diff options
| -rw-r--r-- | doc/man/crystfel_geometry.5 | 6 | ||||
| -rw-r--r-- | libcrystfel/src/datatemplate.c | 7 | ||||
| -rw-r--r-- | libcrystfel/src/datatemplate_priv.h | 4 | ||||
| -rw-r--r-- | libcrystfel/src/image.c | 11 |
4 files changed, 25 insertions, 3 deletions
diff --git a/doc/man/crystfel_geometry.5 b/doc/man/crystfel_geometry.5 index eef98486..b8674f13 100644 --- a/doc/man/crystfel_geometry.5 +++ b/doc/man/crystfel_geometry.5 @@ -94,6 +94,12 @@ mask_good = 0x27 mask_bad = 0x00 .PD 0 +.IP "\fBdetector_shift_x = \fInnn \fB[m|mm]" +.IP "\fBdetector_shift_y = \fInnn \fB[m|mm]" +.PD +These specify that the entire detector should be shifted by this amount in the x and y directions. The units should be specified as \fBm\fR or \fBmm\fR. If units are not specified, the value will be taken as metres. \fInnn\fR can be a file metadata location (e.g. an HDF5 path). + +.PD 0 .IP "\fBpeak_list = \fIloc" .PD This gives the location of the peak list (for \fB--peaks=cxi\fR or \fB--peaks=hdf5\fR - see indexamajig(1)) in the data files. diff --git a/libcrystfel/src/datatemplate.c b/libcrystfel/src/datatemplate.c index 65da1a54..cc028025 100644 --- a/libcrystfel/src/datatemplate.c +++ b/libcrystfel/src/datatemplate.c @@ -756,6 +756,11 @@ static int parse_toplevel(DataTemplate *dt, return 1; } + } else if ( strcmp(key, "detector_shift_x") == 0 ) { + dt->shift_x_from = strdup(val); + + } else if ( strcmp(key, "detector_shift_y") == 0 ) { + dt->shift_y_from = strdup(val); } else if ( strcmp(key, "photon_energy") == 0 ) { return parse_photon_energy(val, @@ -872,6 +877,8 @@ DataTemplate *data_template_new_from_string(const char *string_in) dt->rigid_group_collections = NULL; dt->photon_energy_bandwidth = -1.0; dt->peak_list = NULL; + dt->shift_x_from = NULL; + dt->shift_y_from = NULL; /* The default defaults... */ defaults.orig_min_fs = -1; diff --git a/libcrystfel/src/datatemplate_priv.h b/libcrystfel/src/datatemplate_priv.h index 75492db5..e9ce3ccb 100644 --- a/libcrystfel/src/datatemplate_priv.h +++ b/libcrystfel/src/datatemplate_priv.h @@ -202,6 +202,10 @@ struct _datatemplate int n_rg_collections; char *peak_list; + + /* Shift of whole detector, in m */ + char * shift_x_from; + char * shift_y_from; }; #endif /* DATATEMPLATE_PRIV_H */ diff --git a/libcrystfel/src/image.c b/libcrystfel/src/image.c index 47cbfea7..b70b920f 100644 --- a/libcrystfel/src/image.c +++ b/libcrystfel/src/image.c @@ -340,7 +340,8 @@ static char *get_value_and_units(struct image *image, const char *from, } -static double get_length(struct image *image, const char *from) +static double get_length(struct image *image, const char *from, + double default_scale) { char *units; double value; @@ -348,7 +349,7 @@ static double get_length(struct image *image, const char *from) units = get_value_and_units(image, from, &value); if ( units == NULL ) { - scale = 1.0e-3; + scale = default_scale; } else { if ( strcmp(units, "mm") == 0 ) { scale = 1e-3; @@ -421,13 +422,17 @@ void create_detgeom(struct image *image, const DataTemplate *dtempl) /* NB cnx,cny are in pixels, cnz is in m */ detgeom->panels[i].cnx = dtempl->panels[i].cnx; detgeom->panels[i].cny = dtempl->panels[i].cny; - detgeom->panels[i].cnz = get_length(image, dtempl->panels[i].cnz_from); + detgeom->panels[i].cnz = get_length(image, dtempl->panels[i].cnz_from, 1e-3); /* Apply offset (in m) and then convert cnz from * m to pixels */ detgeom->panels[i].cnz += dtempl->panels[i].cnz_offset; detgeom->panels[i].cnz /= detgeom->panels[i].pixel_pitch; + /* Apply overall shift (already in m) */ + detgeom->panels[i].cnx += get_length(image, dtempl->shift_x_from, 1.0); + detgeom->panels[i].cny += get_length(image, dtempl->shift_y_from, 1.0); + detgeom->panels[i].max_adu = dtempl->panels[i].max_adu; switch ( dtempl->panels[i].adu_scale_unit ) { |