diff options
Diffstat (limited to 'src/indexamajig.c')
| -rw-r--r-- | src/indexamajig.c | 38 |
1 files changed, 31 insertions, 7 deletions
diff --git a/src/indexamajig.c b/src/indexamajig.c index 0fb97bfe..39ceea2b 100644 --- a/src/indexamajig.c +++ b/src/indexamajig.c @@ -59,6 +59,7 @@ struct process_args int config_nomatch; int config_unpolar; int config_sanity; + struct detector *det; IndexingMethod indm; const double *intensities; const unsigned int *counts; @@ -86,6 +87,7 @@ static void show_help(const char *s) " --indexing=<method> Use 'method' for indexing. Choose from:\n" " none : no indexing\n" " dirax : invoke DirAx\n" +" -g. --geometry=<file> Get detector geometry from file.\n" "\n\nWith just the above options, this program does not do much of practical " "use.\nYou should also enable some of the following:\n\n" " --near-bragg Output a list of reflection intensities to stdout.\n" @@ -159,7 +161,7 @@ static struct image *get_simage(struct image *template, int alternate) * - not necessarily the same as the original. */ image->width = 1024; image->height = 1024; - image->det.n_panels = 2; + image->det->n_panels = 2; if ( alternate ) { @@ -183,12 +185,12 @@ static struct image *get_simage(struct image *template, int alternate) panels[1].clen = 56.7e-2; /* 56.7 cm */ panels[1].res = 13333.3; /* 75 microns/pixel */ - image->det.panels = panels; + image->det->panels = panels; } else { /* Copy pointer to old geometry */ - image->det.panels = template->det.panels; + image->det->panels = template->det->panels; } @@ -263,6 +265,7 @@ static void *process_image(void *pargsv) image.filename = filename; image.hits = NULL; image.n_hits = 0; + image.det = pargs->det; /* View head-on (unit cell is tilted) */ image.orientation.w = 1.0; @@ -285,8 +288,6 @@ static void *process_image(void *pargsv) return result; } - #include "geometry-lcls.tmp" - hdf5_read(hdfile, &image); if ( config_cmfilter ) { @@ -372,7 +373,6 @@ static void *process_image(void *pargsv) done: free(image.data); free(image.flags); - free(image.det.panels); image_feature_list_free(image.features); free(image.hits); hdfile_close(hdfile); @@ -409,6 +409,8 @@ int main(int argc, char *argv[]) int config_alternate = 0; int config_unpolar = 0; int config_sanity = 0; + struct detector *det; + char *geometry = NULL; IndexingMethod indm; char *indm_str = NULL; UnitCell *cell; @@ -435,6 +437,7 @@ int main(int argc, char *argv[]) {"near-bragg", 0, &config_nearbragg, 1}, {"write-drx", 0, &config_writedrx, 1}, {"indexing", 1, NULL, 'z'}, + {"geometry", 1, NULL, 'g'}, {"simulate", 0, &config_simulate, 1}, {"filter-cm", 0, &config_cmfilter, 1}, {"filter-noise", 0, &config_noisefilter, 1}, @@ -450,7 +453,8 @@ int main(int argc, char *argv[]) }; /* Short options */ - while ((c = getopt_long(argc, argv, "hi:wp:j:x:", longopts, NULL)) != -1) { + while ((c = getopt_long(argc, argv, "hi:wp:j:x:g:", + longopts, NULL)) != -1) { switch (c) { case 'h' : { @@ -488,6 +492,11 @@ int main(int argc, char *argv[]) break; } + case 'g' : { + geometry = strdup(optarg); + break; + } + case 0 : { break; } @@ -550,6 +559,18 @@ int main(int argc, char *argv[]) } free(indm_str); + if ( geometry == NULL ) { + ERROR("You need to specify a geometry file with --geometry\n"); + return 1; + } + + det = get_detector_geometry(geometry); + if ( det == NULL ) { + ERROR("Failed to read detector geometry from '%s'\n", geometry); + return 1; + } + free(geometry); + cell = load_cell_from_pdb(pdb); if ( cell == NULL ) { if ( pdb == NULL ) { @@ -603,6 +624,7 @@ int main(int argc, char *argv[]) pargs->config_unpolar = config_unpolar; pargs->config_sanity = config_sanity; pargs->cell = cell; + pargs->det = det; pargs->indm = indm; pargs->intensities = intensities; pargs->counts = counts; @@ -695,6 +717,8 @@ int main(int argc, char *argv[]) } free(prefix); + free(det->panels); + free(det); free(cell); fclose(fh); |