facetron: Add options

4 files changed, 93 insertions, 161 deletions

diff --git a/src/facetron.c b/src/facetron.c
index 42589526..c7c22e30 100644
--- a/src/facetron.c
+++ b/src/facetron.c
@@ -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;
 }
diff --git a/src/indexamajig.c b/src/indexamajig.c
index f63936c5..39905fb4 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -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;
diff --git a/src/utils.c b/src/utils.c
index a47f234f..196cda3f 100644
--- a/src/utils.c
+++ b/src/utils.c
@@ -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;
+}
diff --git a/src/utils.h b/src/utils.h
index a8d7aa2d..dfd1913f 100644
--- a/src/utils.h
+++ b/src/utils.h
@@ -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 */