diff options
Diffstat (limited to 'src/indexamajig.c')
| -rw-r--r-- | src/indexamajig.c | 41 |
1 files changed, 11 insertions, 30 deletions
diff --git a/src/indexamajig.c b/src/indexamajig.c index ff4b2243..b139f299 100644 --- a/src/indexamajig.c +++ b/src/indexamajig.c @@ -62,7 +62,6 @@ #include "detector.h" #include "filters.h" #include "thread-pool.h" -#include "beam-parameters.h" #include "geometry.h" #include "stream.h" #include "reflist-utils.h" @@ -90,9 +89,6 @@ static void show_help(const char *s) " methods separated by commas.\n" " See 'man indexamajig' for details.\n" " -g. --geometry=<file> Get detector geometry from file.\n" -" -b, --beam=<file> Get beam parameters from file (provides nominal\n" -" wavelength value if no per-shot value is found in\n" -" the HDF5 files.\n" " -p, --pdb=<file> File (PDB or CrystFEL unit cell format) from which\n" " to get the unit cell. Default: 'molecule.pdb'.\n" " --basename Remove the directory parts of the filenames.\n" @@ -199,6 +195,7 @@ int main(int argc, char *argv[]) char *tempdir = NULL; char *int_diag = NULL; char *geom_filename = NULL; + struct beam_params beam; /* Defaults */ iargs.cell = NULL; @@ -215,7 +212,7 @@ int main(int argc, char *argv[]) iargs.check_hdf5_snr = 0; iargs.det = NULL; iargs.peaks = PEAK_ZAEF; - iargs.beam = NULL; + iargs.beam = &beam; iargs.element = NULL; iargs.hdf5_peak_path = strdup("/processing/hitfinder/peakinfo"); iargs.copyme = NULL; @@ -250,7 +247,6 @@ int main(int argc, char *argv[]) {"output", 1, NULL, 'o'}, {"indexing", 1, NULL, 'z'}, {"geometry", 1, NULL, 'g'}, - {"beam", 1, NULL, 'b'}, {"pdb", 1, NULL, 'p'}, {"prefix", 1, NULL, 'x'}, {"threshold", 1, NULL, 't'}, @@ -300,7 +296,7 @@ int main(int argc, char *argv[]) }; /* Short options */ - while ((c = getopt_long(argc, argv, "hi:o:z:p:x:j:g:t:b:e:", + while ((c = getopt_long(argc, argv, "hi:o:z:p:x:j:g:t:e:v", longopts, NULL)) != -1) { switch (c) { @@ -309,7 +305,7 @@ int main(int argc, char *argv[]) show_help(argv[0]); return 0; - case 99 : + case 'v' : printf("CrystFEL: " CRYSTFEL_VERSIONSTRING "\n"); printf(CRYSTFEL_BOILERPLATE"\n"); return 0; @@ -340,27 +336,12 @@ int main(int argc, char *argv[]) case 'g' : geom_filename = optarg; - iargs.det = get_detector_geometry(optarg); - if ( iargs.det == NULL ) { - ERROR("Failed to read detector geometry from " - "'%s'\n", optarg); - return 1; - } break; case 't' : iargs.threshold = strtof(optarg, NULL); break; - case 'b' : - iargs.beam = get_beam_parameters(optarg); - if ( iargs.beam == NULL ) { - ERROR("Failed to load beam parameters" - " from '%s'\n", optarg); - return 1; - } - break; - case 'e' : iargs.element = strdup(optarg); break; @@ -514,6 +495,12 @@ int main(int argc, char *argv[]) return 1; } + iargs.det = get_detector_geometry(geom_filename, iargs.beam); + if ( iargs.det == NULL ) { + ERROR("Failed to read detector geometry from '%s'\n", optarg); + return 1; + } + if ( indm_str == NULL ) { STATUS("You didn't specify an indexing method, so I won't try " @@ -598,12 +585,6 @@ int main(int argc, char *argv[]) return 1; } - if ( iargs.beam == NULL ) { - ERROR("You need to provide a beam parameters file (please read" - " the manual for more details).\n"); - return 1; - } - add_geom_beam_stuff_to_copy_hdf5(iargs.copyme, iargs.det, iargs.beam); if ( cellfile != NULL ) { @@ -678,7 +659,7 @@ int main(int argc, char *argv[]) /* Prepare the indexer */ if ( indm != NULL ) { ipriv = prepare_indexing(indm, iargs.cell, iargs.det, - iargs.beam, iargs.tols); + iargs.tols); if ( ipriv == NULL ) { ERROR("Failed to prepare indexing.\n"); return 1; |