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-rw-r--r--doc/man/partialator.114
-rw-r--r--src/partialator.c59
2 files changed, 12 insertions, 61 deletions
diff --git a/doc/man/partialator.1 b/doc/man/partialator.1
index c209b97d..12b4de10 100644
--- a/doc/man/partialator.1
+++ b/doc/man/partialator.1
@@ -14,8 +14,6 @@ partialator \- scaling and post-refinement of partial reflections
.B partialator
\fB-i\fR \fIinput.stream\fR
\fB-o\fR \fIoutput.hkl\fR
-\fB-g\fR \fIdetector.geom\fR
-\fB-b\fR \fIbeamline.beam\fR
\fB-y\fR \fIpointgroup\fR
[\fBoptions\fR] \fB...\fR
.PP
@@ -54,18 +52,6 @@ Give the name of the output file. The default is
Merge according to symmetry \fIpointgroup\fR.
.PD 0
-.IP "\fB-g\fR \fIfilename\fR"
-.IP \fB--geometry=\fR\fIfilename\fR
-.PD
-Read the detector geometry description from \fIfilename\fR. See \fBman crystfel_geometry\fR for more information.
-
-.PD 0
-.IP "\fB-b\fR \fIfilename\fR"
-.IP \fB--beam=\fR\fIfilename\fR
-.PD
-Read the beam description from \fIfilename\fR. See \fBman crystfel_geometry\fR for more information.
-
-.PD 0
.IP "\fB-n\fR \fIn\fR"
.IP \fB--iterations=\fR\fIn\fR
.PD
diff --git a/src/partialator.c b/src/partialator.c
index cc65b490..304c2f22 100644
--- a/src/partialator.c
+++ b/src/partialator.c
@@ -3,7 +3,7 @@
*
* Scaling and post refinement for coherent nanocrystallography
*
- * Copyright © 2012-2013 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2012-2014 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
*
* Authors:
@@ -42,14 +42,12 @@
#include <gsl/gsl_errno.h>
#include <image.h>
-#include <detector.h>
#include <utils.h>
#include <symmetry.h>
#include <stream.h>
#include <geometry.h>
#include <peaks.h>
#include <thread-pool.h>
-#include <beam-parameters.h>
#include <reflist.h>
#include <reflist-utils.h>
@@ -68,8 +66,6 @@ static void show_help(const char *s)
"\n"
" -i, --input=<filename> Specify the name of the input 'stream'.\n"
" -o, --output=<filename> Output filename. Default: partialator.hkl.\n"
-" -g. --geometry=<file> Get detector geometry from file.\n"
-" -b, --beam=<file> Get beam parameters from file.\n"
" -y, --symmetry=<sym> Merge according to symmetry <sym>.\n"
" -n, --iterations=<n> Run <n> cycles of scaling and post-refinement.\n"
" --no-scale Fix all the scaling factors at unity.\n"
@@ -140,7 +136,6 @@ static void done_image(void *vqargs, void *task)
static void refine_all(Crystal **crystals, int n_crystals,
- struct detector *det,
RefList *full, int nthreads, PartialityModel pmodel,
struct srdata *srdata)
{
@@ -329,15 +324,12 @@ int main(int argc, char *argv[])
int c;
char *infile = NULL;
char *outfile = NULL;
- char *geomfile = NULL;
char *sym_str = NULL;
SymOpList *sym;
int nthreads = 1;
- struct detector *det;
int i;
struct image *images;
int n_iter = 10;
- struct beam_params *beam = NULL;
RefList *full;
int n_images = 0;
int n_crystals = 0;
@@ -363,8 +355,6 @@ int main(int argc, char *argv[])
{"help", 0, NULL, 'h'},
{"input", 1, NULL, 'i'},
{"output", 1, NULL, 'o'},
- {"geometry", 1, NULL, 'g'},
- {"beam", 1, NULL, 'b'},
{"symmetry", 1, NULL, 'y'},
{"iterations", 1, NULL, 'n'},
{"reference", 1, NULL, 'r'},
@@ -402,10 +392,6 @@ int main(int argc, char *argv[])
infile = strdup(optarg);
break;
- case 'g' :
- geomfile = strdup(optarg);
- break;
-
case 'j' :
nthreads = atoi(optarg);
break;
@@ -426,15 +412,6 @@ int main(int argc, char *argv[])
pmodel_str = strdup(optarg);
break;
- case 'b' :
- beam = get_beam_parameters(optarg);
- if ( beam == NULL ) {
- ERROR("Failed to load beam parameters"
- " from '%s'\n", optarg);
- return 1;
- }
- break;
-
case 'r' :
reference_file = strdup(optarg);
break;
@@ -486,19 +463,6 @@ int main(int argc, char *argv[])
sym = get_pointgroup(sym_str);
free(sym_str);
- /* Get detector geometry */
- det = get_detector_geometry(geomfile);
- if ( det == NULL ) {
- ERROR("Failed to read detector geometry from '%s'\n", geomfile);
- return 1;
- }
- free(geomfile);
-
- if ( beam == NULL ) {
- ERROR("You must provide a beam parameters file.\n");
- return 1;
- }
-
if ( pmodel_str != NULL ) {
if ( strcmp(pmodel_str, "sphere") == 0 ) {
pmodel = PMODEL_SPHERE;
@@ -549,7 +513,9 @@ int main(int argc, char *argv[])
images = images_new;
cur = &images[n_images];
- cur->det = det;
+ cur->div = NAN;
+ cur->bw = NAN;
+ cur->det = NULL;
if ( read_chunk(st, cur) != 0 ) {
break;
}
@@ -557,14 +523,17 @@ int main(int argc, char *argv[])
/* Won't be needing this, if it exists */
image_feature_list_free(cur->features);
cur->features = NULL;
- cur->div = beam->divergence;
- cur->bw = beam->bandwidth;
- cur->width = det->max_fs;
- cur->height = det->max_ss;
+ cur->width = 0;
+ cur->height = 0;
cur->data = NULL;
cur->flags = NULL;
cur->beam = NULL;
+ if ( isnan(cur->div) || isnan(cur->bw) ) {
+ ERROR("Chunk doesn't contain beam parameters.\n");
+ return 1;
+ }
+
n_images++;
for ( i=0; i<cur->n_crystals; i++ ) {
@@ -589,8 +558,6 @@ int main(int argc, char *argv[])
/* Fill in initial estimates of stuff */
crystal_set_osf(cr, 1.0);
- crystal_set_profile_radius(cr, beam->profile_radius);
- crystal_set_mosaicity(cr, 0.0);
crystal_set_user_flag(cr, 0);
/* This is the raw list of reflections */
@@ -679,7 +646,7 @@ int main(int argc, char *argv[])
comp = (reference == NULL) ? full : reference;
select_reflections_for_refinement(crystals, n_crystals,
comp, have_reference);
- refine_all(crystals, n_crystals, det, comp, nthreads, pmodel,
+ refine_all(crystals, n_crystals, comp, nthreads, pmodel,
&srdata);
nobs = 0;
@@ -746,8 +713,6 @@ int main(int argc, char *argv[])
reflist_free(full);
free(sym);
free(outfile);
- free_detector_geometry(det);
- free(beam);
free(crystals);
if ( reference != NULL ) {
reflist_free(reference);
generated by cgit v1.2.3 (git 2.25.1) at 2024-08-26 14:22:43 +0000