diff options
Diffstat (limited to 'src/mosflm.c')
| -rw-r--r-- | src/mosflm.c | 101 |
1 files changed, 98 insertions, 3 deletions
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"); |