Remove ReAx and GrainSpotter

Neither of these ever really worked, and better algorithms exist now.

7 files changed, 4 insertions, 1902 deletions

diff --git a/libcrystfel/Makefile.am b/libcrystfel/Makefile.am
index 989ce434..be7a2556 100644
--- a/libcrystfel/Makefile.am
+++ b/libcrystfel/Makefile.am
@@ -9,11 +9,10 @@ libcrystfel_la_SOURCES = src/reflist.c src/utils.c src/cell.c src/detector.c \
                          src/reflist-utils.c src/filters.c \
                          src/render.c src/index.c src/dirax.c src/mosflm.c \
                          src/cell-utils.c src/integer_matrix.c src/crystal.c \
-                         src/grainspotter.c src/xds.c src/integration.c \
+                         src/xds.c src/integration.c \
                          src/histogram.c src/events.c src/asdf.c
 
 if HAVE_FFTW
-libcrystfel_la_SOURCES += src/reax.c
 endif
 
 libcrystfel_la_includedir=$(includedir)/crystfel/
@@ -26,9 +25,9 @@ libcrystfel_la_include_HEADERS = ${top_srcdir}/version.h \
                                  src/geometry.h src/peaks.h src/stream.h \
                                  src/render.h src/index.h src/image.h \
                                  src/filters.h src/dirax.h src/mosflm.h \
-                                 src/reax.h src/cell-utils.h \
+                                 src/cell-utils.h \
                                  src/integer_matrix.h src/crystal.h \
-                                 src/grainspotter.h src/xds.h \
+                                 src/xds.h \
                                  src/integration.h src/histogram.h \
                                  src/events.h src/asdf.h
 
diff --git a/libcrystfel/src/grainspotter.c b/libcrystfel/src/grainspotter.c
deleted file mode 100644
index 261756d6..00000000
--- a/libcrystfel/src/grainspotter.c
+++ /dev/null
@@ -1,500 +0,0 @@
-/*
- * grainspotter.c
- *
- * Invoke GrainSpotter for multi-crystal autoindexing
- *
- * Copyright © 2013-2014 Deutsches Elektronen-Synchrotron DESY,
- *                       a research centre of the Helmholtz Association.
- *
- * Authors:
- *   2010-2014 Thomas White <taw@physics.org>
- *
- * This file is part of CrystFEL.
- *
- * CrystFEL is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * CrystFEL is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with CrystFEL.  If not, see <http://www.gnu.org/licenses/>.
- *
- */
-
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-
-#include <stdlib.h>
-#include <stdio.h>
-#include <math.h>
-#include <pty.h>
-#include <string.h>
-#include <unistd.h>
-#include <sys/wait.h>
-#include <fcntl.h>
-#include <assert.h>
-#include <sys/ioctl.h>
-#include <errno.h>
-
-#ifdef HAVE_CLOCK_GETTIME
-#include <time.h>
-#else
-#include <sys/time.h>
-#endif
-
-#include "image.h"
-#include "utils.h"
-#include "peaks.h"
-#include "cell.h"
-#include "cell-utils.h"
-#include "grainspotter.h"
-
-
-#define GRAINSPOTTER_VERBOSE 0
-
-
-/* Global private data, prepared once */
-struct grainspotter_private
-{
-	IndexingMethod indm;
-	UnitCell *cell;
-};
-
-
-/* Data needed during the run of Grainspotter */
-struct grainspotter_data {
-
-	struct grainspotter_private *gp;
-
-	/* Low-level stuff */
-	int                     pty;
-	pid_t                   pid;
-	char                    *rbuffer;
-	int                     rbufpos;
-	int                     rbuflen;
-
-};
-
-
-static int read_matrix(struct grainspotter_private *gp, struct image *image,
-                       char *filename)
-{
-	FILE *fh;
-	int d1;
-	float d2;
-	float ubi11, ubi12, ubi13;
-	float ubi21, ubi22, ubi23;
-	float ubi31, ubi32, ubi33;
-	char line[1024];
-	int r;
-
-	fh = fopen(filename, "r");
-	if ( fh == NULL ) {
-		ERROR("Can't open '%s'\n", filename);
-		return 1;
-	}
-
-	/* Read and discard first line */
-	if ( fgets(line, 1024, fh) == NULL ) {
-		ERROR("Failed to read GFF file.\n");
-		return 1;
-	}
-
-	do {
-
-		Crystal *cr;
-		UnitCell *cell;
-
-		/* One line per grain */
-		if ( fgets(line, 1024, fh) == NULL ) {
-			ERROR("Failed to read GFF file.\n");
-			return 1;
-		}
-
-		STATUS("'%s'\n", line);
-
-		r = sscanf(line, "%i %f %f %f %f %f %f %f %f %f %f %f %f"
-			         "%f %f %f %f %f %f %f %f %f %f %f",
-			         &d1, &d2, &d2, &d2, &d2, &d2, &d2, &d2, &d2,
-			         &d2, &d2, &d2, &d2, &d2, &d2,
-			         &ubi11, &ubi12, &ubi13,
-			         &ubi21, &ubi22, &ubi23,
-			         &ubi31, &ubi32, &ubi33);
-
-		if ( r != 24 ) {
-			ERROR("Only %i parameters in GFF file\n", r);
-			return 1;
-		}
-
-		cell = cell_new();
-
-		cell_set_cartesian(cell, ubi12/1e10, ubi13/1e10, ubi11/1e10,
-			                 ubi22/1e10, ubi23/1e10, ubi21/1e10,
-			                 ubi32/1e10, ubi33/1e10, ubi31/1e10);
-
-		cr = crystal_new();
-		if ( cr == NULL ) {
-			ERROR("Failed to allocate crystal.\n");
-			return 0;
-		}
-
-		crystal_set_cell(cr, cell);
-		image_add_crystal(image, cr);
-
-	} while ( !feof(fh) );
-
-	fclose(fh);
-
-	if ( gp->indm & INDEXING_CHECK_PEAKS ) {
-		if ( !peak_sanity_check(image, image->crystals,
-		                        image->n_crystals) )
-		{
-			free_all_crystals(image);
-			return 0;
-		}
-	}
-
-        return 0;
-}
-
-
-static void gs_parseline(char *line, struct image *image,
-                         struct grainspotter_data *gs)
-{
-	#if GRAINSPOTTER_VERBOSE
-	STATUS("%s\n", line);
-	#endif
-}
-
-
-static int grainspotter_readable(struct image *image,
-                                 struct grainspotter_data *gs)
-{
-	int rval;
-	int no_string = 0;
-
-	rval = read(gs->pty, gs->rbuffer+gs->rbufpos, gs->rbuflen-gs->rbufpos);
-
-	if ( (rval == -1) || (rval == 0) ) return 1;
-
-	gs->rbufpos += rval;
-	assert(gs->rbufpos <= gs->rbuflen);
-
-	while ( (!no_string) && (gs->rbufpos > 0) ) {
-
-		int i;
-		int block_ready = 0;
-
-		/* See if there's a full line in the buffer yet */
-		for ( i=0; i<gs->rbufpos-1; i++ ) {
-			/* Means the last value looked at is rbufpos-2 */
-
-			if ( (gs->rbuffer[i] == '\r')
-			  && (gs->rbuffer[i+1] == '\n') ) {
-				block_ready = 1;
-				break;
-			}
-
-		}
-
-		if ( block_ready ) {
-
-			unsigned int new_rbuflen;
-			unsigned int endbit_length;
-			char *block_buffer = NULL;
-
-			block_buffer = malloc(i+1);
-			memcpy(block_buffer, gs->rbuffer, i);
-			block_buffer[i] = '\0';
-
-			if ( block_buffer[0] == '\r' ) {
-				memmove(block_buffer, block_buffer+1, i);
-			}
-
-			gs_parseline(block_buffer, image, gs);
-			free(block_buffer);
-			endbit_length = i+2;
-
-			/* Now the block's been parsed, it should be
-			 * forgotten about */
-			memmove(gs->rbuffer,
-			        gs->rbuffer + endbit_length,
-			        gs->rbuflen - endbit_length);
-
-			/* Subtract the number of bytes removed */
-			gs->rbufpos = gs->rbufpos  - endbit_length;
-			new_rbuflen = gs->rbuflen - endbit_length;
-			if ( new_rbuflen == 0 ) new_rbuflen = 256;
-			gs->rbuffer = realloc(gs->rbuffer, new_rbuflen);
-			gs->rbuflen = new_rbuflen;
-
-		} else {
-
-			if ( gs->rbufpos==gs->rbuflen ) {
-
-				/* More buffer space is needed */
-				gs->rbuffer = realloc(gs->rbuffer,
-				                      gs->rbuflen + 256);
-				gs->rbuflen = gs->rbuflen + 256;
-				/* The new space gets used at the next
-				 * read, shortly... */
-
-			}
-			no_string = 1;
-
-		}
-
-	}
-
-	return 0;
-}
-
-
-static void write_gve(struct image *image, struct grainspotter_private *gp)
-{
-	FILE *fh;
-	int i;
-	char filename[1024];
-	double a, b, c, al, be, ga;
-
-	snprintf(filename, 1023, "xfel-%i.gve", image->id);
-
-	fh = fopen(filename, "w");
-	if ( !fh ) {
-		ERROR("Couldn't open temporary file '%s'\n", filename);
-		return;
-	}
-
-	cell_get_parameters(gp->cell, &a, &b, &c, &al, &be, &ga);
-	fprintf(fh, "%.6f %.6f %.6f %.6f %.6f %.6f P\n", a*1e10, b*1e10, c*1e10,
-	                     rad2deg(al), rad2deg(be), rad2deg(ga));
-	fprintf(fh, "# wavelength = %.6f\n", image->lambda*1e10);
-	fprintf(fh, "# wedge = 0.000000\n");
-	fprintf(fh, "# ds h k l\n");
-	fprintf(fh, "# xr yr zr xc yc ds eta omega\n");
-
-	for ( i=0; i<image_feature_count(image->features); i++ ) {
-
-		struct imagefeature *f;
-
-		f = image_get_feature(image->features, i);
-		if ( f == NULL ) continue;
-
-		fprintf(fh, "%.6f %.6f %.6f 0 0 %.6f %.6f %.6f 0\n",
-		        f->rz/1e10, f->rx/1e10, f->ry/1e10,
-		        modulus(f->rx, f->ry, f->rz)/1e10, /* dstar */
-		        rad2deg(atan2(f->ry, f->rx)), 0.0);   /* eta, omega */
-
-	}
-	fclose(fh);
-}
-
-
-static char *write_ini(struct image *image)
-{
-	FILE *fh;
-	char *filename;
-	double tt;
-
-	filename = malloc(1024);
-	if ( filename == NULL ) return NULL;
-
-	snprintf(filename, 1023, "xfel-%i.ini", image->id);
-
-	fh = fopen(filename, "w");
-	if ( !fh ) {
-		ERROR("Couldn't open temporary file '%s'\n", filename);
-		free(filename);
-		return NULL;
-	}
-
-	get_q_for_panel(image->det->furthest_out_panel,
-	                image->det->furthest_out_fs,
-	                image->det->furthest_out_ss,
-	                &tt, 1.0/image->lambda);
-
-	fprintf(fh, "spacegroup 96\n");
-	fprintf(fh, "!dsrange 0 1.3\n");
-	fprintf(fh, "tthrange 0 %.2f\n", 20.0);
-	fprintf(fh, "etarange 0 360\n");
-	fprintf(fh, "domega 1\n");
-	fprintf(fh, "omegarange -0.5 0.5\n");
-	fprintf(fh, "filespecs xfel-%i.gve xfel-%i.log\n",
-	            image->id, image->id);
-	fprintf(fh, "cuts 3 0.1 0.5\n");
-	fprintf(fh, "eulerstep 8\n");
-	fprintf(fh, "uncertainties 0.1 0.2 .5\n");
-	fprintf(fh, "nsigmas 2\n");
-	fprintf(fh, "minfracg 0.95\n");
-	fprintf(fh, "Nhkls_in_indexing 500\n");
-	fprintf(fh, "random 10000\n");
-	fprintf(fh, "!positionfit\n");
-	fprintf(fh, "genhkl\n");
-	fprintf(fh, "xfelmode\n");
-
-	fclose(fh);
-
-	return filename;
-}
-
-
-int grainspotter_index(struct image *image, IndexingPrivate *ipriv)
-{
-	unsigned int opts;
-	int status;
-	int rval;
-	struct grainspotter_data *grainspotter;
-	struct grainspotter_private *gp = (struct grainspotter_private *)ipriv;
-	char *ini_filename;
-	char gff_filename[1024];
-
-	write_gve(image, gp);
-	ini_filename = write_ini(image);
-
-	if ( ini_filename == NULL ) {
-		ERROR("Failed to write ini file for GrainSpotter.\n");
-		return 0;
-	}
-
-	grainspotter = malloc(sizeof(struct grainspotter_data));
-	if ( grainspotter == NULL ) {
-		ERROR("Couldn't allocate memory for GrainSpotter data.\n");
-		return 0;
-	}
-
-	grainspotter->gp = gp;
-
-	snprintf(gff_filename, 1023, "xfel-%i.gff", image->id);
-	remove(gff_filename);
-
-	grainspotter->pid = forkpty(&grainspotter->pty, NULL, NULL, NULL);
-	if ( grainspotter->pid == -1 ) {
-		ERROR("Failed to fork for GrainSpotter: %s\n", strerror(errno));
-		return 0;
-	}
-	if ( grainspotter->pid == 0 ) {
-
-		/* Child process: invoke GrainSpotter */
-		struct termios t;
-
-		/* Turn echo off */
-		tcgetattr(STDIN_FILENO, &t);
-		t.c_lflag &= ~(ECHO | ECHOE | ECHOK | ECHONL);
-		tcsetattr(STDIN_FILENO, TCSANOW, &t);
-
-		STATUS("Running GrainSpotter.0.93 '%s'\n", ini_filename);
-		execlp("GrainSpotter.0.93", "", ini_filename, (char *)NULL);
-		ERROR("Failed to invoke GrainSpotter.\n");
-		_exit(0);
-
-	}
-	free(ini_filename);
-
-	grainspotter->rbuffer = malloc(256);
-	grainspotter->rbuflen = 256;
-	grainspotter->rbufpos = 0;
-
-	/* Set non-blocking */
-	opts = fcntl(grainspotter->pty, F_GETFL);
-	fcntl(grainspotter->pty, F_SETFL, opts | O_NONBLOCK);
-
-	do {
-
-		fd_set fds;
-		struct timeval tv;
-		int sval;
-
-		FD_ZERO(&fds);
-		FD_SET(grainspotter->pty, &fds);
-
-		tv.tv_sec = 30;
-		tv.tv_usec = 0;
-
-		sval = select(grainspotter->pty+1, &fds, NULL, NULL, &tv);
-
-		if ( sval == -1 ) {
-
-			const int err = errno;
-
-			switch ( err ) {
-
-				case EINTR:
-				STATUS("Restarting select()\n");
-				rval = 0;
-				break;
-
-				default:
-				ERROR("select() failed: %s\n", strerror(err));
-				rval = 1;
-
-			}
-
-		} else if ( sval != 0 ) {
-			rval = grainspotter_readable(image, grainspotter);
-		} else {
-			ERROR("No response from GrainSpotter..\n");
-			rval = 1;
-		}
-
-	} while ( !rval );
-
-	close(grainspotter->pty);
-	free(grainspotter->rbuffer);
-	waitpid(grainspotter->pid, &status, 0);
-
-	if ( status != 0 ) {
-		ERROR("GrainSpotter doesn't seem to be working properly.\n");
-		free(grainspotter);
-		return 0;
-	}
-
-	if ( read_matrix(gp, image, gff_filename) != 0 ) {
-		free(grainspotter);
-		return 0;
-	}
-
-	/* Success! */
-	free(grainspotter);
-	return 1;
-}
-
-
-
-IndexingPrivate *grainspotter_prepare(IndexingMethod *indm, UnitCell *cell,
-                                      struct detector *det, float *ltl)
-{
-	struct grainspotter_private *gp;
-
-	if ( cell == NULL ) {
-		ERROR("GrainSpotter needs a unit cell.\n");
-		return NULL;
-	}
-
-	gp = calloc(1, sizeof(*gp));
-	if ( gp == NULL ) return NULL;
-
-	/* Flags that GrainSpotter knows about */
-	*indm &= INDEXING_METHOD_MASK | INDEXING_CHECK_PEAKS
-	       | INDEXING_USE_LATTICE_TYPE | INDEXING_USE_CELL_PARAMETERS;
-
-	gp->cell = cell;
-	gp->indm = *indm;
-
-	return (IndexingPrivate *)gp;
-}
-
-
-void grainspotter_cleanup(IndexingPrivate *pp)
-{
-	struct grainspotter_private *p;
-
-	p = (struct grainspotter_private *)pp;
-	free(p);
-}
diff --git a/libcrystfel/src/grainspotter.h b/libcrystfel/src/grainspotter.h
deleted file mode 100644
index 3ab823ad..00000000
--- a/libcrystfel/src/grainspotter.h
+++ /dev/null
@@ -1,55 +0,0 @@
-/*
- * grainspotter.h
- *
- * Invoke GrainSpotter for multi-crystal autoindexing
- *
- * Copyright © 2013 Deutsches Elektronen-Synchrotron DESY,
- *                  a research centre of the Helmholtz Association.
- *
- * Authors:
- *   2010-2013 Thomas White <taw@physics.org>
- *
- * This file is part of CrystFEL.
- *
- * CrystFEL is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * CrystFEL is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with CrystFEL.  If not, see <http://www.gnu.org/licenses/>.
- *
- */
-
-#ifndef GRAINSPOTTER_H
-#define GRAINSPOTTER_H
-
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include "cell.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-extern IndexingPrivate *grainspotter_prepare(IndexingMethod *indm,
-                                             UnitCell *cell,
-                                             struct detector *det,
-                                             float *ltl);
-
-extern void grainspotter_cleanup(IndexingPrivate *pp);
-
-extern int grainspotter_index(struct image *image, IndexingPrivate *p);
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif	/* GRAINSPOTTER_H */
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index 6b36af3e..c3aef88e 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -49,11 +49,8 @@
 #include "xds.h"
 #include "detector.h"
 #include "index.h"
-#include "reax.h"
-#include "grainspotter.h"
 #include "geometry.h"
 #include "cell-utils.h"
-#include "grainspotter.h"
 
 
 static int debug_index(struct image *image)
@@ -102,16 +99,7 @@ IndexingPrivate **prepare_indexing(IndexingMethod *indm, UnitCell *cell,
 			break;
 
 			case INDEXING_XDS :
-            iprivs[n] = xds_prepare(&indm[n], cell, det, ltl);
-			break;
-
-			case INDEXING_REAX :
-			iprivs[n] = reax_prepare(&indm[n], cell, det, ltl);
-			break;
-
-			case INDEXING_GRAINSPOTTER :
-			iprivs[n] = grainspotter_prepare(&indm[n], cell,
-			                                 det, ltl);
+			iprivs[n] = xds_prepare(&indm[n], cell, det, ltl);
 			break;
 
 			case INDEXING_DEBUG :
@@ -184,14 +172,6 @@ void cleanup_indexing(IndexingMethod *indms, IndexingPrivate **privs)
 			xds_cleanup(privs[n]);
 			break;
 
-			case INDEXING_REAX :
-			reax_cleanup(privs[n]);
-			break;
-
-			case INDEXING_GRAINSPOTTER :
-			grainspotter_cleanup(privs[n]);
-			break;
-
 			case INDEXING_DEBUG :
 			free(privs[n]);
 			break;
@@ -257,14 +237,6 @@ static int try_indexer(struct image *image, IndexingMethod indm,
 		return run_xds(image, ipriv);
 		break;
 
-		case INDEXING_REAX :
-		return reax_index(ipriv, image);
-		break;
-
-		case INDEXING_GRAINSPOTTER :
-		return grainspotter_index(image, ipriv);
-		break;
-
 		case INDEXING_DEBUG :
 		return debug_index(image);
 
@@ -389,14 +361,6 @@ char *indexer_str(IndexingMethod indm)
 		strcpy(str, "mosflm");
 		break;
 
-		case INDEXING_REAX :
-		strcpy(str, "reax");
-		break;
-
-		case INDEXING_GRAINSPOTTER :
-		strcpy(str, "grainspotter");
-		break;
-
 		case INDEXING_XDS :
 		strcpy(str, "xds");
 		break;
@@ -469,15 +433,9 @@ IndexingMethod *build_indexer_list(const char *str)
 		} else if ( strcmp(methods[i], "mosflm") == 0) {
 			list[++nmeth] = INDEXING_DEFAULTS_MOSFLM;
 
-		} else if ( strcmp(methods[i], "grainspotter") == 0) {
-			list[++nmeth] = INDEXING_DEFAULTS_GRAINSPOTTER;
-
         } else if ( strcmp(methods[i], "xds") == 0) {
 			list[++nmeth] = INDEXING_DEFAULTS_XDS;
 
-		} else if ( strcmp(methods[i], "reax") == 0) {
-			list[++nmeth] = INDEXING_DEFAULTS_REAX;
-
 		} else if ( strcmp(methods[i], "none") == 0) {
 			list[++nmeth] = INDEXING_NONE;
 
diff --git a/libcrystfel/src/index.h b/libcrystfel/src/index.h
index ff1cd5df..12c13df8 100644
--- a/libcrystfel/src/index.h
+++ b/libcrystfel/src/index.h
@@ -48,15 +48,6 @@
                                      | INDEXING_CHECK_CELL_COMBINATIONS        \
                                      | INDEXING_USE_LATTICE_TYPE)
 
-#define INDEXING_DEFAULTS_REAX (INDEXING_REAX | INDEXING_USE_LATTICE_TYPE      \
-                                     | INDEXING_USE_CELL_PARAMETERS            \
-                                     | INDEXING_CHECK_PEAKS)
-
-#define INDEXING_DEFAULTS_GRAINSPOTTER (INDEXING_GRAINSPOTTER                  \
-                                     | INDEXING_USE_LATTICE_TYPE               \
-                                     | INDEXING_USE_CELL_PARAMETERS            \
-                                     | INDEXING_CHECK_PEAKS)
-
 /* Axis check is needed for XDS, because it likes to permute the axes */
 #define INDEXING_DEFAULTS_XDS (INDEXING_XDS | INDEXING_USE_LATTICE_TYPE        \
                                      | INDEXING_USE_CELL_PARAMETERS            \
@@ -68,8 +59,6 @@
  * @INDEXING_NONE: No indexing to be performed
  * @INDEXING_DIRAX: Invoke DirAx
  * @INDEXING_MOSFLM: Invoke MOSFLM
- * @INDEXING_REAX: DPS algorithm using known cell parameters
- * @INDEXING_GRAINSPOTTER: Invoke GrainSpotter
  * @INDEXING_XDS: Invoke XDS
  * @INDEXING_SIMULATION: Dummy value
  * @INDEXING_DEBUG: Results injector for debugging
@@ -95,8 +84,6 @@ typedef enum {
 	/* The core indexing methods themselves */
 	INDEXING_DIRAX  = 1,
 	INDEXING_MOSFLM = 2,
-	INDEXING_REAX   = 3,
-	INDEXING_GRAINSPOTTER = 4,
 	INDEXING_XDS = 5,
 	INDEXING_SIMULATION = 6,
 	INDEXING_DEBUG = 7,
diff --git a/libcrystfel/src/reax.c b/libcrystfel/src/reax.c
deleted file mode 100644
index e2dd249a..00000000
--- a/libcrystfel/src/reax.c
+++ /dev/null
@@ -1,1212 +0,0 @@
-/*
- * reax.c
- *
- * A new auto-indexer
- *
- * Copyright © 2012-2014 Deutsches Elektronen-Synchrotron DESY,
- *                       a research centre of the Helmholtz Association.
- * Copyright © 2014 Takanori Nakane
- *
- * Authors:
- *   2011-2014 Thomas White <taw@physics.org>
- *   2014 Takanori Nakane <nakane.t@gmail.com>
- *
- * This file is part of CrystFEL.
- *
- * CrystFEL is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * CrystFEL is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with CrystFEL.  If not, see <http://www.gnu.org/licenses/>.
- *
- */
-
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-
-#include <stdlib.h>
-#include <stdio.h>
-#include <math.h>
-#include <assert.h>
-#include <fftw3.h>
-#include <fenv.h>
-#include <gsl/gsl_matrix.h>
-#include <gsl/gsl_vector.h>
-#include <gsl/gsl_linalg.h>
-#include <gsl/gsl_eigen.h>
-
-#include "image.h"
-#include "utils.h"
-#include "peaks.h"
-#include "cell.h"
-#include "cell-utils.h"
-#include "index.h"
-#include "reax.h"
-
-
-/* Minimum number of standard deviations above the mean a peak must be in the
- * 1D FT to qualify as a candidate vector */
-#define MIN_SIGMAS (3.0)
-
-
-/* Maximum number of times the angular tolerance that vectors are permitted to
- * be together before they get merged by squash_vectors() */
-#define INC_TOL_MULTIPLIER (3.0)
-
-
-/* Maximum number of candidate vectors to find (we will take the best ones) */
-#define MAX_CANDIDATES (1024)
-
-
-/* Choose the best solution from this many candidate cells */
-#define MAX_REAX_CELL_CANDIDATES (32)
-
-struct dvec
-{
-	double x;
-	double y;
-	double z;
-	double th;
-	double ph;
-};
-
-
-struct reax_candidate
-{
-	struct dvec v;   /* This is the vector for the candidate */
-	double fom;
-};
-
-
-struct reax_search_v
-{
-	unsigned int smin;
-	unsigned int smax;  /* Search for vector in this range */
-
-	struct reax_candidate *cand;  /* Candidate vectors go here */
-	int n_cand;                   /* There are this many candidates */
-	int max_warned;
-};
-
-
-struct reax_search
-{
-	struct reax_search_v *search;  /* Search for these vectors */
-	int n_search;                  /* There are this many vectors to find */
-	double pmax;                   /* The maximum feature resolution */
-};
-
-
-struct reax_private
-{
-	IndexingMethod indm;
-	struct dvec *directions;
-	int n_dir;
-	double angular_inc;
-	UnitCell *cell;
-
-	double *fft_in;
-	fftw_complex *fft_out;
-	fftw_plan plan;
-	int nel;
-
-	fftw_complex *r_fft_in;
-	fftw_complex *r_fft_out;
-	fftw_plan r_plan;
-	int ch;
-	int cw;
-};
-
-
-static void fill_and_transform(struct dvec *dir, ImageFeatureList *flist,
-                        int nel, double pmax, double *fft_in,
-                        fftw_complex *fft_out, fftw_plan plan,
-                        const struct rigid_group *rg, struct detector *det)
-{
-	int n, i;
-
-	for ( i=0; i<nel; i++ ) {
-		fft_in[i] = 0.0;
-	}
-
-	n = image_feature_count(flist);
-	for ( i=0; i<n; i++ ) {
-
-		struct imagefeature *f;
-		double val;
-		int idx;
-
-		f = image_get_feature(flist, i);
-		if ( f == NULL ) continue;
-
-		if ( rg != NULL ) {
-
-			struct panel *p;
-
-			p = find_panel(det, f->fs, f->ss);
-			assert(p != NULL);
-
-			if ( !panel_is_in_rigid_group(rg, p) ) continue;
-
-		}
-
-		val = f->rx*dir->x + f->ry*dir->y + f->rz*dir->z;
-
-		idx = nel/2 + nel*val/(2.0*pmax);
-		fft_in[idx]++;
-
-	}
-
-	fftw_execute_dft_r2c(plan, fft_in, fft_out);
-}
-
-
-static void add_candidate(struct reax_search_v *s, struct reax_candidate *c)
-{
-	int idx;
-
-	if ( s->n_cand == MAX_CANDIDATES ) {
-		if ( !s->max_warned ) {
-			ERROR("WARNING: Too many candidates.\n");
-			s->max_warned = 1;
-		}
-		return;
-	}
-
-	idx = s->n_cand++;
-
-	s->cand[idx].v = c->v;
-	s->cand[idx].fom = c->fom;
-}
-
-
-static double check_dir(struct dvec *dir, ImageFeatureList *flist,
-                        int nel, double pmax, double *fft_in,
-                        fftw_complex *fft_out, fftw_plan plan,
-                        struct reax_search *s,
-                        const struct rigid_group *rg, struct detector *det)
-{
-	int i;
-	double tot;
-
-	fill_and_transform(dir, flist, nel, pmax, fft_in, fft_out,
-	                   plan, rg, det);
-
-	tot = 0.0;
-	for ( i=0; i<s->n_search; i++ ) {
-
-		double tot = 0.0;
-		double peak = 0.0;
-		double peak_mod = 0.0;
-		double mean;
-		double sd = 0.0;
-		int j;
-		int n = 0;
-
-		for ( j=0; j<nel/2+1; j++ ) {
-
-			double re, im, am;
-
-			re = fft_out[j][0];
-			im = fft_out[j][1];
-			am = sqrt(re*re + im*im);
-
-			tot += am;
-			n++;
-
-			if ( ( j >= s->search[i].smin )
-			  && ( j <= s->search[i].smax ) ) {
-				if ( am > peak ) {
-					peak = am;
-					peak_mod = (double)j/(2.0*pmax);
-				}
-			}
-
-		}
-		mean = tot/(double)n;
-
-		for ( j=0; j<nel/2+1; j++ ) {
-
-			double re, im, am;
-
-			re = fft_out[j][0];
-			im = fft_out[j][1];
-			am = sqrt(re*re + im*im);
-
-			sd += pow(am - mean, 2.0);
-
-		}
-		sd = sqrt(sd/(double)n);
-
-		/* If sufficiently strong, add to list of candidates */
-		if ( peak > mean+MIN_SIGMAS*sd ) {
-
-			struct reax_candidate c;
-
-			c.v.x = dir->x * peak_mod;
-			c.v.y = dir->y * peak_mod;
-			c.v.z = dir->z * peak_mod;
-			c.fom = peak;
-
-			add_candidate(&s->search[i],  &c);
-
-		}
-
-	}
-
-	return tot;
-}
-
-
-/* Refine a direct space vector.  From Clegg (1984)
- * with added iteration because more reflections might get included as the
- * refinement proceeds. */
-static double iterate_refine_vector(double *x, double *y, double *z,
-                                    ImageFeatureList *flist)
-{
-	int fi, n, err;
-	gsl_matrix *C;
-	gsl_vector *A;
-	gsl_vector *t;
-	gsl_matrix *s_vec;
-	gsl_vector *s_val;
-	double dtmax;
-
-	A = gsl_vector_calloc(3);
-	C = gsl_matrix_calloc(3, 3);
-
-	n = image_feature_count(flist);
-	fesetround(1);
-	for ( fi=0; fi<n; fi++ ) {
-
-		struct imagefeature *f;
-		double val;
-		double kn, kno;
-		double xv[3];
-		int i, j;
-
-		f = image_get_feature(flist, fi);
-		if ( f == NULL ) continue;
-
-		kno = f->rx*(*x) + f->ry*(*y) + f->rz*(*z);  /* Sorry ... */
-		kn = nearbyint(kno);
-		if ( fabs(kn - kno) > 0.3 ) continue;
-
-		xv[0] = f->rx;  xv[1] = f->ry;  xv[2] = f->rz;
-
-		for ( i=0; i<3; i++ ) {
-
-			val = gsl_vector_get(A, i);
-			gsl_vector_set(A, i, val+xv[i]*kn);
-
-			for ( j=0; j<3; j++ ) {
-				val = gsl_matrix_get(C, i, j);
-				gsl_matrix_set(C, i, j, val+xv[i]*xv[j]);
-			}
-
-		}
-
-	}
-
-	s_val = gsl_vector_calloc(3);
-	s_vec = gsl_matrix_calloc(3, 3);
-	err = gsl_linalg_SV_decomp_jacobi(C, s_vec, s_val);
-	if ( err ) {
-		ERROR("SVD failed: %s\n", gsl_strerror(err));
-		gsl_matrix_free(s_vec);
-		gsl_vector_free(s_val);
-		gsl_matrix_free(C);
-		gsl_vector_free(A);
-		return 0.0;
-	}
-
-	t = gsl_vector_calloc(3);
-	err = gsl_linalg_SV_solve(C, s_vec, s_val, A, t);
-	if ( err ) {
-		ERROR("Matrix solution failed: %s\n", gsl_strerror(err));
-		gsl_matrix_free(s_vec);
-		gsl_vector_free(s_val);
-		gsl_matrix_free(C);
-		gsl_vector_free(A);
-		gsl_vector_free(t);
-		return 0.0;
-	}
-
-	gsl_matrix_free(s_vec);
-	gsl_vector_free(s_val);
-
-	dtmax  = fabs(*x - gsl_vector_get(t, 0));
-	dtmax += fabs(*y - gsl_vector_get(t, 1));
-	dtmax += fabs(*z - gsl_vector_get(t, 2));
-
-	*x = gsl_vector_get(t, 0);
-	*y = gsl_vector_get(t, 1);
-	*z = gsl_vector_get(t, 2);
-
-	gsl_matrix_free(C);
-	gsl_vector_free(A);
-	gsl_vector_free(t);
-
-	return dtmax;
-}
-
-
-static void refine_vector(ImageFeatureList *flist, struct dvec *dir)
-{
-	int i;
-	double sm;
-
-	i = 0;
-	do {
-
-		sm  = iterate_refine_vector(&dir->x, &dir->y, &dir->z, flist);
-		i++;
-
-	} while ( (sm > 0.001e-9) && (i<10) );
-}
-
-
-static void squash_vectors(struct reax_search *s, double tol)
-{
-	int i;
-
-	for ( i=0; i<s->n_search; i++ ) {
-
-		struct reax_search_v *sv;
-		struct reax_candidate *new;
-		int j, k;
-		int n_invalid = 0;
-		int n_copied;
-
-		sv = &s->search[i];
-
-		for ( j=0; j<sv->n_cand; j++ ) {
-		for ( k=0; k<sv->n_cand; k++ ) {
-
-			struct reax_candidate *v1, *v2;
-
-			if ( j == k ) continue;
-
-			v1 = &sv->cand[j];
-			v2 = &sv->cand[k];
-
-			if ( angle_between(v1->v.x, v1->v.y, v1->v.z,
-			                   v2->v.x, v2->v.y, v2->v.z) < tol )
-			{
-				if ( !isnan(v1->fom) && !isnan(v2->fom ) ) {
-					if ( v1->fom > v2->fom ) {
-						v2->fom = NAN;
-					} else {
-						v1->fom = NAN;
-					}
-					n_invalid++;
-				}
-			}
-
-		}
-		}
-
-		new = calloc(sv->n_cand - n_invalid,
-		             sizeof(struct reax_candidate));
-		if ( new == NULL ) {
-			ERROR("Failed to allocate memory for squashed"
-			      " candidate list.\n");
-			return;
-		}
-
-		n_copied = 0;
-		for ( j=0; j<sv->n_cand; j++ ) {
-			if ( !isnan(sv->cand[j].fom) ) {
-
-				new[n_copied] = sv->cand[j];
-				n_copied++;
-
-			}
-		}
-		assert(sv->n_cand - n_invalid == n_copied);
-
-		free(sv->cand);
-		//STATUS("Search vector %i:", i);
-		//STATUS(" squashed %i candidates down to %i\n",
-		//       sv->n_cand, n_copied);
-		sv->n_cand = n_copied;
-		sv->cand = new;
-
-	}
-}
-
-
-static UNUSED void show_vectors(struct reax_search *s, const char *pre)
-{
-	int i;
-
-	/* For each direction being searched for */
-	for ( i=0; i<s->n_search; i++ ) {
-
-		int j;
-
-		for ( j=0; j<s->search[i].n_cand; j++ ) {
-			STATUS("%s: %i/%i: %+6.2f %+6.2f %+6.2f nm %.2f\n", pre,
-			       i, j, s->search[i].cand[j].v.x*1e9,
-			       s->search[i].cand[j].v.y*1e9,
-			       s->search[i].cand[j].v.z*1e9,
-			       s->search[i].cand[j].fom);
-		}
-
-	}
-}
-
-
-static void find_candidates(struct reax_private *p,
-                            ImageFeatureList *flist, double pmax,
-                            double *fft_in, fftw_complex *fft_out,
-                            struct reax_search *s,
-                            const char *rg, struct detector *det)
-{
-	int i;
-
-	for ( i=0; i<s->n_search; i++ ) {
-		s->search[i].cand = calloc(MAX_CANDIDATES,
-		                           sizeof(struct reax_candidate));
-		s->search[i].n_cand = 0;
-	}
-
-	for ( i=0; i<p->n_dir; i++ ) {
-		check_dir(&p->directions[i], flist,
-		                    p->nel, pmax, fft_in, fft_out, p->plan,
-		                    s, NULL, NULL);
-	}
-
-	squash_vectors(s, INC_TOL_MULTIPLIER*p->angular_inc);
-
-	//show_vectors(s, "BEFORE");
-
-	for ( i=0; i<s->n_search; i++ ) {
-
-		struct reax_search_v *sv;
-		int j;
-
-		sv = &s->search[i];
-
-		for ( j=0; j<sv->n_cand; j++ ) {
-			refine_vector(flist, &sv->cand[j].v);
-		}
-
-	}
-
-	//show_vectors(s, "FINAL");
-}
-
-
-/* Set up search parameters to look for all three cell axes */
-static struct reax_search *search_all_axes(UnitCell *cell, double pmax)
-{
-	double ax, ay, az;
-	double bx, by, bz;
-	double cx, cy, cz;
-	double mod_a, mod_b, mod_c;
-	double amin, amax;
-	double bmin, bmax;
-	double cmin, cmax;
-	unsigned int smin, smax;
-	const double ltol = 10.0; /* Direct space axis length tolerance in % */
-	struct reax_search *s;
-
-	cell_get_cartesian(cell, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz);
-	mod_a = modulus(ax, ay, az);
-	amin = mod_a * (1.0-ltol/100.0);
-	amax = mod_a * (1.0+ltol/100.0);
-
-	mod_b = modulus(bx, by, bz);
-	bmin = mod_b * (1.0-ltol/100.0);
-	bmax = mod_b * (1.0+ltol/100.0);
-
-	mod_c = modulus(cx, cy, cz);
-	cmin = mod_c * (1.0-ltol/100.0);
-	cmax = mod_c * (1.0+ltol/100.0);
-
-	s = malloc(3*sizeof(*s));
-	s->pmax = pmax;
-	s->n_search = 3;
-	s->search = malloc(3*sizeof(struct reax_search_v));
-	smin = 2.0*pmax * amin;  smax = 2.0*pmax * amax;
-	s->search[0].smin = smin;  s->search[0].smax = smax;
-	s->search[0].max_warned = 0;
-	smin = 2.0*pmax * bmin;  smax = 2.0*pmax * bmax;
-	s->search[1].smin = smin;  s->search[1].smax = smax;
-	s->search[1].max_warned = 0;
-	smin = 2.0*pmax * cmin;  smax = 2.0*pmax * cmax;
-	s->search[2].smin = smin;  s->search[2].smax = smax;
-	s->search[2].max_warned = 0;
-
-	return s;
-}
-
-
-static double get_model_phase(double x, double y, double z, ImageFeatureList *f,
-                              int nel, double pmax, double *fft_in,
-                              fftw_complex *fft_out, fftw_plan plan,
-                              int smin, int smax, const struct rigid_group *rg,
-                              struct detector *det)
-{
-	struct dvec dir;
-	int s, i;
-	double max;
-	double re, im;
-
-	dir.x = x;  dir.y = y;  dir.z = z;
-
-	fill_and_transform(&dir, f, nel, pmax, fft_in, fft_out, plan, rg, det);
-
-	s = -1;
-	max = 0.0;
-	for ( i=smin; i<=smax; i++ ) {
-
-		double re, im, m;
-
-		re = fft_out[i][0];
-		im = fft_out[i][1];
-		m = sqrt(re*re + im*im);
-		if ( m > max ) {
-			max = m;
-			s = i;
-		}
-
-	}
-
-	re = fft_out[s][0];
-	im = fft_out[s][1];
-
-	return atan2(im, re);
-}
-
-
-static void refine_rigid_group(struct image *image, UnitCell *cell,
-                               const struct rigid_group *rg, double pmax,
-                               double *fft_in, fftw_complex *fft_out,
-                               fftw_plan plan, int smin, int smax,
-                               struct detector *det, struct reax_private *pr)
-{
-	double ax, ay, az, ma;
-	double bx, by, bz, mb;
-	double cx, cy, cz, mc;
-	double pha, phb, phc;
-	int i, j;
-	fftw_complex *r_fft_in;
-	fftw_complex *r_fft_out;
-	double m2m;
-	signed int aix, aiy;
-	signed int bix, biy;
-	signed int cix, ciy;
-
-	cell_get_cartesian(cell, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz);
-
-	ma = modulus(ax, ay, az);
-	mb = modulus(bx, by, bz);
-	mc = modulus(cx, cy, cz);
-
-	pha = get_model_phase(ax/ma, ay/ma, az/ma, image->features,
-	                      pr->nel, pmax, fft_in, fft_out, plan,
-	                      smin, smax, rg, det);
-	phb = get_model_phase(bx/mb, by/mb, bz/mb, image->features,
-	                      pr->nel, pmax, fft_in, fft_out, plan,
-	                      smin, smax, rg, det);
-	phc = get_model_phase(cx/mc, cy/mc, cz/mc, image->features,
-	                      pr->nel, pmax, fft_in, fft_out, plan,
-	                      smin, smax, rg, det);
-
-	r_fft_in = fftw_malloc(pr->cw*pr->ch*sizeof(fftw_complex));
-	r_fft_out = fftw_malloc(pr->cw*pr->ch*sizeof(fftw_complex));
-	for ( i=0; i<pr->cw; i++ ) {
-	for ( j=0; j<pr->ch; j++ ) {
-		r_fft_in[i+pr->cw*j][0] = 0.0;
-		r_fft_in[i+pr->cw*j][1] = 0.0;
-	}
-	}
-
-	ma = modulus(ax, ay, 0.0);
-	mb = modulus(bx, by, 0.0);
-	mc = modulus(cx, cy, 0.0);
-	m2m = ma;
-	if ( mb > m2m ) m2m = mb;
-	if ( mc > m2m ) m2m = mc;
-
-	aix = (pr->cw/2)*ax/m2m;  aiy = (pr->ch/2)*ay/m2m;
-	bix = (pr->cw/2)*bx/m2m;  biy = (pr->ch/2)*by/m2m;
-	cix = (pr->cw/2)*cx/m2m;  ciy = (pr->ch/2)*cy/m2m;
-
-	if ( aix < 0 ) aix += pr->cw/2;
-	if ( bix < 0 ) bix += pr->cw/2;
-	if ( cix < 0 ) cix += pr->cw/2;
-
-	if ( aiy < 0 ) aiy += pr->ch/2;
-	if ( biy < 0 ) biy += pr->ch/2;
-	if ( ciy < 0 ) ciy += pr->ch/2;
-
-	r_fft_in[aix + pr->cw*aiy][0] = cos(pha);
-	r_fft_in[aix + pr->cw*aiy][1] = sin(pha);
-	r_fft_in[pr->cw-aix + pr->cw*(pr->ch-aiy)][0] = cos(pha);
-	r_fft_in[pr->cw-aix + pr->cw*(pr->ch-aiy)][1] = -sin(pha);
-
-	r_fft_in[bix + pr->cw*biy][0] = cos(phb);
-	r_fft_in[bix + pr->cw*biy][1] = sin(phb);
-	r_fft_in[pr->cw-bix + pr->cw*(pr->ch-biy)][0] = cos(phb);
-	r_fft_in[pr->cw-bix + pr->cw*(pr->ch-biy)][1] = -sin(phb);
-
-	r_fft_in[cix + pr->cw*ciy][0] = cos(phc);
-	r_fft_in[cix + pr->cw*ciy][1] = sin(phc);
-	r_fft_in[pr->cw-cix + pr->cw*(pr->ch-ciy)][0] = cos(phc);
-	r_fft_in[pr->cw-cix + pr->cw*(pr->ch-ciy)][1] = -sin(phc);
-
-	const int tidx = 1;
-	r_fft_in[tidx][0] = 1.0;
-	r_fft_in[tidx][1] = 0.0;
-
-//	STATUS("%i %i\n", aix, aiy);
-//	STATUS("%i %i\n", bix, biy);
-//	STATUS("%i %i\n", cix, ciy);
-
-	fftw_execute_dft(pr->r_plan, r_fft_in, r_fft_out);
-
-//	max = 0.0;
-//	FILE *fh = fopen("centering.dat", "w");
-//	for ( i=0; i<pr->cw; i++ ) {
-//	for ( j=0; j<pr->ch; j++ ) {
-//
-//		double re, im, am, ph;
-//
-//		re = r_fft_out[i + pr->cw*j][0];
-//		im = r_fft_out[i + pr->cw*j][1];
-//		am = sqrt(re*re + im*im);
-//		ph = atan2(im, re);
-//
-//		if ( am > max ) {
-//			max = am;
-//			max_i = i;
-//			max_j = j;
-//		}
-//
-//		fprintf(fh, "%f ", am);
-//
-//	}
-//	fprintf(fh, "\n");
-//	}
-//	STATUS("Max at %i, %i\n", max_i, max_j);
-//	fclose(fh);
-//	exit(1);
-
-//	STATUS("Offsets for '%s': %.2f, %.2f pixels\n", rg, dx, dy);
-}
-
-
-static UNUSED void refine_all_rigid_groups(struct image *image, UnitCell *cell,
-                                           double pmax,
-                                           double *fft_in,
-                                           fftw_complex *fft_out,
-                                           fftw_plan plan, int smin, int smax,
-                                           struct detector *det,
-                                           struct reax_private *p)
-{
-	int i;
-
-	for ( i=0; i<image->det->n_rigid_groups; i++ ) {
-		refine_rigid_group(image, cell, image->det->rigid_groups[i],
-		                   pmax, fft_in, fft_out, plan, smin, smax,
-		                   det, p);
-	}
-}
-
-
-static double max_feature_resolution(ImageFeatureList *flist)
-{
-	double pmax;
-	int i, n;
-
-	pmax = 0.0;
-	n = image_feature_count(flist);
-	for ( i=0; i<n; i++ ) {
-
-		struct imagefeature *f;
-		double val;
-
-		f = image_get_feature(flist, i);
-		if ( f == NULL ) continue;
-
-		val = modulus(f->rx, f->ry, f->rz);
-		if ( val > pmax ) pmax = val;
-
-	}
-
-	return pmax;
-}
-
-
-static int right_handed_vec(struct rvec a, struct rvec b, struct rvec c)
-{
-	struct rvec aCb;
-	double aCb_dot_c;
-
-	/* "a" cross "b" */
-	aCb.u = a.v*b.w - a.w*b.v;
-	aCb.v = - (a.u*b.w - a.w*b.u);
-	aCb.w = a.u*b.v - a.v*b.u;
-
-	/* "a cross b" dot "c" */
-	aCb_dot_c = aCb.u*c.u + aCb.v*c.v + aCb.w*c.w;
-
-	if ( aCb_dot_c > 0.0 ) return 1;
-	return 0;
-}
-
-
-struct cell_candidate
-{
-	UnitCell *cell;
-	double fom;
-};
-
-
-struct cell_candidate_list
-{
-	struct cell_candidate *cand;
-	int n_cand;
-};
-
-
-static int check_twinning(UnitCell *c1, UnitCell *c2, int verbose)
-{
-	int i;
-	int n_dup;
-	const int n_trials = 40;
-
-	double asx, asy, asz;
-	double bsx, bsy, bsz;
-	double csx, csy, csz;
-	double ax, ay, az;
-	double bx, by, bz;
-	double cx, cy, cz;
-
-	gsl_rng *rng;
-
-	/* This is a rubbish RNG, but it serves for this purpose: nothing more
-	 * than "I couldn't be bothered to think of n_trials sets of random
-	 * indices". */
-	rng = gsl_rng_alloc(gsl_rng_taus2);
-
-	cell_get_reciprocal(c1, &asx, &asy, &asz,
-	                        &bsx, &bsy, &bsz,
-	                        &csx, &csy, &csz);
-	cell_get_cartesian(c2, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz);
-
-	n_dup = 0;
-	for ( i=0; i<n_trials; i++ ) {
-
-		signed int h, k, l;
-		double h2, k2, l2;
-		double rx, ry, rz;
-		double dev;
-		signed int h2i, k2i, l2i;
-
-		h = gsl_rng_uniform_int(rng, 10);
-		k = gsl_rng_uniform_int(rng, 10);
-		l = gsl_rng_uniform_int(rng, 10);
-
-		/* Position of this (randomly selected)
-		 * reciprocal lattice point */
-		rx = h*asx + k*bsx + l*csx;
-		ry = h*asy + k*bsy + l*csy;
-		rz = h*asz + k*bsz + l*csz;
-
-		/* Indices of this point in the basis of the other cell */
-		h2 = rx*ax + ry*ay + rz*az;
-		k2 = rx*bx + ry*by + rz*bz;
-		l2 = rx*cx + ry*cy + rz*cz;
-
-		h2i = lrint(h2);
-		k2i = lrint(k2);
-		l2i = lrint(l2);
-
-		dev = pow(h2i-h2, 2.0) + pow(k2i-k2, 2.0) + pow(l2i-l2, 2.0);
-
-		if ( verbose ) {
-			STATUS("%3i %3i %3i -> %5.2f %5.2f %5.2f -> "
-			       "%3i %3i %3i -> %5.2f\n", h, k, l,
-			       h2, k2, l2, h2i, k2i, l2i, dev);
-		}
-
-		if ( dev < 0.1 ) {
-			n_dup++;
-		}
-
-	}
-
-	if ( verbose ) {
-		STATUS("%i duplicates.\n", n_dup);
-	}
-
-	gsl_rng_free(rng);
-
-	if ( n_dup > 10 ) return 1;
-	return 0;
-}
-
-
-/* Return true if "cnew" accounts for more than 25% of the peaks predicted by
- * any of the "ncells" cells in "cells". */
-static int twinned(UnitCell *cnew, struct cell_candidate_list *cl)
-{
-	int i;
-
-	for ( i=0; i<cl->n_cand; i++ ) {
-		if ( check_twinning(cnew, cl->cand[i].cell, 0) ) return 1;
-	}
-
-	return 0;
-}
-
-
-static int check_vector_combination(struct dvec *vi, struct dvec *vj,
-                                    struct dvec *vk, UnitCell *cell)
-{
-	double ang;
-	double a, b, c, al, be, ga;
-	const double angtol = deg2rad(5.0);
-
-	cell_get_parameters(cell, &a, &b, &c, &al, &be, &ga);
-
-	ang = angle_between(vi->x, vi->y, vi->z, vj->x, vj->y, vj->z);
-	if ( fabs(ang-ga) > angtol ) return 0;
-
-	ang = angle_between(vi->x, vi->y, vi->z, vk->x, vk->y, vk->z);
-	if ( fabs(ang-be) > angtol ) return 0;
-
-	ang = angle_between(vj->x, vj->y, vj->z, vk->x, vk->y, vk->z);
-	if ( fabs(ang-al) > angtol ) return 0;
-
-	return 1;
-}
-
-
-static void add_cell_candidate(struct cell_candidate_list *cl, UnitCell *cnew,
-                               double fom)
-{
-	struct cell_candidate cshift;
-	int i, cpos;
-
-	cpos = cl->n_cand;
-	for ( i=0; i<cl->n_cand; i++ ) {
-		if ( fom > cl->cand[i].fom ) {
-			cpos = i;
-			break;
-		}
-	}
-
-	cshift.cell = cnew;
-	cshift.fom = fom;
-
-	for ( i=cpos; i<cl->n_cand; i++ ) {
-
-		struct cell_candidate cshift2;
-		cshift2 = cl->cand[i];
-		cl->cand[i] = cshift;
-		cshift = cshift2;
-
-	}
-
-	if ( cl->n_cand >= MAX_REAX_CELL_CANDIDATES ) {
-		/* "cshift" just fell off the end of the list */
-	} else {
-		cl->cand[cl->n_cand++] = cshift;
-	}
-}
-
-
-static int check_cell(struct reax_private *dp, struct image *image,
-                      UnitCell *cell)
-{
-	UnitCell *out;
-	Crystal *cr;
-
-	out = cell_new_from_cell(cell);
-
-	cr = crystal_new();
-	if ( cr == NULL ) {
-		ERROR("Failed to allocate crystal.\n");
-		return 0;
-	}
-
-	crystal_set_cell(cr, out);
-
-	if ( dp->indm & INDEXING_CHECK_PEAKS ) {
-		if ( !peak_sanity_check(image, &cr, 1) ) {
-			crystal_free(cr);  /* Frees the cell as well */
-			return 0;
-		}
-	}
-
-	image_add_crystal(image, cr);
-
-	return 1;
-}
-
-
-static int assemble_cells_from_candidates(struct image *image,
-                                           struct reax_search *s,
-                                           UnitCell *cell,
-                                           struct reax_private *p)
-{
-	int i, j, k;
-	signed int ti, tj, tk;
-	int rval;
-	struct cell_candidate_list cl;
-
-	cl.cand = calloc(MAX_REAX_CELL_CANDIDATES,
-	                 sizeof(struct cell_candidate));
-	if ( cl.cand == NULL ) {
-		ERROR("Failed to allocate cell candidate list.\n");
-		return 0;
-	}
-	cl.n_cand = 0;
-
-	/* Find candidates for axes 0 and 1 which have the right angle */
-	for ( i=0; i<s->search[0].n_cand; i++ ) {
-	for ( j=0; j<s->search[1].n_cand; j++ ) {
-	for ( k=0; k<s->search[2].n_cand; k++ ) {
-	for ( ti=-1; ti<=1; ti+=2 ) {
-	for ( tj=-1; tj<=1; tj+=2 ) {
-	for ( tk=-1; tk<=1; tk+=2 ) {
-
-		struct dvec vi, vj, vk;
-		struct rvec ai, bi, ci;
-		UnitCell *cnew;
-		double fom;
-
-		vi = s->search[0].cand[i].v;
-		vj = s->search[1].cand[j].v;
-		vk = s->search[2].cand[k].v;
-
-		vi.x *= ti;  vi.y *= ti;  vi.z *= ti;
-		vj.x *= tj;  vj.y *= tj;  vj.z *= tj;
-		vk.x *= tk;  vk.y *= tk;  vk.z *= tk;
-
-		if ( !check_vector_combination(&vi, &vj, &vk, cell) ) continue;
-
-		ai.u = vi.x;  ai.v = vi.y;  ai.w = vi.z;
-		bi.u = vj.x;  bi.v = vj.y;  bi.w = vj.z;
-		ci.u = vk.x;  ci.v = vk.y;  ci.w = vk.z;
-
-		if ( !right_handed_vec(ai, bi, ci) ) continue;
-
-		/* We have three vectors with the right angles */
-		cnew = cell_new_from_direct_axes(ai, bi, ci);
-
-		if ( twinned(cnew, &cl) ) {
-			cell_free(cnew);
-			continue;
-		}
-
-		fom = 1.0;
-		add_cell_candidate(&cl, cnew, fom);
-
-	}
-	}
-	}
-	}
-	}
-	}
-
-	for ( i=0; i<cl.n_cand; i++ ) {
-		double a, b, c, al, be, ga;
-		double aA, bA, cA, alA, beA, gaA;
-		int w = 0;
-//		STATUS("%i: %f\n", i, cl.cand[i].fom);
-		cell_get_parameters(cl.cand[i].cell, &a, &b, &c, &al, &be, &ga);
-		cell_get_parameters(cl.cand[i].cell, &aA, &bA, &cA,
-		                                     &alA, &beA, &gaA);
-		if ( fabs(a - aA) > aA/10.0 ) w = 1;
-		if ( fabs(b - bA) > bA/10.0 ) w = 1;
-		if ( fabs(c - cA) > cA/10.0 ) w = 1;
-		if ( fabs(al - alA) > deg2rad(5.0) ) w = 1;
-		if ( fabs(be - beA) > deg2rad(5.0) ) w = 1;
-		if ( fabs(ga - gaA) > deg2rad(5.0) ) w = 1;
-		if ( w ) {
-			STATUS("This cell is a long way from that sought:\n");
-			cell_print(cl.cand[i].cell);
-		}
-	}
-
-	rval = 0;
-	for ( i=0; i<cl.n_cand; i++ ) {
-		if ( check_cell(p,  image, cl.cand[i].cell) ) {
-			rval = 1;
-			break;
-		}
-	}
-
-	free(cl.cand);
-	return rval;
-}
-
-
-int reax_index(IndexingPrivate *pp, struct image *image)
-{
-	struct reax_private *p;
-	double *fft_in;
-	fftw_complex *fft_out;
-	double pmax;
-	struct reax_search *s;
-	int i;
-	int rval = 0;
-
-	p = (struct reax_private *)pp;
-
-	fft_in = fftw_malloc(p->nel*sizeof(double));
-	fft_out = fftw_malloc((p->nel/2 + 1)*sizeof(fftw_complex));
-
-	pmax = max_feature_resolution(image->features);
-
-	/* Sanity check */
-	if ( pmax < 1e4 ) {
-		fftw_free(fft_in);
-		fftw_free(fft_out);
-		return 0;
-	}
-
-	s = search_all_axes(p->cell, pmax);
-	find_candidates(p, image->features, pmax, fft_in, fft_out, s,
-	                NULL, image->det);
-
-//	refine_all_rigid_groups(image, image->candidate_cells[0], pmax,
-//	                        fft_in, fft_out, p->plan, smin, smax,
-//	                        image->det, p);
-
-	rval = assemble_cells_from_candidates(image, s, p->cell, p);
-
-	for ( i=0; i<s->n_search; i++ ) {
-		free(s->search[i].cand);
-	}
-	free(s->search);
-	free(s);
-	fftw_free(fft_in);
-	fftw_free(fft_out);
-	return rval;
-}
-
-
-IndexingPrivate *reax_prepare(IndexingMethod *indm, UnitCell *cell,
-                              struct detector *det, float *ltl)
-{
-	struct reax_private *p;
-	int samp;
-	double th;
-
-	if ( cell == NULL ) {
-		ERROR("ReAx needs a unit cell.\n");
-		return NULL;
-	}
-
-	p = calloc(1, sizeof(*p));
-	if ( p == NULL ) return NULL;
-
-	p->cell = cell;
-
-	/* Flags that ReAx knows about */
-	*indm &= INDEXING_METHOD_MASK | INDEXING_CHECK_PEAKS;
-
-	/* Flags that ReAx requires */
-	*indm |= INDEXING_USE_LATTICE_TYPE;
-	*indm |= INDEXING_USE_CELL_PARAMETERS;
-
-	p->angular_inc = deg2rad(1.0);
-
-	/* Reserve memory, over-estimating the number of directions */
-	samp = 2.0*M_PI / p->angular_inc;
-	p->directions = malloc(samp*samp*sizeof(struct dvec));
-	if ( p == NULL) {
-		free(p);
-		return NULL;
-	}
-	STATUS("Allocated space for %i directions\n", samp*samp);
-
-	/* Generate vectors for 1D Fourier transforms */
-	fesetround(1);  /* Round to nearest */
-	p->n_dir = 0;
-	for ( th=0.0; th<M_PI_2; th+=p->angular_inc ) {
-
-		double ph, phstep, n_phstep;
-
-		n_phstep = 2.0*M_PI*sin(th)/p->angular_inc;
-		n_phstep = nearbyint(n_phstep);
-		phstep = 2.0*M_PI/n_phstep;
-
-		for ( ph=0.0; ph<2.0*M_PI; ph+=phstep ) {
-
-			struct dvec *dir;
-
-			assert(p->n_dir<samp*samp);
-
-			dir = &p->directions[p->n_dir++];
-
-			dir->x = cos(ph) * sin(th);
-			dir->y = sin(ph) * sin(th);
-			dir->z = cos(th);
-			dir->th = th;
-			dir->ph = ph;
-
-		}
-
-	}
-	STATUS("Generated %i directions (angular increment %.3f deg)\n",
-	       p->n_dir, rad2deg(p->angular_inc));
-
-	p->nel = 1024;
-
-	/* These arrays are not actually used */
-	p->fft_in = fftw_malloc(p->nel*sizeof(double));
-	p->fft_out = fftw_malloc((p->nel/2 + 1)*sizeof(fftw_complex));
-
-	p->plan = fftw_plan_dft_r2c_1d(p->nel, p->fft_in, p->fft_out,
-	                               FFTW_MEASURE);
-
-	p->cw = 128; p->ch = 128;
-
-	/* Also not used */
-	p->r_fft_in = fftw_malloc(p->cw*p->ch*sizeof(fftw_complex));
-	p->r_fft_out = fftw_malloc(p->cw*p->ch*sizeof(fftw_complex));
-
-	p->r_plan = fftw_plan_dft_2d(p->cw, p->ch, p->r_fft_in, p->r_fft_out,
-	                             1, FFTW_MEASURE);
-
-	p->indm = *indm;
-
-	return (IndexingPrivate *)p;
-}
-
-
-void reax_cleanup(IndexingPrivate *pp)
-{
-	struct reax_private *p;
-
-	p = (struct reax_private *)pp;
-
-	free(p->directions);
-
-	fftw_destroy_plan(p->plan);
-	fftw_free(p->fft_in);
-	fftw_free(p->fft_out);
-
-	fftw_destroy_plan(p->r_plan);
-	fftw_free(p->r_fft_in);
-	fftw_free(p->r_fft_out);
-
-	free(p);
-}
diff --git a/libcrystfel/src/reax.h b/libcrystfel/src/reax.h
deleted file mode 100644
index 0bc96d9e..00000000
--- a/libcrystfel/src/reax.h
+++ /dev/null
@@ -1,75 +0,0 @@
-/*
- * reax.h
- *
- * A new auto-indexer
- *
- * Copyright © 2012 Deutsches Elektronen-Synchrotron DESY,
- *                  a research centre of the Helmholtz Association.
- *
- * Authors:
- *   2011-2012 Thomas White <taw@physics.org>
- *
- * This file is part of CrystFEL.
- *
- * CrystFEL is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * CrystFEL is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with CrystFEL.  If not, see <http://www.gnu.org/licenses/>.
- *
- */
-
-#ifndef REAX_H
-#define REAX_H
-
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include "index.h"
-#include "cell.h"
-#include "detector.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-#ifdef HAVE_FFTW
-
-extern IndexingPrivate *reax_prepare(IndexingMethod *indm, UnitCell *cell,
-                                     struct detector *det, float *ltl);
-
-extern void reax_cleanup(IndexingPrivate *pp);
-
-extern int reax_index(IndexingPrivate *pp, struct image *image);
-
-#else /* HAVE_FFTW */
-
-static IndexingPrivate *reax_prepare(IndexingMethod *indm, UnitCell *cell,
-                                     struct detector *det, float *ltl)
-{
-	return NULL;
-}
-
-static void reax_cleanup(IndexingPrivate *pp)
-{
-}
-
-static int reax_index(IndexingPrivate *pp, struct image *image)
-{
-}
-
-#endif /* HAVE_FFTW */
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif	/* REAX_H */