diff options
Diffstat (limited to 'src/process_hkl.c')
| -rw-r--r-- | src/process_hkl.c | 71 |
1 files changed, 40 insertions, 31 deletions
diff --git a/src/process_hkl.c b/src/process_hkl.c index d110695b..53ac1169 100644 --- a/src/process_hkl.c +++ b/src/process_hkl.c @@ -37,31 +37,31 @@ static void show_help(const char *s) printf( "Assemble and process FEL Bragg intensities.\n" "\n" -" -h, --help Display this help message.\n" -" -i, --input=<filename> Specify input filename (\"-\" for stdin).\n" -" -o, --output=<filename> Specify output filename for merged intensities\n" -" (don't specify for no output).\n" +" -h, --help Display this help message.\n" +" -i, --input=<filename> Specify input filename (\"-\" for stdin).\n" +" -o, --output=<filename> Specify output filename for merged intensities\n" +" (don't specify for no output).\n" "\n" -" --max-only Take the integrated intensity to be equal to the\n" -" maximum intensity measured for that reflection.\n" -" The default is to use the mean value from all\n" -" measurements.\n" -" -e, --output-every=<n> Analyse figures of merit after every n patterns\n" -" Default: 1000. A value of zero means to do the\n" -" analysis only after reading all the patterns.\n" -" --no-analyse Don't perform any kind of analysis, just merge the\n" -" intensities.\n" -" --sum Sum (rather than average) the intensities for the\n" -" final output list. This is useful for comparing\n" -" results to radially summed powder patterns, but\n" -" will break R-factor analysis.\n" -" -r, --rvsq Output lists of R vs |q| (\"Luzzatti plots\") when\n" -" analysing figures of merit.\n" -" --stop-after=<n> Stop after processing n patterns. Zero means\n" -" keep going until the end of the input, and is the\n" -" default.\n" -" --zone-axis Output an [001] zone axis pattern each time the\n" -" figures of merit are analysed.\n"); +" --max-only Take the integrated intensity to be equal to the\n" +" maximum intensity measured for that reflection.\n" +" The default is to use the mean value from all\n" +" measurements.\n" +" --sum Sum (rather than average) the intensities for the\n" +" final output list. This is useful for comparing\n" +" results to radially summed powder patterns, but\n" +" will break R-factor analysis.\n" +" --stop-after=<n> Stop after processing n patterns. Zero means\n" +" keep going until the end of the input, and is\n" +" the default.\n" +" -c, --compare-with=<file> Compare with reflection intensities in this file\n" +"\n" +" -e, --output-every=<n> Analyse figures of merit after every n patterns\n" +" Default: 1000. A value of zero means to do the\n" +" analysis only after reading all the patterns.\n" +" -r, --rvsq Output lists of R vs |q| (\"Luzzatti plots\")\n" +" when analysing figures of merit.\n" +" --zone-axis Output an [001] zone axis pattern each time the\n" +" figures of merit are analysed.\n"); } @@ -193,8 +193,8 @@ int main(int argc, char *argv[]) int config_rvsq = 0; int config_stopafter = 0; int config_zoneaxis = 0; - int config_noanalyse = 0; int config_sum = 0; + char *intfile = NULL; /* Long options */ const struct option longopts[] = { @@ -203,10 +203,10 @@ int main(int argc, char *argv[]) {"output", 1, NULL, 'o'}, {"max-only", 0, &config_maxonly, 1}, {"output-every", 1, NULL, 'e'}, - {"no-analyse", 0, &config_noanalyse, 1}, {"rvsq", 0, NULL, 'r'}, {"stop-after", 1, NULL, 's'}, {"zone-axis", 0, &config_zoneaxis, 1}, + {"compare-with", 0, NULL, 'c'}, {"sum", 0, &config_sum, 1}, {0, 0, NULL, 0} }; @@ -245,6 +245,11 @@ int main(int argc, char *argv[]) break; } + case 'c' : { + intfile = strdup(optarg); + break; + } + case 0 : { break; } @@ -261,14 +266,18 @@ int main(int argc, char *argv[]) return 1; } + if ( intfile != NULL ) { + STATUS("Comparing against '%s'\n", intfile); + trueref = read_reflections(intfile); + free(intfile); + } else { + trueref = NULL; + } + ref = new_list_intensity(); counts = new_list_count(); mol = load_molecule(); - if ( !config_noanalyse ) { - get_reflections_cached(mol, eV_to_J(2.0e3)); - trueref = ideal_intensities(mol->reflections); - } if ( strcmp(filename, "-") == 0 ) { fh = stdin; @@ -331,7 +340,7 @@ int main(int argc, char *argv[]) fclose(fh); - if ( !config_noanalyse ) { + if ( trueref != NULL ) { process_reflections(ref, trueref, counts, n_patterns, mol->cell, config_rvsq, config_zoneaxis); } |