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diff --git a/tests/prediction_gradient_check.c b/tests/prediction_gradient_check.c
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+/*
+ * prediction_gradient_check.c
+ *
+ * Check partiality gradients for prediction refinement
+ *
+ * Copyright © 2012-2015 Deutsches Elektronen-Synchrotron DESY,
+ * a research centre of the Helmholtz Association.
+ *
+ * Authors:
+ * 2012-2015 Thomas White <taw@physics.org>
+ *
+ * This file is part of CrystFEL.
+ *
+ * CrystFEL is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * CrystFEL is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with CrystFEL. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <gsl/gsl_statistics.h>
+#include <getopt.h>
+
+#include <image.h>
+#include <cell.h>
+#include <cell-utils.h>
+#include <geometry.h>
+#include <reflist.h>
+#include "../src/predict-refine.c"
+
+
+int checkrxy;
+
+
+static void scan(RefList *reflections, RefList *compare,
+ int *valid, long double *vals[3], int idx)
+{
+ int i;
+ Reflection *refl;
+ RefListIterator *iter;
+
+ i = 0;
+ for ( refl = first_refl(reflections, &iter);
+ refl != NULL;
+ refl = next_refl(refl, iter) )
+ {
+ signed int h, k, l;
+ Reflection *refl2;
+ double rlow, rhigh, p;
+ double fs, ss, xh, yh;
+ struct panel *panel;
+
+ get_indices(refl, &h, &k, &l);
+ refl2 = find_refl(compare, h, k, l);
+ if ( refl2 == NULL ) {
+ valid[i] = 0;
+ i++;
+ continue;
+ }
+
+ get_partial(refl2, &rlow, &rhigh, &p);
+ get_detector_pos(refl2, &fs, &ss);
+ panel = get_panel(refl2);
+ twod_mapping(fs, ss, &xh, &yh, panel);
+
+ switch ( checkrxy ) {
+
+ case 0 :
+ vals[idx][i] = (rlow + rhigh)/2.0;
+ break;
+
+ case 1 :
+ vals[idx][i] = xh;
+ break;
+
+ case 2 :
+ vals[idx][i] = yh;
+ break;
+ }
+
+ i++;
+ }
+}
+
+
+static UnitCell *new_shifted_cell(UnitCell *input, int k, double shift)
+{
+ UnitCell *cell;
+ double asx, asy, asz;
+ double bsx, bsy, bsz;
+ double csx, csy, csz;
+
+ cell = cell_new();
+ cell_get_reciprocal(input, &asx, &asy, &asz, &bsx, &bsy, &bsz,
+ &csx, &csy, &csz);
+ switch ( k )
+ {
+ case GPARAM_ASX : asx += shift; break;
+ case GPARAM_ASY : asy += shift; break;
+ case GPARAM_ASZ : asz += shift; break;
+ case GPARAM_BSX : bsx += shift; break;
+ case GPARAM_BSY : bsy += shift; break;
+ case GPARAM_BSZ : bsz += shift; break;
+ case GPARAM_CSX : csx += shift; break;
+ case GPARAM_CSY : csy += shift; break;
+ case GPARAM_CSZ : csz += shift; break;
+ }
+ cell_set_reciprocal(cell, asx, asy, asz, bsx, bsy, bsz, csx, csy, csz);
+
+ return cell;
+}
+
+
+static Crystal *new_shifted_crystal(Crystal *cr, int refine, double incr_val)
+{
+ Crystal *cr_new;
+ UnitCell *cell;
+
+ cr_new = crystal_copy(cr);
+ if ( cr_new == NULL ) {
+ ERROR("Failed to allocate crystal.\n");
+ return NULL;
+ }
+
+ crystal_set_image(cr_new, crystal_get_image(cr));
+
+ switch ( refine ) {
+
+ case GPARAM_ASX :
+ case GPARAM_ASY :
+ case GPARAM_ASZ :
+ case GPARAM_BSX :
+ case GPARAM_BSY :
+ case GPARAM_BSZ :
+ case GPARAM_CSX :
+ case GPARAM_CSY :
+ case GPARAM_CSZ :
+ cell = new_shifted_cell(crystal_get_cell(cr), refine,
+ incr_val);
+ crystal_set_cell(cr_new, cell);
+ break;
+
+ default:
+ ERROR("Can't shift %i\n", refine);
+ break;
+
+ }
+
+ return cr_new;
+}
+
+
+static void calc_either_side(Crystal *cr, double incr_val,
+ int *valid, long double *vals[3], int refine)
+{
+ RefList *compare;
+ struct image *image = crystal_get_image(cr);
+ Crystal *cr_new;
+
+ cr_new = new_shifted_crystal(cr, refine, -incr_val);
+ compare = find_intersections(image, cr_new, PMODEL_SCSPHERE);
+ scan(crystal_get_reflections(cr), compare, valid, vals, 0);
+ cell_free(crystal_get_cell(cr_new));
+ crystal_free(cr_new);
+ reflist_free(compare);
+
+ cr_new = new_shifted_crystal(cr, refine, +incr_val);
+ compare = find_intersections(image, cr_new, PMODEL_SCSPHERE);
+ scan(crystal_get_reflections(cr), compare, valid, vals, 2);
+ cell_free(crystal_get_cell(cr_new));
+ crystal_free(cr_new);
+ reflist_free(compare);
+}
+
+
+static double test_gradients(Crystal *cr, double incr_val, int refine,
+ const char *str, const char *file,
+ int quiet, int plot)
+{
+ Reflection *refl;
+ RefListIterator *iter;
+ long double *vals[3];
+ int i;
+ int *valid;
+ int nref;
+ int n_good, n_invalid, n_small, n_nan, n_bad;
+ RefList *reflections;
+ FILE *fh = NULL;
+ int ntot = 0;
+ double total = 0.0;
+ char tmp[32];
+ double *vec1;
+ double *vec2;
+ int n_line;
+ double cc;
+
+ reflections = find_intersections(crystal_get_image(cr), cr,
+ PMODEL_SCSPHERE);
+ crystal_set_reflections(cr, reflections);
+
+ nref = num_reflections(reflections);
+ if ( nref < 10 ) {
+ ERROR("Too few reflections found. Failing test by default.\n");
+ return 0.0;
+ }
+
+ vals[0] = malloc(nref*sizeof(long double));
+ vals[1] = malloc(nref*sizeof(long double));
+ vals[2] = malloc(nref*sizeof(long double));
+ if ( (vals[0] == NULL) || (vals[1] == NULL) || (vals[2] == NULL) ) {
+ ERROR("Couldn't allocate memory.\n");
+ return 0.0;
+ }
+
+ valid = malloc(nref*sizeof(int));
+ if ( valid == NULL ) {
+ ERROR("Couldn't allocate memory.\n");
+ return 0.0;
+ }
+ for ( i=0; i<nref; i++ ) valid[i] = 1;
+
+ scan(reflections, reflections, valid, vals, 1);
+
+ calc_either_side(cr, incr_val, valid, vals, refine);
+
+ if ( plot ) {
+ snprintf(tmp, 32, "gradient-test-%s.dat", file);
+ fh = fopen(tmp, "w");
+ }
+
+ vec1 = malloc(nref*sizeof(double));
+ vec2 = malloc(nref*sizeof(double));
+ if ( (vec1 == NULL) || (vec2 == NULL) ) {
+ ERROR("Couldn't allocate memory.\n");
+ return 0.0;
+ }
+
+ n_invalid = 0; n_good = 0;
+ n_nan = 0; n_small = 0; n_bad = 0; n_line = 0;
+ i = 0;
+ for ( refl = first_refl(reflections, &iter);
+ refl != NULL;
+ refl = next_refl(refl, iter) )
+ {
+ long double grad1, grad2, grad;
+ double cgrad;
+ signed int h, k, l;
+ struct reflpeak rp;
+
+ get_indices(refl, &h, &k, &l);
+
+ if ( !valid[i] ) {
+ n_invalid++;
+ i++;
+ } else {
+
+ double r1, r2, p;
+
+ grad1 = (vals[1][i] - vals[0][i]) / incr_val;
+ grad2 = (vals[2][i] - vals[1][i]) / incr_val;
+ grad = (grad1 + grad2) / 2.0;
+ i++;
+
+ if ( checkrxy == 0 ) {
+
+ cgrad = r_gradient(crystal_get_cell(cr), refine,
+ refl, crystal_get_image(cr));
+
+ } else {
+
+ struct imagefeature pk;
+ struct image *image;
+
+ pk.fs = 0.0;
+ pk.ss = 0.0;
+
+ image = crystal_get_image(cr);
+ rp.refl = refl;
+ rp.peak = &pk;
+ rp.panel = &image->det->panels[0];
+
+ if ( checkrxy == 1 ) {
+ cgrad = x_gradient(refine, &rp,
+ crystal_get_image(cr)->det,
+ crystal_get_image(cr)->lambda,
+ crystal_get_cell(cr));
+ } else {
+ cgrad = y_gradient(refine, &rp,
+ crystal_get_image(cr)->det,
+ crystal_get_image(cr)->lambda,
+ crystal_get_cell(cr));
+ }
+ }
+
+ get_partial(refl, &r1, &r2, &p);
+
+ if ( isnan(cgrad) ) {
+ n_nan++;
+ continue;
+ }
+
+ if ( plot ) {
+ fprintf(fh, "%e %Le\n", cgrad, grad);
+ }
+
+ vec1[n_line] = cgrad;
+ vec2[n_line] = grad;
+ n_line++;
+
+ if ( (fabs(cgrad) < 5e-12) && (fabs(grad) < 5e-12) ) {
+ n_small++;
+ continue;
+ }
+
+ total += fabs(cgrad - grad);
+ ntot++;
+
+ if ( !within_tolerance(grad, cgrad, 5.0)
+ || !within_tolerance(cgrad, grad, 5.0) )
+ {
+
+ if ( !quiet ) {
+ STATUS("!- %s %3i %3i %3i"
+ " %10.2Le %10.2e ratio = %5.2Lf"
+ " %10.2e %10.2e\n",
+ str, h, k, l, grad, cgrad,
+ cgrad/grad, r1, r2);
+ }
+ n_bad++;
+
+ } else {
+
+ //STATUS("OK %s %3i %3i %3i"
+ // " %10.2Le %10.2e ratio = %5.2Lf"
+ // " %10.2e %10.2e\n",
+ // str, h, k, l, grad, cgrad, cgrad/grad,
+ // r1, r2);
+
+ n_good++;
+
+ }
+
+ }
+
+ }
+
+ STATUS("%3s: %3i within 5%%, %3i outside, %3i nan, %3i invalid, "
+ "%3i small. ", str, n_good, n_bad, n_nan, n_invalid, n_small);
+
+ if ( plot ) {
+ fclose(fh);
+ }
+
+ cc = gsl_stats_correlation(vec1, 1, vec2, 1, n_line);
+ STATUS("CC = %+f\n", cc);
+ return cc;
+}
+
+
+int main(int argc, char *argv[])
+{
+ struct image image;
+ const double incr_frac = 1.0/100000.0;
+ double incr_val;
+ double ax, ay, az;
+ double bx, by, bz;
+ double cx, cy, cz;
+ UnitCell *cell;
+ Crystal *cr;
+ struct quaternion orientation;
+ int fail = 0;
+ int quiet = 0;
+ int plot = 0;
+ int c;
+ gsl_rng *rng;
+ UnitCell *rot;
+ double val;
+
+ const struct option longopts[] = {
+ {"quiet", 0, &quiet, 1},
+ {"plot", 0, &plot, 1},
+ {0, 0, NULL, 0}
+ };
+
+ while ((c = getopt_long(argc, argv, "", longopts, NULL)) != -1) {
+ switch (c) {
+
+ case 0 :
+ break;
+
+ case '?' :
+ break;
+
+ default :
+ ERROR("Unhandled option '%c'\n", c);
+ break;
+
+ }
+
+ }
+
+ image.width = 1024;
+ image.height = 1024;
+ image.det = simple_geometry(&image);
+ image.det->panels[0].res = 13333.3;
+ image.det->panels[0].clen = 80e-3;
+ image.det->panels[0].coffset = 0.0;
+
+ image.lambda = ph_en_to_lambda(eV_to_J(8000.0));
+ image.div = 1e-3;
+ image.bw = 0.01;
+ image.filename = malloc(256);
+
+ cr = crystal_new();
+ if ( cr == NULL ) {
+ ERROR("Failed to allocate crystal.\n");
+ return 1;
+ }
+ crystal_set_mosaicity(cr, 0.0);
+ crystal_set_profile_radius(cr, 0.005e9);
+ crystal_set_image(cr, &image);
+
+ cell = cell_new_from_parameters(10.0e-9, 10.0e-9, 10.0e-9,
+ deg2rad(90.0),
+ deg2rad(90.0),
+ deg2rad(90.0));
+
+ rng = gsl_rng_alloc(gsl_rng_mt19937);
+
+ for ( checkrxy=0; checkrxy<3; checkrxy++ ) {
+
+
+ switch ( checkrxy ) {
+ case 0 :
+ STATUS("Excitation error:\n");
+ break;
+ case 1:
+ STATUS("x coordinate:\n");
+ break;
+ default:
+ case 2:
+ STATUS("y coordinate:\n");
+ break;
+ STATUS("WTF??\n");
+ break;
+ }
+
+ orientation = random_quaternion(rng);
+ rot = cell_rotate(cell, orientation);
+ crystal_set_cell(cr, rot);
+
+ cell_get_reciprocal(rot, &ax, &ay, &az,
+ &bx, &by, &bz, &cx, &cy, &cz);
+
+ if ( checkrxy != 2 ) {
+
+ incr_val = incr_frac * ax;
+ val = test_gradients(cr, incr_val, GPARAM_ASX,
+ "ax*", "ax", quiet, plot);
+ if ( val < 0.99 ) fail = 1;
+ incr_val = incr_frac * bx;
+ val = test_gradients(cr, incr_val, GPARAM_BSX,
+ "bx*", "bx", quiet, plot);
+ if ( val < 0.99 ) fail = 1;
+ incr_val = incr_frac * cx;
+ val = test_gradients(cr, incr_val, GPARAM_CSX,
+ "cx*", "cx", quiet, plot);
+ if ( val < 0.99 ) fail = 1;
+
+ }
+
+ if ( checkrxy != 1 ) {
+
+ incr_val = incr_frac * ay;
+ val = test_gradients(cr, incr_val, GPARAM_ASY,
+ "ay*", "ay", quiet, plot);
+ if ( val < 0.99 ) fail = 1;
+ incr_val = incr_frac * by;
+ val = test_gradients(cr, incr_val, GPARAM_BSY,
+ "by*", "by", quiet, plot);
+ if ( val < 0.99 ) fail = 1;
+ incr_val = incr_frac * cy;
+ val = test_gradients(cr, incr_val, GPARAM_CSY,
+ "cy*", "cy", quiet, plot);
+ if ( val < 0.99 ) fail = 1;
+
+ }
+
+ incr_val = incr_frac * az;
+ val = test_gradients(cr, incr_val, GPARAM_ASZ, "az*", "az",
+ quiet, plot);
+ if ( val < 0.99 ) fail = 1;
+ incr_val = incr_frac * bz;
+ val = test_gradients(cr, incr_val, GPARAM_BSZ, "bz*", "bz",
+ quiet, plot);
+ if ( val < 0.99 ) fail = 1;
+ incr_val = incr_frac * cz;
+ val = test_gradients(cr, incr_val, GPARAM_CSZ, "cz*", "cz",
+ quiet, plot);
+ if ( val < 0.99 ) fail = 1;
+
+ }
+
+ gsl_rng_free(rng);
+
+ return fail;
+}
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