Formatting

7 files changed, 139 insertions, 104 deletions

diff --git a/libcrystfel/src/cell.c b/libcrystfel/src/cell.c
index 8412fc62..31d3b9b1 100644
--- a/libcrystfel/src/cell.c
+++ b/libcrystfel/src/cell.c
@@ -424,7 +424,7 @@ int cell_get_parameters(UnitCell *cell, double *a, double *b, double *c,
 
 	switch ( cell->rep ) {
 
-	case CELL_REP_CRYST:
+		case CELL_REP_CRYST:
 		/* Direct response */
 		*a = cell->a;
 		*b = cell->b;
@@ -434,7 +434,7 @@ int cell_get_parameters(UnitCell *cell, double *a, double *b, double *c,
 		*gamma = cell->gamma;
 		return 0;
 
-	case CELL_REP_CART:
+		case CELL_REP_CART:
 		/* Convert cartesian -> crystallographic */
 		*a = modulus(cell->ax, cell->ay, cell->az);
 		*b = modulus(cell->bx, cell->by, cell->bz);
@@ -448,7 +448,7 @@ int cell_get_parameters(UnitCell *cell, double *a, double *b, double *c,
 		                       cell->bx, cell->by, cell->bz);
 		return 0;
 
-	case CELL_REP_RECIP:
+		case CELL_REP_RECIP:
 		/* Convert reciprocal -> crystallographic.
                  * Start by converting reciprocal -> cartesian */
 		cell_invert(cell->axs, cell->ays, cell->azs,
@@ -480,21 +480,21 @@ int cell_get_cartesian(UnitCell *cell,
 
 	switch ( cell->rep ) {
 
-	case CELL_REP_CRYST:
+		case CELL_REP_CRYST:
 		/* Convert crystallographic -> cartesian. */
 		return cell_crystallographic_to_cartesian(cell,
 		                                          ax, ay, az,
 		                                          bx, by, bz,
 		                                          cx, cy, cz);
 
-	case CELL_REP_CART:
+		case CELL_REP_CART:
 		/* Direct response */
 		*ax = cell->ax;  *ay = cell->ay;  *az = cell->az;
 		*bx = cell->bx;  *by = cell->by;  *bz = cell->bz;
 		*cx = cell->cx;  *cy = cell->cy;  *cz = cell->cz;
 		return 0;
 
-	case CELL_REP_RECIP:
+		case CELL_REP_RECIP:
 		/* Convert reciprocal -> cartesian */
 		return cell_invert(cell->axs, cell->ays, cell->azs,
 		                   cell->bxs, cell->bys, cell->bzs,
@@ -518,7 +518,7 @@ int cell_get_reciprocal(UnitCell *cell,
 
 	switch ( cell->rep ) {
 
-	case CELL_REP_CRYST:
+		case CELL_REP_CRYST:
 		/* Convert crystallographic -> reciprocal */
 		r = cell_crystallographic_to_cartesian(cell,
 		                                       &ax, &ay, &az,
@@ -528,7 +528,7 @@ int cell_get_reciprocal(UnitCell *cell,
 		return cell_invert(ax, ay, az,bx, by, bz, cx, cy, cz,
 		                   asx, asy, asz, bsx, bsy, bsz, csx, csy, csz);
 
-	case CELL_REP_CART:
+		case CELL_REP_CART:
 		/* Convert cartesian -> reciprocal */
 		cell_invert(cell->ax, cell->ay, cell->az,
 		            cell->bx, cell->by, cell->bz,
@@ -536,7 +536,7 @@ int cell_get_reciprocal(UnitCell *cell,
 		            asx, asy, asz, bsx, bsy, bsz, csx, csy, csz);
 		return 0;
 
-	case CELL_REP_RECIP:
+		case CELL_REP_RECIP:
 		/* Direct response */
 		*asx = cell->axs;  *asy = cell->ays;  *asz = cell->azs;
 		*bsx = cell->bxs;  *bsy = cell->bys;  *bsz = cell->bzs;
@@ -569,12 +569,16 @@ const char *cell_get_spacegroup(UnitCell *cell)
 static const char *cell_rep(UnitCell *cell)
 {
 	switch ( cell->rep ) {
-	case CELL_REP_CRYST:
+
+		case CELL_REP_CRYST:
 		return "crystallographic, direct space";
-	case CELL_REP_CART:
+
+		case CELL_REP_CART:
 		return "cartesian, direct space";
-	case CELL_REP_RECIP:
+
+		case CELL_REP_RECIP:
 		return "cartesian, reciprocal space";
+
 	}
 
 	return "unknown";
diff --git a/libcrystfel/src/dirax.c b/libcrystfel/src/dirax.c
index 20f48bd3..43de6c6e 100644
--- a/libcrystfel/src/dirax.c
+++ b/libcrystfel/src/dirax.c
@@ -226,37 +226,37 @@ static void dirax_send_next(struct image *image, struct dirax_data *dirax)
 
 	switch ( dirax->step ) {
 
-	case 1 :
+		case 1 :
 		dirax_sendline("\\echo off\n", dirax);
 		break;
 
-	case 2 :
+		case 2 :
 		snprintf(tmp, 31, "read xfel-%i.drx\n", image->id);
 		dirax_sendline(tmp, dirax);
 		break;
 
-	case 3 :
+		case 3 :
 		dirax_sendline("dmax 1000\n", dirax);
 		break;
 
-	case 4 :
+		case 4 :
 		dirax_sendline("indexfit 2\n", dirax);
 		break;
 
-	case 5 :
+		case 5 :
 		dirax_sendline("levelfit 1000\n", dirax);
 		break;
 
-	case 6 :
+		case 6 :
 		dirax_sendline("go\n", dirax);
 		dirax->finished_ok = 1;
 		break;
 
-	case 7 :
+		case 7 :
 		dirax_sendline("acl\n", dirax);
 		break;
 
-	case 8 :
+		case 8 :
 		if ( dirax->best_acl_nh == 0 ) {
 			/* At this point, DirAx is presenting its ACL prompt
 			 * and waiting for a single number.  Use an extra
@@ -270,11 +270,11 @@ static void dirax_send_next(struct image *image, struct dirax_data *dirax)
 		dirax_sendline(tmp, dirax);
 		break;
 
-	case 9 :
+		case 9 :
 		dirax_sendline("cell\n", dirax);
 		break;
 
-	case 10 :
+		case 10 :
 		if ( dirax->n_acls_tried == MAX_DIRAX_CELL_CANDIDATES ) {
 			dirax_sendline("exit\n", dirax);
 		} else {
@@ -285,7 +285,7 @@ static void dirax_send_next(struct image *image, struct dirax_data *dirax)
 		}
 		break;
 
-	default:
+		default:
 		dirax_sendline("exit\n", dirax);
 		return;
 
diff --git a/libcrystfel/src/hdf5-file.c b/libcrystfel/src/hdf5-file.c
index 88d11bff..9924e665 100644
--- a/libcrystfel/src/hdf5-file.c
+++ b/libcrystfel/src/hdf5-file.c
@@ -719,6 +719,9 @@ char *hdfile_get_string_value(struct hdfile *f, const char *name)
 	hsize_t max_size;
 	hid_t type;
 	hid_t class;
+	herr_t r;
+	int buf;
+	char *tmp;
 
 	dh = H5Dopen2(f->fh, name, H5P_DEFAULT);
 	if ( dh < 0 ) return NULL;
@@ -761,11 +764,8 @@ char *hdfile_get_string_value(struct hdfile *f, const char *name)
 	}
 
 	switch ( class ) {
-	case H5T_FLOAT : {
 
-		herr_t r;
-		double buf;
-		char *tmp;
+		case H5T_FLOAT :
 
 		r = H5Dread(dh, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL,
 		            H5P_DEFAULT, &buf);
@@ -776,12 +776,8 @@ char *hdfile_get_string_value(struct hdfile *f, const char *name)
 
 		return tmp;
 
-	}
-	case H5T_INTEGER : {
+		case H5T_INTEGER :
 
-		herr_t r;
-		int buf;
-		char *tmp;
 
 		r = H5Dread(dh, H5T_NATIVE_INT, H5S_ALL, H5S_ALL,
 		            H5P_DEFAULT, &buf);
@@ -791,6 +787,7 @@ char *hdfile_get_string_value(struct hdfile *f, const char *name)
 		snprintf(tmp, 255, "%d", buf);
 
 		return tmp;
+
 	}
 	default : {
 		goto fail;
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index 3d0f164b..f4bc9d6c 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -83,18 +83,23 @@ IndexingPrivate **prepare_indexing(IndexingMethod *indm, UnitCell *cell,
 	for ( n=0; n<nm; n++ ) {
 
 		switch ( indm[n] ) {
-		case INDEXING_NONE :
+
+			case INDEXING_NONE :
 			ERROR("Tried to prepare INDEXING_NONE!\n");
 			break;
-		case INDEXING_DIRAX :
+
+			case INDEXING_DIRAX :
 			iprivs[n] = indexing_private(indm[n]);
 			break;
-		case INDEXING_MOSFLM :
+
+			case INDEXING_MOSFLM :
 			iprivs[n] = indexing_private(indm[n]);
 			break;
-		case INDEXING_REAX :
+
+			case INDEXING_REAX :
 			iprivs[n] = reax_prepare();
 			break;
+
 		}
 
 	}
@@ -113,18 +118,23 @@ void cleanup_indexing(IndexingPrivate **priv)
 	while ( priv[n] != NULL ) {
 
 		switch ( priv[n]->indm ) {
-		case INDEXING_NONE :
+
+			case INDEXING_NONE :
 			free(priv[n]);
 			break;
-		case INDEXING_DIRAX :
+
+			case INDEXING_DIRAX :
 			free(priv[n]);
 			break;
-		case INDEXING_MOSFLM :
+
+			case INDEXING_MOSFLM :
 			free(priv[n]);
 			break;
-		case INDEXING_REAX :
+
+			case INDEXING_REAX :
 			reax_cleanup(priv[n]);
 			break;
+
 		}
 
 		n++;
@@ -173,17 +183,22 @@ void index_pattern(struct image *image, UnitCell *cell, IndexingMethod *indm,
 
 		/* Index as appropriate */
 		switch ( indm[n] ) {
-		case INDEXING_NONE :
+
+			case INDEXING_NONE :
 			return;
-		case INDEXING_DIRAX :
+
+			case INDEXING_DIRAX :
 			run_dirax(image);
 			break;
-		case INDEXING_MOSFLM :
+
+			case INDEXING_MOSFLM :
 			run_mosflm(image, cell);
 			break;
-		case INDEXING_REAX :
+
+			case INDEXING_REAX :
 			reax_index(ipriv[n], image, cell);
 			break;
+
 		}
 		if ( image->ncells == 0 ) {
 			n++;
@@ -205,20 +220,25 @@ void index_pattern(struct image *image, UnitCell *cell, IndexingMethod *indm,
 
 			/* Match or reduce the cell as appropriate */
 			switch ( cellr ) {
-			case CELLR_NONE :
+
+				case CELLR_NONE :
 				new_cell = cell_new_from_cell(cand);
 				break;
-			case CELLR_REDUCE :
+
+				case CELLR_REDUCE :
 				new_cell = match_cell(cand, cell, verbose,
 				                      ltl, 1);
 				break;
-			case CELLR_COMPARE :
+
+				case CELLR_COMPARE :
 				new_cell = match_cell(cand, cell, verbose,
 				                      ltl, 0);
 				break;
-			case CELLR_COMPARE_AB :
+
+				case CELLR_COMPARE_AB :
 				new_cell = match_cell_ab(cand, cell);
 				break;
+
 			}
 
 			/* No cell?  Move on to the next candidate */
diff --git a/libcrystfel/src/mosflm.c b/libcrystfel/src/mosflm.c
index 3e29a4f8..410b779a 100644
--- a/libcrystfel/src/mosflm.c
+++ b/libcrystfel/src/mosflm.c
@@ -283,13 +283,13 @@ static void mosflm_send_next(struct image *image, struct mosflm_data *mosflm)
 
 	switch ( mosflm->step ) {
 
-	case 1 :
+		case 1 :
 		mosflm_sendline("DETECTOR ROTATION HORIZONTAL"
 		                " ANTICLOCKWISE ORIGIN LL FAST HORIZONTAL"
 		                " RECTANGULAR\n", mosflm);
 		break;
 
-	case 2 :
+		case 2 :
 		if ( mosflm->target_cell != NULL ) {
 			cell_get_parameters(mosflm->target_cell, &a, &b, &c,
 				            &alpha, &beta, &gamma);
@@ -303,7 +303,7 @@ static void mosflm_send_next(struct image *image, struct mosflm_data *mosflm)
 		}
 		break;
 
-	case 3 :
+		case 3 :
 		if ( mosflm->target_cell != NULL ) {
 			sg = cell_get_spacegroup(mosflm->target_cell);
 			/* Remove white space from space group */
@@ -321,31 +321,31 @@ static void mosflm_send_next(struct image *image, struct mosflm_data *mosflm)
 		}
 		break;
 
-	case 4 :
+		case 4 :
 		mosflm_sendline("DISTANCE 67.8\n", mosflm);
 		break;
 
-	case 5 :
+		case 5 :
 		mosflm_sendline("BEAM 0.0 0.0\n", mosflm);
 		break;
 
-	case 6 :
+		case 6 :
 		wavelength = image->lambda*1e10;
 		snprintf(tmp, 255, "WAVELENGTH %10.5f\n", wavelength);
 		mosflm_sendline(tmp, mosflm);
 		break;
 
-	case 7 :
+		case 7 :
 		snprintf(tmp, 255, "NEWMAT %s\n", mosflm->newmatfile);
 		mosflm_sendline(tmp, mosflm);
 		break;
 
-	case 8 :
+		case 8 :
 		snprintf(tmp, 255, "IMAGE %s phi 0 0\n", mosflm->imagefile);
 		mosflm_sendline(tmp, mosflm);
 		break;
 
-	case 9 :
+		case 9 :
 		snprintf(tmp, 255, "AUTOINDEX DPS FILE %s"
 		                   " IMAGE 1 MAXCELL 1000 REFINE\n",
 		         mosflm->sptfile);
@@ -357,7 +357,7 @@ static void mosflm_send_next(struct image *image, struct mosflm_data *mosflm)
 		mosflm_sendline(tmp, mosflm);
 		break;
 
-	case 10 :
+		case 10 :
 		mosflm_sendline("GO\n", mosflm);
 		mosflm->finished_ok = 1;
 		break;
diff --git a/libcrystfel/src/render.c b/libcrystfel/src/render.c
index c9e1f01e..5d0cf9e8 100644
--- a/libcrystfel/src/render.c
+++ b/libcrystfel/src/render.c
@@ -64,34 +64,35 @@ static void render_rgb(double val, double max,
 		s = 6;
 	}
 	switch ( s ) {
-		case 0 : {	/* Black to blue */
-			r = 0;  g = 0;  b = p;
-			break;
-		}
-		case 1 : {	/* Blue to pink */
-			r = p;  g = 0;  b = 1.0;
-			break;
-		}
-		case 2 : {	/* Pink to red */
-			r = 1.0;  g = 0;  b = (1.0-p)*1.0;
-			break;
-		}
-		case 3 : {	/* Red to Orange */
-			r = 1.0;  g = 0.5*p;  b = 0;
-			break;
-		}
-		case 4 : {	/* Orange to Yellow */
-			r = 1.0;  g = 0.5 + 0.5*p;  b = 0;
-			break;
-		}
-		case 5 : {	/* Yellow to White */
-			r = 1.0;  g = 1.0;  b = 1.0*p;
-			break;
-		}
-		case 6 : {	/* Pixel has hit the maximum value */
-			r = 1.0;  g = 1.0;  b = 1.0;
-			break;
-		}
+
+		case 0 :	/* Black to blue */
+		r = 0;  g = 0;  b = p;
+		break;
+
+		case 1 :	/* Blue to pink */
+		r = p;  g = 0;  b = 1.0;
+		break;
+
+		case 2 :	/* Pink to red */
+		r = 1.0;  g = 0;  b = (1.0-p)*1.0;
+		break;
+
+		case 3 :	/* Red to Orange */
+		r = 1.0;  g = 0.5*p;  b = 0;
+		break;
+
+		case 4 :	/* Orange to Yellow */
+		r = 1.0;  g = 0.5 + 0.5*p;  b = 0;
+		break;
+
+		case 5 :	/* Yellow to White */
+		r = 1.0;  g = 1.0;  b = 1.0*p;
+		break;
+
+		case 6 :	/* Pixel has hit the maximum value */
+		r = 1.0;  g = 1.0;  b = 1.0;
+		break;
+
 	}
 
 	*rp = r;
@@ -144,16 +145,20 @@ void render_scale(double val, double max, int scale,
                   double *rp, double *gp, double *bp)
 {
 	switch ( scale ) {
-	case SCALE_COLOUR :
+
+		case SCALE_COLOUR :
 		render_rgb(val, max, rp, gp, bp);
 		break;
-	case SCALE_MONO :
+
+		case SCALE_MONO :
 		render_mono(val, max, rp, gp, bp);
 		break;
-	case SCALE_INVMONO :
+
+		case SCALE_INVMONO :
 		render_invmono(val, max, rp, gp, bp);
 		break;
-	case SCALE_RATIO :
+
+		case SCALE_RATIO :
 		render_ratio(val, max, rp, gp, bp);
 		break;
 	}
diff --git a/libcrystfel/src/statistics.c b/libcrystfel/src/statistics.c
index 6ddf2850..56273fdb 100644
--- a/libcrystfel/src/statistics.c
+++ b/libcrystfel/src/statistics.c
@@ -407,22 +407,28 @@ static double calc_r(double scale, void *params)
 	struct r_params *rp = params;
 
 	switch ( rp->fom ) {
-	case R_1_ZERO :
+
+		case R_1_ZERO :
 		return internal_r1_negstozero(rp->list1, rp->list2, scale);
-	case R_1_IGNORE :
+
+		case R_1_IGNORE :
 		return internal_r1_ignorenegs(rp->list1, rp->list2, scale);
-	case R_2 :
+
+		case R_2 :
 		return internal_r2(rp->list1, rp->list2, scale);
 
-	case R_1_I :
+		case R_1_I :
 		return internal_r_i(rp->list1, rp->list2, scale);
 
-	case R_DIFF_ZERO :
+		case R_DIFF_ZERO :
 		return internal_rdiff_negstozero(rp->list1, rp->list2,scale);
-	case R_DIFF_IGNORE :
+
+		case R_DIFF_IGNORE :
 		return internal_rdiff_ignorenegs(rp->list1, rp->list2, scale);
-	case R_DIFF_INTENSITY :
+
+		case R_DIFF_INTENSITY :
 		return internal_rdiff_intensity(rp->list1, rp->list2, scale);
+
 	}
 
 	ERROR("No such FoM!\n");
@@ -457,17 +463,20 @@ static double r_minimised(RefList *list1, RefList *list2, double *scalep, int fo
 
 		/* Initial guess */
 		switch ( fom ) {
-		case R_1_ZERO :
-		case R_1_IGNORE :
-		case R_DIFF_ZERO :
-		case R_DIFF_IGNORE :
+
+			case R_1_ZERO :
+			case R_1_IGNORE :
+			case R_DIFF_ZERO :
+			case R_DIFF_IGNORE :
 			scale = stat_scale_sqrti(list1, list2);
 			break;
-		case R_2 :
-		case R_1_I :
-		case R_DIFF_INTENSITY :
+
+			case R_2 :
+			case R_1_I :
+			case R_DIFF_INTENSITY :
 			scale = stat_scale_intensity(list1, list2);
 			break;
+
 		}
 		//STATUS("Initial scale factor estimate: %5.2e\n", scale);