Introduce "libcrystfel"

1 files changed, 1233 insertions, 0 deletions

diff --git a/libcrystfel/src/detector.c b/libcrystfel/src/detector.c
new file mode 100644
index 00000000..54bae1d7
--- /dev/null
+++ b/libcrystfel/src/detector.c
@@ -0,0 +1,1233 @@
+/*
+ * 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 "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;
+}