diff options
Diffstat (limited to 'src/indexamajig.c')
| -rw-r--r-- | src/indexamajig.c | 91 |
1 files changed, 37 insertions, 54 deletions
diff --git a/src/indexamajig.c b/src/indexamajig.c index 51461c91..72491450 100644 --- a/src/indexamajig.c +++ b/src/indexamajig.c @@ -36,6 +36,7 @@ #include "thread-pool.h" #include "beam-parameters.h" #include "geometry.h" +#include "stream.h" enum { @@ -50,9 +51,8 @@ struct static_index_args UnitCell *cell; int config_cmfilter; int config_noisefilter; - int config_dumpfound; int config_verbose; - int config_nearbragg; + int stream_flags; int config_polar; int config_satcorr; int config_closer; @@ -109,7 +109,8 @@ 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" -" -o, --output=<filename> Write indexed stream to this file. '-' for stdout.\n" +" -o, --output=<filename> Write output stream to this file. '-' for stdout.\n" +" Default: indexamajig.stream\n" "\n" " --indexing=<methods> Use 'methods' for indexing. Provide one or more\n" " methods separated by commas. Choose from:\n" @@ -129,25 +130,19 @@ static void show_help(const char *s) " This is the default method.\n" " hdf5 : Get from /processing/hitfinder/peakinfo\n" " in the HDF5 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" -" When pixels with fractional indices within 0.1 of\n" -" integer values (the Bragg condition) are found,\n" -" the integral of pixels within a ten pixel radius\n" -" of the nearest-to-Bragg pixel will be reported as\n" -" the intensity. The centroid of the pixels will\n" -" be given as the coordinates, as well as the h,k,l\n" -" (integer) indices of the reflection. If a peak\n" -" was located by the initial peak search close to\n" -" the \"near Bragg\" location, its coordinates will\n" -" be taken as the centre instead.\n" -" --dump-peaks Write the results of the peak search to stdout.\n" -" The intensities in this list are from the\n" -" centroid/integration procedure.\n" -"\n" -"\nFor more control over the process, you might need:\n\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" +"\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" " none : no matching, just use the raw cell.\n" " reduce : full cell reduction.\n" @@ -196,9 +191,7 @@ static void process_image(void *pp, int cookie) UnitCell *cell = pargs->static_args.cell; int config_cmfilter = pargs->static_args.config_cmfilter; int config_noisefilter = pargs->static_args.config_noisefilter; - int config_dumpfound = pargs->static_args.config_dumpfound; int config_verbose = pargs->static_args.config_verbose; - int config_nearbragg = pargs->static_args.config_nearbragg; int config_polar = pargs->static_args.config_polar; IndexingMethod *indm = pargs->static_args.indm; const struct beam_params *beam = pargs->static_args.beam; @@ -274,7 +267,6 @@ static void process_image(void *pp, int cookie) /* Get peaks from HDF5 */ if ( get_peaks(&image, hdfile) ) { ERROR("Failed to get peaks from HDF5 file.\n"); - return; } break; case PEAK_ZAEF : @@ -288,51 +280,44 @@ static void process_image(void *pp, int cookie) free(image.data); image.data = data_for_measurement; - if ( config_dumpfound ) { - dump_peaks(&image, pargs->static_args.ofh, - pargs->static_args.output_mutex); - } - - /* Not indexing? Then there's nothing left to do. */ - if ( indm == NULL ) goto done; - /* Calculate orientation matrix (by magic) */ index_pattern(&image, cell, indm, pargs->static_args.cellr, config_verbose, pargs->static_args.ipriv, pargs->static_args.config_insane); /* No cell at this point? Then we're done. */ - if ( image.indexed_cell == NULL ) goto done; - pargs->indexable = 1; + if ( image.indexed_cell != NULL ) pargs->indexable = 1; /* Measure intensities if requested */ - if ( config_nearbragg ) { - RefList *reflections; + /* Do EITHER: */ - image.div = beam->divergence; - image.bw = beam->bandwidth; - image.profile_radius = 0.0001e9; + //image.div = beam->divergence; + //image.bw = beam->bandwidth; + //image.profile_radius = 0.0001e9; + //image.reflections = find_intersections(&image, + // image.indexed_cell, 0); - //reflections = find_intersections(&image, image.indexed_cell, - // 0); - reflections = find_projected_peaks(&image, image.indexed_cell, - 0, 0.1); + image.reflections = find_projected_peaks(&image, + image.indexed_cell, + 0, 0.1); - output_intensities(&image, image.indexed_cell, reflections, - pargs->static_args.output_mutex, - config_polar, - pargs->static_args.config_closer, - pargs->static_args.ofh); + integrate_reflections(&image, config_polar, + pargs->static_args.config_closer); - reflist_free(reflections); + /* OR */ - } + //image.reflections = integrate_pixels(&image, 0, 0.1, + // config_polar); + + pthread_mutex_lock(pargs->static_args.output_mutex); + write_chunk(pargs->static_args.ofh, &image, + pargs->static_args.stream_flags); + pthread_mutex_unlock(pargs->static_args.output_mutex); /* Only free cell if found */ cell_free(image.indexed_cell); -done: free(image.data); free(image.flags); image_feature_list_free(image.features); @@ -737,9 +722,7 @@ int main(int argc, char *argv[]) qargs.static_args.cell = cell; qargs.static_args.config_cmfilter = config_cmfilter; qargs.static_args.config_noisefilter = config_noisefilter; - qargs.static_args.config_dumpfound = config_dumpfound; qargs.static_args.config_verbose = config_verbose; - qargs.static_args.config_nearbragg = config_nearbragg; qargs.static_args.config_polar = config_polar; qargs.static_args.config_satcorr = config_satcorr; qargs.static_args.config_closer = config_closer; |