GrainSpotter interface (works)

1 files changed, 152 insertions, 13 deletions

diff --git a/libcrystfel/src/grainspotter.c b/libcrystfel/src/grainspotter.c
index 06f65f08..b7e5ce0a 100644
--- a/libcrystfel/src/grainspotter.c
+++ b/libcrystfel/src/grainspotter.c
@@ -50,9 +50,10 @@
 
 
 #include "image.h"
-#include "grainspotter.h"
 #include "utils.h"
 #include "peaks.h"
+#include "cell.h"
+#include "cell-utils.h"
 
 
 #define GRAINSPOTTER_VERBOSE 0
@@ -70,30 +71,99 @@ struct grainspotter_data {
 };
 
 
+static int read_matrix(struct image *image)
+{
+	FILE *fh;
+	int d1;
+	float d2;
+	float ubi11, ubi12, ubi13;
+	float ubi21, ubi22, ubi23;
+	float ubi31, ubi32, ubi33;
+	char filename[1024];
+	char line[1024];
+	int r;
+
+	snprintf(filename, 1023, "xfel-%i.gff", image->id);
+
+	fh = fopen(filename, "r");
+	if ( fh == NULL ) {
+		ERROR("Can't open '%s'\n", filename);
+		return 1;
+	}
+
+	/* Read and discard first line */
+	if ( fgets(line, 1024, fh) == NULL ) {
+		ERROR("Failed to read GFF file.\n");
+		return 1;
+	}
+
+	/* One line per grain */
+	if ( fgets(line, 1024, fh) == NULL ) {
+		ERROR("Failed to read GFF file.\n");
+		return 1;
+	}
+
+	STATUS("'%s'\n", line);
+
+	r = sscanf(line,
+         "%i %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f",
+         &d1, &d2, &d2, &d2, &d2, &d2, &d2, &d2, &d2, &d2, &d2, &d2, &d2, &d2, &d2,
+         &ubi11, &ubi12, &ubi13, &ubi21, &ubi22, &ubi23, &ubi31, &ubi32, &ubi33);
+
+	if ( r != 24 ) {
+		ERROR("Only %i parameters in GFF file\n", r);
+		return 1;
+	}
+
+	fclose(fh);
+
+	image->candidate_cells[0] = cell_new();
+
+//	cell_set_cartesian(image->candidate_cells[0],
+//	                   ubi11/1e10, ubi12/1e10, ubi13/1e10,
+//	                   ubi21/1e10, ubi22/1e10, ubi23/1e10,
+//	                   ubi31/1e10, ubi32/1e10, ubi33/1e10);
+
+	cell_set_cartesian(image->candidate_cells[0],
+	                   ubi12/1e10, ubi13/1e10, ubi11/1e10,
+	                   ubi22/1e10, ubi23/1e10, ubi21/1e10,
+	                   ubi32/1e10, ubi33/1e10, ubi31/1e10);
+
+
+        image->ncells = 1;
+        cell_print(image->candidate_cells[0]);
+
+        return 0;
+}
+
+
 static int grainspotter_readable(struct image *image,
                                  struct grainspotter_data *grainspotter)
 {
 	int rval;
 
 	rval = read(grainspotter->pty,
-	            grainspotter->rbuffer+grainspotter->rbufpos,
-	            grainspotter->rbuflen-grainspotter->rbufpos);
+	            grainspotter->rbuffer, grainspotter->rbuflen);
 
-	if ( (rval == -1) || (rval == 0) ) return 1;
+	if ( rval == -1 ) {
+		ERROR("Read failed: %s\n", strerror(errno));
+		return 1;
+	}
+
+	grainspotter->rbuffer[rval] = '\0';
 
-	/* FIXME! (if needed) */
-	//grainspotter->rbufpos += rval;
-	//assert(grainspotter->rbufpos <= grainspotter->rbuflen);
+	printf("GrainSpotter: '%s'\n", grainspotter->rbuffer);
 
 	return 0;
 }
 
 
-static void write_gve(struct image *image)
+static void write_gve(struct image *image, UnitCell *cell)
 {
 	FILE *fh;
 	int i;
 	char filename[1024];
+	double a, b, c, al, be, ga;
 
 	snprintf(filename, 1023, "xfel-%i.gve", image->id);
 
@@ -102,7 +172,14 @@ static void write_gve(struct image *image)
 		ERROR("Couldn't open temporary file '%s'\n", filename);
 		return;
 	}
-	fprintf(fh, "%f\n", 0.5);  /* Lie about the wavelength.  */
+
+	cell_get_parameters(cell, &a, &b, &c, &al, &be, &ga);
+	fprintf(fh, "%.6f %.6f %.6f %.6f %.6f %.6f P\n", a*1e10, b*1e10, c*1e10,
+	                     rad2deg(al), rad2deg(be), rad2deg(ga));
+	fprintf(fh, "# wavelength = %.6f\n", image->lambda*1e10);
+	fprintf(fh, "# wedge = 0.000000\n");
+	fprintf(fh, "# ds h k l\n");
+	fprintf(fh, "# xr yr zr xc yc ds eta omega\n");
 
 	for ( i=0; i<image_feature_count(image->features); i++ ) {
 
@@ -111,11 +188,60 @@ static void write_gve(struct image *image)
 		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);
+		fprintf(fh, "%.6f %.6f %.6f 0 0 %.6f %.6f %.6f 0\n",
+		        f->rz/1e10, f->rx/1e10, f->ry/1e10,
+		        modulus(f->rx, f->ry, f->rz)/1e10, /* dstar */
+		        atan2(f->ry, f->rx), 0.0);   /* eta, omega */
+
+	}
+	fclose(fh);
+}
+
+
+static char *write_ini(struct image *image)
+{
+	FILE *fh;
+	char *filename;
+	double tt;
+
+	filename = malloc(1024);
+	if ( filename == NULL ) return NULL;
 
+	snprintf(filename, 1023, "xfel-%i.ini", image->id);
+
+	fh = fopen(filename, "w");
+	if ( !fh ) {
+		ERROR("Couldn't open temporary file '%s'\n", filename);
+		free(filename);
+		return NULL;
 	}
+
+	get_q_for_panel(image->det->furthest_out_panel,
+	                    image->det->furthest_out_fs,
+	                    image->det->furthest_out_ss,
+	                    &tt, 1.0/image->lambda);
+
+	fprintf(fh, "spacegroup 96\n");
+	fprintf(fh, "!dsrange 0 1.3\n");
+	fprintf(fh, "tthrange 0 %.2f\n", 20.0);
+	fprintf(fh, "etarange 0 360\n");
+	fprintf(fh, "domega 1\n");
+	fprintf(fh, "omegarange -0.5 0.5\n");
+	fprintf(fh, "filespecs xfel-%i.gve xfel-%i.log\n",
+	            image->id, image->id);
+	fprintf(fh, "cuts 3 0.1 0.5\n");
+	fprintf(fh, "eulerstep 8\n");
+	fprintf(fh, "uncertainties 0.1 0.2 .5\n");
+	fprintf(fh, "nsigmas 2\n");
+	fprintf(fh, "minfracg 0.95\n");
+	fprintf(fh, "Nhkls_in_indexing 500\n");
+	fprintf(fh, "random 10000\n");
+	fprintf(fh, "!positionfit\n");
+	fprintf(fh, "genhkl\n");
+
 	fclose(fh);
+
+	return filename;
 }
 
 
@@ -125,8 +251,15 @@ void run_grainspotter(struct image *image, UnitCell *cell)
 	int status;
 	int rval;
 	struct grainspotter_data *grainspotter;
+	char *ini_filename;
+
+	write_gve(image, cell);
+	ini_filename = write_ini(image);
 
-	write_gve(image);
+	if ( ini_filename == NULL ) {
+		ERROR("Failed to write ini file for GrainSpotter.\n");
+		return;
+	}
 
 	grainspotter = malloc(sizeof(struct grainspotter_data));
 	if ( grainspotter == NULL ) {
@@ -149,11 +282,13 @@ void run_grainspotter(struct image *image, UnitCell *cell)
 		t.c_lflag &= ~(ECHO | ECHOE | ECHOK | ECHONL);
 		tcsetattr(STDIN_FILENO, TCSANOW, &t);
 
-		execlp("GrainSpotter.0.90", "", (char *)NULL);
+		STATUS("Running GrainSpotter.0.90 '%s'\n", ini_filename);
+		execlp("GrainSpotter.0.90", "", ini_filename, (char *)NULL);
 		ERROR("Failed to invoke GrainSpotter.\n");
 		_exit(0);
 
 	}
+	free(ini_filename);
 
 	grainspotter->rbuffer = malloc(256);
 	grainspotter->rbuflen = 256;
@@ -210,5 +345,9 @@ void run_grainspotter(struct image *image, UnitCell *cell)
 		ERROR("GrainSpotter doesn't seem to be working properly.\n");
 	}
 
+	if ( read_matrix(image) != 0 ) {
+		ERROR("Failed to read matrix\n");
+	}
+
 	free(grainspotter);
 }