mosflm almost functional

3 files changed, 108 insertions, 11 deletions

diff --git a/src/index.c b/src/index.c
index 01e7aa4b..5a2704f4 100644
--- a/src/index.c
+++ b/src/index.c
@@ -109,6 +109,8 @@ static void write_drx(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 */
@@ -116,7 +118,7 @@ struct sptline {
 	double s; /* sigma of peak */
 };
 
-/* need to sort mosflm peaks by intensity... */
+
 static int compare_vals(const void *ap, const void *bp)
 {
 	const struct sptline a = *(struct sptline *)ap;
@@ -127,7 +129,7 @@ static int compare_vals(const void *ap, const void *bp)
 	return 0;
 }
 
-/* write .spt file for mosflm */
+
 static void write_spt(struct image *image)
 {
 	FILE *fh;
@@ -201,9 +203,9 @@ void write_img(struct image *image)
 	unsigned short int * intimage;
 	
 	intimage = malloc(sizeof(unsigned short int));
-	intimage[0] = 0;
+	intimage[0] = 1;
 	
-	snprintf(filename, 1023, "xfel-%i.img", image->id);
+	snprintf(filename, 1023, "xfel-%i_001.img", image->id);
 	
 	fh = fopen(filename, "w");
 	if ( !fh ) {
@@ -219,7 +221,7 @@ void write_img(struct image *image)
 	fprintf(fh,"SIZE2=1;\n");
 	fprintf(fh,"}\n");
 	while ( ftell(fh) < 512 ) { fprintf(fh," "); };
-	fwrite(fh,sizeof(unsigned short int),1,fh);
+	fwrite(intimage,sizeof(unsigned short int),1,fh);
 	fclose(fh);
 }
 
@@ -262,8 +264,8 @@ void index_pattern(struct image *image, UnitCell *cell, IndexingMethod indm,
 		break;
 	case INDEXING_MOSFLM :
 		write_spt(image);
-		write_img(image); /* don't do this every time? */
-		run_mosflm(image);
+		write_img(image); /* dummy image. not needed for each frame.*/
+		run_mosflm(image,cell);
 		break;
 	case INDEXING_TEMPLATE :
 		match_templates(image, ipriv);
diff --git a/src/mosflm.c b/src/mosflm.c
index aed22720..1a2beb7b 100644
--- a/src/mosflm.c
+++ b/src/mosflm.c
@@ -391,17 +391,112 @@ static int dirax_readable(struct image *image)
 }
 
 
+static int read_newmat(const char * filename, struct image *image)
+{
+	FILE * fh;
+	float asx, asy, asz;
+	float bsx, bsy, bsz;
+	float csx, csy, csz;
+	int n;
+	double c;
+	
+	fh = fopen(filename,"r");
+	if (fh == NULL){ 
+		return 1;
+	}
+	n  = fscanf(fh,"%f %f %f\n",&asx,&bsx,&csx);
+	n += fscanf(fh,"%f %f %f\n",&asy,&bsy,&csy);
+	n += fscanf(fh,"%f %f %f\n",&asz,&bsz,&csz);
+	if (n != 9) {
+		return 1;
+	}
+	fclose(fh);
+	
+	/* mosflm A matrix is multiplied by lambda, so fix this */
+	c = 1e-10/image->lambda;
+	
+	cell_set_reciprocal(image->candidate_cells[0],
+                            asz*c, asy*c, asx*c,
+                            bsz*c, bsy*c, bsx*c,
+                            csz*c, csy*c, csx*c);
+               
+        image->ncells = 1;
+        
+        return 0;
+}
 
 
-
-void run_mosflm(struct image *image)
+void run_mosflm(struct image *image, UnitCell *cell)
 {
 	unsigned int opts;
 	int status;
 	int rval;
+	int i,j;
+	char mos_cmd[1024];
+	char symm[64];
+	const char *sg;
+	double a,b,c,alpha,beta,gamma;
+	double wavelength; /* angstrom */
+	const char newmatfile[128];
+	int fail;
+	
+	printf("Mosflm is not fully implemented.  Using DirAx for now.\n");
+	
+	wavelength = image->lambda*1e10;
+	cell_get_parameters(cell, &a, &b, &c, &alpha, &beta, &gamma);
+	sg = cell_get_spacegroup(cell);
+	sprintf(newmatfile,"xfel-%i.newmat",image->id);
+	
+	/* need to remove white space from spacegroup... */
+	j = 0;
+	for(i = 0; i < strlen(sg);i++)
+	{
+		if (sg[i] != ' ') {
+			symm[j] = sg[i];
+			j++;
+		}
+	}
+	symm[j] = '\0';	
+	
+	
+	/* build a script to run mosflm */
+	sprintf(mos_cmd,"%s","ipmosflm << eof-mosflm >> /dev/null\n");
+	sprintf(mos_cmd,"%s%s",mos_cmd,
+	                     "DETECTOR ROTATION HORIZONTAL ANTICLOCKWISE"
+	                     " ORIGIN LL FAST HORIZONTAL RECTANGULAR\n");
+	sprintf(mos_cmd,"%sCELL %6.2f %6.2f %6.2f %6.2f %6.2f %6.2f\n",
+	                   mos_cmd,
+	                   a*1e10,b*1e10,c*1e10,
+	                   rad2deg(alpha),rad2deg(beta),rad2deg(gamma));
+	sprintf(mos_cmd,"%sSYMM %s\n",mos_cmd,symm);
+	sprintf(mos_cmd,"%sDISTANCE %8.4f\n",mos_cmd,67.8);
+	sprintf(mos_cmd,"%sBEAM %8.4f %8.4f\n",mos_cmd,0.0,0.0);
+	sprintf(mos_cmd,"%sWAVELENGTH %10.5f\n",mos_cmd,wavelength);
+	sprintf(mos_cmd,"%sNEWMAT %s\n",mos_cmd,newmatfile);
+	sprintf(mos_cmd,"%sIMAGE xfel-%i_001.img phi 0 0\n",mos_cmd,image->id);
+	sprintf(mos_cmd,"%sAUTOINDEX DPS FILE xfel-%i.spt IMAGE 1\n",
+	                      mos_cmd,image->id);
+	sprintf(mos_cmd,"%sGO\n",mos_cmd);
+	sprintf(mos_cmd,"%s%s",mos_cmd,"eof-mosflm\n");
+
+	/* Run the mosflm script */
+	fail = system(mos_cmd);
+	if (fail) { 
+		ERROR("mosflm execution failed.\n");
+		return; 
+	}
 
-	printf("Mosflm is not yet implemented.  Using DirAx for now.\n");
+	/* Read the mosflm NEWMAT file and set cell candidate */ 
+	/* Existence of this file means possible success. Pretty shady. */
+	fail = read_newmat(newmatfile,image);
+	if (fail) {
+		printf("Failed to read mosflm NEWMAT file.\n"); 
+		return;
+	}
 
+	/* remove the mosflm NEWMAT file */
+	remove(newmatfile);
+	
 	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/mosflm.h b/src/mosflm.h
index 8d09d8d5..53939902 100644
--- a/src/mosflm.h
+++ b/src/mosflm.h
@@ -22,7 +22,7 @@
 #include "utils.h"
 
 
-extern void run_mosflm(struct image *image);
+extern void run_mosflm(struct image *image, UnitCell *cell);
 
 
 #endif	/* MOSFLM_H */