panel(struct detector *det, const char *name)
-{
- struct panel *new;
-
- det->n_panels++;
- det->panels = realloc(det->panels, det->n_panels*sizeof(struct panel));
-
- new = &det->panels[det->n_panels-1];
- memcpy(new, &det->defaults, sizeof(struct panel));
-
- /* Create a new copy of the camera length location if needed */
- if ( new->clen_from != NULL ) {
- new->clen_from = strdup(new->clen_from);
- }
- strcpy(new->name, name);
-
- return new;
-}
-
-
-static struct badregion *new_bad_region(struct detector *det, const char *name)
-{
- struct badregion *new;
-
- det->n_bad++;
- det->bad = realloc(det->bad, det->n_bad*sizeof(struct badregion));
-
- new = &det->bad[det->n_bad-1];
- new->min_x = NAN;
- new->max_x = NAN;
- new->min_y = NAN;
- new->max_y = NAN;
- strcpy(new->name, name);
-
- return new;
-}
-
-
-struct panel *find_panel_by_name(struct detector *det, const char *name)
-{
- int i;
-
- for ( i=0; i<det->n_panels; i++ ) {
- if ( strcmp(det->panels[i].name, name) == 0 ) {
- return &det->panels[i];
- }
- }
-
- return NULL;
-}
-
-
-static struct badregion *find_bad_region_by_name(struct detector *det,
- const char *name)
-{
- int i;
-
- for ( i=0; i<det->n_bad; i++ ) {
- if ( strcmp(det->bad[i].name, name) == 0 ) {
- return &det->bad[i];
- }
- }
-
- return NULL;
-}
-
-
-static char *find_or_add_rg(struct detector *det, const char *name)
-{
- int i;
- char **new;
- char *tmp;
-
- for ( i=0; i<det->num_rigid_groups; i++ ) {
-
- if ( strcmp(det->rigid_groups[i], name) == 0 ) {
- return det->rigid_groups[i];
- }
-
- }
-
- new = realloc(det->rigid_groups,
- (1+det->num_rigid_groups)*sizeof(char *));
- if ( new == NULL ) return NULL;
-
- det->rigid_groups = new;
-
- tmp = strdup(name);
- det->rigid_groups[det->num_rigid_groups] = tmp;
-
- det->num_rigid_groups++;
-
- return tmp;
-}
-
-
-static int parse_field_for_panel(struct panel *panel, const char *key,
- const char *val, struct detector *det)
-{
- int reject = 0;
-
- if ( strcmp(key, "min_fs") == 0 ) {
- panel->min_fs = atof(val);
- } else if ( strcmp(key, "max_fs") == 0 ) {
- panel->max_fs = atof(val);
- } else if ( strcmp(key, "min_ss") == 0 ) {
- panel->min_ss = atof(val);
- } else if ( strcmp(key, "max_ss") == 0 ) {
- panel->max_ss = atof(val);
- } else if ( strcmp(key, "corner_x") == 0 ) {
- panel->cnx = atof(val);
- } else if ( strcmp(key, "corner_y") == 0 ) {
- panel->cny = atof(val);
- } else if ( strcmp(key, "rigid_group") == 0 ) {
- panel->rigid_group = find_or_add_rg(det, val);
- } else if ( strcmp(key, "clen") == 0 ) {
-
- char *end;
- double v = strtod(val, &end);
- if ( end == val ) {
- /* This means "fill in later" */
- panel->clen = -1.0;
- panel->clen_from = strdup(val);
- } else {
- panel->clen = v;
- panel->clen_from = NULL;
- }
-
- } else if ( strcmp(key, "coffset") == 0) {
- panel->coffset = atof(val);
- } else if ( strcmp(key, "res") == 0 ) {
- panel->res = atof(val);
- } else if ( strcmp(key, "peak_sep") == 0 ) {
- panel->peak_sep = atof(val);
- } else if ( strcmp(key, "integr_radius") == 0 ) {
- panel->integr_radius = atof(val);
- } else if ( strcmp(key, "badrow_direction") == 0 ) {
- panel->badrow = val[0]; /* First character only */
- if ( (panel->badrow != 'x') && (panel->badrow != 'y')
- && (panel->badrow != 'f') && (panel->badrow != 's')
- && (panel->badrow != '-') ) {
- ERROR("badrow_direction must be x, y, f, s or '-'\n");
- ERROR("Assuming '-'\n.");
- panel->badrow = '-';
- }
- if ( panel->badrow == 'x' ) panel->badrow = 'f';
- if ( panel->badrow == 'y' ) panel->badrow = 's';
- } else if ( strcmp(key, "no_index") == 0 ) {
- panel->no_index = atob(val);
- } else if ( strcmp(key, "fs") == 0 ) {
- if ( dir_conv(val, &panel->fsx, &panel->fsy) != 0 ) {
- ERROR("Invalid fast scan direction '%s'\n", val);
- reject = 1;
- }
- } else if ( strcmp(key, "ss") == 0 ) {
- if ( dir_conv(val, &panel->ssx, &panel->ssy) != 0 ) {
- ERROR("Invalid slow scan direction '%s'\n", val);
- reject = 1;
- }
- } else {
- ERROR("Unrecognised field '%s'\n", key);
- }
-
- return reject;
-}
-
-
-static int parse_field_bad(struct badregion *panel, const char *key,
- const char *val)
-{
- int reject = 0;
-
- if ( strcmp(key, "min_x") == 0 ) {
- panel->min_x = atof(val);
- } else if ( strcmp(key, "max_x") == 0 ) {
- panel->max_x = atof(val);
- } else if ( strcmp(key, "min_y") == 0 ) {
- panel->min_y = atof(val);
- } else if ( strcmp(key, "max_y") == 0 ) {
- panel->max_y = atof(val);
- } else {
- ERROR("Unrecognised field '%s'\n", key);
- }
-
- return reject;
-}
-
-
-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 ) {
-
- char *end;
- double v = strtod(val, &end);
-
- if ( end != val ) {
- det->mask_bad = v;
- }
-
- } else if ( strcmp(key, "mask_good") == 0 ) {
-
- char *end;
- double v = strtod(val, &end);
-
- if ( end != val ) {
- det->mask_good = v;
- }
-
- } else if ( strcmp(key, "peak_sep") == 0 ) {
- det->defaults.peak_sep = atof(val);
- } else if ( strcmp(key, "integr_radius") == 0 ) {
- det->defaults.integr_radius = atof(val);
- } else if ( parse_field_for_panel(&det->defaults, key, val, det) ) {
- ERROR("Unrecognised top level field '%s'\n", key);
- }
-}
-
-
-struct detector *get_detector_geometry(const char *filename)
-{
- FILE *fh;
- struct detector *det;
- char *rval;
- char **bits;
- int i;
- int reject = 0;
- int x, y, max_fs, max_ss;
-
- fh = fopen(filename, "r");
- if ( fh == NULL ) return NULL;
-
- det = calloc(1, sizeof(struct detector));
- if ( det == NULL ) {
- fclose(fh);
- return NULL;
- }
-
- det->n_panels = 0;
- det->panels = NULL;
- det->n_bad = 0;
- det->bad = NULL;
- det->mask_good = 0;
- det->mask_bad = 0;
- det->mask = NULL;
- det->num_rigid_groups = 0;
- det->rigid_groups = NULL;
-
- /* The default defaults... */
- det->defaults.min_fs = -1;
- det->defaults.min_ss = -1;
- det->defaults.max_fs = -1;
- det->defaults.max_ss = -1;
- det->defaults.cnx = NAN;
- det->defaults.cny = NAN;
- det->defaults.clen = -1.0;
- det->defaults.coffset = 0.0;
- det->defaults.res = -1.0;
- det->defaults.badrow = '-';
- det->defaults.no_index = 0;
- det->defaults.peak_sep = 50.0;
- det->defaults.integr_radius = 3.0;
- det->defaults.fsx = 1.0;
- det->defaults.fsy = 0.0;
- det->defaults.ssx = 0.0;
- det->defaults.ssy = 1.0;
- det->defaults.rigid_group = NULL;
- strncpy(det->defaults.name, "", 1023);
-
- do {
-
- int n1, n2;
- char **path;
- char line[1024];
- struct badregion *badregion = NULL;
- struct panel *panel = NULL;
- char *key;
- char wholeval[1024];
-
- rval = fgets(line, 1023, fh);
- if ( rval == NULL ) break;
- chomp(line);
-
- if ( line[0] == ';' ) continue;
-
- n1 = assplode(line, " \t", &bits, ASSPLODE_NONE);
- if ( n1 < 3 ) {
- for ( i=0; i<n1; i++ ) free(bits[i]);
- free(bits);
- continue;
- }
-
- /* Stitch the pieces of the "value" back together */
- wholeval[0] = '\0'; /* Empty string */
- for ( i=2; i<n1; i++ ) {
- if ( bits[i][0] == ';' ) break; /* Stop on comment */
- strncat(wholeval, bits[i], 1023);
- }
-
- if ( bits[1][0] != '=' ) {
- for ( i=0; i<n1; i++ ) free(bits[i]);
- free(bits);
- continue;
- }
-
- n2 = assplode(bits[0], "/\\.", &path, ASSPLODE_NONE);
- if ( n2 < 2 ) {
- /* This was a top-level option, not handled above. */
- parse_toplevel(det, bits[0], bits[2]);
- for ( i=0; i<n1; i++ ) free(bits[i]);
- free(bits);
- for ( i=0; i<n2; i++ ) free(path[i]);
- free(path);
- continue;
- }
-
- if ( strncmp(path[0], "bad", 3) == 0 ) {
- badregion = find_bad_region_by_name(det, path[0]);
- if ( badregion == NULL ) {
- badregion = new_bad_region(det, path[0]);
- }
- } else {
- panel = find_panel_by_name(det, path[0]);
- if ( panel == NULL ) {
- panel = new_panel(det, path[0]);
- }
- }
-
- key = path[1];
-
- if ( panel != NULL ) {
- if ( parse_field_for_panel(panel, path[1],
- wholeval, det) )
- {
- reject = 1;
- }
- } else {
- if ( parse_field_bad(badregion, path[1], wholeval) ) {
- reject = 1;
- }
- }
-
- for ( i=0; i<n1; i++ ) free(bits[i]);
- for ( i=0; i<n2; i++ ) free(path[i]);
- free(bits);
- free(path);
-
- } while ( rval != NULL );
-
- if ( det->n_panels == -1 ) {
- ERROR("No panel descriptions in geometry file.\n");
- fclose(fh);
- free(det);
- return NULL;
- }
-
- max_fs = 0;
- max_ss = 0;
- for ( i=0; i<det->n_panels; i++ ) {
-
- if ( det->panels[i].min_fs < 0 ) {
- ERROR("Please specify the minimum FS coordinate for"
- " panel %s\n", det->panels[i].name);
- reject = 1;
- }
- if ( det->panels[i].max_fs < 0 ) {
- ERROR("Please specify the maximum FS coordinate for"
- " panel %s\n", det->panels[i].name);
- reject = 1;
- }
- if ( det->panels[i].min_ss < 0 ) {
- ERROR("Please specify the minimum SS coordinate for"
- " panel %s\n", det->panels[i].name);
- reject = 1;
- }
- if ( det->panels[i].max_ss < 0 ) {
- ERROR("Please specify the maximum SS coordinate for"
- " panel %s\n", det->panels[i].name);
- reject = 1;
- }
- if ( isnan(det->panels[i].cnx) ) {
- ERROR("Please specify the corner X coordinate for"
- " panel %s\n", det->panels[i].name);
- reject = 1;
- }
- if ( isnan(det->panels[i].cny) ) {
- ERROR("Please specify the corner Y coordinate for"
- " panel %s\n", det->panels[i].name);
- reject = 1;
- }
- if ( (det->panels[i].clen < 0.0)
- && (det->panels[i].clen_from == NULL) ) {
- ERROR("Please specify the camera length for"
- " panel %s\n", det->panels[i].name);
- reject = 1;
- }
- if ( det->panels[i].res < 0 ) {
- ERROR("Please specify the resolution for"
- " panel %s\n", det->panels[i].name);
- reject = 1;
- }
- /* It's OK if the badrow direction is '0' */
- /* It's not a problem if "no_index" is still zero */
- /* The default peak_sep is OK (maybe) */
- /* The default transformation matrix is at least valid */
-
- if ( det->panels[i].max_fs > max_fs ) {
- max_fs = det->panels[i].max_fs;
- }
- if ( det->panels[i].max_ss > max_ss ) {
- max_ss = det->panels[i].max_ss;
- }
-
- }
-
- for ( i=0; i<det->n_bad; i++ ) {
-
- if ( isnan(det->bad[i].min_x) ) {
- ERROR("Please specify the minimum x coordinate for"
- " bad region %s\n", det->bad[i].name);
- reject = 1;
- }
- if ( isnan(det->bad[i].min_y) ) {
- ERROR("Please specify the minimum y coordinate for"
- " bad region %s\n", det->bad[i].name);
- reject = 1;
- }
- if ( isnan(det->bad[i].max_x) ) {
- ERROR("Please specify the maximum x coordinate for"
- " bad region %s\n", det->bad[i].name);
- reject = 1;
- }
- if ( isnan(det->bad[i].max_y) ) {
- ERROR("Please specify the maximum y coordinate for"
- " bad region %s\n", det->bad[i].name);
- reject = 1;
- }
- }
-
- for ( x=0; x<=max_fs; x++ ) {
- for ( y=0; y<=max_ss; y++ ) {
- if ( find_panel(det, x, y) == NULL ) {
- ERROR("Detector geometry invalid: contains gaps.\n");
- reject = 1;
- goto out;
- }
- }
- }
-
-out:
- det->max_fs = max_fs;
- det->max_ss = max_ss;
-
- /* Calculate matrix inverse */
- for ( i=0; i<det->n_panels; i++ ) {
-
- struct panel *p;
- double d;
-
- p = &det->panels[i];
-
- 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;
- p->xfs = p->ssy / d;
- p->yfs = -p->ssx / d;
- p->xss = -p->fsy / d;
- p->yss = p->fsx / d;
-
- }
-
- if ( reject ) return NULL;
-
- fclose(fh);
-
- return det;
-}
-
-
-void free_detector_geometry(struct detector *det)
-{
- int i;
-
- for ( i=0; i<det->num_rigid_groups; i++ ) {
- free(det->rigid_groups[i]);
- }
- free(det->rigid_groups);
-
- free(det->panels);
- free(det->bad);
- free(det->mask);
- free(det);
-}
-
-
-struct detector *copy_geom(const struct detector *in)
-{
- struct detector *out;
- int i;
-
- 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));
-
- out->bad = malloc(out->n_bad * sizeof(struct badregion));
- memcpy(out->bad, in->bad, out->n_bad * sizeof(struct badregion));
-
- if ( in->rigid_groups != NULL ) {
-
- out->rigid_groups = malloc(out->num_rigid_groups*sizeof(char *));
- memcpy(out->rigid_groups, in->rigid_groups,
- out->num_rigid_groups*sizeof(char *));
-
- for ( i=0; i<in->num_rigid_groups; i++ ) {
- out->rigid_groups[i] = strdup(in->rigid_groups[i]);
- }
-
- }
-
- for ( i=0; i<out->n_panels; i++ ) {
-
- struct panel *p;
-
- p = &out->panels[i];
-
- if ( p->clen_from != NULL ) {
- /* Make a copy of the clen_from fields unique to this
- * copy of the structure. */
- p->clen_from = strdup(p->clen_from);
- }
-
- }
-
- for ( i=0; i<in->num_rigid_groups; i++ ) {
-
- int j;
- char *rg = in->rigid_groups[i];
- char *rgn = out->rigid_groups[i];
-
- for ( j=0; j<in->n_panels; j++ ) {
-
- if ( in->panels[j].rigid_group == rg ) {
- out->panels[j].rigid_group = rgn;
- }
-
- }
-
- }
-
- return out;
-}
-
-
-struct detector *simple_geometry(const struct image *image)
-{
- struct detector *geom;
-
- geom = calloc(1, sizeof(struct detector));
-
- geom->n_panels = 1;
- geom->panels = calloc(1, sizeof(struct panel));
-
- geom->panels[0].min_fs = 0;
- geom->panels[0].max_fs = image->width-1;
- geom->panels[0].min_ss = 0;
- geom->panels[0].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].fsx = 1;
- geom->panels[0].fsy = 0;
- geom->panels[0].ssx = 0;
- geom->panels[0].ssy = 1;
-
- geom->panels[0].xfs = 1;
- geom->panels[0].xss = 0;
- geom->panels[0].yfs = 0;
- geom->panels[0].yss = 1;
-
- return geom;
-}
-
-
-int reverse_2d_mapping(double x, double y, double *pfs, double *pss,
- struct detector *det)
-{
- int i;
-
- for ( i=0; i<det->n_panels; i++ ) {
-
- struct panel *p = &det->panels[i];
- double cx, cy, fs, ss;
-
- /* Get position relative to corner */
- cx = x - p->cnx;
- cy = y - p->cny;
-
- /* Reverse the transformation matrix */
- fs = cx*p->xfs + cy*p->yfs;
- ss = cx*p->xss + cy*p->yss;
-
- /* In range? */
- if ( fs < 0 ) continue;
- if ( ss < 0 ) continue;
- if ( fs > (p->max_fs-p->min_fs+1) ) continue;
- if ( ss > (p->max_ss-p->min_ss+1) ) continue;
-
- *pfs = fs + p->min_fs;
- *pss = ss + p->min_ss;
- return 0;
-
- }
-
- return 1;
-}
-
-
-static void check_extents(struct panel p, double *min_x, double *min_y,
- double *max_x, double *max_y, double fs, double ss)
-{
- double xs, ys, rx, ry;
-
- xs = fs*p.fsx + ss*p.ssx;
- ys = fs*p.fsy + ss*p.ssy;
-
- rx = xs + p.cnx;
- ry = ys + p.cny;
-
- if ( rx > *max_x ) *max_x = rx;
- if ( ry > *max_y ) *max_y = ry;
- if ( rx < *min_x ) *min_x = rx;
- if ( ry < *min_y ) *min_y = ry;
-}
-
-
-double largest_q(struct image *image)
-{
- int fs, ss;
- double ttm = 0.0;
- double qmax = 0.0;
-
- for ( fs=0; fs<image->width; fs++ ) {
- for ( ss=0; ss<image->height; ss++ ) {
-
- struct rvec q;
- double tt;
-
- q = get_q(image, fs, ss, &tt, 1.0/image->lambda);
-
- if ( tt > ttm ) {
- qmax = modulus(q.u, q.v, q.w);
- ttm = tt;
- }
-
- }
- }
-
- return qmax;
-}
-
-
-double smallest_q(struct image *image)
-{
- int fs, ss;
- double ttm = +INFINITY;
- double qmin = +INFINITY;
- for ( fs=0; fs<image->width; fs++ ) {
- for ( ss=0; ss<image->height; ss++ ) {
-
- struct rvec q;
- double tt;
-
- q = get_q(image, fs, ss, &tt, 1.0/image->lambda);
-
- if ( tt < ttm ) {
- qmin = modulus(q.u, q.v, q.w);
- ttm = tt;
- }
-
- }
- }
-
- return qmin;
-}
-
-
-void get_pixel_extents(struct detector *det,
- double *min_x, double *min_y,
- double *max_x, double *max_y)
-{
- int i;
-
- *min_x = 0.0;
- *max_x = 0.0;
- *min_y = 0.0;
- *max_y = 0.0;
-
- /* To determine the maximum extents of the detector, put all four
- * corners of each panel through the transformations and watch for the
- * biggest */
-
- for ( i=0; i<det->n_panels; i++ ) {
-
- check_extents(det->panels[i], min_x, min_y, max_x, max_y,
- 0.0,
- 0.0);
-
- check_extents(det->panels[i], min_x, min_y, max_x, max_y,
- 0.0,
- det->panels[i].max_ss-det->panels[i].min_ss+1);
-
- check_extents(det->panels[i], min_x, min_y, max_x, max_y,
- det->panels[i].max_fs-det->panels[i].min_fs+1,
- 0.0);
-
- check_extents(det->panels[i], min_x, min_y, max_x, max_y,
- det->panels[i].max_fs-det->panels[i].min_fs+1,
- det->panels[i].max_ss-det->panels[i].min_ss+1);
-
-
- }
-}
-
-
-int write_detector_geometry(const char *filename, struct detector *det)
-{
- struct panel *p;
- int pi;
- FILE *fh;
-
- if ( filename == NULL ) return 2;
- if ( det->n_panels < 1 ) return 3;
-
- fh = fopen(filename, "w");
- if ( fh == NULL ) return 1;
-
- for ( pi=0; pi<det->n_panels; pi++) {
-
- p = &(det->panels[pi]);
-
- if ( p == NULL ) return 4;
-
- if ( pi > 0 ) fprintf(fh, "\n");
-
- fprintf(fh, "%s/min_fs = %d\n", p->name, p->min_fs);
- fprintf(fh, "%s/min_ss = %d\n", p->name, p->min_ss);
- fprintf(fh, "%s/max_fs = %d\n", p->name, p->max_fs);
- fprintf(fh, "%s/max_ss = %d\n", p->name, p->max_ss);
- fprintf(fh, "%s/badrow_direction = %C\n", p->name, p->badrow);
- fprintf(fh, "%s/res = %g\n", p->name, p->res);
- fprintf(fh, "%s/peak_sep = %g\n", p->name, p->peak_sep);
- fprintf(fh, "%s/clen = %s\n", p->name, p->clen_from);
- fprintf(fh, "%s/fs = %+fx %+fy\n", p->name, p->fsx, p->fsy);
- fprintf(fh, "%s/ss = %+fx %+fy\n", p->name, p->ssx, p->ssy);
- fprintf(fh, "%s/corner_x = %g\n", p->name, p->cnx);
- fprintf(fh, "%s/corner_y = %g\n", p->name, p->cny);
-
- if ( p->no_index ) {
- fprintf(fh, "%s/no_index = 1\n", p->name);
- } /* else don't clutter up the file */
-
- if ( p->rigid_group != NULL ) {
- fprintf(fh, "%s/rigid_group = %s\n",
- p->name, p->rigid_group);
- }
-
- }
- fclose(fh);
-
- return 0;
-}
generated by cgit v1.2.3 (git 2.25.1) at 2024-07-10 05:18:26 +0000