Introduce "libcrystfel"

1 files changed, 0 insertions, 1234 deletions

diff --git a/src/detector.c b/src/detector.c
deleted file mode 100644
index 7f29ec82..00000000
--- 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;
-}