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/*
* detector.c
*
* Detector properties
*
* (c) 2006-2010 Thomas White <taw@physics.org>
*
* Part of CrystFEL - crystallography with a FEL
*
*/
#include <stdlib.h>
#include <math.h>
#include <stdio.h>
#include <string.h>
#include "image.h"
#include "utils.h"
#include "diffraction.h"
#include "detector.h"
#include "parameters-lcls.tmp"
/* x,y in pixels relative to image origin */
int map_position(struct image *image, double dx, double dy,
double *rx, double *ry, double *rz)
{
double d;
double twotheta, psi;
const double k = 1.0 / image->lambda;
struct panel *p;
double x = 0.0;
double y = 0.0;
p = find_panel(image->det, dx, dy);
if ( p == NULL ) return 1;
x = ((double)dx - p->cx);
y = ((double)dy - p->cy);
/* Convert pixels to metres */
x /= p->res;
y /= p->res; /* Convert pixels to metres */
d = sqrt((x*x) + (y*y));
twotheta = atan2(d, p->clen);
psi = atan2(y, x);
*rx = k*sin(twotheta)*cos(psi);
*ry = k*sin(twotheta)*sin(psi);
*rz = k - k*cos(twotheta);
return 0;
}
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;
/* How many photons are scattered per electron? */
area = M_PI*pow(BEAM_RADIUS, 2.0);
total_energy = FLUENCE * ph_lambda_to_en(image->lambda);
energy_density = total_energy / area;
ph_per_e = (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",
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 dsq, proj_area;
struct panel *p;
intensity = (double)image->data[x + image->width*y];
if ( isinf(intensity) ) {
ERROR("Infinity at %i,%i\n", x, y);
}
if ( intensity < 0.0 ) {
ERROR("Negative at %i,%i\n", x, y);
}
if ( isnan(intensity) ) {
ERROR("NaN at %i,%i\n", x, y);
}
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 */
dsq = pow(((double)x - p->cx) / p->res, 2.0);
dsq += pow(((double)y - p->cy) / p->res, 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 * DQE);
} else {
cf = intensity * ph_per_e * sa * DQE;
counts = cf;
}
image->data[x + image->width*y] = counts * DETECTOR_GAIN;
if ( isinf(image->data[x+image->width*y]) ) {
ERROR("Processed infinity at %i,%i\n", x, y);
}
if ( isnan(image->data[x+image->width*y]) ) {
ERROR("Processed NaN at %i,%i\n", x, y);
}
if ( image->data[x+image->width*y] < 0.0 ) {
ERROR("Processed negative at %i,%i %f\n", x, y, counts);
}
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 (halve this to get the"
" voxel size for a synthesis)\n",
rad2deg(max_tt), (image->lambda/(2.0*sin(max_tt/2.0)))/1e-9);
}
struct panel *find_panel(struct detector *det, int x, int y)
{
int p;
for ( p=0; p<det->n_panels; p++ ) {
if ( (x >= det->panels[p].min_x)
&& (x <= det->panels[p].max_x)
&& (y >= det->panels[p].min_y)
&& (y <= det->panels[p].max_y) ) {
return &det->panels[p];
}
}
ERROR("No mapping found for %i,%i\n", x, y);
return NULL;
}
struct detector *get_detector_geometry(const char *filename)
{
FILE *fh;
struct detector *det;
char *rval;
char **bits;
int n_panels = -1;
int i;
fh = fopen(filename, "r");
if ( fh == NULL ) return NULL;
det = malloc(sizeof(struct detector));
if ( det == NULL ) {
fclose(fh);
return NULL;
}
do {
int n1, n2;
char **path;
char line[1024];
int np;
rval = fgets(line, 1023, fh);
if ( rval == NULL ) break;
chomp(line);
n1 = assplode(line, " \t", &bits, ASSPLODE_NONE);
if ( n1 < 3 ) continue;
if ( bits[1][0] != '=' ) continue;
if ( strcmp(bits[0], "n_panels") == 0 ) {
if ( n_panels != -1 ) {
ERROR("Duplicate n_panels statement.\n");
fclose(fh);
free(det);
return NULL;
}
n_panels = atoi(bits[2]);
det->panels = malloc(n_panels * sizeof(struct panel));
continue;
}
n2 = assplode(bits[0], "/\\.", &path, ASSPLODE_NONE);
np = atoi(path[0]);
if ( strcmp(path[1], "min_x") == 0 ) {
det->panels[np].min_x = atof(bits[2]);
} else if ( strcmp(path[1], "max_x") == 0 ) {
det->panels[np].max_x = atof(bits[2]);
} else if ( strcmp(path[1], "min_y") == 0 ) {
det->panels[np].min_y = atof(bits[2]);
} else if ( strcmp(path[1], "max_y") == 0 ) {
det->panels[np].max_y = atof(bits[2]);
} else if ( strcmp(path[1], "cx") == 0 ) {
det->panels[np].cx = atof(bits[2]);
} else if ( strcmp(path[1], "cy") == 0 ) {
det->panels[np].cy = atof(bits[2]);
} else if ( strcmp(path[1], "clen") == 0 ) {
det->panels[np].clen = atof(bits[2]);
} else if ( strcmp(path[1], "res") == 0 ) {
det->panels[np].res = atof(bits[2]);
} else {
ERROR("Unrecognised field '%s'\n", path[1]);
}
} while ( rval != NULL );
if ( n_panels == -1 ) {
ERROR("No panel descriptions in geometry file.\n");
fclose(fh);
free(det->panels);
free(det);
return NULL;
}
for ( i=0; i<n_panels; i++ ) {
STATUS("Panel %i, min_x = %i\n", i, det->panels[i].min_x);
STATUS("Panel %i, max_x = %i\n", i, det->panels[i].max_x);
STATUS("Panel %i, min_y = %i\n", i, det->panels[i].min_y);
STATUS("Panel %i, max_y = %i\n", i, det->panels[i].max_y);
STATUS("Panel %i, cx = %f\n", i, det->panels[i].cx);
STATUS("Panel %i, cy = %f\n", i, det->panels[i].cy);
STATUS("Panel %i, clen = %f\n", i, det->panels[i].clen);
STATUS("Panel %i, res = %f\n", i, det->panels[i].res);
}
return det;
}
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