Copy and Replace when saving geometry

6 files changed, 68 insertions, 52 deletions

diff --git a/libcrystfel/src/detector.c b/libcrystfel/src/detector.c
index 9533e264..39a84b6c 100644
--- a/libcrystfel/src/detector.c
+++ b/libcrystfel/src/detector.c
@@ -1604,60 +1604,61 @@ void get_pixel_extents(struct detector *det,
 }
 
 
-int write_detector_geometry(const char *filename, struct detector *det)
+int write_detector_geometry(const char* geometry_filename,
+                            const char *output_filename, struct detector *det)
 {
-	struct panel *p;
-	int pi;
+        FILE *ifh;
 	FILE *fh;
 
-	if ( filename == NULL ) return 2;
+	if ( geometry_filename == NULL ) return 2;
+	if ( output_filename == NULL ) return 2;
 	if ( det->n_panels < 1 ) return 3;
 
-	fh = fopen(filename, "w");
-	if ( fh == NULL ) return 1;
+	ifh = fopen(geometry_filename, "r");
+	if ( ifh == NULL ) return 1;
 
-	for ( pi=0; pi<det->n_panels; pi++) {
+	fh = fopen(output_filename, "w");
+	if ( fh == NULL ) return 1;
 
-		p = &(det->panels[pi]);
+	do {
 
-		if ( p == NULL ) return 4;
+		char *rval;
+		char line[1024];
+		int n_bits;
+		char **bits;
+		int i;
+		struct panel *p;
 
-		if ( pi > 0 ) fprintf(fh, "\n");
+		rval = fgets(line, 1023, ifh);
+		if ( rval == NULL ) break;
 
-		fprintf(fh, "%s/min_fs = %d\n", p->name, p->min_fs);
-		fprintf(fh, "%s/min_ss = %d\n", p->name, p->min_ss);
-		fprintf(fh, "%s/max_fs = %d\n", p->name, p->max_fs);
-		fprintf(fh, "%s/max_ss = %d\n", p->name, p->max_ss);
-		fprintf(fh, "%s/badrow_direction = %C\n", p->name, p->badrow);
-		fprintf(fh, "%s/res = %g\n", p->name, p->res);
-		fprintf(fh, "%s/clen = %s\n", p->name, p->clen_from);
-		fprintf(fh, "%s/fs = %+fx %+fy\n", p->name, p->fsx, p->fsy);
-		fprintf(fh, "%s/ss = %+fx %+fy\n", p->name, p->ssx, p->ssy);
-		fprintf(fh, "%s/corner_x = %g\n", p->name, p->cnx);
-		fprintf(fh, "%s/corner_y = %g\n", p->name, p->cny);
-		fprintf(fh, "%s/adu_per_eV = %g\n", p->name, p->adu_per_eV);
-		fprintf(fh, "%s/max_adu = %g\n", p->name, p->max_adu);
+		n_bits = assplode(line, "/", &bits, ASSPLODE_NONE);
 
-		if ( p->no_index ) {
-			fprintf(fh, "%s/no_index = 1\n", p->name);
-		} /* else don't clutter up the file */
+		if ( n_bits < 2 || n_bits > 2 ) {
+			for ( i=0; i<n_bits; i++ ) free(bits[i]);
+			fputs(line, fh);
+		} else {
+			p = find_panel_by_name(det, bits[0]);
+
+			if ( strncmp(bits[1], "fs = ", 5) == 0) {
+				fprintf(fh, "%s/fs = %+fx %+fy\n", p->name, p->fsx, p->fsy);
+			} else if ( strncmp(bits[1], "ss = ", 5) == 0) {
+				fprintf(fh, "%s/ss = %+fx %+fy\n", p->name, p->ssx, p->ssy);
+			} else if ( strncmp(bits[1], "corner_x = ", 11) == 0) {
+				fprintf(fh, "%s/corner_x = %g\n", p->name, p->cnx);
+			} else if ( strncmp(bits[1], "corner_y = ", 11) == 0) {
+				fprintf(fh, "%s/corner_y = %g\n", p->name, p->cny);
+			} else {
+				fputs(line, fh);
+			}
 
-		if ( p->rigid_group != NULL ) {
-			fprintf(fh, "%s/rigid_group = %s\n",
-			        p->name, p->rigid_group->name);
-		}
+			for ( i=0; i<n_bits; i++ ) free(bits[i]);
 
-		if ( p->data != NULL ) {
-			fprintf(fh, "%s/data = %s\n",
-					p->name, p->data);
 		}
 
-		if ( p->mask != NULL ) {
-			fprintf(fh, "%s/mask = %s\n",
-			        p->name, p->mask);
-		}
+	} while ( 1 );
 
-	}
+	fclose(ifh);
 	fclose(fh);
 
 	return 0;
diff --git a/libcrystfel/src/detector.h b/libcrystfel/src/detector.h
index 1cd4c607..2cec61c2 100644
--- a/libcrystfel/src/detector.h
+++ b/libcrystfel/src/detector.h
@@ -221,7 +221,9 @@ extern double smallest_q(struct image *image);
 
 extern struct panel *find_panel_by_name(struct detector *det, const char *name);
 
-extern int write_detector_geometry(const char *filename, struct detector *det);
+extern int write_detector_geometry(const char* geometry_filename,
+                                   const char *output_filename, struct detector *det);
+
 
 extern void mark_resolution_range_as_bad(struct image *image,
                                          double min, double max);
diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c
index 07568024..988570bc 100644
--- a/libcrystfel/src/stream.c
+++ b/libcrystfel/src/stream.c
@@ -266,7 +266,8 @@ static RefList *read_stream_reflections_2_3(FILE *fh, struct detector *det)
 			double ph;
 			char *v;
 			struct panel *p;
-			float write_fs, write_ss;
+			float write_fs = 0;
+			float write_ss = 0;
 
 			refl = add_refl(out, h, k, l);
 			set_intensity(refl, intensity);
diff --git a/src/dw-hdfsee.c b/src/dw-hdfsee.c
index f4655d0a..e9b6ee86 100644
--- a/src/dw-hdfsee.c
+++ b/src/dw-hdfsee.c
@@ -1176,7 +1176,7 @@ static gint displaywindow_about(GtkWidget *widget, DisplayWindow *dw)
 static int save_geometry_file(DisplayWindow *dw)
 {
 	GtkWidget *d;
-	gchar * filename;
+	gchar * output_filename;
 	int w;
 
 	d = gtk_file_chooser_dialog_new("Save Detector Geometry",
@@ -1187,10 +1187,11 @@ static int save_geometry_file(DisplayWindow *dw)
 	                                NULL);
 
 	gtk_dialog_run (GTK_DIALOG (d));
-	filename = gtk_file_chooser_get_filename(GTK_FILE_CHOOSER (d));
-	w = write_detector_geometry(filename, dw->image->det);
+	output_filename = gtk_file_chooser_get_filename(GTK_FILE_CHOOSER (d));
+	w = write_detector_geometry(dw->geom_filename, output_filename,
+                                    dw->image->det);
 	gtk_widget_destroy(d);
-	g_free(filename);
+	g_free(output_filename);
 	return w;
 }
 
@@ -2429,7 +2430,8 @@ static gint displaywindow_keypress(GtkWidget *widget, GdkEventKey *event,
 }
 
 
-DisplayWindow *displaywindow_open(char *filename, const char *peaks,
+DisplayWindow *displaywindow_open(char *filename, char *geom_filename,
+                                  const char *peaks,
                                   double boost, int binning,
                                   int noisefilter, int calibmode, int colscale,
                                   const char *element,
@@ -2479,6 +2481,7 @@ DisplayWindow *displaywindow_open(char *filename, const char *peaks,
 	dw->multi_event = 0;
 	dw->curr_event = 0;
 	dw->ev_list = NULL;
+	dw->geom_filename = strdup(geom_filename);
 
 	dw->image->det = det_geom;
 	dw->image->beam = beam;
@@ -2488,6 +2491,7 @@ DisplayWindow *displaywindow_open(char *filename, const char *peaks,
 	dw->hdfile = hdfile_open(filename);
 	if ( dw->hdfile == NULL ) {
 		ERROR("Couldn't open file: %s\n", filename);
+		free(dw->geom_filename);
 		free(dw);
 		return NULL;
 	}
@@ -2502,6 +2506,7 @@ DisplayWindow *displaywindow_open(char *filename, const char *peaks,
 		if ( dw->ev_list == NULL ) {
 			ERROR("Error while parsing file structure\n");
 			free_event_list(dw->ev_list);
+			free(dw->geom_filename);
 			free(dw);
 			return NULL;
 		}
@@ -2509,6 +2514,7 @@ DisplayWindow *displaywindow_open(char *filename, const char *peaks,
 			ERROR("Multi-event geometry file but no events found "
 			      "in data file\n");
 			free_event_list(dw->ev_list);
+			free(dw->geom_filename);
 			free(dw);
 			return NULL;
 		} else {
@@ -2532,8 +2538,9 @@ DisplayWindow *displaywindow_open(char *filename, const char *peaks,
 	}
 	if ( check ) {
 		ERROR("Couldn't load file\n");
-		free(dw);
+		free(dw->geom_filename);
 		hdfile_close(dw->hdfile);
+		free(dw->geom_filename);
 		return NULL;
 	}
 
diff --git a/src/dw-hdfsee.h b/src/dw-hdfsee.h
index fc16594d..14c17287 100644
--- a/src/dw-hdfsee.h
+++ b/src/dw-hdfsee.h
@@ -90,11 +90,13 @@ typedef struct {
 
 	int             not_ready_yet;
 
-    struct detector* simple_geom;
+	struct detector* simple_geom;
 
-    struct hdfile	*hdfile;
+	struct hdfile	*hdfile;
 	struct image	*image;
 
+	char            *geom_filename;
+
 	/* Dialog boxes */
 	BinningDialog  *binning_dialog;
 	BoostIntDialog *boostint_dialog;
@@ -137,7 +139,7 @@ typedef struct {
 } DisplayWindow;
 
 /* Open an image display window showing the given filename, or NULL */
-extern DisplayWindow *displaywindow_open(char *filename,
+extern DisplayWindow *displaywindow_open(char *filename, char *geom_filename,
                                          const char *peaks, double boost,
                                          int binning,
                                          int noisefilter, int calibmode,
diff --git a/src/hdfsee.c b/src/hdfsee.c
index cc35b6e0..cdf4ae92 100644
--- a/src/hdfsee.c
+++ b/src/hdfsee.c
@@ -117,6 +117,7 @@ int main(int argc, char *argv[])
 	size_t i;
 	int nfiles;
 	char *peaks = NULL;
+	char *geom_filename = NULL;
 	double boost = 1.0;
 	int binning = 2;
 	int config_noisefilter = 0;
@@ -213,7 +214,9 @@ int main(int argc, char *argv[])
 			break;
 
 			case 'g' :
-			det_geom = get_detector_geometry(optarg, &cbeam);
+			geom_filename = strdup(optarg);
+			det_geom = get_detector_geometry(geom_filename, &cbeam);
+
 			if ( det_geom == NULL ) {
 				ERROR("Failed to read detector geometry from '%s'\n",
 				       optarg);
@@ -293,8 +296,8 @@ int main(int argc, char *argv[])
 	free(cscale);
 
 	for ( i=0; i<nfiles; i++ ) {
-		main_window_list[i] = displaywindow_open(argv[optind+i], peaks,
-		                                         boost, binning,
+		main_window_list[i] = displaywindow_open(argv[optind+i], geom_filename,
+		                                         peaks, boost, binning,
 		                                         config_noisefilter,
 		                                         config_calibmode,
 		                                         colscale, element,