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Commit 8bb2c7e3 authored by Thomas White's avatar Thomas White
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Move stream handling functions to a separate module

parent 7b3e7208
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Makefile.am
View file @ 8bb2c7e3
......@@ -9,5 +9,6 @@ EXTRA_DIST = configure src/cell.h src/hdf5-file.h src/image.h \
src/povray.h src/index-priv.h src/geometry.h src/templates.h \
data/sfac/Ca.nff data/sfac/C.nff data/sfac/Fe.nff data/sfac/H.nff \
data/sfac/Mg.nff data/sfac/N.nff data/sfac/O.nff data/sfac/P.nff \
data/sfac/S.nff data/sfac/f0_WaasKirf.dat src/render_hkl.h
data/sfac/S.nff data/sfac/f0_WaasKirf.dat src/render_hkl.h \
src/stream.h
SUBDIRS = src data doc scripts
Makefile.in
View file @ 8bb2c7e3
......@@ -207,7 +207,8 @@ EXTRA_DIST = configure src/cell.h src/hdf5-file.h src/image.h \
src/povray.h src/index-priv.h src/geometry.h src/templates.h \
data/sfac/Ca.nff data/sfac/C.nff data/sfac/Fe.nff data/sfac/H.nff \
data/sfac/Mg.nff data/sfac/N.nff data/sfac/O.nff data/sfac/P.nff \
data/sfac/S.nff data/sfac/f0_WaasKirf.dat src/render_hkl.h
data/sfac/S.nff data/sfac/f0_WaasKirf.dat src/render_hkl.h \
src/stream.h
SUBDIRS = src data doc scripts
all: config.h
......
src/Makefile.am
View file @ 8bb2c7e3
......@@ -18,7 +18,7 @@ endif
pattern_sim_LDADD = @LIBS@
process_hkl_SOURCES = process_hkl.c sfac.c statistics.c cell.c utils.c \
reflections.c symmetry.c
reflections.c symmetry.c stream.c
process_hkl_LDADD = @LIBS@
indexamajig_SOURCES = indexamajig.c hdf5-file.c utils.c cell.c image.c \
......@@ -62,11 +62,11 @@ facetron_SOURCES = facetron.c cell.c hdf5-file.c utils.c detector.c peaks.c \
facetron_LDADD = @LIBS@
cubeit_SOURCES = cubeit.c cell.c hdf5-file.c utils.c detector.c diffraction.c \
sfac.c render.c filters.c image.c symmetry.c
sfac.c render.c filters.c image.c symmetry.c stream.c
cubeit_LDADD = @LIBS@
reintegrate_SOURCES = reintegrate.c cell.c hdf5-file.c utils.c detector.c \
peaks.c image.c diffraction.c sfac.c geometry.c
peaks.c image.c diffraction.c sfac.c geometry.c stream.c
reintegrate_LDADD = @LIBS@
INCLUDES = "-I$(top_srcdir)/data"
src/Makefile.in
View file @ 8bb2c7e3
......@@ -67,7 +67,8 @@ compare_hkl_DEPENDENCIES =
am_cubeit_OBJECTS = cubeit.$(OBJEXT) cell.$(OBJEXT) \
hdf5-file.$(OBJEXT) utils.$(OBJEXT) detector.$(OBJEXT) \
diffraction.$(OBJEXT) sfac.$(OBJEXT) render.$(OBJEXT) \
filters.$(OBJEXT) image.$(OBJEXT) symmetry.$(OBJEXT)
filters.$(OBJEXT) image.$(OBJEXT) symmetry.$(OBJEXT) \
stream.$(OBJEXT)
cubeit_OBJECTS = $(am_cubeit_OBJECTS)
cubeit_DEPENDENCIES =
am_facetron_OBJECTS = facetron.$(OBJEXT) cell.$(OBJEXT) \
......@@ -118,13 +119,13 @@ powder_plot_OBJECTS = $(am_powder_plot_OBJECTS)
powder_plot_DEPENDENCIES =
am_process_hkl_OBJECTS = process_hkl.$(OBJEXT) sfac.$(OBJEXT) \
statistics.$(OBJEXT) cell.$(OBJEXT) utils.$(OBJEXT) \
reflections.$(OBJEXT) symmetry.$(OBJEXT)
reflections.$(OBJEXT) symmetry.$(OBJEXT) stream.$(OBJEXT)
process_hkl_OBJECTS = $(am_process_hkl_OBJECTS)
process_hkl_DEPENDENCIES =
am_reintegrate_OBJECTS = reintegrate.$(OBJEXT) cell.$(OBJEXT) \
hdf5-file.$(OBJEXT) utils.$(OBJEXT) detector.$(OBJEXT) \
peaks.$(OBJEXT) image.$(OBJEXT) diffraction.$(OBJEXT) \
sfac.$(OBJEXT) geometry.$(OBJEXT)
sfac.$(OBJEXT) geometry.$(OBJEXT) stream.$(OBJEXT)
reintegrate_OBJECTS = $(am_reintegrate_OBJECTS)
reintegrate_DEPENDENCIES =
am_render_hkl_OBJECTS = render_hkl.$(OBJEXT) cell.$(OBJEXT) \
......@@ -265,7 +266,7 @@ pattern_sim_SOURCES = pattern_sim.c diffraction.c utils.c image.c \
$(am__append_2)
pattern_sim_LDADD = @LIBS@
process_hkl_SOURCES = process_hkl.c sfac.c statistics.c cell.c utils.c \
reflections.c symmetry.c
reflections.c symmetry.c stream.c
process_hkl_LDADD = @LIBS@
indexamajig_SOURCES = indexamajig.c hdf5-file.c utils.c cell.c image.c \
......@@ -301,11 +302,11 @@ facetron_SOURCES = facetron.c cell.c hdf5-file.c utils.c detector.c peaks.c \
facetron_LDADD = @LIBS@
cubeit_SOURCES = cubeit.c cell.c hdf5-file.c utils.c detector.c diffraction.c \
sfac.c render.c filters.c image.c symmetry.c
sfac.c render.c filters.c image.c symmetry.c stream.c
cubeit_LDADD = @LIBS@
reintegrate_SOURCES = reintegrate.c cell.c hdf5-file.c utils.c detector.c \
peaks.c image.c diffraction.c sfac.c geometry.c
peaks.c image.c diffraction.c sfac.c geometry.c stream.c
reintegrate_LDADD = @LIBS@
INCLUDES = "-I$(top_srcdir)/data"
......@@ -453,6 +454,7 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/render_hkl.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/sfac.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/statistics.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/stream.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/symmetry.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/templates.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/utils.Po@am__quote@
......
src/cubeit.c
View file @ 8bb2c7e3
......@@ -31,6 +31,7 @@
#include "diffraction.h"
#include "render.h"
#include "symmetry.h"
#include "stream.h"
#define MAX_THREADS (256)
......@@ -383,75 +384,6 @@ static void write_slice(const char *filename, double *vals, int z,
}
static UnitCell *read_orientation_matrix(FILE *fh)
{
float u, v, w;
struct rvec as, bs, cs;
UnitCell *cell;
char line[1024];
if ( fgets(line, 1023, fh) == NULL ) return NULL;
if ( sscanf(line, "astar = %f %f %f", &u, &v, &w) != 3 ) {
ERROR("Couldn't read a-star\n");
return NULL;
}
as.u = u*1e9; as.v = v*1e9; as.w = w*1e9;
if ( fgets(line, 1023, fh) == NULL ) return NULL;
if ( sscanf(line, "bstar = %f %f %f", &u, &v, &w) != 3 ) {
ERROR("Couldn't read b-star\n");
return NULL;
}
bs.u = u*1e9; bs.v = v*1e9; bs.w = w*1e9;
if ( fgets(line, 1023, fh) == NULL ) return NULL;
if ( sscanf(line, "cstar = %f %f %f", &u, &v, &w) != 3 ) {
ERROR("Couldn't read c-star\n");
return NULL;
}
cs.u = u*1e9; cs.v = v*1e9; cs.w = w*1e9;
cell = cell_new_from_axes(as, bs, cs);
return cell;
}
static int find_chunk(FILE *fh, UnitCell **cell, char **filename)
{
char line[1024];
char *rval = NULL;
do {
rval = fgets(line, 1023, fh);
if ( rval == NULL ) continue;
chomp(line);
if ( strncmp(line, "Reflections from indexing", 25) != 0 ) {
continue;
}
*filename = strdup(line+29);
/* Skip two lines (while checking for errors) */
rval = fgets(line, 1023, fh);
if ( rval == NULL ) continue;
rval = fgets(line, 1023, fh);
if ( rval == NULL ) continue;
*cell = read_orientation_matrix(fh);
if ( *cell == NULL ) {
STATUS("Got filename but no cell for %s\n", *filename);
continue;
}
return 0;
} while ( rval != NULL );
return 1;
}
static void add_to_mean(UnitCell *cell, double *ast, double *bst, double *cst,
double *alst, double *best, double *gast)
{
......
src/process_hkl.c
View file @ 8bb2c7e3
......@@ -26,6 +26,7 @@
#include "sfac.h"
#include "reflections.h"
#include "symmetry.h"
#include "stream.h"
/* Number of divisions for intensity histograms */
......@@ -535,26 +536,6 @@ static void merge_all(FILE *fh, double **pmodel, ReflItemList **pobserved,
}
static int count_patterns(FILE *fh)
{
char *rval;
int n_total_patterns = 0;
do {
char line[1024];
rval = fgets(line, 1023, fh);
if ( rval == NULL ) continue;
if ( (strncmp(line, "Reflections from indexing", 25) == 0)
|| (strncmp(line, "New pattern", 11) == 0) ) {
n_total_patterns++;
}
} while ( rval != NULL );
return n_total_patterns;
}
int main(int argc, char *argv[])
{
int c;
......
src/reintegrate.c
View file @ 8bb2c7e3
......@@ -28,6 +28,7 @@
#include "hdf5-file.h"
#include "symmetry.h"
#include "peaks.h"
#include "stream.h"
#define MAX_THREADS (256)
......@@ -147,75 +148,6 @@ static void *worker_thread(void *pargsv)
}
static UnitCell *read_orientation_matrix(FILE *fh)
{
float u, v, w;
struct rvec as, bs, cs;
UnitCell *cell;
char line[1024];
if ( fgets(line, 1023, fh) == NULL ) return NULL;
if ( sscanf(line, "astar = %f %f %f", &u, &v, &w) != 3 ) {
ERROR("Couldn't read a-star\n");
return NULL;
}
as.u = u*1e9; as.v = v*1e9; as.w = w*1e9;
if ( fgets(line, 1023, fh) == NULL ) return NULL;
if ( sscanf(line, "bstar = %f %f %f", &u, &v, &w) != 3 ) {
ERROR("Couldn't read b-star\n");
return NULL;
}
bs.u = u*1e9; bs.v = v*1e9; bs.w = w*1e9;
if ( fgets(line, 1023, fh) == NULL ) return NULL;
if ( sscanf(line, "cstar = %f %f %f", &u, &v, &w) != 3 ) {
ERROR("Couldn't read c-star\n");
return NULL;
}
cs.u = u*1e9; cs.v = v*1e9; cs.w = w*1e9;
cell = cell_new_from_axes(as, bs, cs);
return cell;
}
static int find_chunk(FILE *fh, UnitCell **cell, char **filename)
{
char line[1024];
char *rval = NULL;
do {
rval = fgets(line, 1023, fh);
if ( rval == NULL ) continue;
chomp(line);
if ( strncmp(line, "Reflections from indexing", 25) != 0 ) {
continue;
}
*filename = strdup(line+29);
/* Skip two lines (while checking for errors) */
rval = fgets(line, 1023, fh);
if ( rval == NULL ) continue;
rval = fgets(line, 1023, fh);
if ( rval == NULL ) continue;
*cell = read_orientation_matrix(fh);
if ( *cell == NULL ) {
STATUS("Got filename but no cell for %s\n", *filename);
continue;
}
return 0;
} while ( rval != NULL );
return 1;
}
static void integrate_all(int nthreads, struct detector *det, FILE *fh,
int config_basename, const char *prefix)
{
......
src/stream.c 0 → 100644
View file @ 8bb2c7e3
/*
* stream.c
*
* Indexed stream tools
*
* (c) 2006-2010 Thomas White <taw@physics.org>
*
* Part of CrystFEL - crystallography with a FEL
*
*/
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include "cell.h"
#include "utils.h"
int count_patterns(FILE *fh)
{
char *rval;
int n_total_patterns = 0;
do {
char line[1024];
rval = fgets(line, 1023, fh);
if ( rval == NULL ) continue;
if ( (strncmp(line, "Reflections from indexing", 25) == 0)
|| (strncmp(line, "New pattern", 11) == 0) ) {
n_total_patterns++;
}
} while ( rval != NULL );
return n_total_patterns;
}
static UnitCell *read_orientation_matrix(FILE *fh)
{
float u, v, w;
struct rvec as, bs, cs;
UnitCell *cell;
char line[1024];
if ( fgets(line, 1023, fh) == NULL ) return NULL;
if ( sscanf(line, "astar = %f %f %f", &u, &v, &w) != 3 ) {
ERROR("Couldn't read a-star\n");
return NULL;
}
as.u = u*1e9; as.v = v*1e9; as.w = w*1e9;
if ( fgets(line, 1023, fh) == NULL ) return NULL;
if ( sscanf(line, "bstar = %f %f %f", &u, &v, &w) != 3 ) {
ERROR("Couldn't read b-star\n");
return NULL;
}
bs.u = u*1e9; bs.v = v*1e9; bs.w = w*1e9;
if ( fgets(line, 1023, fh) == NULL ) return NULL;
if ( sscanf(line, "cstar = %f %f %f", &u, &v, &w) != 3 ) {
ERROR("Couldn't read c-star\n");
return NULL;
}
cs.u = u*1e9; cs.v = v*1e9; cs.w = w*1e9;
cell = cell_new_from_axes(as, bs, cs);
return cell;
}
int find_chunk(FILE *fh, UnitCell **cell, char **filename)
{
char line[1024];
char *rval = NULL;
do {
rval = fgets(line, 1023, fh);
if ( rval == NULL ) continue;
chomp(line);
if ( strncmp(line, "Reflections from indexing", 25) != 0 ) {
continue;
}
*filename = strdup(line+29);
/* Skip two lines (while checking for errors) */
rval = fgets(line, 1023, fh);
if ( rval == NULL ) continue;
rval = fgets(line, 1023, fh);
if ( rval == NULL ) continue;
*cell = read_orientation_matrix(fh);
if ( *cell == NULL ) {
STATUS("Got filename but no cell for %s\n", *filename);
continue;
}
return 0;
} while ( rval != NULL );
return 1;
}
src/stream.h 0 → 100644
View file @ 8bb2c7e3
/*
* stream.h
*
* Indexed stream tools
*
* (c) 2006-2010 Thomas White <taw@physics.org>
*
* Part of CrystFEL - crystallography with a FEL
*
*/
#ifndef STREAM_H
#define STREAM_H
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
extern int count_patterns(FILE *fh);
extern int find_chunk(FILE *fh, UnitCell **cell, char **filename);
#endif /* STREAM_H */
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