diff options
Diffstat (limited to 'src/indexamajig.c')
| -rw-r--r-- | src/indexamajig.c | 54 |
1 files changed, 44 insertions, 10 deletions
diff --git a/src/indexamajig.c b/src/indexamajig.c index 245d1a81..d59132c5 100644 --- a/src/indexamajig.c +++ b/src/indexamajig.c @@ -43,10 +43,12 @@ static void show_help(const char *s) "\n" " -i, --input=<filename> Specify file containing list of images to process.\n" " '-' means stdin, which is the default.\n" -" --no-index Do everything else (including fine peak search and\n" -" writing 'xfel.drx' if DirAx is being used), but\n" -" don't actually index.\n" -" --dirax Use DirAx for indexing.\n" +" --indexing=<method> Use 'method' for indexing. Choose from:\n" +" none : no indexing\n" +" dirax : invoke DirAx\n" +" --write-drx Write 'xfel.drx' for visualisation of reciprocal\n" +" space. Implied by any indexing method other than" +" 'none'.\n" " --dump-peaks Write the results of the peak search to stdout.\n" " --near-bragg Output a list of reflection intensities to stdout.\n" " --simulate Simulate the diffraction pattern using the indexed\n" @@ -65,9 +67,11 @@ int main(int argc, char *argv[]) int n_hits; int config_noindex = 0; int config_dumpfound = 0; - int config_dirax = 0; int config_nearbragg = 0; + int config_writedrx = 0; int config_simulate = 0; + IndexingMethod indm; + char *indm_str = NULL; /* Long options */ const struct option longopts[] = { @@ -76,7 +80,8 @@ int main(int argc, char *argv[]) {"no-index", 0, &config_noindex, 1}, {"dump-peaks", 0, &config_dumpfound, 1}, {"near-bragg", 0, &config_nearbragg, 1}, - {"dirax", 0, &config_dirax, 1}, + {"write-drx", 0, &config_writedrx, 1}, + {"indexing", 1, NULL, 'z'}, {"simulate", 0, &config_simulate, 1}, {0, 0, NULL, 0} }; @@ -95,6 +100,11 @@ int main(int argc, char *argv[]) break; } + case 'z' : { + indm_str = strdup(optarg); + break; + } + case 0 : { break; } @@ -120,6 +130,20 @@ int main(int argc, char *argv[]) return 1; } + if ( indm_str == NULL ) { + STATUS("You didn't specify an indexing method, so I won't" + " try to index anything. If that isn't what you\n" + " wanted, re-run with --indexing=<method>.\n"); + indm = INDEXING_NONE; + } else if ( strcmp(indm_str, "none") == 0 ) { + indm = INDEXING_NONE; + } else if ( strcmp(indm_str, "dirax") == 0) { + indm = INDEXING_DIRAX; + } else { + ERROR("Unrecognised indexing method '%s'\n", indm_str); + return 1; + } + n_images = 0; n_hits = 0; do { @@ -160,13 +184,22 @@ int main(int argc, char *argv[]) if ( config_dumpfound ) dump_peaks(&image); - /* Not indexing? Then there's nothing left to do. */ - if ( config_noindex ) goto done; + /* Not indexing nor writing xfel.drx? + * Then there's nothing left to do. */ + if ( (!config_writedrx) && (indm == INDEXING_NONE) ) { + goto done; + } /* Calculate orientation matrix (by magic) */ - index_pattern(&image, config_noindex, config_dirax); + if ( config_writedrx || (indm != INDEXING_NONE) ) { + index_pattern(&image, indm); + } + + /* No cell at this point? Then we're done. */ if ( image.indexed_cell == NULL ) goto done; + /* Simulation or intensity measurements both require + * Ewald sphere vectors */ if ( config_nearbragg || config_simulate ) { /* Simulate a diffraction pattern */ @@ -184,11 +217,12 @@ int main(int argc, char *argv[]) } + /* Measure intensities if requested */ if ( config_nearbragg ) { - /* Read h,k,l,I */ output_intensities(&image, image.indexed_cell); } + /* Simulate pattern if requested */ if ( config_simulate ) { image.data = NULL; |