Skip to content
GitLab
Commit 2c238039 authored by Thomas White's avatar Thomas White
Browse files

Move the "indexed reflection array" thing to where it can't do any harm

parent 3c896e87
Hide whitespace changes
Inline Side-by-side
Makefile.am
View file @ 2c238039
......@@ -35,12 +35,14 @@ LDADD += $(top_builddir)/libcrystfel/libcrystfel.la
src_partial_sim_SOURCES = src/partial_sim.c
src_pattern_sim_SOURCES = src/pattern_sim.c
src_pattern_sim_SOURCES = src/pattern_sim.c src/diffraction.c \
src/diffraction-gpu.c
if HAVE_OPENCL
TESTS += tests/gpu_sim_check
noinst_PROGRAMS += tests/gpu_sim_check
tests_gpu_sim_check_SOURCES = tests/gpu_sim_check.c
tests_gpu_sim_check_SOURCES = tests/gpu_sim_check.c src/diffraction.c \
src/diffraction-gpu.c
endif
src_process_hkl_SOURCES = src/process_hkl.c
......@@ -88,7 +90,7 @@ EXTRA_DIST += src/dw-hdfsee.h src/hdfsee.h src/render_hkl.h \
src/post-refinement.h src/hrs-scaling.h src/scaling-report.h
crystfeldir = $(datadir)/crystfel
crystfel_DATA = data/diffraction.cl data/defs.h data/hdfsee.ui
crystfel_DATA = data/diffraction.cl data/hdfsee.ui
EXTRA_DIST += $(crystfel_DATA)
......
Makefile.in
View file @ 2c238039
......@@ -142,7 +142,8 @@ src_partialator_OBJECTS = $(am_src_partialator_OBJECTS)
src_partialator_LDADD = $(LDADD)
src_partialator_DEPENDENCIES = $(top_builddir)/lib/libgnu.a \
$(top_builddir)/libcrystfel/libcrystfel.la
am_src_pattern_sim_OBJECTS = src/pattern_sim.$(OBJEXT)
am_src_pattern_sim_OBJECTS = src/pattern_sim.$(OBJEXT) \
src/diffraction.$(OBJEXT) src/diffraction-gpu.$(OBJEXT)
src_pattern_sim_OBJECTS = $(am_src_pattern_sim_OBJECTS)
src_pattern_sim_LDADD = $(LDADD)
src_pattern_sim_DEPENDENCIES = $(top_builddir)/lib/libgnu.a \
......@@ -163,9 +164,12 @@ src_render_hkl_OBJECTS = $(am_src_render_hkl_OBJECTS)
src_render_hkl_LDADD = $(LDADD)
src_render_hkl_DEPENDENCIES = $(top_builddir)/lib/libgnu.a \
$(top_builddir)/libcrystfel/libcrystfel.la
am__tests_gpu_sim_check_SOURCES_DIST = tests/gpu_sim_check.c
am__tests_gpu_sim_check_SOURCES_DIST = tests/gpu_sim_check.c \
src/diffraction.c src/diffraction-gpu.c
@HAVE_OPENCL_TRUE@am_tests_gpu_sim_check_OBJECTS = \
@HAVE_OPENCL_TRUE@ tests/gpu_sim_check.$(OBJEXT)
@HAVE_OPENCL_TRUE@ tests/gpu_sim_check.$(OBJEXT) \
@HAVE_OPENCL_TRUE@ src/diffraction.$(OBJEXT) \
@HAVE_OPENCL_TRUE@ src/diffraction-gpu.$(OBJEXT)
tests_gpu_sim_check_OBJECTS = $(am_tests_gpu_sim_check_OBJECTS)
tests_gpu_sim_check_LDADD = $(LDADD)
tests_gpu_sim_check_DEPENDENCIES = $(top_builddir)/lib/libgnu.a \
......@@ -567,8 +571,12 @@ AM_CPPFLAGS = -DDATADIR=\""$(datadir)"\" -I$(top_builddir)/lib \
LDADD = $(top_builddir)/lib/libgnu.a @IGNORE_UNUSED_LIBRARIES_CFLAGS@ \
$(top_builddir)/libcrystfel/libcrystfel.la
src_partial_sim_SOURCES = src/partial_sim.c
src_pattern_sim_SOURCES = src/pattern_sim.c
@HAVE_OPENCL_TRUE@tests_gpu_sim_check_SOURCES = tests/gpu_sim_check.c
src_pattern_sim_SOURCES = src/pattern_sim.c src/diffraction.c \
src/diffraction-gpu.c
@HAVE_OPENCL_TRUE@tests_gpu_sim_check_SOURCES = tests/gpu_sim_check.c src/diffraction.c \
@HAVE_OPENCL_TRUE@ src/diffraction-gpu.c
src_process_hkl_SOURCES = src/process_hkl.c
src_indexamajig_SOURCES = src/indexamajig.c
@BUILD_HDFSEE_TRUE@src_hdfsee_SOURCES = src/hdfsee.c src/dw-hdfsee.c
......@@ -588,7 +596,7 @@ tests_pr_gradient_check_SOURCES = tests/pr_gradient_check.c \
INCLUDES = -I$(top_srcdir)/libcrystfel/src -I$(top_srcdir)/data
crystfeldir = $(datadir)/crystfel
crystfel_DATA = data/diffraction.cl data/defs.h data/hdfsee.ui
crystfel_DATA = data/diffraction.cl data/hdfsee.ui
man_MANS = doc/man/indexamajig.1 doc/man/process_hkl.1 doc/man/pattern_sim.1 \
doc/man/crystfel_geometry.1 doc/man/powder_plot.1
......@@ -777,6 +785,10 @@ src/partialator$(EXEEXT): $(src_partialator_OBJECTS) $(src_partialator_DEPENDENC
$(AM_V_CCLD)$(LINK) $(src_partialator_OBJECTS) $(src_partialator_LDADD) $(LIBS)
src/pattern_sim.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
src/diffraction.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
src/diffraction-gpu.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
src/pattern_sim$(EXEEXT): $(src_pattern_sim_OBJECTS) $(src_pattern_sim_DEPENDENCIES) src/$(am__dirstamp)
@rm -f src/pattern_sim$(EXEEXT)
$(AM_V_CCLD)$(LINK) $(src_pattern_sim_OBJECTS) $(src_pattern_sim_LDADD) $(LIBS)
......@@ -832,6 +844,8 @@ mostlyclean-compile:
-rm -f src/calibrate_detector.$(OBJEXT)
-rm -f src/check_hkl.$(OBJEXT)
-rm -f src/compare_hkl.$(OBJEXT)
-rm -f src/diffraction-gpu.$(OBJEXT)
-rm -f src/diffraction.$(OBJEXT)
-rm -f src/dw-hdfsee.$(OBJEXT)
-rm -f src/get_hkl.$(OBJEXT)
-rm -f src/hdfsee.$(OBJEXT)
......@@ -857,6 +871,8 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/calibrate_detector.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/check_hkl.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/compare_hkl.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/diffraction-gpu.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/diffraction.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/dw-hdfsee.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/get_hkl.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/hdfsee.Po@am__quote@
......
data/defs.h deleted 100644 → 0
View file @ 3c896e87
/*
* defs.h
*
* Constant definitions which must be consistent throughout
*
* (c) 2006-2010 Thomas White <taw@physics.org>
*
* Part of CrystFEL - crystallography with a FEL
*
*/
#ifndef DEFS_H
#define DEFS_H
/* Maxmimum index to hold values up to (can be increased if necessary) */
#define INDMAX 140
/* Array size */
#define IDIM (INDMAX*2 +1)
#endif /* DEFS_H */
data/diffraction.cl
View file @ 2c238039
......@@ -10,7 +10,11 @@
*/
#include <defs.h>
/* Maxmimum index to hold values up to (can be increased if necessary)
* WARNING: Altering this value constitutes an ABI change, and means you must
* update src/pattern_sim.h then recompile and reinstall everything. */
#define INDMAX 140
#ifndef M_PI
#define M_PI ((float)(3.14159265))
#endif
......
libcrystfel/Makefile.am
View file @ 2c238039
lib_LTLIBRARIES = libcrystfel.la
libcrystfel_la_SOURCES = src/reflist.c src/utils.c src/cell.c src/detector.c \
src/thread-pool.c src/image.c src/hdf5-file.c \
src/beam-parameters.c src/geometry.c src/statistics.c \
src/symmetry.c src/stream.c src/peaks.c \
src/reflist-utils.c src/filters.c src/diffraction.c \
src/diffraction-gpu.c src/cl-utils.c src/render.c \
src/index.c src/dirax.c src/mosflm.c src/reax.c
src/reflist-utils.c src/filters.c src/cl-utils.c \
src/render.c src/index.c src/dirax.c src/mosflm.c \
src/reax.c
libcrystfel_la_includedir=$(includedir)/crystfel/
libcrystfel_la_include_HEADERS = src/beam-parameters.h src/diffraction-gpu.h \
src/hdf5-file.h src/reflist.h src/symmetry.h \
src/cell.h src/diffraction.h src/image.h \
libcrystfel_la_include_HEADERS = src/beam-parameters.h src/hdf5-file.h \
src/reflist.h src/symmetry.h src/cell.h \
src/reflist-utils.h src/thread-pool.h \
src/cl-utils.h src/filters.h src/list_tmp.h \
src/cl-utils.h src/filters.h \
src/statistics.h src/utils.h src/detector.h \
src/geometry.h src/peaks.h src/stream.h \
src/render.h src/index.h \
../data/defs.h
src/render.h src/index.h src/image.h
INCLUDES = "-I$(top_srcdir)/data"
AM_CPPFLAGS = -DDATADIR=\""$(datadir)"\" -I$(top_builddir)/lib
......
libcrystfel/Makefile.in
View file @ 2c238039
......@@ -88,9 +88,9 @@ am_libcrystfel_la_OBJECTS = src/reflist.lo src/utils.lo src/cell.lo \
src/detector.lo src/thread-pool.lo src/image.lo \
src/hdf5-file.lo src/beam-parameters.lo src/geometry.lo \
src/statistics.lo src/symmetry.lo src/stream.lo src/peaks.lo \
src/reflist-utils.lo src/filters.lo src/diffraction.lo \
src/diffraction-gpu.lo src/cl-utils.lo src/render.lo \
src/index.lo src/dirax.lo src/mosflm.lo src/reax.lo
src/reflist-utils.lo src/filters.lo src/cl-utils.lo \
src/render.lo src/index.lo src/dirax.lo src/mosflm.lo \
src/reax.lo
libcrystfel_la_OBJECTS = $(am_libcrystfel_la_OBJECTS)
AM_V_lt = $(am__v_lt_$(V))
am__v_lt_ = $(am__v_lt_$(AM_DEFAULT_VERBOSITY))
......@@ -351,20 +351,18 @@ libcrystfel_la_SOURCES = src/reflist.c src/utils.c src/cell.c src/detector.c \
src/thread-pool.c src/image.c src/hdf5-file.c \
src/beam-parameters.c src/geometry.c src/statistics.c \
src/symmetry.c src/stream.c src/peaks.c \
src/reflist-utils.c src/filters.c src/diffraction.c \
src/diffraction-gpu.c src/cl-utils.c src/render.c \
src/index.c src/dirax.c src/mosflm.c src/reax.c
src/reflist-utils.c src/filters.c src/cl-utils.c \
src/render.c src/index.c src/dirax.c src/mosflm.c \
src/reax.c
libcrystfel_la_includedir = $(includedir)/crystfel/
libcrystfel_la_include_HEADERS = src/beam-parameters.h src/diffraction-gpu.h \
src/hdf5-file.h src/reflist.h src/symmetry.h \
src/cell.h src/diffraction.h src/image.h \
libcrystfel_la_include_HEADERS = src/beam-parameters.h src/hdf5-file.h \
src/reflist.h src/symmetry.h src/cell.h \
src/reflist-utils.h src/thread-pool.h \
src/cl-utils.h src/filters.h src/list_tmp.h \
src/cl-utils.h src/filters.h \
src/statistics.h src/utils.h src/detector.h \
src/geometry.h src/peaks.h src/stream.h \
src/render.h src/index.h \
../data/defs.h
src/render.h src/index.h src/image.h
INCLUDES = "-I$(top_srcdir)/data"
AM_CPPFLAGS = -DDATADIR=\""$(datadir)"\" -I$(top_builddir)/lib \
......@@ -457,9 +455,6 @@ src/peaks.lo: src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
src/reflist-utils.lo: src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
src/filters.lo: src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
src/diffraction.lo: src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
src/diffraction-gpu.lo: src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
src/cl-utils.lo: src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
src/render.lo: src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
src/index.lo: src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
......@@ -479,10 +474,6 @@ mostlyclean-compile:
-rm -f src/cl-utils.lo
-rm -f src/detector.$(OBJEXT)
-rm -f src/detector.lo
-rm -f src/diffraction-gpu.$(OBJEXT)
-rm -f src/diffraction-gpu.lo
-rm -f src/diffraction.$(OBJEXT)
-rm -f src/diffraction.lo
-rm -f src/dirax.$(OBJEXT)
-rm -f src/dirax.lo
-rm -f src/filters.$(OBJEXT)
......@@ -525,8 +516,6 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/cell.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/cl-utils.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/detector.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/diffraction-gpu.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/diffraction.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/dirax.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/filters.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/geometry.Plo@am__quote@
......
libcrystfel/src/peaks.c
View file @ 2c238039
......@@ -29,7 +29,6 @@
#include "peaks.h"
#include "detector.h"
#include "filters.h"
#include "diffraction.h"
#include "reflist-utils.h"
#include "beam-parameters.h"
......
libcrystfel/src/reflist-utils.c
View file @ 2c238039
......@@ -34,76 +34,6 @@
**/
double *intensities_from_list(RefList *list)
{
Reflection *refl;
RefListIterator *iter;
double *out = new_list_intensity();
for ( refl = first_refl(list, &iter);
refl != NULL;
refl = next_refl(refl, iter) ) {
signed int h, k, l;
double intensity = get_intensity(refl);
get_indices(refl, &h, &k, &l);
set_intensity(out, h, k, l, intensity);
}
return out;
}
double *phases_from_list(RefList *list)
{
Reflection *refl;
RefListIterator *iter;
double *out = new_list_phase();
for ( refl = first_refl(list, &iter);
refl != NULL;
refl = next_refl(refl, iter) ) {
signed int h, k, l;
double phase = get_phase(refl, NULL);
get_indices(refl, &h, &k, &l);
set_phase(out, h, k, l, phase);
}
return out;
}
unsigned char *flags_from_list(RefList *list)
{
Reflection *refl;
RefListIterator *iter;
unsigned char *out = new_list_flag();
for ( refl = first_refl(list, &iter);
refl != NULL;
refl = next_refl(refl, iter) ) {
signed int h, k, l;
get_indices(refl, &h, &k, &l);
set_flag(out, h, k, l, 1);
}
return out;
}
int check_list_symmetry(RefList *list, const SymOpList *sym)
{
Reflection *refl;
......
libcrystfel/src/reflist-utils.h
View file @ 2c238039
......@@ -33,10 +33,6 @@ extern RefList *read_reflections_from_file(FILE *fh);
extern RefList *read_reflections(const char *filename);
extern double *intensities_from_list(RefList *list);
extern double *phases_from_list(RefList *list);
extern unsigned char *flags_from_list(RefList *list);
extern int check_list_symmetry(RefList *list, const SymOpList *sym);
extern int find_equiv_in_list(RefList *list, signed int h, signed int k,
signed int l, const SymOpList *sym, signed int *hu,
......
libcrystfel/src/utils.h
View file @ 2c238039
......@@ -175,32 +175,6 @@ static inline int within_tolerance(double a, double b, double percent)
#define UNUSED __attribute__((unused))
/* -------------------- Indexed lists for specified types ------------------- */
#include "defs.h"
#define LIST_SIZE (IDIM*IDIM*IDIM)
/* Create functions for storing reflection intensities indexed as h,k,l */
#define LABEL(x) x##_intensity
#define TYPE double
#include "list_tmp.h"
/* CAs above, but for phase values */
#define LABEL(x) x##_phase
#define TYPE double
#include "list_tmp.h"
/* As above, but for (unsigned) integer counts */
#define LABEL(x) x##_count
#define TYPE unsigned int
#include "list_tmp.h"
/* As above, but for simple flags */
#define LABEL(x) x##_flag
#define TYPE unsigned char
#include "list_tmp.h"
/* ------------------------------ Message macros ---------------------------- */
......
libcrystfel/src/diffraction-gpu.c → src/diffraction-gpu.c
View file @ 2c238039
......@@ -31,6 +31,7 @@
#include "diffraction.h"
#include "cl-utils.h"
#include "beam-parameters.h"
#include "pattern_sim.h"
#define SAMPLING (4)
......
libcrystfel/src/diffraction.c → src/diffraction.c
View file @ 2c238039
......@@ -24,6 +24,7 @@
#include "diffraction.h"
#include "beam-parameters.h"
#include "symmetry.h"
#include "pattern_sim.h"
#define SAMPLING (4)
......
src/pattern_sim.c
View file @ 2c238039
......@@ -33,6 +33,7 @@
#include "symmetry.h"
#include "reflist.h"
#include "reflist-utils.h"
#include "pattern_sim.h"
static void show_help(const char *s)
......@@ -141,6 +142,76 @@ static void show_details()
}
static double *intensities_from_list(RefList *list)
{
Reflection *refl;
RefListIterator *iter;
double *out = new_list_intensity();
for ( refl = first_refl(list, &iter);
refl != NULL;
refl = next_refl(refl, iter) ) {
signed int h, k, l;
double intensity = get_intensity(refl);
get_indices(refl, &h, &k, &l);
set_intensity(out, h, k, l, intensity);
}
return out;
}
static double *phases_from_list(RefList *list)
{
Reflection *refl;
RefListIterator *iter;
double *out = new_list_phase();
for ( refl = first_refl(list, &iter);
refl != NULL;
refl = next_refl(refl, iter) ) {
signed int h, k, l;
double phase = get_phase(refl, NULL);
get_indices(refl, &h, &k, &l);
set_phase(out, h, k, l, phase);
}
return out;
}
static unsigned char *flags_from_list(RefList *list)
{
Reflection *refl;
RefListIterator *iter;
unsigned char *out = new_list_flag();
for ( refl = first_refl(list, &iter);
refl != NULL;
refl = next_refl(refl, iter) ) {
signed int h, k, l;
get_indices(refl, &h, &k, &l);
set_flag(out, h, k, l, 1);
}
return out;
}
static struct quaternion read_quaternion()
{
do {
......
src/pattern_sim.h 0 → 100644
View file @ 2c238039
/*
* pattern_sim.h
*
* Simulate diffraction patterns from small crystals
*
* (c) 2006-2011 Thomas White <taw@physics.org>
*
* Part of CrystFEL - crystallography with a FEL
*
*/
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#ifndef PATTERN_SIM_H
#define PATTERN_SIM_H
/* Maxmimum index to hold values up to (can be increased if necessary)
* WARNING: Altering this value constitutes an ABI change, and means you must
* update data/diffraction.cl then recompile and reinstall everything. */
#define INDMAX 140
/* Array size */
#define IDIM (INDMAX*2 +1)
#define LIST_SIZE (IDIM*IDIM*IDIM)
/* Create functions for storing reflection intensities indexed as h,k,l */
#define LABEL(x) x##_intensity
#define TYPE double
#include "list_tmp.h"
/* CAs above, but for phase values */
#define LABEL(x) x##_phase
#define TYPE double
#include "list_tmp.h"
/* As above, but for (unsigned) integer counts */
#define LABEL(x) x##_count
#define TYPE unsigned int
#include "list_tmp.h"
/* As above, but for simple flags */
#define LABEL(x) x##_flag
#define TYPE unsigned char
#include "list_tmp.h"
#endif /* PATTERN_SIM_H */
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment

imprint | privacy | Conditions of Use