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Commit 4e0fe58f authored by Thomas White's avatar Thomas White
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Formatting

parent 781b32aa
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libcrystfel/src/cell.c
View file @ 4e0fe58f
......@@ -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";
......
libcrystfel/src/dirax.c
View file @ 4e0fe58f
......@@ -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;
......
libcrystfel/src/hdf5-file.c
View file @ 4e0fe58f
......@@ -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;
......
libcrystfel/src/index.c
View file @ 4e0fe58f
......@@ -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 */
......
libcrystfel/src/mosflm.c
View file @ 4e0fe58f
......@@ -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;
......
libcrystfel/src/render.c
View file @ 4e0fe58f
......@@ -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;
}
......
libcrystfel/src/statistics.c
View file @ 4e0fe58f
......@@ -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);
......
src/check_hkl.c
View file @ 4e0fe58f
......@@ -339,43 +339,44 @@ int main(int argc, char *argv[])
while ((c = getopt_long(argc, argv, "hy:p:", longopts, NULL)) != -1) {
switch (c) {
case 'h' :
case 'h' :
show_help(argv[0]);
return 0;
case 'y' :
case 'y' :
sym_str = strdup(optarg);
break;
case 'p' :
case 'p' :
pdb = strdup(optarg);
break;
case 0 :
case 0 :
break;
case 2 :
case 2 :
if ( sscanf(optarg, "%e", &rmin_fix) != 1 ) {
ERROR("Invalid value for --rmin\n");
return 1;
}
break;
case 3 :
case 3 :
if ( sscanf(optarg, "%e", &rmax_fix) != 1 ) {
ERROR("Invalid value for --rmax\n");
return 1;
}
break;
case 4 :
case 4 :
if ( sscanf(optarg, "%f", &sigma_cutoff) != 1 ) {
ERROR("Invalid value for --sigma-cutoff\n");
return 1;
}
break;
default :
default :
return 1;
}
......
src/cl-utils.c
View file @ 4e0fe58f
......@@ -46,28 +46,71 @@
const char *clError(cl_int err)
{
switch ( err ) {
case CL_SUCCESS : return "no error";
case CL_INVALID_PLATFORM : return "invalid platform";
case CL_INVALID_KERNEL : return "invalid kernel";
case CL_INVALID_ARG_INDEX : return "invalid argument index";
case CL_INVALID_ARG_VALUE : return "invalid argument value";
case CL_INVALID_MEM_OBJECT : return "invalid memory object";
case CL_INVALID_SAMPLER : return "invalid sampler";
case CL_INVALID_ARG_SIZE : return "invalid argument size";
case CL_INVALID_COMMAND_QUEUE : return "invalid command queue";
case CL_INVALID_CONTEXT : return "invalid context";
case CL_INVALID_VALUE : return "invalid value";
case CL_INVALID_EVENT_WAIT_LIST : return "invalid wait list";
case CL_MAP_FAILURE : return "map failure";
case CL_MEM_OBJECT_ALLOCATION_FAILURE : return "object allocation failure";
case CL_OUT_OF_HOST_MEMORY : return "out of host memory";
case CL_OUT_OF_RESOURCES : return "out of resources";
case CL_INVALID_KERNEL_NAME : return "invalid kernel name";
case CL_INVALID_KERNEL_ARGS : return "invalid kernel arguments";
case CL_INVALID_WORK_GROUP_SIZE : return "invalid work group size";
case CL_IMAGE_FORMAT_NOT_SUPPORTED : return "image format not supported";
case CL_INVALID_WORK_DIMENSION : return "invalid work dimension";
default :
case CL_SUCCESS :
return "no error";