Break off integrate_rings_once()

3 files changed, 319 insertions, 181 deletions

diff --git a/tests/.gitignore b/tests/.gitignore
index 31ce158f..fabb48f3 100644
--- a/tests/.gitignore
+++ b/tests/.gitignore
@@ -10,4 +10,5 @@ symmetry_check
 centering_check
 transformation_check
 cell_check
+ring_check
 .dirstamp
diff --git a/tests/integration_check.c b/tests/integration_check.c
index ac871581..4b302955 100644
--- a/tests/integration_check.c
+++ b/tests/integration_check.c
@@ -1,10 +1,9 @@
 /*
  * integration_check.c
  *
- * Check peak integration
+ * Check reflection integration
  *
- * Copyright © 2012 Thomas White <taw@physics.org>
- * Copyright © 2012 Andrew Martin <andrew.martin@desy.de>
+ * Copyright © 2013 Thomas White <taw@physics.org>
  *
  * This file is part of CrystFEL.
  *
@@ -35,126 +34,9 @@
 #include <utils.h>
 #include <beam-parameters.h>
 
-#include "../libcrystfel/src/peaks.c"
+#include "../libcrystfel/src/integration.c"
 
 
-/* The third integration check draws a Poisson background and checks that, on
- * average, it gets subtracted by the background subtraction. */
-static void third_integration_check(struct image *image, int n_trials,
-                                    int *fail)
-{
-	double mean_intensity = 0.0;
-	double mean_bg = 0.0;
-	double mean_max = 0.0;
-	double mean_sigma = 0.0;
-	int i;
-	int fs, ss;
-	int nfail = 0;
-
-	for ( i=0; i<n_trials; i++ ) {
-
-		double intensity, sigma;
-		double fsp, ssp;
-		int r;
-
-		for ( fs=0; fs<image->width; fs++ ) {
-		for ( ss=0; ss<image->height; ss++ ) {
-			image->data[fs+image->width*ss] = poisson_noise(1000.0);
-		}
-		}
-
-		r = integrate_peak(image, 64, 64, &fsp, &ssp,
-		                   &intensity, &sigma, 10.0, 15.0, 17.0,
-		                   NULL, NULL);
-
-		if ( r == 0 ) {
-			mean_intensity += intensity;
-			mean_sigma += sigma;
-		} else {
-			nfail++;
-		}
-
-	}
-	mean_intensity /= n_trials;
-	mean_bg /= n_trials;
-	mean_max /= n_trials;
-	mean_sigma /= n_trials;
-
-	STATUS("  Third check (mean values): intensity = %.2f, sigma = %.2f,"
-	       " integration failed %i/%i times\n",
-	       mean_intensity, mean_sigma, nfail, n_trials);
-
-/* These values are always wrong, because the integration sucks */
-//	if ( fabs(mean_intensity) > 5.0 ) {
-//		ERROR("Mean intensity should be close to zero.\n");
-//		*fail = 1;
-//	}
-//	if ( fabs(mean_intensity) > mean_sigma/10.0 ) {
-//		ERROR("Mean intensity should be much less than mean sigma.\n");
-//		*fail = 1;
-//	}
-}
-
-
-/* The fourth integration check draws a Poisson background and draws a peak on
- * top of it, then checks that the intensity of the peak is correctly recovered
- * accounting for the background. */
-static void fourth_integration_check(struct image *image, int n_trials,
-                                     int *fail)
-{
-	double mean_intensity = 0.0;
-	double mean_sigma = 0.0;
-	int i;
-	int fs, ss;
-	int pcount = 0;
-	int nfail = 0;
-
-	for ( i=0; i<n_trials; i++ ) {
-
-		double intensity, sigma;
-		double fsp, ssp;
-		int r;
-
-		for ( fs=0; fs<image->width; fs++ ) {
-		for ( ss=0; ss<image->height; ss++ ) {
-			int idx = fs+image->width*ss;
-			image->data[idx] = poisson_noise(1000.0);
-			if ( (fs-64)*(fs-64) + (ss-64)*(ss-64) > 9*9 ) continue;
-			image->data[idx] += 1000.0;
-			pcount++;
-		}
-		}
-
-		r = integrate_peak(image, 64, 64, &fsp, &ssp,
-		                   &intensity, &sigma, 10.0, 15.0, 17.0,
-		                   NULL, NULL);
-
-		if ( r == 0 ) {
-			mean_intensity += intensity;
-			mean_sigma += sigma;
-		} else {
-			nfail++;
-		}
-
-	}
-	mean_intensity /= n_trials;
-	mean_sigma /= n_trials;
-	pcount /= n_trials;
-
-	STATUS(" Fourth check (mean values): intensity = %.2f, sigma = %.2f,"
-	       " integration failed %i/%i times\n",
-	       mean_intensity, mean_sigma, nfail, n_trials);
-
-	if ( fabs(mean_intensity - pcount*1000.0) > 4000.0 ) {
-		ERROR("Mean intensity should be close to %f\n", pcount*1000.0);
-		*fail = 1;
-	}
-	if ( fabs(mean_intensity) < mean_sigma ) {
-		ERROR("Mean intensity should be greater than mean sigma.\n");
-		*fail = 1;
-	}
-}
-
 
 int main(int argc, char *argv[])
 {
@@ -164,7 +46,6 @@ int main(int argc, char *argv[])
 	FILE *fh;
 	unsigned int seed;
 	int fail = 0;
-	const int n_trials = 100;
 	int r, npx;
 	double ex;
 
@@ -208,65 +89,7 @@ int main(int argc, char *argv[])
 	image.n_crystals = 0;
 	image.crystals = NULL;
 
-	/* First check: no intensity -> no peak, or very low intensity */
-	r = integrate_peak(&image, 64, 64, &fsp, &ssp, &intensity, &sigma,
-	                   10.0, 15.0, 17.0, NULL, NULL);
-	STATUS("  First check: integrate_peak() returned %i", r);
-	if ( r == 0 ) {
-
-		STATUS(", intensity = %.2f, sigma = %.2f\n", intensity, sigma);
-
-		if ( fabs(intensity) > 0.01 ) {
-			ERROR("Intensity should be very close to zero.\n");
-			fail = 1;
-		}
-
-	} else {
-		STATUS(" (correct)\n");
-	}
-
-	/* Second check: uniform peak gives correct I and low sigma(I) */
-	npx = 0;
-	for ( fs=0; fs<image.width; fs++ ) {
-	for ( ss=0; ss<image.height; ss++ ) {
-		if ( (fs-64)*(fs-64) + (ss-64)*(ss-64) > 9*9 ) continue;
-		image.data[fs+image.width*ss] = 1000.0;
-		npx++;
-	}
-	}
-
-	r = integrate_peak(&image, 64, 64, &fsp, &ssp, &intensity, &sigma,
-	                   10.0, 15.0, 17.0, NULL, NULL);
-	if ( r ) {
-		ERROR(" Second check: integrate_peak() returned %i (wrong).\n",
-		      r);
-		fail = 1;
-	} else {
-
-		STATUS(" Second check: intensity = %.2f, sigma = %.2f\n",
-		       intensity, sigma);
-
-		ex = npx*1000.0;
-		if ( within_tolerance(ex, intensity, 1.0) == 0 ) {
-			ERROR("Intensity should be close to %f\n", ex);
-			fail = 1;
-		}
-
-		ex = sqrt(npx*1000.0);
-		if ( within_tolerance(ex, sigma, 1.0) == 0 ) {
-			ERROR("Sigma should be roughly %f.\n", ex);
-			fail = 1;
-		}
-
-	}
-
-	/* Third check: Poisson background should get mostly subtracted */
-	third_integration_check(&image, n_trials, &fail);
-
-	/* Fourth check: peak on Poisson background */
-	fourth_integration_check(&image, n_trials, &fail);
-
-	/* Fifth check: uniform peak on uniform background */
+	/* Uniform peak on uniform background */
 	npx = 0;
 	for ( fs=0; fs<image.width; fs++ ) {
 	for ( ss=0; ss<image.height; ss++ ) {
diff --git a/tests/ring_check.c b/tests/ring_check.c
new file mode 100644
index 00000000..ac871581
--- /dev/null
+++ b/tests/ring_check.c
@@ -0,0 +1,314 @@
+/*
+ * integration_check.c
+ *
+ * Check peak integration
+ *
+ * Copyright © 2012 Thomas White <taw@physics.org>
+ * Copyright © 2012 Andrew Martin <andrew.martin@desy.de>
+ *
+ * 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 <image.h>
+#include <utils.h>
+#include <beam-parameters.h>
+
+#include "../libcrystfel/src/peaks.c"
+
+
+/* The third integration check draws a Poisson background and checks that, on
+ * average, it gets subtracted by the background subtraction. */
+static void third_integration_check(struct image *image, int n_trials,
+                                    int *fail)
+{
+	double mean_intensity = 0.0;
+	double mean_bg = 0.0;
+	double mean_max = 0.0;
+	double mean_sigma = 0.0;
+	int i;
+	int fs, ss;
+	int nfail = 0;
+
+	for ( i=0; i<n_trials; i++ ) {
+
+		double intensity, sigma;
+		double fsp, ssp;
+		int r;
+
+		for ( fs=0; fs<image->width; fs++ ) {
+		for ( ss=0; ss<image->height; ss++ ) {
+			image->data[fs+image->width*ss] = poisson_noise(1000.0);
+		}
+		}
+
+		r = integrate_peak(image, 64, 64, &fsp, &ssp,
+		                   &intensity, &sigma, 10.0, 15.0, 17.0,
+		                   NULL, NULL);
+
+		if ( r == 0 ) {
+			mean_intensity += intensity;
+			mean_sigma += sigma;
+		} else {
+			nfail++;
+		}
+
+	}
+	mean_intensity /= n_trials;
+	mean_bg /= n_trials;
+	mean_max /= n_trials;
+	mean_sigma /= n_trials;
+
+	STATUS("  Third check (mean values): intensity = %.2f, sigma = %.2f,"
+	       " integration failed %i/%i times\n",
+	       mean_intensity, mean_sigma, nfail, n_trials);
+
+/* These values are always wrong, because the integration sucks */
+//	if ( fabs(mean_intensity) > 5.0 ) {
+//		ERROR("Mean intensity should be close to zero.\n");
+//		*fail = 1;
+//	}
+//	if ( fabs(mean_intensity) > mean_sigma/10.0 ) {
+//		ERROR("Mean intensity should be much less than mean sigma.\n");
+//		*fail = 1;
+//	}
+}
+
+
+/* The fourth integration check draws a Poisson background and draws a peak on
+ * top of it, then checks that the intensity of the peak is correctly recovered
+ * accounting for the background. */
+static void fourth_integration_check(struct image *image, int n_trials,
+                                     int *fail)
+{
+	double mean_intensity = 0.0;
+	double mean_sigma = 0.0;
+	int i;
+	int fs, ss;
+	int pcount = 0;
+	int nfail = 0;
+
+	for ( i=0; i<n_trials; i++ ) {
+
+		double intensity, sigma;
+		double fsp, ssp;
+		int r;
+
+		for ( fs=0; fs<image->width; fs++ ) {
+		for ( ss=0; ss<image->height; ss++ ) {
+			int idx = fs+image->width*ss;
+			image->data[idx] = poisson_noise(1000.0);
+			if ( (fs-64)*(fs-64) + (ss-64)*(ss-64) > 9*9 ) continue;
+			image->data[idx] += 1000.0;
+			pcount++;
+		}
+		}
+
+		r = integrate_peak(image, 64, 64, &fsp, &ssp,
+		                   &intensity, &sigma, 10.0, 15.0, 17.0,
+		                   NULL, NULL);
+
+		if ( r == 0 ) {
+			mean_intensity += intensity;
+			mean_sigma += sigma;
+		} else {
+			nfail++;
+		}
+
+	}
+	mean_intensity /= n_trials;
+	mean_sigma /= n_trials;
+	pcount /= n_trials;
+
+	STATUS(" Fourth check (mean values): intensity = %.2f, sigma = %.2f,"
+	       " integration failed %i/%i times\n",
+	       mean_intensity, mean_sigma, nfail, n_trials);
+
+	if ( fabs(mean_intensity - pcount*1000.0) > 4000.0 ) {
+		ERROR("Mean intensity should be close to %f\n", pcount*1000.0);
+		*fail = 1;
+	}
+	if ( fabs(mean_intensity) < mean_sigma ) {
+		ERROR("Mean intensity should be greater than mean sigma.\n");
+		*fail = 1;
+	}
+}
+
+
+int main(int argc, char *argv[])
+{
+	struct image image;
+	double fsp, ssp, intensity, sigma;
+	int fs, ss;
+	FILE *fh;
+	unsigned int seed;
+	int fail = 0;
+	const int n_trials = 100;
+	int r, npx;
+	double ex;
+
+	fh = fopen("/dev/urandom", "r");
+	fread(&seed, sizeof(seed), 1, fh);
+	fclose(fh);
+	srand(seed);
+
+	image.data = malloc(128*128*sizeof(float));
+	image.flags = NULL;
+	image.beam = NULL;
+	image.lambda = ph_eV_to_lambda(1000.0);
+
+	image.det = calloc(1, sizeof(struct detector));
+	image.det->n_panels = 1;
+	image.det->panels = calloc(1, sizeof(struct panel));
+
+	image.det->panels[0].min_fs = 0;
+	image.det->panels[0].max_fs = 128;
+	image.det->panels[0].min_ss = 0;
+	image.det->panels[0].max_ss = 128;
+	image.det->panels[0].fsx = 1.0;
+	image.det->panels[0].fsy = 0.0;
+	image.det->panels[0].ssx = 0.0;
+	image.det->panels[0].ssy = 1.0;
+	image.det->panels[0].xfs = 1.0;
+	image.det->panels[0].yfs = 0.0;
+	image.det->panels[0].xss = 0.0;
+	image.det->panels[0].yss = 1.0;
+	image.det->panels[0].cnx = -64.0;
+	image.det->panels[0].cny = -64.0;
+	image.det->panels[0].clen = 1.0;
+	image.det->panels[0].res = 1.0;
+	image.det->panels[0].adu_per_eV = 1.0/1000.0;  /* -> 1 adu per photon */
+	image.det->panels[0].max_adu = +INFINITY;  /* No cutoff */
+
+	image.width = 128;
+	image.height = 128;
+	memset(image.data, 0, 128*128*sizeof(float));
+
+	image.n_crystals = 0;
+	image.crystals = NULL;
+
+	/* First check: no intensity -> no peak, or very low intensity */
+	r = integrate_peak(&image, 64, 64, &fsp, &ssp, &intensity, &sigma,
+	                   10.0, 15.0, 17.0, NULL, NULL);
+	STATUS("  First check: integrate_peak() returned %i", r);
+	if ( r == 0 ) {
+
+		STATUS(", intensity = %.2f, sigma = %.2f\n", intensity, sigma);
+
+		if ( fabs(intensity) > 0.01 ) {
+			ERROR("Intensity should be very close to zero.\n");
+			fail = 1;
+		}
+
+	} else {
+		STATUS(" (correct)\n");
+	}
+
+	/* Second check: uniform peak gives correct I and low sigma(I) */
+	npx = 0;
+	for ( fs=0; fs<image.width; fs++ ) {
+	for ( ss=0; ss<image.height; ss++ ) {
+		if ( (fs-64)*(fs-64) + (ss-64)*(ss-64) > 9*9 ) continue;
+		image.data[fs+image.width*ss] = 1000.0;
+		npx++;
+	}
+	}
+
+	r = integrate_peak(&image, 64, 64, &fsp, &ssp, &intensity, &sigma,
+	                   10.0, 15.0, 17.0, NULL, NULL);
+	if ( r ) {
+		ERROR(" Second check: integrate_peak() returned %i (wrong).\n",
+		      r);
+		fail = 1;
+	} else {
+
+		STATUS(" Second check: intensity = %.2f, sigma = %.2f\n",
+		       intensity, sigma);
+
+		ex = npx*1000.0;
+		if ( within_tolerance(ex, intensity, 1.0) == 0 ) {
+			ERROR("Intensity should be close to %f\n", ex);
+			fail = 1;
+		}
+
+		ex = sqrt(npx*1000.0);
+		if ( within_tolerance(ex, sigma, 1.0) == 0 ) {
+			ERROR("Sigma should be roughly %f.\n", ex);
+			fail = 1;
+		}
+
+	}
+
+	/* Third check: Poisson background should get mostly subtracted */
+	third_integration_check(&image, n_trials, &fail);
+
+	/* Fourth check: peak on Poisson background */
+	fourth_integration_check(&image, n_trials, &fail);
+
+	/* Fifth check: uniform peak on uniform background */
+	npx = 0;
+	for ( fs=0; fs<image.width; fs++ ) {
+	for ( ss=0; ss<image.height; ss++ ) {
+		image.data[fs+image.width*ss] = 1000.0;
+		if ( (fs-64)*(fs-64) + (ss-64)*(ss-64) > 9*9 ) continue;
+		image.data[fs+image.width*ss] += 1000.0;
+		npx++;
+	}
+	}
+
+	r = integrate_peak(&image, 64, 64, &fsp, &ssp, &intensity, &sigma,
+	                   10.0, 15.0, 17.0, NULL, NULL);
+	if ( r ) {
+		ERROR("   Fifth check: integrate_peak() returned %i (wrong).\n",
+		      r);
+		fail = 1;
+	} else {
+
+		STATUS("  Fifth check: intensity = %.2f, sigma = %.2f\n",
+		       intensity, sigma);
+
+		ex = npx*1000.0;
+		if ( within_tolerance(ex, intensity, 1.0) == 0 ) {
+			ERROR("Intensity should be close to %f\n", ex);
+			fail = 1;
+		}
+
+		ex = sqrt(npx*1000.0);
+		if ( within_tolerance(ex, sigma, 1.0) == 0 ) {
+			ERROR("Sigma should be roughly %f.\n", ex);
+			fail = 1;
+		}
+
+	}
+
+
+	free(image.beam);
+	free(image.det->panels);
+	free(image.det);
+	free(image.data);
+
+	if ( fail ) return 1;
+
+	return 0;
+}