PR gradient check

1 files changed, 270 insertions, 0 deletions

diff --git a/tests/pr_gradient_check.c b/tests/pr_gradient_check.c
new file mode 100644
index 00000000..617de4df
--- /dev/null
+++ b/tests/pr_gradient_check.c
@@ -0,0 +1,270 @@
+/*
+ * pr_gradient_check.c
+ *
+ * Check gradients for post refinement
+ *
+ * (c) 2011 Thomas White <taw@physics.org>
+ *
+ * Part of CrystFEL - crystallography with a FEL
+ *
+ */
+
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+
+#include <stdlib.h>
+#include <stdio.h>
+
+#include "../src/image.h"
+#include "../src/cell.h"
+#include "../src/geometry.h"
+#include "../src/reflist.h"
+#include "../src/post-refinement.h"
+
+
+static void scan_partialities(RefList *reflections, RefList *compare,
+                              int *valid, 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;
+		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 calc_either_side(struct image *image, double incr_val,
+                             int *valid, double *vals[3], int refine)
+{
+	RefList *compare;
+	UnitCell *cell;
+
+	cell = new_shifted_cell(image->indexed_cell, refine, -incr_val);
+	compare = find_intersections(image, cell, 0);
+	scan_partialities(image->reflections, compare, valid, vals, 0);
+	cell_free(cell);
+
+	cell = new_shifted_cell(image->indexed_cell, refine, +incr_val);
+	compare = find_intersections(image, cell, 0);
+	scan_partialities(image->reflections, compare, valid, vals, 2);
+	cell_free(cell);
+}
+
+
+static int test_gradients(struct image *image, double incr_val, int refine,
+                          const char *str)
+{
+	Reflection *refl;
+	RefListIterator *iter;
+	double *vals[3];
+	int i;
+	int *valid;
+	int nref;
+	int n_acc, n_valid;
+
+	image->reflections = find_intersections(image, image->indexed_cell, 0);
+
+	nref = num_reflections(image->reflections);
+	if ( nref < 10 ) {
+		ERROR("Too few reflections found.  Failing test by default.\n");
+		return -1;
+	}
+
+	vals[0] = malloc(nref*sizeof(double));
+	vals[1] = malloc(nref*sizeof(double));
+	vals[2] = malloc(nref*sizeof(double));
+	if ( (vals[0] == NULL) || (vals[1] == NULL) || (vals[2] == NULL) ) {
+		ERROR("Couldn't allocate memory.\n");
+		return -1;
+	}
+
+	valid = malloc(nref*sizeof(int));
+	if ( valid == NULL ) {
+		ERROR("Couldn't allocate memory.\n");
+		return -1;
+	}
+	for ( i=0; i<nref; i++ ) valid[i] = 1;
+
+	scan_partialities(image->reflections, image->reflections,
+	                  valid, vals, 1);
+
+	calc_either_side(image, incr_val, valid, vals, refine);
+
+	n_valid = nref;  n_acc = 0;
+	i = 0;
+	for ( refl = first_refl(image->reflections, &iter);
+	      refl != NULL;
+	      refl = next_refl(refl, iter) )
+	{
+
+		double grad1, grad2, grad;
+		double cgrad;
+		signed int h, k, l;
+
+		get_indices(refl, &h, &k, &l);
+
+		if ( !valid[i] ) {
+			n_valid--;
+		} else {
+
+			grad1 = (vals[1][i] - vals[0][i]) / incr_val;
+			grad2 = (vals[2][i] - vals[1][i]) / incr_val;
+			grad = (grad1 + grad2) / 2.0;
+
+			cgrad = gradient(image, refine, refl,
+			                 image->profile_radius);
+
+			if ( !within_tolerance(grad, cgrad, 10.0) ) {
+				STATUS("!- %s %5.2f %5.2f %5.2f"
+				       " -> %10.2e %10.2e -> %10.2e %10.2e\n",
+				       str, vals[0][i], vals[1][i], vals[2][i],
+				       grad1, grad2, grad, cgrad);
+			} else {
+				//STATUS("OK %s %5.2f %5.2f %5.2f"
+				//       " -> %10.2e %10.2e"
+				//       " -> %10.2e %10.2e\n",
+				//       str, vals[0][i], vals[1][i], vals[2][i],
+				//       grad1, grad2, grad, cgrad);
+				n_acc++;
+			}
+
+		}
+
+		i++;
+
+	}
+
+	STATUS("%s: %i out of %i valid gradients were accurate.\n",
+	       str, n_acc, n_valid);
+
+	if ( n_acc != n_valid ) return 1;
+
+	return 0;
+}
+
+int main(int argc, char *argv[])
+{
+	struct image image;
+	const double incr_frac = 1.0/1000.0;
+	double incr_val;
+	double ax, ay, az;
+	double bx, by, bz;
+	double cx, cy, cz;
+	UnitCell *cell;
+	struct quaternion orientation;
+
+	image.width = 1024;
+	image.height = 1024;
+	image.det = simple_geometry(&image);
+
+	image.lambda = ph_en_to_lambda(eV_to_J(2000.0));
+	image.div = 0.009;
+	image.bw = 0.01;
+	image.m = 0.0;
+	image.profile_radius = 0.005e9;
+	image.i0_available = 0;
+	image.filename = malloc(256);
+
+	cell = cell_new_from_parameters(10.0e-9,
+	                                              10.0e-9,
+	                                              10.0e-9,
+	                                              deg2rad(90.0),
+	                                              deg2rad(90.0),
+	                                              deg2rad(90.0));
+
+	orientation = random_quaternion();
+	image.indexed_cell = cell_rotate(cell, orientation);
+
+	cell_get_reciprocal(image.indexed_cell,
+	                    &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz);
+
+	incr_val = incr_frac * ax;
+	test_gradients(&image, incr_val, REF_ASX, "ax*");
+	incr_val = incr_frac * ay;
+	test_gradients(&image, incr_val, REF_ASY, "ay*");
+	incr_val = incr_frac * az;
+	test_gradients(&image, incr_val, REF_ASZ, "az*");
+
+	incr_val = incr_frac * bx;
+	test_gradients(&image, incr_val, REF_BSX, "bx*");
+	incr_val = incr_frac * by;
+	test_gradients(&image, incr_val, REF_BSY, "by*");
+	incr_val = incr_frac * bz;
+	test_gradients(&image, incr_val, REF_BSZ, "bz*");
+
+	incr_val = incr_frac * cx;
+	test_gradients(&image, incr_val, REF_CSX, "cx*");
+	incr_val = incr_frac * cy;
+	test_gradients(&image, incr_val, REF_CSY, "cy*");
+	incr_val = incr_frac * cz;
+	test_gradients(&image, incr_val, REF_CSZ, "cz*");
+
+	return 0;
+}