aboutsummaryrefslogtreecommitdiff
path: root/libcrystfel
diff options
context:
space:
mode:
Diffstat (limited to 'libcrystfel')
-rw-r--r--libcrystfel/src/cell.c28
-rw-r--r--libcrystfel/src/dirax.c22
-rw-r--r--libcrystfel/src/hdf5-file.c15
-rw-r--r--libcrystfel/src/index.c52
-rw-r--r--libcrystfel/src/mosflm.c20
-rw-r--r--libcrystfel/src/render.c69
-rw-r--r--libcrystfel/src/statistics.c37
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);
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-14 09:53:27 +0000