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/*
* calibrate_detector.c
*
* Attempt to refine detector geometry
*
* (c) 2011 Rick Kirian <rkirian@asu.edu>
* (c) 2006-2011 Thomas White <taw@physics.org>
*
* Part of CrystFEL - crystallography with a FEL
*
*/
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include <stdarg.h>
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <unistd.h>
#include <getopt.h>
#include <fenv.h>
#include <math.h>
#include <gsl/gsl_linalg.h>
#include "utils.h"
#include "image.h"
#include "detector.h"
#include "index.h"
#include "hdf5-file.h"
#include "stream.h"
#include "peaks.h"
static void show_help(const char *s)
{
printf("Syntax: %s [options] -i <file.h5>\n\n", s);
printf(
"Stream-based optimisation of detector geometry.\n"
"\n"
" -h, --help Display this help message.\n"
" -g. --geometry=<file> Get detector geometry from file.\n"
" -i, --input=<file> Input filename.\n"
" -m, --method=<method> The calibration method. Choose from:\n"
" xy Determine panel shifts in plane of detector\n"
" -o, --output=<file> Name of output geometry file.\n"
" -n, --npeaks=<number> Don't refine unless this many peaks are found\n"
" in the whole stream.\n"
"\n");
}
static int calculate_projected_peak(struct panel *panel, struct rvec q,
double kk, double *fs, double *ss)
{
if ( panel == NULL ) return 1;
double xd, yd, cl;
double plx, ply;
const double den = kk + q.w;
/* Camera length for this panel */
cl = panel->clen;
/* Coordinates of peak relative to central beam, in m */
xd = cl * q.u / den;
yd = cl * q.v / den;
/* Convert to pixels */
xd *= panel->res;
yd *= panel->res;
/* Convert to relative to the panel corner */
plx = xd - panel->cnx;
ply = yd - panel->cny;
*fs = panel->xfs*plx + panel->yfs*ply;
*ss = panel->xss*plx + panel->yss*ply;
*fs += panel->min_fs;
*ss += panel->min_ss;
/* Now, is this on this panel? */
if ( *fs < panel->min_fs ) return 3;
if ( *fs > panel->max_fs ) return 3;
if ( *ss < panel->min_ss ) return 3;
if ( *ss > panel->max_ss ) return 3;
return 0;
}
static struct rvec nearest_bragg(struct image *image, struct rvec q)
{
struct rvec g;
double ax, ay, az;
double bx, by, bz;
double cx, cy, cz;
double hd, kd, ld;
double h, k, l;
int s;
double U[9];
double hvec[3];
/* Miller indices of nearest Bragg reflection */
cell_get_cartesian(image->indexed_cell, &ax, &ay, &az,
&bx, &by, &bz,
&cx, &cy, &cz);
hd = q.u * ax + q.v * ay + q.w * az;
kd = q.u * bx + q.v * by + q.w * bz;
ld = q.u * cx + q.v * cy + q.w * cz;
h = lrint(hd);
k = lrint(kd);
l = lrint(ld);
/* Now get scattering vector for reflection hkl
* by solving the equation U*q = h */
U[0] = ax; U[1] = ay; U[2] = az;
U[3] = bx; U[4] = by; U[5] = bz;
U[6] = cx; U[7] = cy; U[8] = cz;
hvec[0] = h; hvec[1] = k; hvec[2] = l;
gsl_matrix_view m = gsl_matrix_view_array(U, 3, 3);
gsl_vector_view b = gsl_vector_view_array(hvec, 3);
gsl_vector *x = gsl_vector_alloc(3);
gsl_permutation *perm = gsl_permutation_alloc(3);
gsl_linalg_LU_decomp(&m.matrix, perm, &s);
gsl_linalg_LU_solve(&m.matrix, perm, &b.vector, x);
/* Outgoing wavevector for hkl */
g.u = x->data[0];
g.v = x->data[1];
g.w = x->data[2];
return g;
}
static void refine_xy(FILE *fh, struct image *image, int minpeaks,
const char *outfilename)
{
double *weightedSumFS;
double *weightedSumSS;
double *summedWeights;
double *meanShiftFS;
double *meanShiftSS;
int *peaksFound;
double cnx, cny;
double xsh, ysh;
int pi;
int nChunks;
weightedSumFS = calloc(sizeof(double), image->det->n_panels);
weightedSumSS = calloc(sizeof(double), image->det->n_panels);
summedWeights = calloc(sizeof(double), image->det->n_panels);
peaksFound = calloc(sizeof(int), image->det->n_panels);
meanShiftFS = calloc(sizeof(double), image->det->n_panels);
meanShiftSS = calloc(sizeof(double), image->det->n_panels);
/* Initialize arrays */
for (pi=0; pi<image->det->n_panels; pi++) {
weightedSumFS[pi] = 0;
weightedSumSS[pi] = 0;
summedWeights[pi] = 0;
peaksFound[pi] = 0;
meanShiftFS[pi] = 0;
meanShiftSS[pi] = 0;
}
fesetround(1); /* Round towards nearest */
nChunks = 0;
while ( 1 ) {
int fail;
int nFeatures;
int i;
/* Get next chunk */
fail = read_chunk(fh, image);
if ( fail ) break;
nChunks += 1;
/* Skip if no peaks found */
if ( image->features == NULL ) {
continue;
}
/* Loop through peaks to determine mean panel shift */
nFeatures = image_feature_count(image->features);
for ( i=0; i<nFeatures; i++ ) {
struct panel *p;
struct imagefeature *thisFeature;
struct rvec q;
double twotheta;
struct rvec g;
double fs, ss; /* Observed peaks */
double pfs, pss; /* Predicted peaks */
double dfs, dss; /* Observed - predicted */
int pi;
double thisWeight;
/* If we find a feature, determine peak
* position */
thisFeature = image_get_feature(image->features, i);
if ( thisFeature == NULL ) {
continue;
}
fs = thisFeature->fs;
ss = thisFeature->ss;
p = find_panel(image->det, fs, ss);
if ( p == NULL ) {
continue;
}
if ( p->no_index ) continue;
/* Now determine the predicted peak position.
* Scattering vector of this peak */
q = get_q(image, fs, ss, &twotheta, 1.0/image->lambda);
/* Scattering vector of nearest bragg peak */
g = nearest_bragg(image, q);
/* Coordinate of this predicted peak */
fail = calculate_projected_peak(p, g, 1.0/image->lambda,
&pfs, &pss);
if ( fail != 0 ) continue;
/* Finally, we have the shift for this peak */
dfs = pfs - fs;
dss = pss - ss;
/* Add this shift to the weighted sum over shifts */
pi = find_panel_number(image->det,fs,ss);
thisWeight = 1.0;
weightedSumFS[pi] += thisWeight*dfs;
weightedSumSS[pi] += thisWeight*dss;
summedWeights[pi] += thisWeight;
peaksFound[pi] += 1;
}
}
/* Calculate weighted average shift in peak positions */
for ( pi=0; pi<image->det->n_panels; pi++ ) {
meanShiftFS[pi] = weightedSumFS[pi]/summedWeights[pi];
meanShiftSS[pi] = weightedSumSS[pi]/summedWeights[pi];
}
/* Populate the image structure with new geometry info */
for ( pi=0; pi<image->det->n_panels; pi++ ) {
struct panel *p;
p = &image->det->panels[pi];
xsh = 0;
ysh = 0;
if ( peaksFound[pi] >= minpeaks ) {
/* Convert shifts from raw coords to lab frame */
xsh = meanShiftFS[pi]*p->fsx + meanShiftSS[pi]*p->ssx;
ysh = meanShiftFS[pi]*p->fsy + meanShiftSS[pi]*p->ssy;
/* Add shifts to original panel corner locations */
cnx = p->cnx + xsh;
cny = p->cny + ysh;
} else {
/* Not refined? use original coordinates */
cnx = p->cnx;
cny = p->cny;
}
image->det->panels[pi].cnx = cnx;
image->det->panels[pi].cny = cny;
if ( peaksFound[pi] < minpeaks) {
image->det->panels[pi].no_index = 1;
}
STATUS("Panel %s, # peaks: %10d, mean shifts: %f %f\n",
p->name, peaksFound[pi], xsh, ysh);
}
/* Write the new geometry file */
write_detector_geometry(outfilename, image->det);
}
int main(int argc, char *argv[])
{
char c;
struct image image;
char *filename = NULL;
char *geometry = NULL;
char *method = NULL;
char *outputfile = NULL;
FILE *fh = NULL;
FILE *outfh = NULL;
int minpeaks = 0;
/* Long options */
const struct option longopts[] = {
{"help", 0, NULL, 'h'},
{"input", 1, NULL, 'i'},
{"geometry", 1, NULL, 'g'},
{"method", 1, NULL, 'm'},
{"output", 1, NULL, 'o'},
{"npeaks", 1, NULL, 'n'},
{0, 0, NULL, 0}
};
/* Short options */
while ((c = getopt_long(argc, argv, "hi:g:m:o:n:",
longopts, NULL)) != -1) {
switch (c) {
case 'h' :
show_help(argv[0]);
return 0;
case 'i' :
filename = strdup(optarg);
break;
case 'g' :
geometry = strdup(optarg);
break;
case 'm' :
method = strdup(optarg);
break;
case 'o' :
outputfile = strdup(optarg);
break;
case 'n' :
minpeaks = atoi(optarg);
break;
case 0 :
break;
default :
return 1;
}
}
if ( filename == NULL ) {
ERROR("You must specify the input filename with -i\n");
return 1;
}
fh = fopen(filename,"r");
if ( fh == NULL ) {
ERROR("Couldn't open file '%s'\n", filename);
return 1;
}
if ( geometry == NULL ) {
ERROR("You need to specify a geometry file with --geometry\n");
return 1;
}
image.det = get_detector_geometry(geometry);
if ( image.det == NULL ) {
ERROR("Failed to read detector geometry from %s\n", geometry);
return 1;
}
free(geometry);
image.width = image.det->max_fs;
image.height = image.det->max_ss;
if ( outputfile != NULL ) {
STATUS("Writing result to '%s'\n", outputfile);
outfh = fopen(outputfile, "w");
} else {
ERROR("You need to specify an output file.\n");
return 1;
}
if ( minpeaks == 0 ) {
minpeaks = 1;
STATUS("You did not specify minimum number of peaks.\n");
STATUS("Using default value of %d\n", minpeaks);
}
if ( method == NULL ) {
STATUS("You did not specify a refinement method "
"- using default.\n");
method = strdup("xy");
}
if ( strcmp(method,"xy") == 0 ) {
STATUS("Using refinement method %s\n", method);
refine_xy(fh, &image, minpeaks, outputfile);
} else {
printf("Refinement method %s not recognized\n",method);
return 1;
}
fclose(outfh);
return 0;
}
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