diff options
Diffstat (limited to 'src')
| -rw-r--r-- | src/index.c | 40 | ||||
| -rw-r--r-- | src/mosflm.c | 43 |
2 files changed, 41 insertions, 42 deletions
diff --git a/src/index.c b/src/index.c index 866c5c3b..edfa33e5 100644 --- a/src/index.c +++ b/src/index.c @@ -142,7 +142,7 @@ static void write_spt(struct image *image) double height=100; double sigma=1; int nPeaks = image_feature_count(image->features); - + snprintf(filename, 1023, "xfel-%i.spt", image->id); fh = fopen(filename, "w"); @@ -150,70 +150,70 @@ static void write_spt(struct image *image) ERROR("Couldn't open temporary file xfel.spt\n"); return; } - + fprintf(fh, "%10d %10d %10.8f %10.6f %10.6f\n", 1, 1, fpix, 1.0, 0.0); fprintf(fh, "%10d %10d\n", 1, 1); fprintf(fh, "%10.5f %10.5f\n", 0.0, 0.0); - + struct sptline *sptlines; sptlines = malloc(sizeof(struct sptline)*nPeaks); - + for ( i=0; i<nPeaks; i++ ) { struct imagefeature *f; - + f = image_get_feature(image->features, i); if ( f == NULL ) continue; struct panel *pan; pan = find_panel(image->det,f->x,f->y); if ( pan == NULL ) continue; - + pix = 1000/pan->res; /* pixel size in mm */ height = f->intensity; - + sptlines[i].x = (f->y - pan->cy)*pix*fclen/pan->clen/1000; sptlines[i].y = -(f->x - pan->cx)*pix*fclen/pan->clen/1000; sptlines[i].h = height; sptlines[i].s = sigma; - + } - + qsort(sptlines, nPeaks, sizeof(struct sptline), compare_vals); - + for ( i=0; i<nPeaks; i++ ) { - + fprintf(fh, "%10.2f %10.2f %10.2f %10.2f %10.2f %10.2f\n", - sptlines[i].x, sptlines[i].y, - 0.0, 0.0, + sptlines[i].x, sptlines[i].y, + 0.0, 0.0, sptlines[i].h, sptlines[i].s); - + } - + fprintf(fh,"%10.2f %10.2f %10.2f %10.2f %10.2f %10.2f\n", -999.0,-999.0,-999.0,-999.0,-999.0,-999.0); fclose(fh); } -/* write a dummy 1x1 pixel image file for mosflm. Without post refinement, +/* write a dummy 1x1 pixel image file for mosflm. Without post refinement, mosflm will ignore this, but it must be present.*/ void write_img(struct image *image) { FILE *fh; char filename[1024]; unsigned short int * intimage; - + intimage = malloc(sizeof(unsigned short int)); intimage[0] = 1; - + snprintf(filename, 1023, "xfel-%i_001.img", image->id); - + fh = fopen(filename, "w"); if ( !fh ) { ERROR("Couldn't open temporary file xfel.spt\n"); return; } - + fprintf(fh,"{\nHEADER_BYTES=512;\n"); fprintf(fh,"BYTE_ORDER=little_endian;\n"); fprintf(fh,"TYPE=unsigned_short;\n"); diff --git a/src/mosflm.c b/src/mosflm.c index c5f81ee0..072ba4f1 100644 --- a/src/mosflm.c +++ b/src/mosflm.c @@ -48,11 +48,11 @@ todo ** properly read the newmat file (don't use fscanf-- spaces between numers are not guaranteed) -** "success" is indicated by existence of NEWMAT file written by mosflm. +** "success" is indicated by existence of NEWMAT file written by mosflm. Better to interact with mosflm directly in order to somehow verify success. - + ** investigate how these keywords affect mosflms behavior: - + MOSAICITY DISPERSION DIVERGENCE @@ -62,7 +62,7 @@ todo PREREFINE ON EXTRA ON POSTREF ON - + These did not seem to affect the results by my (Rick's) experience, probably because they are only used conjunction with image intensity data, but it's worth another look at the documentation. @@ -82,10 +82,10 @@ static int read_newmat(const char * filename, struct image *image) float csx, csy, csz; int n; double c; - + fh = fopen(filename,"r"); if (fh == NULL){ - STATUS("found newmat.\n"); + STATUS("found newmat.\n"); return 1; } n = fscanf(fh,"%f %f %f\n",&asx,&bsx,&csx); @@ -96,19 +96,19 @@ static int read_newmat(const char * filename, struct image *image) return 1; } fclose(fh); - + /* mosflm A matrix is multiplied by lambda, so fix this */ c = 1/image->lambda; - + image->candidate_cells[0] = cell_new(); - + 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; } @@ -123,12 +123,12 @@ void run_mosflm(struct image *image, UnitCell *cell) double wavelength; /* angstrom */ char newmatfile[128]; int fail; - + 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++) @@ -138,9 +138,9 @@ void run_mosflm(struct image *image, UnitCell *cell) j++; } } - symm[j] = '\0'; - - + 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, @@ -163,22 +163,21 @@ void run_mosflm(struct image *image, UnitCell *cell) /* Run the mosflm script */ fail = system(mos_cmd); - if (fail) { + if (fail) { ERROR("mosflm execution failed.\n"); - return; + return; } - /* Read the mosflm NEWMAT file and set cell candidate */ + /* 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"); + printf("Failed to read mosflm NEWMAT file.\n"); return; } /* remove the mosflm NEWMAT file */ //remove(newmatfile); - + return; } - |