New stream writing

1 files changed, 123 insertions, 29 deletions

diff --git a/src/stream.c b/src/stream.c
index fbe0abad..4e34a48c 100644
--- a/src/stream.c
+++ b/src/stream.c
@@ -21,6 +21,63 @@
 #include "cell.h"
 #include "utils.h"
 #include "image.h"
+#include "stream.h"
+
+
+static void exclusive(const char *a, const char *b)
+{
+	ERROR("The stream options '%s' and '%s' are mutually exclusive.\n",
+	      a, b);
+}
+
+
+int parse_stream_flags(const char *a)
+{
+	int n, i;
+	int ret = STREAM_NONE;
+	char **flags;
+
+	n = assplode(a, ",", &flags, ASSPLODE_NONE);
+
+	for ( i=0; i<n; i++ ) {
+
+		if ( strcmp(flags[i], "pixels") == 0) {
+			if ( ret & STREAM_INTEGRATED ) {
+				exclusive("pixels", "integrated");
+				return -1;
+			}
+			ret |= STREAM_PIXELS;
+		} else if ( strcmp(flags[i], "integrated") == 0) {
+			if ( ret & STREAM_PIXELS ) {
+				exclusive("pixels", "integrated");
+				return -1;
+			}
+			ret |= STREAM_INTEGRATED;
+		} else if ( strcmp(flags[i], "peaks") == 0) {
+			if ( ret & STREAM_PEAKS_IF_INDEXED ) {
+				exclusive("peaks", "peaksifindexed");
+				return -1;
+			}
+			ret |= STREAM_PEAKS;
+		} else if ( strcmp(flags[i], "peaksifindexed") == 0) {
+			if ( ret & STREAM_PEAKS ) {
+				exclusive("peaks", "peaksifindexed");
+				return -1;
+			}
+			ret |= STREAM_PEAKS_IF_INDEXED;
+		} else {
+			ERROR("Unrecognised stream flag '%s'\n", flags[i]);
+			return 0;
+		}
+
+		free(flags[i]);
+
+	}
+	free(flags);
+
+	return ret;
+
+}
 
 
 int count_patterns(FILE *fh)
@@ -76,6 +133,31 @@ static UnitCell *read_orientation_matrix(FILE *fh)
 
 static void write_reflections(struct image *image, FILE *ofh)
 {
+	Reflection *refl;
+	RefListIterator *iter;
+
+	fprintf(ofh, "Reflections measured after indexing\n");
+	/* FIXME: Unify this with write_reflections() over in reflections.c */
+	fprintf(ofh, "  h   k   l          I    phase   sigma(I) "
+		     " 1/d(nm^-1)  counts\n");
+
+	for ( refl = first_refl(image->reflections, &iter);
+	      refl != NULL;
+	      refl = next_refl(refl, iter) ) {
+
+		signed int h, k, l;
+		double intensity, esd_i, s;
+
+		get_indices(refl, &h, &k, &l);
+		intensity = get_intensity(refl);
+		esd_i = 0.0; /* FIXME! */
+		s = 0.0; /* FIXME! */
+
+		/* h, k, l, I, sigma(I), s */
+		fprintf(ofh, "%3i %3i %3i %10.2f %s %10.2f  %10.2f %7i\n",
+		        h, k, l, intensity, "       -", esd_i, s/1.0e9, 1);
+
+	}
 }
 
 
@@ -83,7 +165,7 @@ static void write_peaks(struct image *image, FILE *ofh)
 {
 	int i;
 
-	fprintf(ofh, "Peaks from peak search in %s\n", image->filename);
+	fprintf(ofh, "Peaks from peak search\n");
 	fprintf(ofh, "  x/px     y/px   (1/d)/nm^-1    Intensity\n");
 
 	for ( i=0; i<image_feature_count(image->features); i++ ) {
@@ -102,13 +184,10 @@ static void write_peaks(struct image *image, FILE *ofh)
 		       f->x, f->y, q/1.0e9, f->intensity);
 
 	}
-
-	fprintf(ofh, "\n");
 }
 
 
-
-void write_chunk(FILE *ofh, struct image *image, int flags)
+void write_chunk(FILE *ofh, struct image *i, int f)
 {
 	double asx, asy, asz;
 	double bsx, bsy, bsz;
@@ -117,36 +196,51 @@ void write_chunk(FILE *ofh, struct image *image, int flags)
 
 	fprintf(ofh, "----- Begin chunk -----\n");
 
-	fprintf(ofh, "Image filename: %s\n", image->filename);
-
-	cell_get_parameters(image->indexed_cell, &a, &b, &c, &al, &be, &ga);
-	fprintf(ofh, "Cell parameters %7.5f %7.5f %7.5f nm,"
-	             " %7.5f %7.5f %7.5f deg\n",
-	             a*1.0e9, b*1.0e9, c*1.0e9,
-	             rad2deg(al), rad2deg(be), rad2deg(ga));
-
-	cell_get_reciprocal(image->indexed_cell, &asx, &asy, &asz,
-	                          &bsx, &bsy, &bsz,
-	                          &csx, &csy, &csz);
-	fprintf(ofh, "astar = %+9.7f %+9.7f %+9.7f nm^-1\n",
-	        asx/1e9, asy/1e9, asz/1e9);
-	fprintf(ofh, "bstar = %+9.7f %+9.7f %+9.7f nm^-1\n",
-	        bsx/1e9, bsy/1e9, bsz/1e9);
-	fprintf(ofh, "cstar = %+9.7f %+9.7f %+9.7f nm^-1\n",
-	       csx/1e9, csy/1e9, csz/1e9);
-
-	if ( image->f0_available ) {
-		fprintf(ofh, "I0 = %7.5f (arbitrary gas detector units)\n",
-		       image->f0);
+	fprintf(ofh, "Image filename: %s\n", i->filename);
+
+	if ( i->indexed_cell != NULL ) {
+		cell_get_parameters(i->indexed_cell, &a, &b, &c,
+		                                         &al, &be, &ga);
+		fprintf(ofh, "Cell parameters %7.5f %7.5f %7.5f nm,"
+			     " %7.5f %7.5f %7.5f deg\n",
+			     a*1.0e9, b*1.0e9, c*1.0e9,
+			     rad2deg(al), rad2deg(be), rad2deg(ga));
+
+		cell_get_reciprocal(i->indexed_cell, &asx, &asy, &asz,
+			                  &bsx, &bsy, &bsz,
+			                  &csx, &csy, &csz);
+		fprintf(ofh, "astar = %+9.7f %+9.7f %+9.7f nm^-1\n",
+			asx/1e9, asy/1e9, asz/1e9);
+		fprintf(ofh, "bstar = %+9.7f %+9.7f %+9.7f nm^-1\n",
+			bsx/1e9, bsy/1e9, bsz/1e9);
+		fprintf(ofh, "cstar = %+9.7f %+9.7f %+9.7f nm^-1\n",
+		       csx/1e9, csy/1e9, csz/1e9);
+
+	} else {
+
+		fprintf(ofh, "No unit cell from indexing.\n");
+
+	}
+
+	if ( i->i0_available ) {
+		fprintf(ofh, "I0 = %7.5f (arbitrary units)\n", i->i0);
 	} else {
 		fprintf(ofh, "I0 = invalid\n");
 	}
 
 	fprintf(ofh, "photon_energy_eV = %f\n",
-	        J_to_eV(ph_lambda_to_en(image->lambda)));
+	        J_to_eV(ph_lambda_to_en(i->lambda)));
+
+	if ( (f & STREAM_PEAKS)
+	  || ((f & STREAM_PEAKS_IF_INDEXED) && (i->indexed_cell != NULL)) ) {
+		fprintf(ofh, "\n");
+		write_peaks(i, ofh);
+	}
 
-	write_peaks(image, ofh);
-	write_reflections(image, ofh);
+	if ( (f & STREAM_PIXELS) || (f & STREAM_INTEGRATED) ) {
+		fprintf(ofh, "\n");
+		write_reflections(i, ofh);
+	}
 
 	fprintf(ofh, "----- End chunk -----\n\n");
 }