diff options
| -rw-r--r-- | src/index.c | 16 | ||||
| -rw-r--r-- | src/mosflm.c | 101 | ||||
| -rw-r--r-- | src/mosflm.h | 2 |
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 */ |