diff options
| -rw-r--r-- | doc/man/crystfel_geometry.5 | 24 | ||||
| -rw-r--r-- | doc/man/partialator.1 | 2 | ||||
| -rw-r--r-- | src/compare_hkl.c | 1 | ||||
| -rw-r--r-- | src/dw-hdfsee.c | 2 | ||||
| -rw-r--r-- | src/dw-hdfsee.h | 2 | ||||
| -rw-r--r-- | src/get_hkl.c | 6 | ||||
| -rw-r--r-- | src/hdfsee.c | 8 |
7 files changed, 28 insertions, 17 deletions
diff --git a/doc/man/crystfel_geometry.5 b/doc/man/crystfel_geometry.5 index 216aec15..ecee06f5 100644 --- a/doc/man/crystfel_geometry.5 +++ b/doc/man/crystfel_geometry.5 @@ -104,6 +104,16 @@ panel0/peak_sep = 6.0 .br panel0/clen = /LCLS/detectorPosition +; The camera length offset (in metres) for this panel. +.br +; This number will be added to the camera length (\fBclen\fR). This can be +.br +; useful if the camera length is taken from the HDF5 file and you need to make +.br +; an adjustment, such as that from a calibration experiment. +.br +panel0/coffset = 0.0 + ; For this panel, the fast and slow scan directions correspond to the given .br ; directions in the lab coordinate system described above, measured in pixels. @@ -138,9 +148,7 @@ panel0/no_index = 0 .br ; a region will not be integrated nor indexed. Bad regions are specified in .br -; pixel units, but in the lab coordinate system (i.e. "y" points at the ceiling, -.br -; "z" is the beam direction and "x" completes the right-handed system). +; pixel units, but in the lab coordinate system (see above). .br badregionA/min_x = -20.0 .br @@ -156,9 +164,9 @@ badregionA/max_y = +100.0 .br ; give its path within each HDF5 file, and two bitmasks. The pixel is .br -; considered good if all of the bits which are set in "mask_good" are set, AND +; considered good if all of the bits which are set in \fBmask_good\fR are set, .br -; if none of the bits which are set in "mask_bad" are set. +; \fIand\fR if none of the bits which are set in \fBmask_bad\fR are set. .br mask = /processing/hitfinder/masks .br @@ -170,8 +178,10 @@ mask_bad = 0x00 .br peak_sep = 6.0 .br -; in which case the value will be used for all *subsequent* panels. - +; in which case the value will be used for all \fBsubsequent\fR panels appearing +.br +; in the file. +.br ; The maximum value, in ADU, before the pixel will be considered as bad. .br max_adu = 3500 diff --git a/doc/man/partialator.1 b/doc/man/partialator.1 index 6d675ae8..38292975 100644 --- a/doc/man/partialator.1 +++ b/doc/man/partialator.1 @@ -90,7 +90,7 @@ Run \fIn\fR analyses in parallel. .SH BUGS -This program is an \fIexperimental\fR in this version of CrystFEL. It is not +This program is \fIexperimental\fR in this version of CrystFEL. It is not yet considered ready for processing experimental data. Your pet kitten may explode if you attempt to solve a structure using intensities calculated by this program. diff --git a/src/compare_hkl.c b/src/compare_hkl.c index c3e7a547..f0484ede 100644 --- a/src/compare_hkl.c +++ b/src/compare_hkl.c @@ -464,6 +464,7 @@ static int get_bin(struct shells *s, Reflection *refl, UnitCell *cell) /* Allow for slight rounding errors */ if ( (bin == -1) && (d <= s->rmins[0]) ) bin = 0; + if ( (bin == -1) && (d >= s->rmaxs[s->nshells-1]) ) bin = 0; assert(bin != -1); return bin; diff --git a/src/dw-hdfsee.c b/src/dw-hdfsee.c index ee3b55f0..c4eabaf2 100644 --- a/src/dw-hdfsee.c +++ b/src/dw-hdfsee.c @@ -1778,7 +1778,7 @@ static gint displaywindow_press(GtkWidget *widget, GdkEventButton *event, DisplayWindow *displaywindow_open(const char *filename, const char *peaks, - int boost, int binning, int cmfilter, + double boost, int binning, int cmfilter, int noisefilter, int colscale, const char *element, const char *geometry, int show_rings, double *ring_radii, diff --git a/src/dw-hdfsee.h b/src/dw-hdfsee.h index 6d8c9782..84095a41 100644 --- a/src/dw-hdfsee.h +++ b/src/dw-hdfsee.h @@ -117,7 +117,7 @@ typedef struct { /* Open an image display window showing the given filename, or NULL */ extern DisplayWindow *displaywindow_open(const char *filename, - const char *peaks, int boost, + const char *peaks, double boost, int binning, int cmfilter, int noisefilter, int colscale, const char *element, diff --git a/src/get_hkl.c b/src/get_hkl.c index c879a51a..e69beb51 100644 --- a/src/get_hkl.c +++ b/src/get_hkl.c @@ -254,9 +254,9 @@ static RefList *expand_reflections(RefList *in, const SymOpList *initial, RefList *out; SymOpMask *m; - if ( !is_subgroup(target, initial) ) { - ERROR("%s is not a subgroup of %s!\n", symmetry_name(initial), - symmetry_name(target)); + if ( !is_subgroup(initial, target) ) { + ERROR("%s is not a subgroup of %s!\n", symmetry_name(target), + symmetry_name(initial)); return NULL; } diff --git a/src/hdfsee.c b/src/hdfsee.c index 894b8af9..36472e46 100644 --- a/src/hdfsee.c +++ b/src/hdfsee.c @@ -111,7 +111,7 @@ int main(int argc, char *argv[]) size_t i; int nfiles; char *peaks = NULL; - int boost = 1; + double boost = 1.0; int binning = 2; int config_cmfilter = 0; int config_noisefilter = 0; @@ -161,10 +161,10 @@ int main(int argc, char *argv[]) break; case 'i' : - boost = atoi(optarg); - if ( boost < 1 ) { + boost = atof(optarg); + if ( boost <= 0 ) { ERROR("Intensity boost must be a positive" - " integer.\n"); + " number.\n"); return 1; } break; |