diff options
Diffstat (limited to 'src/indexamajig.c')
| -rw-r--r-- | src/indexamajig.c | 37 |
1 files changed, 25 insertions, 12 deletions
diff --git a/src/indexamajig.c b/src/indexamajig.c index 72491450..320439b3 100644 --- a/src/indexamajig.c +++ b/src/indexamajig.c @@ -52,7 +52,7 @@ struct static_index_args int config_cmfilter; int config_noisefilter; int config_verbose; - int stream_flags; + int stream_flags; /* What goes into the output? */ int config_polar; int config_satcorr; int config_closer; @@ -62,7 +62,7 @@ struct static_index_args struct detector *det; IndexingMethod *indm; IndexingPrivate **ipriv; - int peaks; + int peaks; /* Peak detection method */ int cellr; struct beam_params *beam; const char *element; @@ -132,15 +132,20 @@ static void show_help(const char *s) " in the HDF5 file.\n" "\n\n" "You can control what information is included in the output stream using\n" -"' --record=<flags>'. Possible flags are:\n" -"pixels Include a list of sums of pixel values within the\n" -" integration domain, correcting for individual pixel\n" -" solid angles.\n" -"integrated Include a list of reflection intensities, produced by\n" -" integrating around predicted peak locations.\n" -" The flags 'pixels' and 'integrated' are mutually exclusive.\n" -"peaks Include peak locations and intensities from the peak search.\n" -"peaksifindexed Include peak locations only if the pattern could be indexed.\n" +"' --record=<flags>'. Possible flags are:\n\n" +" pixels Include a list of sums of pixel values within the\n" +" integration domain, correcting for individual pixel\n" +" solid angles.\n" +"\n" +" integrated Include a list of reflection intensities, produced by\n" +" integrating around predicted peak locations.\n" +"\n" +" peaks Include peak locations and intensities from the peak search.\n" +"\n" +" peaksifindexed As 'peaks', but only if the pattern could be indexed.\n\n" +"\n" +"The default is '--record=integrated'. The flags 'pixels' and 'integrated'\n" +"are mutually exclusive, as are the flags 'peaks' and 'peaksifindexed'.\n" "\n\n" "For more control over the process, you might need:\n\n" " --cell-reduction=<m> Use <m> as the cell reduction method. Choose from:\n" @@ -162,7 +167,7 @@ static void show_help(const char *s) " --min-gradient=<n> Minimum gradient for Zaefferer peak search.\n" " Default: 100,000.\n" " -e, --image=<element> Use this image from the HDF5 file.\n" -" Example: /data/data0." +" Example: /data/data0.\n" " Default: The first one found.\n" "\n" "\nOptions for greater performance or verbosity:\n\n" @@ -431,6 +436,7 @@ int main(int argc, char *argv[]) struct beam_params *beam = NULL; char *element = NULL; double nominal_photon_energy; + int stream_flags = STREAM_INTEGRATED; /* Long options */ const struct option longopts[] = { @@ -460,6 +466,7 @@ int main(int argc, char *argv[]) {"insane", 0, &config_insane, 1}, {"image", 1, NULL, 'e'}, {"basename", 0, &config_basename, 1}, + {"record", 1, NULL, 5}, {0, 0, NULL, 0} }; @@ -529,6 +536,11 @@ int main(int argc, char *argv[]) element = strdup(optarg); break; + case 5 : + stream_flags = parse_stream_flags(optarg); + if ( stream_flags < 0 ) return 1; + break; + case 0 : break; @@ -673,6 +685,7 @@ int main(int argc, char *argv[]) free(pdb); /* Start by writing the entire command line to stdout */ + fprintf(ofh, "CrystFEL stream format 2.0\n"); fprintf(ofh, "Command line:"); for ( i=0; i<argc; i++ ) { fprintf(ofh, " %s", argv[i]); |