Remove --write-drx option and simplify code

4 files changed, 158 insertions, 167 deletions

diff --git a/src/dirax.c b/src/dirax.c
index 0930f8f9..ebb53f25 100644
--- a/src/dirax.c
+++ b/src/dirax.c
@@ -385,12 +385,45 @@ static int dirax_readable(struct image *image)
 }
 
 
+static void write_drx(struct image *image)
+{
+	FILE *fh;
+	int i;
+	char filename[1024];
+
+	snprintf(filename, 1023, "xfel-%i.drx", image->id);
+
+	fh = fopen(filename, "w");
+	if ( !fh ) {
+		ERROR("Couldn't open temporary file xfel.drx\n");
+		return;
+	}
+	fprintf(fh, "%f\n", 0.5);  /* Lie about the wavelength.  */
+
+	for ( i=0; i<image_feature_count(image->features); i++ ) {
+
+		struct imagefeature *f;
+
+		f = image_get_feature(image->features, i);
+		if ( f == NULL ) continue;
+
+		fprintf(fh, "%10f %10f %10f %8f\n",
+		        f->rx/1e10, f->ry/1e10, f->rz/1e10, 1.0);
+
+	}
+	fclose(fh);
+}
+
+
+
 void run_dirax(struct image *image)
 {
 	unsigned int opts;
 	int status;
 	int rval;
 
+	write_drx(image);
+
 	image->dirax_pid = forkpty(&image->dirax_pty, NULL, NULL, NULL);
 	if ( image->dirax_pid == -1 ) {
 		ERROR("Failed to fork for DirAx\n");
diff --git a/src/index.c b/src/index.c
index 4d2a158f..69711b42 100644
--- a/src/index.c
+++ b/src/index.c
@@ -108,152 +108,6 @@ void cleanup_indexing(IndexingPrivate **priv)
 }
 
 
-static void write_drx(struct image *image)
-{
-	FILE *fh;
-	int i;
-	char filename[1024];
-
-	snprintf(filename, 1023, "xfel-%i.drx", image->id);
-
-	fh = fopen(filename, "w");
-	if ( !fh ) {
-		ERROR("Couldn't open temporary file xfel.drx\n");
-		return;
-	}
-	fprintf(fh, "%f\n", 0.5);  /* Lie about the wavelength.  */
-
-	for ( i=0; i<image_feature_count(image->features); i++ ) {
-
-		struct imagefeature *f;
-
-		f = image_get_feature(image->features, i);
-		if ( f == NULL ) continue;
-
-		fprintf(fh, "%10f %10f %10f %8f\n",
-		        f->rx/1e10, f->ry/1e10, f->rz/1e10, 1.0);
-
-	}
-	fclose(fh);
-}
-
-
-/* write .spt file for mosflm */
-/* need to sort mosflm peaks by intensity... */
-struct sptline {
-	double x; /* x coordinate of peak */
-	double y; /* y coordinate of peak */
-	double h; /* height of peak */
-	double s; /* sigma of peak */
-};
-
-
-static int compare_vals(const void *ap, const void *bp)
-{
-	const struct sptline a = *(struct sptline *)ap;
-	const struct sptline b = *(struct sptline *)bp;
-
-	if ( a.h < b.h ) return 1;
-	if ( a.h > b.h ) return -1;
-	return 0;
-}
-
-
-static void write_spt(struct image *image)
-{
-	FILE *fh;
-	int i;
-	char filename[1024];
-	double fclen=67.8;  /* fake camera length in mm */
-	double fpix=0.075;  /* fake pixel size in mm */
-	double pix;
-	double height=100;
-	double sigma=1;
-	int nPeaks = image_feature_count(image->features);
-
-	snprintf(filename, 1023, "xfel-%i.spt", image->id);
-
-	fh = fopen(filename, "w");
-	if ( !fh ) {
-		ERROR("Couldn't open temporary file xfel.spt\n");
-		return;
-	}
-
-	fprintf(fh, "%10d %10d %10.8f %10.6f %10.6f\n", 1, 1, fpix, 1.0, 0.0);
-	fprintf(fh, "%10d %10d\n", 1, 1);
-	fprintf(fh, "%10.5f %10.5f\n", 0.0, 0.0);
-
-	struct sptline *sptlines;
-	sptlines = malloc(sizeof(struct sptline)*nPeaks);
-
-	for ( i=0; i<nPeaks; i++ ) {
-
-		struct imagefeature *f;
-
-		f = image_get_feature(image->features, i);
-		if ( f == NULL ) continue;
-
-		struct panel *pan;
-		pan = find_panel(image->det,f->x,f->y);
-		if ( pan == NULL ) continue;
-
-		pix = 1000/pan->res; /* pixel size in mm */
-		height = f->intensity;
-
-		sptlines[i].x = (f->y - pan->cy)*pix*fclen/pan->clen/1000;
-		sptlines[i].y = -(f->x - pan->cx)*pix*fclen/pan->clen/1000;
-		sptlines[i].h = height;
-		sptlines[i].s = sigma;
-
-	}
-
-	qsort(sptlines, nPeaks, sizeof(struct sptline), compare_vals);
-
-	for ( i=0; i<nPeaks; i++ ) {
-
-		fprintf(fh, "%10.2f %10.2f %10.2f %10.2f %10.2f %10.2f\n",
-		        sptlines[i].x, sptlines[i].y,
-		        0.0, 0.0,
-		        sptlines[i].h, sptlines[i].s);
-
-	}
-
-	fprintf(fh,"%10.2f %10.2f %10.2f %10.2f %10.2f %10.2f\n",
-	           -999.0,-999.0,-999.0,-999.0,-999.0,-999.0);
-	fclose(fh);
-}
-
-/* write a dummy 1x1 pixel image file for mosflm.  Without post refinement,
-   mosflm will ignore this, but it must be present.*/
-void write_img(struct image *image)
-{
-	FILE *fh;
-	char filename[1024];
-	unsigned short int * intimage;
-
-	intimage = malloc(sizeof(unsigned short int));
-	intimage[0] = 1;
-
-	snprintf(filename, 1023, "xfel-%i_001.img", image->id);
-
-	fh = fopen(filename, "w");
-	if ( !fh ) {
-		ERROR("Couldn't open temporary file xfel.spt\n");
-		return;
-	}
-
-	fprintf(fh,"{\nHEADER_BYTES=512;\n");
-	fprintf(fh,"BYTE_ORDER=little_endian;\n");
-	fprintf(fh,"TYPE=unsigned_short;\n");
-	fprintf(fh,"DIM=2;\n");
-	fprintf(fh,"SIZE1=1;\n");
-	fprintf(fh,"SIZE2=1;\n");
-	fprintf(fh,"}\n");
-	while ( ftell(fh) < 512 ) { fprintf(fh," "); };
-	fwrite(intimage,sizeof(unsigned short int),1,fh);
-	fclose(fh);
-}
-
 void map_all_peaks(struct image *image)
 {
 	int i;
@@ -292,13 +146,10 @@ void index_pattern(struct image *image, UnitCell *cell, IndexingMethod *indm,
 			return;
 		case INDEXING_DIRAX :
 			STATUS("Running DirAx...\n");
-			write_drx(image);
 			run_dirax(image);
 			break;
 		case INDEXING_MOSFLM :
 			STATUS("Running MOSFLM...\n");
-			write_spt(image);
-			write_img(image); /* dummy image */
 			run_mosflm(image, cell);
 			break;
 		case INDEXING_TEMPLATE :
diff --git a/src/indexamajig.c b/src/indexamajig.c
index de50383c..83eee4d1 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -53,7 +53,6 @@ struct static_index_args
 	UnitCell *cell;
 	int config_cmfilter;
 	int config_noisefilter;
-	int config_writedrx;
 	int config_dumpfound;
 	int config_verbose;
 	int config_alternate;
@@ -161,10 +160,6 @@ static void show_help(const char *s)
 "                           as \"simulated.h5\".  You can TRY to combine this\n"
 "                           with \"-j <n>\" with n greater than 1, but it's\n"
 "                           not a good idea.\n"
-"     --write-drx          Write 'xfel.drx' for visualisation of reciprocal\n"
-"                           space.  Implied by any indexing method other than\n"
-"                           'none'.  Beware: the units in this file are\n"
-"                           reciprocal Angstroms.\n"
 "     --dump-peaks         Write the results of the peak search to stdout.\n"
 "                           The intensities in this list are from the\n"
 "                           centroid/integration procedure.\n"
@@ -318,7 +313,6 @@ static void process_image(void *pp, int cookie)
 	UnitCell *cell = pargs->static_args.cell;
 	int config_cmfilter = pargs->static_args.config_cmfilter;
 	int config_noisefilter = pargs->static_args.config_noisefilter;
-	int config_writedrx = pargs->static_args.config_writedrx;
 	int config_dumpfound = pargs->static_args.config_dumpfound;
 	int config_verbose = pargs->static_args.config_verbose;
 	int config_alternate  = pargs->static_args.config_alternate;
@@ -397,17 +391,12 @@ static void process_image(void *pp, int cookie)
 		           pargs->static_args.output_mutex);
 	}
 
-	/* Not indexing nor writing xfel.drx?
-	 * Then there's nothing left to do. */
-	if ( (!config_writedrx) && (indm == INDEXING_NONE) ) {
-		goto done;
-	}
+	/* Not indexing? Then there's nothing left to do. */
+	if ( indm == NULL ) goto done;
 
 	/* Calculate orientation matrix (by magic) */
-	if ( config_writedrx || (indm != INDEXING_NONE) ) {
-		index_pattern(&image, cell, indm, pargs->static_args.cellr,
-		              config_verbose, pargs->static_args.ipriv);
-	}
+	index_pattern(&image, cell, indm, pargs->static_args.cellr,
+		      config_verbose, pargs->static_args.ipriv);
 
 	/* No cell at this point?  Then we're done. */
 	if ( image.indexed_cell == NULL ) goto done;
@@ -527,7 +516,6 @@ int main(int argc, char *argv[])
 	int config_noindex = 0;
 	int config_dumpfound = 0;
 	int config_nearbragg = 0;
-	int config_writedrx = 0;
 	int config_simulate = 0;
 	int config_cmfilter = 0;
 	int config_noisefilter = 0;
@@ -582,7 +570,6 @@ int main(int argc, char *argv[])
 		{"peaks",              1, NULL,                2},
 		{"cell-reduction",     1, NULL,                3},
 		{"near-bragg",         0, &config_nearbragg,   1},
-		{"write-drx",          0, &config_writedrx,    1},
 		{"indexing",           1, NULL,               'z'},
 		{"geometry",           1, NULL,               'g'},
 		{"beam",               1, NULL,               'b'},
@@ -886,7 +873,6 @@ int main(int argc, char *argv[])
 	qargs.static_args.cell = cell;
 	qargs.static_args.config_cmfilter = config_cmfilter;
 	qargs.static_args.config_noisefilter = config_noisefilter;
-	qargs.static_args.config_writedrx = config_writedrx;
 	qargs.static_args.config_dumpfound = config_dumpfound;
 	qargs.static_args.config_verbose = config_verbose;
 	qargs.static_args.config_alternate = config_alternate;
diff --git a/src/mosflm.c b/src/mosflm.c
index 40780451..974b82c5 100644
--- a/src/mosflm.c
+++ b/src/mosflm.c
@@ -102,6 +102,124 @@ static int read_newmat(const char * filename, struct image *image)
 }
 
 
+/* write .spt file for mosflm */
+/* need to sort mosflm peaks by intensity... */
+struct sptline {
+	double x; /* x coordinate of peak */
+	double y; /* y coordinate of peak */
+	double h; /* height of peak */
+	double s; /* sigma of peak */
+};
+
+
+static int compare_vals(const void *ap, const void *bp)
+{
+	const struct sptline a = *(struct sptline *)ap;
+	const struct sptline b = *(struct sptline *)bp;
+
+	if ( a.h < b.h ) return 1;
+	if ( a.h > b.h ) return -1;
+	return 0;
+}
+
+
+static void write_spt(struct image *image)
+{
+	FILE *fh;
+	int i;
+	char filename[1024];
+	double fclen=67.8;  /* fake camera length in mm */
+	double fpix=0.075;  /* fake pixel size in mm */
+	double pix;
+	double height=100;
+	double sigma=1;
+	int nPeaks = image_feature_count(image->features);
+
+	snprintf(filename, 1023, "xfel-%i.spt", image->id);
+
+	fh = fopen(filename, "w");
+	if ( !fh ) {
+		ERROR("Couldn't open temporary file xfel.spt\n");
+		return;
+	}
+
+	fprintf(fh, "%10d %10d %10.8f %10.6f %10.6f\n", 1, 1, fpix, 1.0, 0.0);
+	fprintf(fh, "%10d %10d\n", 1, 1);
+	fprintf(fh, "%10.5f %10.5f\n", 0.0, 0.0);
+
+	struct sptline *sptlines;
+	sptlines = malloc(sizeof(struct sptline)*nPeaks);
+
+	for ( i=0; i<nPeaks; i++ ) {
+
+		struct imagefeature *f;
+
+		f = image_get_feature(image->features, i);
+		if ( f == NULL ) continue;
+
+		struct panel *pan;
+		pan = find_panel(image->det,f->x,f->y);
+		if ( pan == NULL ) continue;
+
+		pix = 1000/pan->res; /* pixel size in mm */
+		height = f->intensity;
+
+		sptlines[i].x = (f->y - pan->cy)*pix*fclen/pan->clen/1000;
+		sptlines[i].y = -(f->x - pan->cx)*pix*fclen/pan->clen/1000;
+		sptlines[i].h = height;
+		sptlines[i].s = sigma;
+
+	}
+
+	qsort(sptlines, nPeaks, sizeof(struct sptline), compare_vals);
+
+	for ( i=0; i<nPeaks; i++ ) {
+
+		fprintf(fh, "%10.2f %10.2f %10.2f %10.2f %10.2f %10.2f\n",
+		        sptlines[i].x, sptlines[i].y,
+		        0.0, 0.0,
+		        sptlines[i].h, sptlines[i].s);
+
+	}
+
+	fprintf(fh,"%10.2f %10.2f %10.2f %10.2f %10.2f %10.2f\n",
+	           -999.0,-999.0,-999.0,-999.0,-999.0,-999.0);
+	fclose(fh);
+}
+
+
+/* Write a dummy 1x1 pixel image file for mosflm.  Without post refinement,
+ * mosflm will ignore this, but it must be present. */
+static void write_img(struct image *image)
+{
+	FILE *fh;
+	char filename[1024];
+	unsigned short int * intimage;
+
+	intimage = malloc(sizeof(unsigned short int));
+	intimage[0] = 1;
+
+	snprintf(filename, 1023, "xfel-%i_001.img", image->id);
+
+	fh = fopen(filename, "w");
+	if ( !fh ) {
+		ERROR("Couldn't open temporary file xfel.spt\n");
+		return;
+	}
+
+	fprintf(fh,"{\nHEADER_BYTES=512;\n");
+	fprintf(fh,"BYTE_ORDER=little_endian;\n");
+	fprintf(fh,"TYPE=unsigned_short;\n");
+	fprintf(fh,"DIM=2;\n");
+	fprintf(fh,"SIZE1=1;\n");
+	fprintf(fh,"SIZE2=1;\n");
+	fprintf(fh,"}\n");
+	while ( ftell(fh) < 512 ) { fprintf(fh," "); };
+	fwrite(intimage,sizeof(unsigned short int),1,fh);
+	fclose(fh);
+}
+
+
 void run_mosflm(struct image *image, UnitCell *cell)
 {
 	int i,j;
@@ -113,6 +231,9 @@ void run_mosflm(struct image *image, UnitCell *cell)
 	char newmatfile[128];
 	int fail;
 
+	write_spt(image);
+	write_img(image); /* dummy image */
+
 	wavelength = image->lambda*1e10;
 	cell_get_parameters(cell, &a, &b, &c, &alpha, &beta, &gamma);
 	sg = cell_get_spacegroup(cell);