Add tests/pr_pl_gradient_check for testing gradient of total correction factors

2 files changed, 518 insertions, 0 deletions

diff --git a/tests/.gitignore b/tests/.gitignore
index 1a5ece46..31ce158f 100644
--- a/tests/.gitignore
+++ b/tests/.gitignore
@@ -5,6 +5,7 @@ gpu_sim_check
 integration_check
 pr_l_gradient_check
 pr_p_gradient_check
+pr_pl_gradient_check
 symmetry_check
 centering_check
 transformation_check
diff --git a/tests/pr_pl_gradient_check.c b/tests/pr_pl_gradient_check.c
new file mode 100644
index 00000000..a102ac18
--- /dev/null
+++ b/tests/pr_pl_gradient_check.c
@@ -0,0 +1,517 @@
+/*
+ * pr_p_gradient_check.c
+ *
+ * Check partiality gradients for post refinement
+ *
+ * Copyright © 2012-2013 Deutsches Elektronen-Synchrotron DESY,
+ *                       a research centre of the Helmholtz Association.
+ *
+ * Authors:
+ *   2012-2013 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/post-refinement.h"
+
+
+static void scan_partialities(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 r1, r2, p;
+		int clamp_low, clamp_high;
+
+		get_indices(refl, &h, &k, &l);
+		refl2 = find_refl(compare, h, k, l);
+		if ( refl2 == NULL ) {
+			valid[i] = 0;
+			i++;
+			continue;
+		}
+
+		get_partial(refl2, &r1, &r2, &p, &clamp_low, &clamp_high);
+		if ( clamp_low && clamp_high ) {
+			if ( !within_tolerance(p, 1.0, 0.001) ) {
+
+				signed int h, k, l;
+
+				get_indices(refl, &h, &k, &l);
+
+				ERROR("%3i %3i %3i - double clamped but"
+				      " partiality not close to 1.0 (%5.2f)\n",
+				      h, k, l, p);
+
+			}
+			valid[i] = 0;
+		}
+
+		vals[idx][i] = p * get_lorentz(refl2);
+		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 REF_ASX :  asx += shift;  break;
+		case REF_ASY :  asy += shift;  break;
+		case REF_ASZ :  asz += shift;  break;
+		case REF_BSX :  bsx += shift;  break;
+		case REF_BSY :  bsy += shift;  break;
+		case REF_BSZ :  bsz += shift;  break;
+		case REF_CSX :  csx += shift;  break;
+		case REF_CSY :  csy += shift;  break;
+		case REF_CSZ :  csz += shift;  break;
+	}
+	cell_set_reciprocal(cell, asx, asy, asz, bsx, bsy, bsz, csx, csy, csz);
+
+	return cell;
+}
+
+
+static void shift_parameter(struct image *image, int k, double shift)
+{
+	switch ( k )
+	{
+		case REF_DIV : image->div += shift;  break;
+	}
+}
+
+
+static Crystal *new_shifted_crystal(Crystal *cr, int refine, double incr_val)
+{
+	Crystal *cr_new;
+	double r;
+	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));
+	r = crystal_get_profile_radius(cr_new);
+
+	switch ( refine ) {
+
+		case REF_ASX :
+		case REF_ASY :
+		case REF_ASZ :
+		case REF_BSX :
+		case REF_BSY :
+		case REF_BSZ :
+		case REF_CSX :
+		case REF_CSY :
+		case REF_CSZ :
+		cell = new_shifted_cell(crystal_get_cell(cr), refine,
+		                        incr_val);
+		crystal_set_cell(cr_new, cell);
+		break;
+
+		case REF_R :
+		cell = cell_new_from_cell(crystal_get_cell(cr));
+		crystal_set_cell(cr_new, cell);
+		crystal_set_profile_radius(cr_new, r + incr_val);
+		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);
+
+	if ( (refine != REF_DIV) ) {
+
+		Crystal *cr_new;
+
+		/* Crystal properties */
+		cr_new = new_shifted_crystal(cr, refine, -incr_val);
+		compare = find_intersections(image, cr_new);
+		scan_partialities(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);
+		scan_partialities(crystal_get_reflections(cr), compare, valid,
+		                  vals, 2);
+		cell_free(crystal_get_cell(cr_new));
+		crystal_free(cr_new);
+		reflist_free(compare);
+
+	} else {
+
+		struct image im_moved;
+
+		/* "Image" properties */
+		im_moved = *image;
+		shift_parameter(&im_moved, refine, -incr_val);
+		compare = find_intersections(&im_moved, cr);
+		scan_partialities(crystal_get_reflections(cr), compare,
+		                  valid, vals, 0);
+		reflist_free(compare);
+
+		im_moved = *image;
+		shift_parameter(&im_moved, refine, +incr_val);
+		compare = find_intersections(&im_moved, cr);
+		scan_partialities(crystal_get_reflections(cr), compare,
+		                  valid, vals, 2);
+		reflist_free(compare);
+
+	}
+}
+
+
+
+static double test_gradients(Crystal *cr, double incr_val, int refine,
+                             const char *str, const char *file,
+                             PartialityModel pmodel, 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;
+	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);
+	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_partialities(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;
+
+		get_indices(refl, &h, &k, &l);
+
+		if ( !valid[i] ) {
+			n_invalid++;
+			i++;
+		} else {
+
+			double r1, r2, p, lor;
+			int cl, ch;
+
+			grad1 = (vals[1][i] - vals[0][i]) / incr_val;
+			grad2 = (vals[2][i] - vals[1][i]) / incr_val;
+			grad = (grad1 + grad2) / 2.0;
+			i++;
+
+			get_partial(refl, &r1, &r2, &p, &cl, &ch);
+			lor = get_lorentz(refl);
+
+			cgrad  = p_gradient(cr, refine, refl, pmodel) * lor;
+			cgrad += l_gradient(cr, refine, refl, pmodel) * 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-8) && (fabs(grad) < 5e-8) ) {
+				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 = 1.0/1000000.0;
+	double incr_val;
+	double ax, ay, az;
+	double bx, by, bz;
+	double cx, cy, cz;
+	UnitCell *cell;
+	Crystal *cr;
+	struct quaternion orientation;
+	int i;
+	const PartialityModel pmodel = PMODEL_SPHERE;
+	int fail = 0;
+	int quiet = 0;
+	int plot = 0;
+	int c;
+
+	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));
+
+	for ( i=0; i<1; i++ ) {
+
+		UnitCell *rot;
+		double val;
+
+		orientation = random_quaternion();
+		rot = cell_rotate(cell, orientation);
+		crystal_set_cell(cr, rot);
+
+		cell_get_reciprocal(rot,
+			            &ax, &ay, &az, &bx, &by,
+			            &bz, &cx, &cy, &cz);
+
+		incr_val = incr_frac * image.div;
+		val =  test_gradients(cr, incr_val, REF_DIV, "div", "div",
+		                      pmodel, quiet, plot);
+		if ( val < 0.99 ) fail = 1;
+
+		incr_val = incr_frac * crystal_get_profile_radius(cr);
+		val = test_gradients(cr, incr_val, REF_R, "R", "R", pmodel,
+		                     quiet, plot);
+		if ( val < 0.99 ) fail = 1;
+
+		incr_val = incr_frac * ax;
+		val = test_gradients(cr, incr_val, REF_ASX, "ax*", "x", pmodel,
+		                     quiet, plot);
+		if ( val < 0.99 ) fail = 1;
+		incr_val = incr_frac * bx;
+		val = test_gradients(cr, incr_val, REF_BSX, "bx*", "x", pmodel,
+		                     quiet, plot);
+		if ( val < 0.99 ) fail = 1;
+		incr_val = incr_frac * cx;
+		val = test_gradients(cr, incr_val, REF_CSX, "cx*", "x", pmodel,
+		                     quiet, plot);
+		if ( val < 0.99 ) fail = 1;
+
+		incr_val = incr_frac * ay;
+		val = test_gradients(cr, incr_val, REF_ASY, "ay*", "y", pmodel,
+		                     quiet, plot);
+		if ( val < 0.99 ) fail = 1;
+		incr_val = incr_frac * by;
+		val = test_gradients(cr, incr_val, REF_BSY, "by*", "y", pmodel,
+		                     quiet, plot);
+		if ( val < 0.99 ) fail = 1;
+		incr_val = incr_frac * cy;
+		val = test_gradients(cr, incr_val, REF_CSY, "cy*", "y", pmodel,
+		                     quiet, plot);
+		if ( val < 0.99 ) fail = 1;
+
+		incr_val = incr_frac * az;
+		val = test_gradients(cr, incr_val, REF_ASZ, "az*", "z", pmodel,
+		                     quiet, plot);
+		if ( val < 0.99 ) fail = 1;
+		incr_val = incr_frac * bz;
+		val = test_gradients(cr, incr_val, REF_BSZ, "bz*", "z", pmodel,
+		                     quiet, plot);
+		if ( val < 0.99 ) fail = 1;
+		incr_val = incr_frac * cz;
+		val = test_gradients(cr, incr_val, REF_CSZ, "cz*", "z", pmodel,
+		                     quiet, plot);
+		if ( val < 0.99 ) fail = 1;
+
+	}
+
+	return fail;
+}