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Commit 4a235243 authored by Thomas White's avatar Thomas White
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facetron: Add options

parent fcee934f
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src/facetron.c
View file @ 4a235243
......@@ -39,7 +39,10 @@ static void show_help(const char *s)
"\n"
" -i, --input=<filename> Specify the name of the input stream.\n"
" Can be '-' for stdin.\n"
" -g. --geometry=<file> Get detector geometry from file.\n"
" -g. --geometry=<file> Get detector geometry from file.\n"
" -x, --prefix=<p> Prefix filenames from input file with <p>.\n"
" --basename Remove the directory parts of the filenames.\n"
" --no-check-prefix Don't attempt to correct the --prefix.\n"
);
}
......@@ -113,122 +116,28 @@ static int find_chunk(FILE *fh, UnitCell **cell, char **filename)
}
static void get_trial_cell(UnitCell *out, UnitCell *in, int i, double step)
static char *twiddle_filename(char *filename, int config_basename,
const char *prefix)
{
double asx, asy, asz;
double bsx, bsy, bsz;
double csx, csy, csz;
cell_get_reciprocal(in, &asx, &asy, &asz, &bsx, &bsy, &bsz,
&csx, &csy, &csz);
switch ( i ) {
case 0 : asx += step; break;
case 1 : asx -= step; break;
case 2 : asy += step; break;
case 3 : asy -= step; break;
case 4 : asz += step; break;
case 5 : asz -= step; break;
case 6 : bsx += step; break;
case 7 : bsx -= step; break;
case 8 : bsy += step; break;
case 9 : bsy -= step; break;
case 10 : bsz += step; break;
case 11 : bsz -= step; break;
case 12 : csx += step; break;
case 13 : csx -= step; break;
case 14 : csy += step; break;
case 15 : csy -= step; break;
case 16 : csz += step; break;
case 17 : csz -= step; break;
default : break;
char *f3;
size_t len;
if ( config_basename ) {
char *f2;
/* Happy with either the GNU or non-GNU versions of basename()
* here. Because _GNU_SOURCE is defined in configure.ac, we
* should have the GNU version. */
f2 = strdup(basename(filename));
free(filename);
filename = f2;
}
cell_set_reciprocal(out, asx, asy, asz, bsx, bsy, bsz, csx, csy, csz);
}
static void try_refine(struct image *image, UnitCell *cell,
double da, double dw, double step)
{
struct reflhit *hits;
int np;
double itot;
UnitCell *trial_cell;
int did_something;
trial_cell = cell_new();
hits = find_intersections(image, cell, da, dw, &np, 0);
itot = integrate_all(image, hits, np);
STATUS("%f\n", itot);
do {
int i;
did_something = 0;
for ( i=0; i<18; i++ ) {
struct reflhit *trial_hits;
double trial_itot;
get_trial_cell(trial_cell, cell, i, step);
trial_hits = find_intersections(image, trial_cell,
da, dw, &np, 0);
trial_itot = integrate_all(image, hits, np);
if ( trial_itot > itot ) {
double asx, asy, asz;
double bsx, bsy, bsz;
double csx, csy, csz;
cell_get_reciprocal(trial_cell, &asx, &asy,
&asz, &bsx, &bsy, &bsz,
&csx, &csy, &csz);
cell_set_reciprocal(cell, asx, asy, asz, bsx,
bsy, bsz, csx, csy, csz);
itot = trial_itot;
free(hits);
hits = trial_hits;
did_something = 1;
len = strlen(prefix)+strlen(filename)+1;
f3 = malloc(len);
snprintf(f3, len, "%s%s", prefix, filename);
} else {
free(trial_hits);
}
}
} while ( did_something );
free(trial_cell);
}
/* Predict peaks */
static void pre_refine(struct image *image, UnitCell *cell,
double *da, double *dw)
{
double asx, asy, asz;
double bsx, bsy, bsz;
double csx, csy, csz;
double istep, step;
/* Start by changing parameters by 1% */
cell_get_reciprocal(cell, &asx, &asy,
&asz, &bsx, &bsy, &bsz,
&csx, &csy, &csz);
istep = (asx+asy+asz+bsx+bsy+bsz+csx+csy+csz)/900.0;
for ( step=istep; step>istep/100.0; step-=istep/100.0 ) {
try_refine(image, cell, *da, *dw, step);
}
free(filename);
return f3;
}
......@@ -241,17 +150,23 @@ int main(int argc, char *argv[])
char *filename;
struct detector *det;
char *geometry = NULL;
char *prefix = NULL;
int config_basename = 0;
int config_checkprefix = 1;
/* Long options */
const struct option longopts[] = {
{"help", 0, NULL, 'h'},
{"input", 1, NULL, 'i'},
{"geometry", 1, NULL, 'g'},
{"prefix", 1, NULL, 'x'},
{"basename", 0, &config_basename, 1},
{"no-check-prefix", 0, &config_checkprefix, 0},
{0, 0, NULL, 0}
};
/* Short options */
while ((c = getopt_long(argc, argv, "hi:g:", longopts, NULL)) != -1) {
while ((c = getopt_long(argc, argv, "hi:g:x:", longopts, NULL)) != -1) {
switch (c) {
case 'h' :
......@@ -266,6 +181,10 @@ int main(int argc, char *argv[])
geometry = strdup(optarg);
break;
case 'x' :
prefix = strdup(optarg);
break;
case 0 :
break;
......@@ -287,6 +206,14 @@ int main(int argc, char *argv[])
return ENOENT;
}
if ( prefix == NULL ) {
prefix = strdup("");
} else {
if ( config_checkprefix ) {
prefix = check_prefix(prefix);
}
}
det = get_detector_geometry(geometry);
if ( det == NULL ) {
ERROR("Failed to read detector geometry from '%s'\n", geometry);
......@@ -299,9 +226,11 @@ int main(int argc, char *argv[])
struct image image;
struct hdfile *hdfile;
double da, dw;
struct reflhit *hits;
int np;
filename = twiddle_filename(filename, config_basename, prefix);
STATUS("Integrating intensities from '%s'\n", filename);
image.det = det;
......@@ -316,12 +245,7 @@ int main(int argc, char *argv[])
hdf5_read(hdfile, &image, 0);
da = 5.0e-3; /* Initial divergence */
dw = 3.0/100.0; /* Initial bandwidth */
pre_refine(&image, cell, &da, &dw);
find_intersections(&image, cell, da, dw, &np, 1);
hits = find_intersections(&image, cell, 5.0e-3, 0.0001, &np, 1);
hdfile_close(hdfile);
cell_free(cell);
......@@ -334,6 +258,7 @@ int main(int argc, char *argv[])
free(det->panels);
free(det);
fclose(fh);
free(prefix);
return 0;
}
src/indexamajig.c
View file @ 4a235243
......@@ -24,8 +24,6 @@
#include <gsl/gsl_errno.h>
#include <pthread.h>
#include <sys/time.h>
#include <sys/types.h>
#include <sys/stat.h>
#include "utils.h"
#include "hdf5-file.h"
......@@ -171,44 +169,6 @@ static void show_help(const char *s)
}
static char *check_prefix(char *prefix)
{
int r;
struct stat statbuf;
char *new;
size_t len;
/* Is "prefix" a directory? */
r = stat(prefix, &statbuf);
if ( r != 0 ) {
/* "prefix" probably doesn't exist. This is fine - assume
* the user knows what they're doing, and that "prefix"
* suffixed with the actual filename will produce something
* sensible. */
return prefix;
}
if ( !S_ISDIR(statbuf.st_mode) ) {
/* Also fine, as above. */
return prefix;
}
/* Does the prefix end in a slash? */
if ( prefix[strlen(prefix)-1] == '/' ) {
/* This looks sensible. */
return prefix;
}
STATUS("Your prefix ('%s') is a directory, but doesn't end"
" with a slash. I'm going to add it for you.\n", prefix);
len = strlen(prefix)+2;
new = malloc(len);
snprintf(new, len, "%s/", prefix);
free(prefix);
return new;
}
static struct image *get_simage(struct image *template, int alternate)
{
struct image *image;
......
src/utils.c
View file @ 4a235243
......@@ -13,6 +13,8 @@
#include <string.h>
#include <stdio.h>
#include <unistd.h>
#include <sys/types.h>
#include <sys/stat.h>
#include "utils.h"
#include "image.h"
......@@ -442,3 +444,42 @@ ReflItemList *intersection_items(ReflItemList *i1, ReflItemList *i2)
return res;
}
char *check_prefix(char *prefix)
{
int r;
struct stat statbuf;
char *new;
size_t len;
/* Is "prefix" a directory? */
r = stat(prefix, &statbuf);
if ( r != 0 ) {
/* "prefix" probably doesn't exist. This is fine - assume
* the user knows what they're doing, and that "prefix"
* suffixed with the actual filename will produce something
* sensible. */
return prefix;
}
if ( !S_ISDIR(statbuf.st_mode) ) {
/* Also fine, as above. */
return prefix;
}
/* Does the prefix end in a slash? */
if ( prefix[strlen(prefix)-1] == '/' ) {
/* This looks sensible. */
return prefix;
}
STATUS("Your prefix ('%s') is a directory, but doesn't end"
" with a slash. I'm going to add it for you.\n", prefix);
STATUS("If this isn't what you want, run with --no-check-prefix.\n");
len = strlen(prefix)+2;
new = malloc(len);
snprintf(new, len, "%s/", prefix);
free(prefix);
return new;
}
src/utils.h
View file @ 4a235243
......@@ -203,10 +203,16 @@ extern void union_op_items(ReflItemList *items, ReflItemList *newi);
extern void union_items(ReflItemList *items, ReflItemList *newi);
extern ReflItemList *intersection_items(ReflItemList *i1, ReflItemList *i2);
/* ------------------------------ Message macros ---------------------------- */
#define ERROR(...) fprintf(stderr, __VA_ARGS__)
#define STATUS(...) fprintf(stderr, __VA_ARGS__)
/* ------------------------------ File handling ----------------------------- */
extern char *check_prefix(char *prefix);
#endif /* UTILS_H */
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