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-rw-r--r--src/indexamajig.c91
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;