aboutsummaryrefslogtreecommitdiff
path: root/src
diff options
context:
space:
mode:
authorThomas White <taw@physics.org>2021-02-12 13:28:18 +0100
committerThomas White <taw@physics.org>2021-02-12 17:27:44 +0100
commit1f896954b41f6379bc933b591164487445cde624 (patch)
tree82ee6c04aa8a8b973273585856d69bcf9703ca8a /src
parent5ceed23ffdae85bb42b4d2f01a7a02485dd8c954 (diff)
GUI: Implement basic MTZ export
Diffstat (limited to 'src')
-rw-r--r--src/gui_export.c175
1 files changed, 159 insertions, 16 deletions
diff --git a/src/gui_export.c b/src/gui_export.c
index 4f300594..95e3d56b 100644
--- a/src/gui_export.c
+++ b/src/gui_export.c
@@ -36,11 +36,18 @@
#include <gtk/gtk.h>
#include <assert.h>
+#ifdef HAVE_LIBCCP4
+#include <ccp4/cmtzlib.h>
+#include <ccp4/csymlib.h>
+#include <ccp4/ccp4_parser.h>
+#endif
+
#include <utils.h>
#include <reflist-utils.h>
#include <cell-utils.h>
#include <symmetry.h>
+#include "version.h"
#include "gui_project.h"
#include "crystfel_gui.h"
#include "gtk-util-routines.h"
@@ -58,22 +65,6 @@ struct export_window
};
-static int export_to_mtz(struct gui_merge_result *result,
- const char *filename, UnitCell *cell,
- double min_res, double max_res)
-{
- return 1;
-}
-
-
-static int export_to_mtz_bij(struct gui_merge_result *result,
- const char *filename, UnitCell *cell,
- double min_res, double max_res)
-{
- return 1;
-}
-
-
struct point_group_conversion
{
char centering;
@@ -139,6 +130,23 @@ static int space_group_for_xds(const char *sym_str, char cen)
}
+static const char *space_group_for_mtz(const char *sym_str, char cen)
+{
+ int i = 0;
+ do {
+ if ( (pg_conversions[i].centering == cen)
+ && (strcmp(sym_str, pg_conversions[i].crystfel) == 0) )
+ {
+ return pg_conversions[i].ccp4;
+ }
+ i++;
+ } while (pg_conversions[i].centering != '*');
+
+ ERROR("Couldn't derive CCP4 representation of symmetry.\n");
+ return NULL;
+}
+
+
static int export_to_xds(struct gui_merge_result *result,
const char *filename, UnitCell *cell,
double min_res, double max_res)
@@ -210,6 +218,141 @@ static int export_to_xds(struct gui_merge_result *result,
}
+#ifdef HAVE_LIBCCP4
+static int add_mtz_symmetry_header(MTZ *mtz, const char *spg_name)
+{
+ CCP4SPG *spg;
+ float rsymx[192][4][4];
+ char ltypex[2];
+ int i;
+
+ spg = ccp4spg_load_by_spgname(spg_name);
+ if ( spg == NULL ) {
+ ERROR("Couldn't look up CCP4 space group '%s'\n", spg_name);
+ return 1;
+ }
+
+ for ( i=0; i<spg->nsymop; i++ ) {
+ rotandtrn_to_mat4(rsymx[i], spg->symop[i]);
+ }
+ ltypex[0] = spg->symbol_old[0];
+ ltypex[1] = '\0';
+
+ ccp4_lwsymm(mtz, spg->nsymop, spg->nsymop_prim,
+ rsymx, ltypex, spg->spg_ccp4_num, spg->symbol_old,
+ spg->point_group);
+
+ ccp4spg_free(&spg);
+
+ return 0;
+}
+#endif
+
+
+static int export_to_mtz(struct gui_merge_result *result,
+ const char *filename, UnitCell *cell,
+ double min_res, double max_res)
+{
+#ifdef HAVE_LIBCCP4
+ MTZ *mtz;
+ MTZXTAL *cr;
+ MTZSET *ds;
+ MTZCOL *columns[5];
+ double a, b, c, al, be, ga;
+ int r;
+ char tmp[128];
+ float cellp[6];
+ int refl_i;
+ RefList *reflist;
+ Reflection *refl;
+ RefListIterator *iter;
+ char *sym_str = NULL;
+ const char *spg;
+
+ reflist = read_reflections_2(result->hkl, &sym_str);
+ if ( reflist == NULL ) return 1;
+ if ( sym_str == NULL ) return 1;
+
+ spg = space_group_for_mtz(sym_str, cell_get_centering(cell));
+ if ( spg == NULL ) {
+ reflist_free(reflist);
+ return 1;
+ }
+
+ mtz = MtzMalloc(0, 0);
+
+ snprintf(tmp, 128, "Data exported via CrystFEL GUI, version %s",
+ crystfel_version_string());
+ ccp4_lwtitl(mtz, tmp, 0);
+
+ mtz->refs_in_memory = 0;
+ mtz->fileout = MtzOpenForWrite(filename);
+
+ if ( add_mtz_symmetry_header(mtz, spg) ) {
+ return 1;
+ }
+
+ cell_get_parameters(cell, &a, &b, &c, &al, &be, &ga);
+ cellp[0] = a*1e10;
+ cellp[1] = b*1e10;
+ cellp[2] = c*1e10;
+ cellp[3] = rad2deg(al);
+ cellp[4] = rad2deg(be);
+ cellp[5] = rad2deg(ga);
+
+ /* FIXME: Proposed labelling:
+ * title = as above
+ * project = basename of folder containing crystfel.project
+ * crystal = name of indexing results run
+ * dataset = name of merge results run */
+ cr = MtzAddXtal(mtz, "Crystal_name", "Project_name", cellp);
+ ds = MtzAddDataset(mtz, cr, result->name, 0.0);
+ columns[0] = MtzAddColumn(mtz, ds, "H", "H");
+ columns[1] = MtzAddColumn(mtz, ds, "K", "H");
+ columns[2] = MtzAddColumn(mtz, ds, "L", "H");
+ columns[3] = MtzAddColumn(mtz, ds, "IOBS", "J");
+ columns[4] = MtzAddColumn(mtz, ds, "SIGIOBS", "Q");
+
+ refl_i = 1;
+ for ( refl = first_refl(reflist, &iter);
+ refl != NULL;
+ refl = next_refl(refl, iter) )
+ {
+ signed int h, k, l;
+ double one_over_d;
+
+ get_indices(refl, &h, &k, &l);
+
+ one_over_d = 2.0*resolution(cell, h, k, l);
+ if ( (one_over_d > min_res) && (one_over_d < max_res) ) {
+ float refldata[5];
+ refldata[0] = h;
+ refldata[1] = k;
+ refldata[2] = l;
+ refldata[3] = get_intensity(refl);
+ refldata[4] = get_esd_intensity(refl);
+ ccp4_lwrefl(mtz, refldata, columns, 5, refl_i++);
+ }
+ }
+
+ r = MtzPut(mtz, " ");
+ MtzFree(mtz);
+ reflist_free(reflist);
+ return 1-r; /* Yes, really. MtzPut return values are backwards */
+#else
+ return 1;
+#endif
+}
+
+
+static int export_to_mtz_bij(struct gui_merge_result *result,
+ const char *filename, UnitCell *cell,
+ double min_res, double max_res)
+{
+ return 1;
+}
+
+
static int export_data(struct export_window *win, char *filename)
{
gchar *cell_filename;