Move processing pipeline to separate file

1 files changed, 1 insertions, 209 deletions

diff --git a/src/im-sandbox.c b/src/im-sandbox.c
index 504c52c4..290f811f 100644
--- a/src/im-sandbox.c
+++ b/src/im-sandbox.c
@@ -41,8 +41,6 @@
 #include <string.h>
 #include <unistd.h>
 #include <getopt.h>
-#include <hdf5.h>
-#include <gsl/gsl_errno.h>
 #include <pthread.h>
 #include <sys/wait.h>
 #include <fcntl.h>
@@ -55,36 +53,14 @@
 #include <sys/time.h>
 #endif
 
-#include "utils.h"
-#include "hdf5-file.h"
-#include "index.h"
-#include "peaks.h"
-#include "detector.h"
-#include "filters.h"
-#include "thread-pool.h"
-#include "beam-parameters.h"
-#include "geometry.h"
-#include "stream.h"
-#include "reflist-utils.h"
-
 #include "im-sandbox.h"
+#include "process_image.h"
 
 
 /* Write statistics at APPROXIMATELY this interval */
 #define STATS_EVERY_N_SECONDS (5)
 
 
-/* Information about the indexing process for one pattern */
-struct pattern_args
-{
-	/* "Input" */
-	char *filename;
-
-	/* "Output" */
-	int n_crystals;
-};
-
-
 struct sb_reader
 {
 	pthread_mutex_t lock;
@@ -194,190 +170,6 @@ static char *get_pattern(FILE *fh, char **use_this_one_instead,
 }
 
 
-static void process_image(const struct index_args *iargs,
-                          struct pattern_args *pargs, Stream *st,
-                          int cookie)
-{
-	float *data_for_measurement;
-	size_t data_size;
-	int check;
-	struct hdfile *hdfile;
-	struct image image;
-	int i;
-	char filename[1024];
-
-	/* Prefix to jump out of temporary folder */
-	if ( pargs->filename[0] != '/' ) {
-		snprintf(filename, 1023, "../../%s", pargs->filename);
-	} else {
-		snprintf(filename, 1023, "%s", pargs->filename);
-	}
-
-	image.features = NULL;
-	image.data = NULL;
-	image.flags = NULL;
-	image.copyme = iargs->copyme;
-	image.id = cookie;
-	image.filename = pargs->filename;  /* Relative to top level */
-	image.beam = iargs->beam;
-	image.det = iargs->det;
-	image.crystals = NULL;
-	image.n_crystals = 0;
-
-	hdfile = hdfile_open(filename);  /* Relative to temporary folder */
-	if ( hdfile == NULL ) return;
-
-	if ( iargs->element != NULL ) {
-
-		int r;
-		r = hdfile_set_image(hdfile, iargs->element);
-		if ( r ) {
-			ERROR("Couldn't select path '%s'\n", iargs->element);
-			hdfile_close(hdfile);
-			return;
-		}
-
-	} else {
-
-		int r;
-		r = hdfile_set_first_image(hdfile, "/");
-		if ( r ) {
-			ERROR("Couldn't select first path\n");
-			hdfile_close(hdfile);
-			return;
-		}
-
-	}
-
-	check = hdf5_read(hdfile, &image, 1);
-	if ( check ) {
-		hdfile_close(hdfile);
-		return;
-	}
-
-	if ( (image.width != image.det->max_fs + 1 )
-	  || (image.height != image.det->max_ss + 1))
-	{
-		ERROR("Image size doesn't match geometry size"
-			" - rejecting image.\n");
-		ERROR("Image size: %i,%i.  Geometry size: %i,%i\n",
-		      image.width, image.height,
-		      image.det->max_fs + 1, image.det->max_ss + 1);
-		hdfile_close(hdfile);
-		return;
-	}
-
-	fill_in_values(image.det, hdfile);
-	fill_in_beam_parameters(image.beam, hdfile);
-
-	image.lambda = ph_en_to_lambda(eV_to_J(image.beam->photon_energy));
-
-	if ( (image.beam->photon_energy < 0.0) || (image.lambda > 1000) ) {
-		/* Error message covers a silly value in the beam file or in
-		 * the HDF5 file. */
-		ERROR("Nonsensical wavelength (%e m or %e eV) value for %s.\n",
-		      image.lambda, image.beam->photon_energy, image.filename);
-		hdfile_close(hdfile);
-		return;
-	}
-
-	if ( iargs->cmfilter ) filter_cm(&image);
-
-	/* Take snapshot of image after CM subtraction but before
-	 * the aggressive noise filter. */
-	data_size = image.width * image.height * sizeof(float);
-	data_for_measurement = malloc(data_size);
-
-	if ( iargs->noisefilter ) {
-		filter_noise(&image, data_for_measurement);
-	} else {
-		memcpy(data_for_measurement, image.data, data_size);
-	}
-
-	switch ( iargs->peaks ) {
-
-		case PEAK_HDF5:
-		// Get peaks from HDF5
-		if (get_peaks(&image, hdfile,
-			iargs->hdf5_peak_path)) {
-			ERROR("Failed to get peaks from HDF5 file.\n");
-		}
-		if ( !iargs->no_revalidate ) {
-			validate_peaks(&image, iargs->min_int_snr,
-				       iargs->ir_inn, iargs->ir_mid,
-				       iargs->ir_out, iargs->use_saturated);
-		}
-		break;
-
-		case PEAK_ZAEF:
-		search_peaks(&image, iargs->threshold,
-		             iargs->min_gradient, iargs->min_snr,
-		             iargs->ir_inn, iargs->ir_mid, iargs->ir_out,
-		             iargs->use_saturated);
-		break;
-
-	}
-
-	/* Get rid of noise-filtered version at this point
-	 * - it was strictly for the purposes of peak detection. */
-	free(image.data);
-	image.data = data_for_measurement;
-
-	/* Index the pattern */
-	index_pattern(&image, iargs->indm, iargs->ipriv);
-
-	pargs->n_crystals = image.n_crystals;
-
-	/* Default beam parameters */
-	image.div = image.beam->divergence;
-	image.bw = image.beam->bandwidth;
-
-	/* Integrate each crystal's diffraction spots */
-	for ( i=0; i<image.n_crystals; i++ ) {
-
-		RefList *reflections;
-
-		/* Set default crystal parameter(s) */
-		crystal_set_profile_radius(image.crystals[i],
-		                           image.beam->profile_radius);
-
-		if ( iargs->integrate_found ) {
-			reflections = select_intersections(&image,
-			                                   image.crystals[i]);
-		} else {
-			reflections = find_intersections(&image,
-			                                 image.crystals[i]);
-		}
-
-		crystal_set_reflections(image.crystals[i], reflections);
-
-	}
-
-	/* Integrate all the crystals at once - need all the crystals so that
-	 * overlaps can be detected. */
-	integrate_reflections(&image, iargs->closer,
-	                              iargs->bgsub,
-	                              iargs->min_int_snr,
-	                              iargs->ir_inn,
-	                              iargs->ir_mid,
-	                              iargs->ir_out,
-	                              iargs->integrate_saturated,
-	                              iargs->res_cutoff);
-
-	write_chunk(st, &image, hdfile,
-	            iargs->stream_peaks, iargs->stream_refls);
-
-	for ( i=0; i<image.n_crystals; i++ ) {
-		crystal_free(image.crystals[i]);
-	}
-
-	free(image.data);
-	if ( image.flags != NULL ) free(image.flags);
-	image_feature_list_free(image.features);
-	hdfile_close(hdfile);
-}
-
-
 static void run_work(const struct index_args *iargs,
                      int filename_pipe, int results_pipe, Stream *st,
                      int cookie)