Tidy up and remove debug

3 files changed, 46 insertions, 53 deletions

diff --git a/src/dirax.c b/src/dirax.c
index c4afbce..79b20ea 100644
--- a/src/dirax.c
+++ b/src/dirax.c
@@ -387,11 +387,9 @@ static void dirax_send_random_selection(ReflectionList *r, int n, FILE *fh)
 		ra = ((long long int)random() * (long long int)n);
 		ra /= RAND_MAX;
 		if ( used[ra] == 'U' ) {
-			printf("%lli - already used\n", ra);
 			continue;
 		}
 
-		printf("Selected reflection %lli\n", ra);
 
 		/* Dig out the correct reflection. A little faffy
 		 * because of the linked list */
@@ -401,10 +399,10 @@ static void dirax_send_random_selection(ReflectionList *r, int n, FILE *fh)
 		}
 
 		/* Limit resolution of reflections */
-		if (	( (ref->x/1e9)*(ref->x/1e9)
-			+ (ref->y/1e9)*(ref->y/1e9)
-			+ (ref->z/1e9)*(ref->z/1e9) ) > (20e9)*(20e9) )
-				continue;
+//		if (	( (ref->x/1e9)*(ref->x/1e9)
+//			+ (ref->y/1e9)*(ref->y/1e9)
+//			+ (ref->z/1e9)*(ref->z/1e9) ) > (20e9)*(20e9) )
+//				continue;
 
 		fprintf(fh, "%10f %10f %10f %8f\n",
 					ref->x/1e10, ref->y/1e10,
diff --git a/src/itrans-stat.c b/src/itrans-stat.c
index ee41817..0e03ead 100644
--- a/src/itrans-stat.c
+++ b/src/itrans-stat.c
@@ -441,7 +441,7 @@ static gsl_matrix *itrans_peaksearch_stat_floodfill(gsl_matrix *m,
 					gsl_matrix_set(p, 2, n, val);
 					n++;
 					if ( n == size ) {
-					printf("expanding %i->%i\n", size, size*2);
+
 		p = itrans_peaksearch_stat_matrix_expand(p, size, size*2);
 						size *= 2;
 					}
@@ -450,14 +450,10 @@ static gsl_matrix *itrans_peaksearch_stat_floodfill(gsl_matrix *m,
 			}
 		}
 	}
-	//printf("ff: ending loop, found %d\n",n);
 
 	*count = n;
 	if ( n > 0 ) {
-		//printf("pcheck s1=%d s2=%d\n",p->size1,p->size2);
-		printf("expandingg %i->%i\n", size, n);
 		p = itrans_peaksearch_stat_matrix_expand(p, size, n);
-		//printf("pcheck s1=%d s2=%d\n",p->size1,p->size2);
 	}
 
 	return p;
diff --git a/src/reproject.c b/src/reproject.c
index e1ce13e..c41aa3f 100644
--- a/src/reproject.c
+++ b/src/reproject.c
@@ -23,24 +23,24 @@
 void reproject_partner_features(ImageFeatureList *rflist, ImageRecord *image) {
 
 	int i;
-	
+
 	for ( i=0; i<rflist->n_features; i++ ) {
-	
+
 		//if ( !reflection_is_easy(rflist->features[i].reflection) ) continue;
-		
+
 		double d = 0.0;
 		ImageFeature *partner;
 		int idx;
-		
+
 		partner = image_feature_closest(image->features, rflist->features[i].x, rflist->features[i].y, &d, &idx);
-		
+
 		if ( (d <= 20.0) && partner ) {
 			rflist->features[i].partner = partner;
 			rflist->features[i].partner_d = d;
 		} else {
 			rflist->features[i].partner = NULL;
 		}
-	
+
 	}
 
 }
@@ -55,12 +55,12 @@ ImageFeatureList *reproject_get_reflections(ImageRecord *image, ReflectionList *
 	double kx, ky, kz;			/* Electron wavevector ("normal" times 1/lambda */
 	double ux, uy, uz, uxt, uyt, uzt;	/* "up" vector (and calculation intermediates) */
 	//int done_debug = 0;
-			
+
 	flist = image_feature_list_new();
-	
+
 	tilt = image->tilt;
 	omega = image->omega;
-	
+
 	/* Calculate the (normalised) incident electron wavevector
 	 *	n is rotated "into" the reconstruction, so only one omega step. */
 	nxt = 0.0;  nyt = 0.0;  nzt = 1.0;
@@ -71,7 +71,7 @@ ImageFeatureList *reproject_get_reflections(ImageRecord *image, ReflectionList *
 	ky = ny / image->lambda;
 	kz = nz / image->lambda;	/* This is the centre of the Ewald sphere */
 	//reflection_add(ctx->reflectionlist, kx, ky, kz, 1, REFLECTION_VECTOR_MARKER_1);
-	
+
 	/* Determine where "up" is
 	 *	See above. */
 	uxt = 0.0;  uyt = 1.0;  uzt = 0.0;
@@ -79,19 +79,19 @@ ImageFeatureList *reproject_get_reflections(ImageRecord *image, ReflectionList *
 	uxt = ux;  uyt = uy;  uzt = uz;
 	ux = uxt*cos(-omega) + uyt*-sin(omega);  uy = -uxt*sin(omega) + uyt*cos(omega);  uz = uzt;
 	//reflection_add(ctx->reflectionlist, ux*50e9, uy*50e9, uz*50e9, 1, REFLECTION_VECTOR_MARKER_2);
-	
+
 	reflection = reflectionlist->reflections;
 	do {
-	
+
 		double xl, yl, zl;
 		double a, b, c;
 		double A1, A2, s1, s2, s;
-		
+
 		/* Get the coordinates of the reciprocal lattice point */
 		xl = reflection->x;
 		yl = reflection->y;
 		zl = reflection->z;
-		
+
 		/* Next, solve the relrod equation to calculate the excitation error */
 		a = 1.0;
 		b = -2.0*(xl*nx + yl*ny + zl*nz);
@@ -101,37 +101,37 @@ ImageFeatureList *reproject_get_reflections(ImageRecord *image, ReflectionList *
 		s1 = 1.0/image->lambda - A1;
 		s2 = 1.0/image->lambda - A2;
 		if ( fabs(s1) < fabs(s2) ) s = s1; else s = s2;
-		
+
 		/* Skip this reflection if s is large */
 		if ( fabs(s) <= smax ) {
-		
+
 			double xi, yi, zi;
 			double gx, gy, gz;
 			double cx, cy, cz;
 			double theta;
 			double x, y;
 			double rx, ry, rz;
-			
+
 			/* Determine the intersection point */
 			xi = xl + s*nx;  yi = yl + s*ny;  zi = zl + s*nz;
-			
+
 			/* Calculate Bragg angle */
 			gx = xi - kx;
 			gy = yi - ky;
 			gz = zi - kz;	/* This is the vector from the centre of the sphere to the intersection */
 			theta = angle_between(-kx, -ky, -kz, gx, gy, gz);
-			
+
 			if ( theta > 0.0 ) {
-			
+
 				double psi, disc;
-				
+
 				//reflection_add(ctx->reflectionlist, xl, yl, zl, 1, REFLECTION_GENERATED);
 				//reflection_add(ctx->reflectionlist, xi, yi, zi, 1, REFLECTION_MARKER);
-				
+
 				/* Calculate azimuth of point in image (clockwise from "up", will be changed later) */
 				cx = yi*nz-zi*ny;  cy = nx*zi-nz*xi;  cz = ny*xi-nx*yi;  /* c = i x n */
 				psi = angle_between(cx, cy, cz, ux, uy, uz);
-				
+
 				/* Finally, resolve the +/- Pi ambiguity from the previous step */
 				rx = cy*nz-cz*ny;  ry = nx*cz-nz*cx;  rz = ny*cx-nx*cy;  /* r = [i x n] x n */
 				disc = angle_between(rx, ry, rz, ux, uy, uz);
@@ -154,15 +154,15 @@ ImageFeatureList *reproject_get_reflections(ImageRecord *image, ReflectionList *
 					psi = 3*M_PI_2 + psi;	/* Case 4 */
 			//		if ( (i==20) && !done_debug ) printf("case 4\n");
 				}
-				
+
 			//	if ( (i==20) && !done_debug ) printf("final psi=%f clockwise from 'up'\n", rad2deg(psi));
 				psi = M_PI_2 - psi;	/* Anticlockwise from "+x" instead of clockwise from "up" */
 			//	if ( (i==20) && !done_debug ) printf("final psi=%f anticlockwise from +x\n", rad2deg(psi));
-				
+
 				psi += omega;
 			//	if ( (i==20) && !done_debug ) printf("final psi=%f anticlockwise from +tilt axis\n", rad2deg(psi));
 			//	if ( (i==20) && !done_debug ) done_debug = 1;
-				
+
 				/* Calculate image coordinates from polar representation */
 				if ( image->fmode == FORMULATION_CLEN ) {
 					x = image->camera_len*tan(theta)*cos(psi);
@@ -178,36 +178,36 @@ ImageFeatureList *reproject_get_reflections(ImageRecord *image, ReflectionList *
 					fprintf(stderr, "Unrecognised formulation mode in reproject_get_reflections()\n");
 					return NULL;
 				}
-				
+
 				x += image->x_centre;
 				y += image->y_centre;
-				
+
 				/* Sanity check */
 				if ( (x>=0) && (x<image->width) && (y>=0) && (y<image->height) ) {
-				
+
 					/* Record the reflection */
 					image_add_feature_reflection(flist, x, y, image, reflection->intensity, reflection);
 					/* Intensity should be multiplied by relrod spike function except
 					 * reprojected reflections aren't used quantitatively for anything */
-					
+
 					//printf("Reflection at %f, %f\n", x, y);
-				
+
 				} /* else it's outside the picture somewhere */
-				
+
 			} /* else this is the central beam so don't worry about it */
-		
+
 		}
-		
+
 		reflection = reflection->next;
-	
+
 	} while ( reflection );
-	
+
 	/* Partner features only if the image has a feature list.  This allows the test
 	 *	program to use this function to generate simulated data. */
 	if ( image->features != NULL ) {
 		reproject_partner_features(flist, image);
 	}
-	
+
 	return flist;
 
 }
@@ -216,21 +216,21 @@ ImageFeatureList *reproject_get_reflections(ImageRecord *image, ReflectionList *
 void reproject_cell_to_lattice(ControlContext *ctx) {
 
 	int i;
-	
+
 	if ( ctx->cell_lattice ) {
 		reflection_list_from_new_cell(ctx->cell_lattice, ctx->cell);
 	} else {
 		ctx->cell_lattice = reflection_list_from_cell(ctx->cell);
 	}
-	
+
 	displaywindow_enable_cell_functions(ctx->dw, TRUE);
-	
+
 	/* Invalidate all the reprojected feature lists */
 	for ( i=0; i<ctx->images->n_images; i++ ) {
 		image_feature_list_free(ctx->images->images[i].rflist);
 		ctx->images->images[i].rflist = NULL;
 	}
-	
+
 }
 
 /* Notify that ctx->cell has changed (also need to call displaywindow_update) */
@@ -240,4 +240,3 @@ void reproject_lattice_changed(ControlContext *ctx) {
 	displaywindow_update_imagestack(ctx->dw);
 
 }
-