From 0014a606ed074e7438c6536cf0fc5a7d5bd790c9 Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Wed, 7 Mar 2012 17:50:06 +0100
Subject: indexamajig: Remove polarization correction

It was totally broken and wrong, and just added noise to the data, and it
should be done at the scaling stage instead of now.
---
 libcrystfel/src/peaks.c | 26 +++++---------------------
 libcrystfel/src/peaks.h |  5 ++---
 2 files changed, 7 insertions(+), 24 deletions(-)

(limited to 'libcrystfel')

diff --git a/libcrystfel/src/peaks.c b/libcrystfel/src/peaks.c
index d0183371..66907298 100644
--- a/libcrystfel/src/peaks.c
+++ b/libcrystfel/src/peaks.c
@@ -153,7 +153,7 @@ static int cull_peaks(struct image *image)
 int integrate_peak(struct image *image, int cfs, int css,
                    double *pfs, double *pss, double *intensity,
                    double *pbg, double *pmax, double *sigma,
-                   int do_polar, int centroid, int bgsub)
+                   int centroid, int bgsub)
 {
 	signed int fs, ss;
 	double lim, out_lim, mid_lim;
@@ -227,21 +227,6 @@ int integrate_peak(struct image *image, int cfs, int css,
 
 		val = image->data[idx];
 
-		if ( do_polar ) {
-
-			int err;
-
-			tt = get_tt(image, fs+cfs, ss+css, &err);
-
-			phi = atan2(ss+css, fs+cfs);
-			pa = pow(sin(phi)*sin(tt), 2.0);
-			pb = pow(cos(tt), 2.0);
-			pol = 1.0 - 2.0*POL*(1-pa) + POL*(1.0+pb);
-
-			val /= pol;
-
-		}
-
 		if ( val > max ) max = val;
 
 		/* If outside inner mask, estimate noise from this region */
@@ -416,7 +401,7 @@ static void search_peaks_in_panel(struct image *image, float threshold,
 		 * intensity of this peak is only an estimate at this stage. */
 		r = integrate_peak(image, mask_fs, mask_ss,
 		                   &f_fs, &f_ss, &intensity,
-		                   &pbg, &pmax, &sigma, 0, 1, 1);
+		                   &pbg, &pmax, &sigma, 1, 1);
 
 		if ( r ) {
 			/* Bad region - don't detect peak */
@@ -619,8 +604,8 @@ static struct integr_ind *sort_reflections(RefList *list, UnitCell *cell,
 
 
 /* Integrate the list of predicted reflections in "image" */
-void integrate_reflections(struct image *image, int polar, int use_closer,
-                           int bgsub, double min_snr)
+void integrate_reflections(struct image *image, int use_closer, int bgsub,
+                           double min_snr)
 {
 	struct integr_ind *il;
 	int n, i;
@@ -669,8 +654,7 @@ void integrate_reflections(struct image *image, int polar, int use_closer,
 		}
 
 		r = integrate_peak(image, pfs, pss, &fs, &ss,
-		                   &intensity, &bg, &max, &sigma, polar, 0,
-		                   bgsub);
+		                   &intensity, &bg, &max, &sigma, 0, bgsub);
 
 		/* Record intensity and set redundancy to 1 on success */
 		if ( r == 0 ) {
diff --git a/libcrystfel/src/peaks.h b/libcrystfel/src/peaks.h
index 2360dc42..8b64a081 100644
--- a/libcrystfel/src/peaks.h
+++ b/libcrystfel/src/peaks.h
@@ -37,8 +37,7 @@ extern void search_peaks(struct image *image, float threshold,
                          float min_gradient, float min_snr);
 
 extern void integrate_reflections(struct image *image,
-                                  int polar, int use_closer, int bgsub,
-                                  double min_snr);
+                                  int use_closer, int bgsub, double min_snr);
 
 extern double peak_lattice_agreement(struct image *image, UnitCell *cell,
                                      double *pst);
@@ -49,7 +48,7 @@ extern int peak_sanity_check(struct image *image);
 extern int integrate_peak(struct image *image, int cfs, int css,
                           double *pfs, double *pss, double *intensity,
                           double *pbg, double *pmax, double *sigma,
-                          int do_polar, int centroid, int bgsub);
+                          int centroid, int bgsub);
 
 extern void estimate_resolution(RefList *list, UnitCell *cell,
                                 double *min, double *max);
-- 
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