Move indexing and rendering to libcrystfel

11 files changed, 0 insertions, 2809 deletions

diff --git a/src/dirax.c b/src/dirax.c
deleted file mode 100644
index bb1cb808..00000000
--- a/src/dirax.c
+++ /dev/null
@@ -1,529 +0,0 @@
-/*
- * dirax.c
- *
- * Invoke the DirAx auto-indexing program
- *
- * (c) 2006-2010 Thomas White <taw@physics.org>
- *
- * Part of CrystFEL - crystallography with a FEL
- *
- */
-
-
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-
-#include <stdlib.h>
-#include <stdio.h>
-#include <math.h>
-#include <string.h>
-#include <unistd.h>
-#include <sys/wait.h>
-#include <fcntl.h>
-#include <assert.h>
-#include <sys/ioctl.h>
-#include <errno.h>
-
-#if HAVE_FORKPTY_LINUX
-#include <pty.h>
-#elif HAVE_FORKPTY_BSD
-#include <util.h>
-#endif
-
-
-#include "image.h"
-#include "dirax.h"
-#include "utils.h"
-#include "peaks.h"
-
-
-#define DIRAX_VERBOSE 0
-
-#define MAX_DIRAX_CELL_CANDIDATES (5)
-
-
-typedef enum {
-	DIRAX_INPUT_NONE,
-	DIRAX_INPUT_LINE,
-	DIRAX_INPUT_PROMPT,
-	DIRAX_INPUT_ACL
-} DirAxInputType;
-
-
-struct dirax_data {
-
-	/* DirAx auto-indexing low-level stuff */
-	int                     pty;
-	pid_t                   pid;
-	char                    *rbuffer;
-	int                     rbufpos;
-	int                     rbuflen;
-
-	/* DirAx auto-indexing high-level stuff */
-	int                     step;
-	int                     finished_ok;
-	int                     read_cell;
-	int                     best_acl;
-	int                     best_acl_nh;
-	int                     acls_tried[MAX_CELL_CANDIDATES];
-	int                     n_acls_tried;
-
-};
-
-
-static void dirax_parseline(const char *line, struct image *image,
-                            struct dirax_data *dirax)
-{
-	int rf, i, di, acl, acl_nh;
-	float d;
-
-	#if DIRAX_VERBOSE
-	char *copy;
-
-	copy = strdup(line);
-	for ( i=0; i<strlen(copy); i++ ) {
-		if ( copy[i] == '\r' ) copy[i]='r';
-		if ( copy[i] == '\n' ) copy[i]='\0';
-	}
-	STATUS("DirAx: %s\n", copy);
-	free(copy);
-	#endif
-
-	if ( strstr(line, "reflections from file") ) {
-		ERROR("DirAx can't understand this data.\n");
-		return;
-	}
-
-	/* Is this the first line of a unit cell specification? */
-	rf = 0; i = 0;
-	while ( (i<strlen(line)) && ((line[i] == 'R')
-				|| (line[i] == 'D') || (line[i] == ' ')) ) {
-		if ( line[i] == 'R' ) rf = 1;
-		if ( (line[i] == 'D') && rf ) {
-			dirax->read_cell = 1;
-			image->candidate_cells[image->ncells] = cell_new();
-			return;
-		}
-		i++;
-	}
-
-	/* Parse unit cell vectors as appropriate */
-	if ( dirax->read_cell == 1 ) {
-		/* First row of unit cell values */
-		float ax, ay, az;
-		int r;
-		r = sscanf(line, "%f %f %f %f %f %f",
-		           &d, &d, &d, &ax, &ay, &az);
-		if ( r != 6 ) {
-			ERROR("Couldn't understand cell line:\n");
-			ERROR("'%s'\n", line);
-			dirax->read_cell = 0;
-			cell_free(image->candidate_cells[image->ncells]);
-			return;
-		}
-		cell_set_cartesian_a(image->candidate_cells[image->ncells],
-		                     ax*1e-10, ay*1e-10, az*1e-10);
-		dirax->read_cell++;
-		return;
-	} else if ( dirax->read_cell == 2 ) {
-		/* Second row of unit cell values */
-		float bx, by, bz;
-		int r;
-		r = sscanf(line, "%f %f %f %f %f %f",
-		           &d, &d, &d, &bx, &by, &bz);
-		if ( r != 6 ) {
-			ERROR("Couldn't understand cell line:\n");
-			ERROR("'%s'\n", line);
-			dirax->read_cell = 0;
-			cell_free(image->candidate_cells[image->ncells]);
-			return;
-		}
-		cell_set_cartesian_b(image->candidate_cells[image->ncells],
-		                     bx*1e-10, by*1e-10, bz*1e-10);
-		dirax->read_cell++;
-		return;
-	} else if ( dirax->read_cell == 3 ) {
-		/* Third row of unit cell values */
-		float cx, cy, cz;
-		int r;
-		r = sscanf(line, "%f %f %f %f %f %f",
-		           &d, &d, &d, &cx, &cy, &cz);
-		if ( r != 6 ) {
-			ERROR("Couldn't understand cell line:\n");
-			ERROR("'%s'\n", line);
-			dirax->read_cell = 0;
-			cell_free(image->candidate_cells[image->ncells]);
-			return;
-		}
-		cell_set_cartesian_c(image->candidate_cells[image->ncells++],
-		                     cx*1e-10, cy*1e-10, cz*1e-10);
-		dirax->read_cell = 0;
-		return;
-	}
-
-	dirax->read_cell = 0;
-
-	if ( sscanf(line, "%i %i %f %f %f %f %f %f %i", &acl, &acl_nh,
-	                               &d, &d, &d, &d, &d, &d, &di) == 9 ) {
-		if ( acl_nh > dirax->best_acl_nh ) {
-
-			int i, found = 0;
-
-			for ( i=0; i<dirax->n_acls_tried; i++ ) {
-				if ( dirax->acls_tried[i] == acl ) found = 1;
-			}
-
-			if ( !found ) {
-				dirax->best_acl_nh = acl_nh;
-				dirax->best_acl = acl;
-			}
-
-		}
-	}
-}
-
-
-static void dirax_sendline(const char *line, struct dirax_data *dirax)
-{
-	#if DIRAX_VERBOSE
-	char *copy;
-	int i;
-
-	copy = strdup(line);
-	for ( i=0; i<strlen(copy); i++ ) {
-		if ( copy[i] == '\r' ) copy[i]='\0';
-		if ( copy[i] == '\n' ) copy[i]='\0';
-	}
-	STATUS("To DirAx: '%s'\n", copy);
-	free(copy);
-	#endif
-
-	write(dirax->pty, line, strlen(line));
-}
-
-
-static void dirax_send_next(struct image *image, struct dirax_data *dirax)
-{
-	char tmp[32];
-
-	switch ( dirax->step ) {
-
-	case 1 :
-		dirax_sendline("\\echo off\n", dirax);
-		break;
-
-	case 2 :
-		snprintf(tmp, 31, "read xfel-%i.drx\n", image->id);
-		dirax_sendline(tmp, dirax);
-		break;
-
-	case 3 :
-		dirax_sendline("dmax 1000\n", dirax);
-		break;
-
-	case 4 :
-		dirax_sendline("indexfit 2\n", dirax);
-		break;
-
-	case 5 :
-		dirax_sendline("levelfit 1000\n", dirax);
-		break;
-
-	case 6 :
-		dirax_sendline("go\n", dirax);
-		dirax->finished_ok = 1;
-		break;
-
-	case 7 :
-		dirax_sendline("acl\n", dirax);
-		break;
-
-	case 8 :
-		if ( dirax->best_acl_nh == 0 ) {
-			/* At this point, DirAx is presenting its ACL prompt
-			 * and waiting for a single number.  Use an extra
-			 * newline to choose automatic ACL selection before
-			 * exiting. */
-			dirax_sendline("\nexit\n", dirax);
-			break;
-		}
-		snprintf(tmp, 31, "%i\n", dirax->best_acl);
-		dirax->acls_tried[dirax->n_acls_tried++] = dirax->best_acl;
-		dirax_sendline(tmp, dirax);
-		break;
-
-	case 9 :
-		dirax_sendline("cell\n", dirax);
-		break;
-
-	case 10 :
-		if ( dirax->n_acls_tried == MAX_DIRAX_CELL_CANDIDATES ) {
-			dirax_sendline("exit\n", dirax);
-		} else {
-			/* Go back round for another cell */
-			dirax->best_acl_nh = 0;
-			dirax->step = 7;
-			dirax_sendline("acl\n", dirax);
-		}
-		break;
-
-	default:
-		dirax_sendline("exit\n", dirax);
-		return;
-
-	}
-
-	dirax->step++;
-}
-
-
-static int dirax_readable(struct image *image, struct dirax_data *dirax)
-{
-	int rval;
-	int no_string = 0;
-
-	rval = read(dirax->pty, dirax->rbuffer+dirax->rbufpos,
-	            dirax->rbuflen-dirax->rbufpos);
-
-	if ( (rval == -1) || (rval == 0) ) return 1;
-
-	dirax->rbufpos += rval;
-	assert(dirax->rbufpos <= dirax->rbuflen);
-
-	while ( (!no_string) && (dirax->rbufpos > 0) ) {
-
-		int i;
-		int block_ready = 0;
-		DirAxInputType type = DIRAX_INPUT_NONE;
-
-		/* See if there's a full line in the buffer yet */
-		for ( i=0; i<dirax->rbufpos-1; i++ ) {
-			/* Means the last value looked at is rbufpos-2 */
-
-			/* Is there a prompt in the buffer? */
-			if ( (i+7 <= dirax->rbufpos)
-			  && (!strncmp(dirax->rbuffer+i, "Dirax> ", 7)) ) {
-				block_ready = 1;
-				type = DIRAX_INPUT_PROMPT;
-				break;
-			}
-
-			/* How about an ACL prompt? */
-			if ( (i+10 <= dirax->rbufpos)
-			  && (!strncmp(dirax->rbuffer+i, "acl/auto [", 10)) ) {
-				block_ready = 1;
-				type = DIRAX_INPUT_ACL;
-				break;
-			}
-
-			if ( (dirax->rbuffer[i] == '\r')
-			  && (dirax->rbuffer[i+1] == '\n') ) {
-				block_ready = 1;
-				type = DIRAX_INPUT_LINE;
-				break;
-			}
-
-		}
-
-		if ( block_ready ) {
-
-			unsigned int new_rbuflen;
-			unsigned int endbit_length;
-			char *block_buffer = NULL;
-
-			switch ( type ) {
-
-			case DIRAX_INPUT_LINE :
-
-				block_buffer = malloc(i+1);
-				memcpy(block_buffer, dirax->rbuffer, i);
-				block_buffer[i] = '\0';
-
-				if ( block_buffer[0] == '\r' ) {
-					memmove(block_buffer, block_buffer+1, i);
-				}
-
-				dirax_parseline(block_buffer, image, dirax);
-				free(block_buffer);
-				endbit_length = i+2;
-				break;
-
-			case DIRAX_INPUT_PROMPT :
-
-				dirax_send_next(image, dirax);
-				endbit_length = i+7;
-				break;
-
-			case DIRAX_INPUT_ACL :
-
-				dirax_send_next(image,dirax );
-				endbit_length = i+10;
-				break;
-
-			default :
-
-				/* Obviously, this never happens :) */
-				ERROR("Unrecognised DirAx input mode! "
-				      "I don't know how to understand DirAx\n");
-				return 1;
-
-			}
-
-			/* Now the block's been parsed, it should be
-			 * forgotten about */
-			memmove(dirax->rbuffer,
-			        dirax->rbuffer + endbit_length,
-			        dirax->rbuflen - endbit_length);
-
-			/* Subtract the number of bytes removed */
-			dirax->rbufpos = dirax->rbufpos
-			                       - endbit_length;
-			new_rbuflen = dirax->rbuflen - endbit_length;
-			if ( new_rbuflen == 0 ) new_rbuflen = 256;
-			dirax->rbuffer = realloc(dirax->rbuffer,
-			                               new_rbuflen);
-			dirax->rbuflen = new_rbuflen;
-
-		} else {
-
-			if ( dirax->rbufpos==dirax->rbuflen ) {
-
-				/* More buffer space is needed */
-				dirax->rbuffer = realloc(
-				                    dirax->rbuffer,
-				                    dirax->rbuflen + 256);
-				dirax->rbuflen = dirax->rbuflen
-				                                          + 256;
-				/* The new space gets used at the next
-				 * read, shortly... */
-
-			}
-			no_string = 1;
-
-		}
-
-	}
-
-	return 0;
-}
-
-
-static void write_drx(struct image *image)
-{
-	FILE *fh;
-	int i;
-	char filename[1024];
-
-	snprintf(filename, 1023, "xfel-%i.drx", image->id);
-
-	fh = fopen(filename, "w");
-	if ( !fh ) {
-		ERROR("Couldn't open temporary file '%s'\n", filename);
-		return;
-	}
-	fprintf(fh, "%f\n", 0.5);  /* Lie about the wavelength.  */
-
-	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, "%10f %10f %10f %8f\n",
-		        f->rx/1e10, f->ry/1e10, f->rz/1e10, 1.0);
-
-	}
-	fclose(fh);
-}
-
-
-void run_dirax(struct image *image)
-{
-	unsigned int opts;
-	int status;
-	int rval;
-	struct dirax_data *dirax;
-
-	write_drx(image);
-
-	dirax = malloc(sizeof(struct dirax_data));
-	if ( dirax == NULL ) {
-		ERROR("Couldn't allocate memory for DirAx data.\n");
-		return;
-	}
-
-	dirax->pid = forkpty(&dirax->pty, NULL, NULL, NULL);
-	if ( dirax->pid == -1 ) {
-		ERROR("Failed to fork for DirAx\n");
-		return;
-	}
-	if ( dirax->pid == 0 ) {
-
-		/* Child process: invoke DirAx */
-		struct termios t;
-
-		/* Turn echo off */
-		tcgetattr(STDIN_FILENO, &t);
-		t.c_lflag &= ~(ECHO | ECHOE | ECHOK | ECHONL);
-		tcsetattr(STDIN_FILENO, TCSANOW, &t);
-
-		execlp("dirax", "", (char *)NULL);
-		ERROR("Failed to invoke DirAx.\n");
-		_exit(0);
-
-	}
-
-	dirax->rbuffer = malloc(256);
-	dirax->rbuflen = 256;
-	dirax->rbufpos = 0;
-
-	/* Set non-blocking */
-	opts = fcntl(dirax->pty, F_GETFL);
-	fcntl(dirax->pty, F_SETFL, opts | O_NONBLOCK);
-
-	dirax->step = 1;	/* This starts the "initialisation" procedure */
-	dirax->finished_ok = 0;
-	dirax->read_cell = 0;
-	dirax->n_acls_tried = 0;
-	dirax->best_acl_nh = 0;
-
-	do {
-
-		fd_set fds;
-		struct timeval tv;
-		int sval;
-
-		FD_ZERO(&fds);
-		FD_SET(dirax->pty, &fds);
-
-		tv.tv_sec = 10;
-		tv.tv_usec = 0;
-
-		sval = select(dirax->pty+1, &fds, NULL, NULL, &tv);
-
-		if ( sval == -1 ) {
-			int err = errno;
-			ERROR("select() failed: %s\n", strerror(err));
-			rval = 1;
-		} else if ( sval != 0 ) {
-			rval = dirax_readable(image, dirax);
-		} else {
-			ERROR("No response from DirAx..\n");
-			rval = 1;
-		}
-
-	} while ( !rval );
-
-	close(dirax->pty);
-	free(dirax->rbuffer);
-	waitpid(dirax->pid, &status, 0);
-
-	if ( dirax->finished_ok == 0 ) {
-		ERROR("DirAx doesn't seem to be working properly.\n");
-	}
-
-	free(dirax);
-}
diff --git a/src/dirax.h b/src/dirax.h
deleted file mode 100644
index 8c429710..00000000
--- a/src/dirax.h
+++ /dev/null
@@ -1,26 +0,0 @@
-/*
- * dirax.h
- *
- * Invoke the DirAx auto-indexing program
- *
- * (c) 2006-2010 Thomas White <taw@physics.org>
- *
- * Part of CrystFEL - crystallography with a FEL
- *
- */
-
-
-#ifndef DIRAX_H
-#define DIRAX_H
-
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include "utils.h"
-
-
-extern void run_dirax(struct image *image);
-
-
-#endif	/* DIRAX_H */
diff --git a/src/index-priv.h b/src/index-priv.h
deleted file mode 100644
index 3d8c8a22..00000000
--- a/src/index-priv.h
+++ /dev/null
@@ -1,29 +0,0 @@
-/*
- * index-priv.h
- *
- * Indexing private data
- *
- * (c) 2006-2010 Thomas White <taw@physics.org>
- *
- * Part of CrystFEL - crystallography with a FEL
- *
- */
-
-
-#ifndef INDEXPRIV_H
-#define INDEXPRIV_H
-
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-
-#include "index.h"
-
-struct _indexingprivate
-{
-	IndexingMethod indm;
-};
-
-
-#endif	/* INDEXPRIV_H */
diff --git a/src/index.c b/src/index.c
deleted file mode 100644
index d5e76c50..00000000
--- a/src/index.c
+++ /dev/null
@@ -1,274 +0,0 @@
-/*
- * index.c
- *
- * Perform indexing (somehow)
- *
- * (c) 2006-2011 Thomas White <taw@physics.org>
- * (c) 2010 Richard Kirian <rkirian@asu.edu>
- *
- * Part of CrystFEL - crystallography with a FEL
- *
- */
-
-
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <stdlib.h>
-#include <stdio.h>
-#include <math.h>
-#include <string.h>
-#include <assert.h>
-
-#include "image.h"
-#include "utils.h"
-#include "peaks.h"
-#include "dirax.h"
-#include "mosflm.h"
-#include "detector.h"
-#include "index.h"
-#include "index-priv.h"
-#include "reax.h"
-#include "geometry.h"
-
-
-/* Base class constructor for unspecialised indexing private data */
-IndexingPrivate *indexing_private(IndexingMethod indm)
-{
-	struct _indexingprivate *priv;
-	priv = calloc(1, sizeof(struct _indexingprivate));
-	priv->indm = indm;
-	return priv;
-}
-
-
-static const char *maybes(int n)
-{
-	if ( n == 1 ) return "";
-	return "s";
-}
-
-
-IndexingPrivate **prepare_indexing(IndexingMethod *indm, UnitCell *cell,
-                                   const char *filename, struct detector *det,
-                                   double nominal_photon_energy)
-{
-	int n;
-	int nm = 0;
-	IndexingPrivate **iprivs;
-
-	while ( indm[nm] != INDEXING_NONE ) nm++;
-	STATUS("Preparing %i indexing method%s.\n", nm, maybes(nm));
-	iprivs = malloc((nm+1) * sizeof(IndexingPrivate *));
-
-	for ( n=0; n<nm; n++ ) {
-
-		switch ( indm[n] ) {
-		case INDEXING_NONE :
-			ERROR("Tried to prepare INDEXING_NONE!\n");
-			break;
-		case INDEXING_DIRAX :
-			iprivs[n] = indexing_private(indm[n]);
-			break;
-		case INDEXING_MOSFLM :
-			iprivs[n] = indexing_private(indm[n]);
-			break;
-		case INDEXING_REAX :
-			iprivs[n] = reax_prepare();
-			break;
-		}
-
-	}
-	iprivs[n] = NULL;
-
-	return iprivs;
-}
-
-
-void cleanup_indexing(IndexingPrivate **priv)
-{
-	int n = 0;
-
-	if ( priv == NULL ) return;  /* Nothing to do */
-
-	while ( priv[n] != NULL ) {
-
-		switch ( priv[n]->indm ) {
-		case INDEXING_NONE :
-			free(priv[n]);
-			break;
-		case INDEXING_DIRAX :
-			free(priv[n]);
-			break;
-		case INDEXING_MOSFLM :
-			free(priv[n]);
-			break;
-		case INDEXING_REAX :
-			reax_cleanup(priv[n]);
-			break;
-		}
-
-		n++;
-
-	}
-}
-
-
-void map_all_peaks(struct image *image)
-{
-	int i, n;
-
-	n = image_feature_count(image->features);
-
-	/* Map positions to 3D */
-	for ( i=0; i<n; i++ ) {
-
-		struct imagefeature *f;
-		struct rvec r;
-
-		f = image_get_feature(image->features, i);
-		if ( f == NULL ) continue;
-
-		r = get_q(image, f->fs, f->ss, NULL, 1.0/image->lambda);
-		f->rx = r.u;  f->ry = r.v;  f->rz = r.w;
-
-	}
-}
-
-
-void index_pattern(struct image *image, UnitCell *cell, IndexingMethod *indm,
-                   int cellr, int verbose, IndexingPrivate **ipriv,
-                   int config_insane)
-{
-	int i;
-	int n = 0;
-
-	if ( indm == NULL ) return;
-
-	map_all_peaks(image);
-	image->indexed_cell = NULL;
-
-	while ( indm[n] != INDEXING_NONE ) {
-
-		image->ncells = 0;
-
-		/* Index as appropriate */
-		switch ( indm[n] ) {
-		case INDEXING_NONE :
-			return;
-		case INDEXING_DIRAX :
-			run_dirax(image);
-			break;
-		case INDEXING_MOSFLM :
-			run_mosflm(image, cell);
-			break;
-		case INDEXING_REAX :
-			reax_index(ipriv[n], image, cell);
-			break;
-		}
-		if ( image->ncells == 0 ) {
-			n++;
-			continue;
-		}
-
-		for ( i=0; i<image->ncells; i++ ) {
-
-			UnitCell *new_cell = NULL;
-			UnitCell *cand = image->candidate_cells[i];
-
-			if ( verbose ) {
-				STATUS("--------------------\n");
-				STATUS("Candidate cell %i (before matching):\n",
-				       i);
-				cell_print(image->candidate_cells[i]);
-				STATUS("--------------------\n");
-			}
-
-			/* Match or reduce the cell as appropriate */
-			switch ( cellr ) {
-			case CELLR_NONE :
-				new_cell = cell_new_from_cell(cand);
-				break;
-			case CELLR_REDUCE :
-				new_cell = match_cell(cand, cell, verbose, 1);
-				break;
-			case CELLR_COMPARE :
-				new_cell = match_cell(cand, cell, verbose, 0);
-				break;
-			case CELLR_COMPARE_AB :
-				new_cell = match_cell_ab(cand, cell);
-				break;
-			}
-
-			/* No cell?  Move on to the next candidate */
-			if ( new_cell == NULL ) continue;
-
-			/* Sanity check */
-			image->reflections = find_intersections(image, new_cell);
-			image->indexed_cell = new_cell;
-			
-			if ( !config_insane && !peak_sanity_check(image) ) {
-				cell_free(new_cell);
-				image->indexed_cell = NULL;
-				continue;
-			}
-
-			goto done;  /* Success */
-
-		}
-
-		for ( i=0; i<image->ncells; i++ ) {
-			cell_free(image->candidate_cells[i]);
-			image->candidate_cells[i] = NULL;
-		}
-
-		/* Move on to the next indexing method */
-		n++;
-
-	}
-
-done:
-	for ( i=0; i<image->ncells; i++ ) {
-		/* May free(NULL) if all algorithms were tried and no success */
-		cell_free(image->candidate_cells[i]);
-	}
-}
-
-
-IndexingMethod *build_indexer_list(const char *str, int *need_cell)
-{
-	int n, i;
-	char **methods;
-	IndexingMethod *list;
-	int tmp;
-
-	if ( need_cell == NULL ) need_cell = &tmp;
-	*need_cell = 0;
-
-	n = assplode(str, ",", &methods, ASSPLODE_NONE);
-	list = malloc((n+1)*sizeof(IndexingMethod));
-
-	for ( i=0; i<n; i++ ) {
-
-		if ( strcmp(methods[i], "dirax") == 0) {
-			list[i] = INDEXING_DIRAX;
-		} else if ( strcmp(methods[i], "mosflm") == 0) {
-			list[i] = INDEXING_MOSFLM;
-		} else if ( strcmp(methods[i], "reax") == 0) {
-			list[i] = INDEXING_REAX;
-			*need_cell = 1;
-		} else {
-			ERROR("Unrecognised indexing method '%s'\n",
-			      methods[i]);
-			return NULL;
-		}
-
-		free(methods[i]);
-
-	}
-	free(methods);
-	list[i] = INDEXING_NONE;
-
-	return list;
-}
diff --git a/src/index.h b/src/index.h
deleted file mode 100644
index 9d4b69bd..00000000
--- a/src/index.h
+++ /dev/null
@@ -1,63 +0,0 @@
-/*
- * index.h
- *
- * Perform indexing (somehow)
- *
- * (c) 2006-2010 Thomas White <taw@physics.org>
- *
- * Part of CrystFEL - crystallography with a FEL
- *
- */
-
-
-#ifndef INDEX_H
-#define INDEX_H
-
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-
-#include "cell.h"
-#include "image.h"
-#include "detector.h"
-
-
-/* Indexing methods */
-typedef enum {
-	INDEXING_NONE,
-	INDEXING_DIRAX,
-	INDEXING_MOSFLM,
-	INDEXING_REAX,
-} IndexingMethod;
-
-
-/* Cell reduction methods */
-enum {
-	CELLR_NONE,
-	CELLR_REDUCE,
-	CELLR_COMPARE,
-	CELLR_COMPARE_AB,
-};
-
-
-typedef struct _indexingprivate IndexingPrivate;
-
-extern IndexingPrivate *indexing_private(IndexingMethod indm);
-
-extern IndexingPrivate **prepare_indexing(IndexingMethod *indm, UnitCell *cell,
-                                         const char *filename,
-                                         struct detector *det,
-                                         double nominal_photon_energy);
-
-extern void map_all_peaks(struct image *image);
-
-extern void index_pattern(struct image *image, UnitCell *cell,
-                          IndexingMethod *indm, int cellr, int verbose,
-                          IndexingPrivate **priv, int config_insane);
-
-extern void cleanup_indexing(IndexingPrivate **priv);
-
-extern IndexingMethod *build_indexer_list(const char *str, int *need_cell);
-
-#endif	/* INDEX_H */
diff --git a/src/mosflm.c b/src/mosflm.c
deleted file mode 100644
index 5df5af21..00000000
--- a/src/mosflm.c
+++ /dev/null
@@ -1,609 +0,0 @@
-/*
- * mosflm.c
- *
- * Invoke the DPS auto-indexing algorithm through MOSFLM
- *
- * (c) 2010 Richard Kirian <rkirian@asu.edu>
- * (c) 2006-2010 Thomas White <taw@physics.org>
- *
- * Part of CrystFEL - crystallography with a FEL
- *
- */
-
-/* TODO:
- *
- * Properly read the newmat file (don't use fscanf-- spaces between numers
- *  are not guaranteed)
- *
- * "Success" is indicated by existence of NEWMAT file written by mosflm.
- *  Better to interact with mosflm directly in order to somehow verify success.
- *
- * Investigate how these keywords affect mosflms behavior:
- *
- *  MOSAICITY
- *  DISPERSION
- *  DIVERGENCE
- *  POLARISATION
- *  POSTREF BEAM
- *  POSTREF USEBEAM OFF
- *  PREREFINE ON
- *  EXTRA ON
- *  POSTREF ON
- *
- *  These did not seem to affect the results by my (Rick's) experience, probably
- *  because they are only used conjunction with image intensity data, but it's
- *  worth another look at the documentation.
- */
-
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-
-#include <stdlib.h>
-#include <stdio.h>
-#include <math.h>
-#include <string.h>
-#include <sys/types.h>
-#include <sys/wait.h>
-#include <unistd.h>
-#include <assert.h>
-#include <fcntl.h>
-#include <errno.h>
-
-#if HAVE_FORKPTY_LINUX
-#include <pty.h>
-#elif HAVE_FORKPTY_BSD
-#include <util.h>
-#endif
-
-
-#include "image.h"
-#include "mosflm.h"
-#include "utils.h"
-#include "peaks.h"
-
-
-#define MOSFLM_VERBOSE 0
-
-
-typedef enum {
-	MOSFLM_INPUT_NONE,
-	MOSFLM_INPUT_LINE,
-	MOSFLM_INPUT_PROMPT
-} MOSFLMInputType;
-
-
-struct mosflm_data {
-
-	/* MOSFLM auto-indexing low-level stuff */
-	int                     pty;
-	pid_t                   pid;
-	char                    *rbuffer;
-	int                     rbufpos;
-	int                     rbuflen;
-
-	/* MOSFLM high-level stuff */
-	char                    newmatfile[128];
-	char                    imagefile[128];
-	char                    sptfile[128];
-	int                     step;
-	int                     finished_ok;
-	UnitCell                *target_cell;
-
-};
-
-
-static void mosflm_parseline(const char *line, struct image *image,
-                             struct mosflm_data *dirax)
-{
-	#if MOSFLM_VERBOSE
-	char *copy;
-	int i;
-
-	copy = strdup(line);
-	for ( i=0; i<strlen(copy); i++ ) {
-		if ( copy[i] == '\r' ) copy[i]='r';
-		if ( copy[i] == '\n' ) copy[i]='\0';
-	}
-	STATUS("MOSFLM: %s\n", copy);
-	free(copy);
-	#endif
-}
-
-
-static int read_newmat(const char *filename, struct image *image)
-{
-	FILE * fh;
-	float asx, asy, asz;
-	float bsx, bsy, bsz;
-	float csx, csy, csz;
-	int n;
-	double c;
-
-	fh = fopen(filename, "r");
-	if ( fh == NULL ) {
-		return 1;
-	}
-	n  = fscanf(fh, "%f %f %f\n", &asx, &bsx, &csx);
-	n += fscanf(fh, "%f %f %f\n", &asy, &bsy, &csy);
-	n += fscanf(fh, "%f %f %f\n", &asz, &bsz, &csz);
-	if ( n != 9 ) {
-		STATUS("Fewer than 9 parameters found in NEWMAT file.\n");
-		return 1;
-	}
-	fclose(fh);
-
-	/* MOSFLM "A" matrix is multiplied by lambda, so fix this */
-	c = 1/image->lambda;
-
-	image->candidate_cells[0] = cell_new();
-
-	cell_set_reciprocal(image->candidate_cells[0],
-                            asz*c, asy*c, asx*c,
-                            bsz*c, bsy*c, bsx*c,
-                            csz*c, csy*c, csx*c);
-
-        image->ncells = 1;
-
-        return 0;
-}
-
-
-/* Need to sort mosflm peaks by intensity... */
-struct sptline {
-	double x; /* x coordinate of peak */
-	double y; /* y coordinate of peak */
-	double h; /* height of peak */
-	double s; /* sigma of peak */
-};
-
-
-static int compare_vals(const void *ap, const void *bp)
-{
-	const struct sptline a = *(struct sptline *)ap;
-	const struct sptline b = *(struct sptline *)bp;
-
-	if ( a.h < b.h ) return 1;
-	if ( a.h > b.h ) return -1;
-	return 0;
-}
-
-
-/* Write .spt file for mosflm */
-static void write_spt(struct image *image, const char *filename)
-{
-	FILE *fh;
-	int i;
-	double fclen = 67.8;  /* fake camera length in mm */
-	double fpix = 0.075;  /* fake pixel size in mm */
-	double pix;
-	double height = 100.0;
-	double sigma = 1.0;
-	int nPeaks = image_feature_count(image->features);
-	struct sptline *sptlines;
-
-	fh = fopen(filename, "w");
-	if ( !fh ) {
-		ERROR("Couldn't open temporary file '%s'\n", filename);
-		return;
-	}
-
-	fprintf(fh, "%10d %10d %10.8f %10.6f %10.6f\n", 1, 1, fpix, 1.0, 0.0);
-	fprintf(fh, "%10d %10d\n", 1, 1);
-	fprintf(fh, "%10.5f %10.5f\n", 0.0, 0.0);
-
-	sptlines = malloc(sizeof(struct sptline)*nPeaks);
-
-	for ( i=0; i<nPeaks; i++ ) {
-
-		struct imagefeature *f;
-		struct panel *p;
-		double xs, ys, rx, ry;
-
-		f = image_get_feature(image->features, i);
-		if ( f == NULL ) continue;
-
-		p = find_panel(image->det, f->fs, f->ss);
-		if ( p == NULL ) continue;
-
-		pix = 1000.0/p->res; /* pixel size in mm */
-		height = f->intensity;
-
-		xs = (f->fs-p->min_fs)*p->fsx + (f->ss-p->min_ss)*p->ssx;
-		ys = (f->ss-p->min_fs)*p->fsy + (f->ss-p->min_ss)*p->ssy;
-		rx = xs + p->cnx;
-		ry = ys + p->cny;
-
-		sptlines[i].x = ry*pix*fclen/p->clen/1000.0;
-		sptlines[i].y = -rx*pix*fclen/p->clen/1000.0;
-		sptlines[i].h = height;
-		sptlines[i].s = sigma/1000.0;
-
-	}
-
-	qsort(sptlines, nPeaks, sizeof(struct sptline), compare_vals);
-
-	for ( i=0; i<nPeaks; i++ ) {
-
-		fprintf(fh, "%10.2f %10.2f %10.2f %10.2f %10.2f %10.2f\n",
-		        sptlines[i].x, sptlines[i].y,
-		        0.0, 0.0,
-		        sptlines[i].h, sptlines[i].s);
-
-	}
-
-	free(sptlines);
-
-	fprintf(fh,"%10.2f %10.2f %10.2f %10.2f %10.2f %10.2f\n",
-	           -999.0,-999.0,-999.0,-999.0,-999.0,-999.0);
-	fclose(fh);
-}
-
-
-/* Write a dummy 1x1 pixel image file for MOSFLM.  Without post refinement,
- * MOSFLM will ignore this, but it must be present. */
-static void write_img(struct image *image, const char *filename)
-{
-	FILE *fh;
-	unsigned short int *intimage;
-
-	intimage = malloc(sizeof(unsigned short int));
-	intimage[0] = 1;
-
-	fh = fopen(filename, "w");
-	if ( !fh ) {
-		ERROR("Couldn't open temporary file '%s'\n", filename);
-		return;
-	}
-
-	/* Write header */
-	fprintf(fh, "{\nHEADER_BYTES=512;\n");
-	fprintf(fh, "BYTE_ORDER=little_endian;\n");
-	fprintf(fh, "TYPE=unsigned_short;\n");
-	fprintf(fh, "DIM=2;\n");
-	fprintf(fh, "SIZE1=1;\n");
-	fprintf(fh, "SIZE2=1;\n");
-	fprintf(fh, "}\n");
-
-	/* Header padding */
-	while ( ftell(fh) < 512 ) fprintf(fh," ");
-
-	fwrite(intimage, sizeof(unsigned short int), 1, fh);
-	free(intimage);
-	fclose(fh);
-}
-
-
-static void mosflm_sendline(const char *line, struct mosflm_data *mosflm)
-{
-	#if MOSFLM_VERBOSE
-	char *copy;
-	int i;
-
-	copy = strdup(line);
-	for ( i=0; i<strlen(copy); i++ ) {
-		if ( copy[i] == '\r' ) copy[i]='\0';
-		if ( copy[i] == '\n' ) copy[i]='\0';
-	}
-	STATUS("To MOSFLM: '%s'\n", copy);
-	free(copy);
-	#endif
-
-	write(mosflm->pty, line, strlen(line));
-}
-
-
-static void mosflm_send_next(struct image *image, struct mosflm_data *mosflm)
-{
-	char tmp[256];
-	char symm[32];
-	const char *sg;
-	double wavelength;
-	double a, b, c, alpha, beta, gamma;
-	int i, j;
-
-	switch ( mosflm->step ) {
-
-	case 1 :
-		mosflm_sendline("DETECTOR ROTATION HORIZONTAL"
-		                " ANTICLOCKWISE ORIGIN LL FAST HORIZONTAL"
-		                " RECTANGULAR\n", mosflm);
-		break;
-
-	case 2 :
-		if ( mosflm->target_cell != NULL ) {
-			cell_get_parameters(mosflm->target_cell, &a, &b, &c,
-				            &alpha, &beta, &gamma);
-			snprintf(tmp, 255,
-			         "CELL %6.2f %6.2f %6.2f %6.2f %6.2f %6.2f\n",
-		                 a*1e10, b*1e10, c*1e10,
-		                 rad2deg(alpha), rad2deg(beta), rad2deg(gamma));
-			mosflm_sendline(tmp, mosflm);
-		} else {
-			mosflm_sendline("# Do nothing\n", mosflm);
-		}
-		break;
-
-	case 3 :
-		if ( mosflm->target_cell != NULL ) {
-			sg = cell_get_spacegroup(mosflm->target_cell);
-			/* Remove white space from space group */
-			j = 0;
-			for ( i=0; i<strlen(sg); i++ ) {
-				if (sg[i] != ' ') {
-					symm[j++] = sg[i];
-				}
-			}
-			symm[j] = '\0';
-			snprintf(tmp, 255, "SYMM %s\n", symm);
-			mosflm_sendline(tmp, mosflm);
-		} else {
-			mosflm_sendline("SYMM P1\n", mosflm);
-		}
-		break;
-
-	case 4 :
-		mosflm_sendline("DISTANCE 67.8\n", mosflm);
-		break;
-
-	case 5 :
-		mosflm_sendline("BEAM 0.0 0.0\n", mosflm);
-		break;
-
-	case 6 :
-		wavelength = image->lambda*1e10;
-		snprintf(tmp, 255, "WAVELENGTH %10.5f\n", wavelength);
-		mosflm_sendline(tmp, mosflm);
-		break;
-
-	case 7 :
-		snprintf(tmp, 255, "NEWMAT %s\n", mosflm->newmatfile);
-		mosflm_sendline(tmp, mosflm);
-		break;
-
-	case 8 :
-		snprintf(tmp, 255, "IMAGE %s phi 0 0\n", mosflm->imagefile);
-		mosflm_sendline(tmp, mosflm);
-		break;
-
-	case 9 :
-		snprintf(tmp, 255, "AUTOINDEX DPS FILE %s"
-		                   " IMAGE 1 MAXCELL 1000 REFINE\n",
-		         mosflm->sptfile);
-
-		/* "This option is only available if you e-mail Andrew Leslie
-		 * and ask for it." - MOSFLM
-		 * snprintf(tmp, 255, "AUTOINDEX NODISPLAY IMAGE 1 FILE %s\n",
-		 *         mosflm->sptfile); */
-		mosflm_sendline(tmp, mosflm);
-		break;
-
-	case 10 :
-		mosflm_sendline("GO\n", mosflm);
-		mosflm->finished_ok = 1;
-		break;
-
-	default:
-		mosflm_sendline("exit\n", mosflm);
-		return;
-
-	}
-
-	mosflm->step++;
-}
-
-
-static int mosflm_readable(struct image *image, struct mosflm_data *mosflm)
-{
-	int rval;
-	int no_string = 0;
-
-	rval = read(mosflm->pty, mosflm->rbuffer+mosflm->rbufpos,
-	            mosflm->rbuflen-mosflm->rbufpos);
-
-	if ( (rval == -1) || (rval == 0) ) return 1;
-
-	mosflm->rbufpos += rval;
-	assert(mosflm->rbufpos <= mosflm->rbuflen);
-
-	while ( (!no_string) && (mosflm->rbufpos > 0) ) {
-
-		int i;
-		int block_ready = 0;
-		MOSFLMInputType type = MOSFLM_INPUT_NONE;
-
-		/* See if there's a full line in the buffer yet */
-		for ( i=0; i<mosflm->rbufpos-1; i++ ) {
-			/* Means the last value looked at is rbufpos-2 */
-
-			/* Is there a prompt in the buffer? */
-			if ( (i+10 <= mosflm->rbufpos)
-			  && (!strncmp(mosflm->rbuffer+i, "MOSFLM => ", 10)) ) {
-				block_ready = 1;
-				type = MOSFLM_INPUT_PROMPT;
-				break;
-			}
-
-			if ( (mosflm->rbuffer[i] == '\r')
-			  && (mosflm->rbuffer[i+1] == '\n') ) {
-				block_ready = 1;
-				type = MOSFLM_INPUT_LINE;
-				break;
-			}
-
-		}
-
-		if ( block_ready ) {
-
-			unsigned int new_rbuflen;
-			unsigned int endbit_length;
-			char *block_buffer = NULL;
-
-			switch ( type ) {
-
-			case MOSFLM_INPUT_LINE :
-
-				block_buffer = malloc(i+1);
-				memcpy(block_buffer, mosflm->rbuffer, i);
-				block_buffer[i] = '\0';
-
-				if ( block_buffer[0] == '\r' ) {
-					memmove(block_buffer, block_buffer+1, i);
-				}
-
-				mosflm_parseline(block_buffer, image, mosflm);
-				free(block_buffer);
-				endbit_length = i+2;
-				break;
-
-			case MOSFLM_INPUT_PROMPT :
-
-				mosflm_send_next(image, mosflm);
-				endbit_length = i+7;
-				break;
-
-			default :
-
-				/* Obviously, this never happens :) */
-				ERROR("Unrecognised MOSFLM input mode! "
-				      "I don't know how to understand MOSFLM\n");
-				return 1;
-
-			}
-
-			/* Now the block's been parsed, it should be
-			 * forgotten about */
-			memmove(mosflm->rbuffer,
-			        mosflm->rbuffer + endbit_length,
-			        mosflm->rbuflen - endbit_length);
-
-			/* Subtract the number of bytes removed */
-			mosflm->rbufpos = mosflm->rbufpos
-			                       - endbit_length;
-			new_rbuflen = mosflm->rbuflen - endbit_length;
-			if ( new_rbuflen == 0 ) new_rbuflen = 256;
-			mosflm->rbuffer = realloc(mosflm->rbuffer,
-			                               new_rbuflen);
-			mosflm->rbuflen = new_rbuflen;
-
-		} else {
-
-			if ( mosflm->rbufpos==mosflm->rbuflen ) {
-
-				/* More buffer space is needed */
-				mosflm->rbuffer = realloc(
-				                    mosflm->rbuffer,
-				                    mosflm->rbuflen + 256);
-				mosflm->rbuflen = mosflm->rbuflen + 256;
-				/* The new space gets used at the next
-				 * read, shortly... */
-
-			}
-			no_string = 1;
-
-		}
-
-	}
-
-	return 0;
-}
-
-
-void run_mosflm(struct image *image, UnitCell *cell)
-{
-	struct mosflm_data *mosflm;
-	unsigned int opts;
-	int status;
-	int rval;
-
-	mosflm = malloc(sizeof(struct mosflm_data));
-	if ( mosflm == NULL ) {
-		ERROR("Couldn't allocate memory for MOSFLM data.\n");
-		return;
-	}
-
-	mosflm->target_cell = cell;
-
-	snprintf(mosflm->imagefile, 127, "xfel-%i_001.img", image->id);
-	write_img(image, mosflm->imagefile); /* Dummy image */
-
-	snprintf(mosflm->sptfile, 127, "xfel-%i_001.spt", image->id);
-	write_spt(image, mosflm->sptfile);
-
-	snprintf(mosflm->newmatfile, 127, "xfel-%i.newmat", image->id);
-	remove(mosflm->newmatfile);
-
-	mosflm->pid = forkpty(&mosflm->pty, NULL, NULL, NULL);
-	if ( mosflm->pid == -1 ) {
-		ERROR("Failed to fork for MOSFLM\n");
-		free(mosflm);
-		return;
-	}
-	if ( mosflm->pid == 0 ) {
-
-		/* Child process: invoke MOSFLM */
-		struct termios t;
-
-		/* Turn echo off */
-		tcgetattr(STDIN_FILENO, &t);
-		t.c_lflag &= ~(ECHO | ECHOE | ECHOK | ECHONL);
-		tcsetattr(STDIN_FILENO, TCSANOW, &t);
-
-		execlp("ipmosflm", "", (char *)NULL);
-		ERROR("Failed to invoke MOSFLM.\n");
-		_exit(0);
-
-	}
-
-	mosflm->rbuffer = malloc(256);
-	mosflm->rbuflen = 256;
-	mosflm->rbufpos = 0;
-
-	/* Set non-blocking */
-	opts = fcntl(mosflm->pty, F_GETFL);
-	fcntl(mosflm->pty, F_SETFL, opts | O_NONBLOCK);
-
-	mosflm->step = 1;	/* This starts the "initialisation" procedure */
-	mosflm->finished_ok = 0;
-
-	do {
-
-		fd_set fds;
-		struct timeval tv;
-		int sval;
-
-		FD_ZERO(&fds);
-		FD_SET(mosflm->pty, &fds);
-
-		tv.tv_sec = 10;
-		tv.tv_usec = 0;
-
-		sval = select(mosflm->pty+1, &fds, NULL, NULL, &tv);
-
-		if ( sval == -1 ) {
-			int err = errno;
-			ERROR("select() failed: %s\n", strerror(err));
-			rval = 1;
-		} else if ( sval != 0 ) {
-			rval = mosflm_readable(image, mosflm);
-		} else {
-			ERROR("No response from MOSFLM..\n");
-			rval = 1;
-		}
-
-	} while ( !rval );
-
-	close(mosflm->pty);
-	free(mosflm->rbuffer);
-	waitpid(mosflm->pid, &status, 0);
-
-	if ( mosflm->finished_ok == 0 ) {
-		ERROR("MOSFLM doesn't seem to be working properly.\n");
-	} else {
-		/* Read the mosflm NEWMAT file and get cell if found */
-		read_newmat(mosflm->newmatfile, image);
-	}
-
-	free(mosflm);
-}
diff --git a/src/mosflm.h b/src/mosflm.h
deleted file mode 100644
index 82b80a44..00000000
--- a/src/mosflm.h
+++ /dev/null
@@ -1,27 +0,0 @@
-/*
- * mosflm.h
- *
- * Invoke the DPS auto-indexing algorithm through MOSFLM
- *
- * (c) 2010 Richard Kirian <rkirian@asu.edu>
- * (c) 2006-2010 Thomas White <taw@physics.org>
- *
- * Part of CrystFEL - crystallography with a FEL
- *
- */
-
-
-#ifndef MOSFLM_H
-#define MOSFLM_H
-
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include "utils.h"
-
-
-extern void run_mosflm(struct image *image, UnitCell *cell);
-
-
-#endif	/* MOSFLM_H */
diff --git a/src/reax.c b/src/reax.c
deleted file mode 100644
index ff1ea582..00000000
--- a/src/reax.c
+++ /dev/null
@@ -1,728 +0,0 @@
-/*
- * reax.c
- *
- * A new auto-indexer
- *
- * (c) 2011 Thomas White <taw@physics.org>
- *
- * Part of CrystFEL - crystallography with a FEL
- *
- */
-
-
-#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 <gsl/gsl_blas.h>
-
-#include "image.h"
-#include "utils.h"
-#include "peaks.h"
-#include "cell.h"
-#include "index.h"
-#include "index-priv.h"
-
-
-struct dvec
-{
-	double x;
-	double y;
-	double z;
-	double th;
-	double ph;
-};
-
-
-struct reax_private
-{
-	IndexingPrivate base;
-	struct dvec *directions;
-	int n_dir;
-	double angular_inc;
-
-	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 double check_dir(struct dvec *dir, ImageFeatureList *flist,
-                        int nel, double pmax, double *fft_in,
-                        fftw_complex *fft_out, fftw_plan plan,
-                        int smin, int smax,
-                        const char *rg, struct detector *det)
-{
-	int n, i;
-	double tot;
-
-	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 ( p->rigid_group != rg ) 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);
-
-	tot = 0.0;
-	for ( i=smin; i<=smax; i++ ) {
-		double re, im;
-		re = fft_out[i][0];
-		im = fft_out[i][1];
-		tot += sqrt(re*re + im*im);
-	}
-
-	return tot;
-}
-
-
-/* Refine a direct space vector.  From Clegg (1984) */
-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 ( 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);
-
-	return dtmax;
-}
-
-
-static void refine_cell(struct image *image, UnitCell *cell,
-                        ImageFeatureList *flist)
-{
-	double ax, ay, az;
-	double bx, by, bz;
-	double cx, cy, cz;
-	int i;
-	double sm;
-
-	cell_get_cartesian(cell, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz);
-	i = 0;
-	do {
-
-		sm  = iterate_refine_vector(&ax, &ay, &az, flist);
-		sm += iterate_refine_vector(&bx, &by, &bz, flist);
-		sm += iterate_refine_vector(&cx, &cy, &cz, flist);
-		i++;
-
-	} while ( (sm > 0.001e-9) && (i<10) );
-
-	cell_set_cartesian(cell, ax, ay, az, bx, by, bz, cx, cy, cz);
-
-	if ( i == 10 ) {
-		cell_free(image->indexed_cell);
-		image->indexed_cell = NULL;
-	}
-}
-
-
-static void fine_search(struct reax_private *p, ImageFeatureList *flist,
-                        int nel, double pmax, double *fft_in,
-                        fftw_complex *fft_out, fftw_plan plan,
-                        int smin, int smax, double th_cen, double ph_cen,
-                        double *x, double *y, double *z)
-{
-	double fom = 0.0;
-	double th, ph;
-	double inc;
-	struct dvec dir;
-	int i, s;
-	double max, modv;
-
-	inc = p->angular_inc / 100.0;
-
-	for ( th=th_cen-p->angular_inc; th<=th_cen+p->angular_inc; th+=inc ) {
-	for ( ph=ph_cen-p->angular_inc; ph<=ph_cen+p->angular_inc; ph+=inc ) {
-
-		double new_fom;
-
-		dir.x = cos(ph) * sin(th);
-		dir.y = sin(ph) * sin(th);
-		dir.z = cos(th);
-
-		new_fom = check_dir(&dir, flist, nel, pmax, fft_in, fft_out,
-		                    plan, smin, smax, NULL, NULL);
-
-		if ( new_fom > fom ) {
-			fom = new_fom;
-			*x = dir.x;  *y = dir.y;  *z = dir.z;
-		}
-
-	}
-	}
-
-	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;
-		}
-
-	}
-	assert(s>0);
-
-	modv = (double)s / (2.0*pmax);
-	*x *= modv;  *y *= modv;  *z *= modv;
-}
-
-
-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 char *rg,
-                              struct detector *det)
-{
-	struct dvec dir;
-	int s, i;
-	double max;
-	double re, im;
-
-	dir.x = x;  dir.y = y;  dir.z = z;
-
-	check_dir(&dir, f, nel, pmax, fft_in,fft_out, plan, smin, smax,
-	          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 char *rg, int nel, 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;
-	struct panel *p;
-	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;
-	double max;
-	int max_i, max_j;
-
-	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, nel, pmax,
-	                      fft_in, fft_out, plan, smin, smax, rg, det);
-	phb = get_model_phase(bx/mb, by/mb, bz/mb, image->features, nel, pmax,
-	                      fft_in, fft_out, plan, smin, smax, rg, det);
-	phc = get_model_phase(cx/mc, cy/mc, cz/mc, image->features, nel, pmax,
-	                      fft_in, fft_out, plan, smin, smax, rg, det);
-
-	for ( i=0; i<det->n_panels; i++ ) {
-		if ( det->panels[i].rigid_group == rg ) {
-			p = &det->panels[i];
-			break;
-		}
-	}
-
-	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 void refine_all_rigid_groups(struct image *image, UnitCell *cell,
-                                    int nel, 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->num_rigid_groups; i++ ) {
-		refine_rigid_group(image, cell, image->det->rigid_groups[i],
-		                   nel, pmax, fft_in, fft_out, plan, smin, smax,
-		                   det, p);
-	}
-}
-
-
-void reax_index(IndexingPrivate *pp, struct image *image, UnitCell *cell)
-{
-	int i;
-	struct reax_private *p;
-	double fom;
-	double ax, ay, az;
-	double bx, by, bz;
-	double cx, cy, cz;
-	double mod_a, mod_b, mod_c;
-	double al, be, ga;
-	double th, ph;
-	double *fft_in;
-	fftw_complex *fft_out;
-	int smin, smax;
-	double amin, amax;
-	double bmin, bmax;
-	double cmin, cmax;
-	double pmax;
-	int n;
-	const double ltol = 5.0;             /* Direct space axis length
-	                                      * tolerance in percent */
-	const double angtol = deg2rad(1.5);  /* Direct space angle tolerance
-	                                      * in radians */
-
-	assert(pp->indm == INDEXING_REAX);
-	p = (struct reax_private *)pp;
-
-	fft_in = fftw_malloc(p->nel*sizeof(double));
-	fft_out = fftw_malloc((p->nel/2 + 1)*sizeof(fftw_complex));
-
-	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);
-
-	al = angle_between(bx, by, bz, cx, cy, cz);
-	be = angle_between(ax, ay, az, cx, cy, cz);
-	ga = angle_between(ax, ay, az, bx, by, bz);
-
-	pmax = 0.0;
-	n = image_feature_count(image->features);
-	for ( i=0; i<n; i++ ) {
-
-		struct imagefeature *f;
-		double val;
-
-		f = image_get_feature(image->features, i);
-		if ( f == NULL ) continue;
-
-		val = modulus(f->rx, f->ry, f->rz);
-		if ( val > pmax ) pmax = val;
-
-	}
-
-	/* Sanity check */
-	if ( pmax < 1e4 ) return;
-
-	/* Search for a */
-	smin = 2.0*pmax * amin;
-	smax = 2.0*pmax * amax;
-	fom = 0.0;  th = 0.0;  ph = 0.0;
-	for ( i=0; i<p->n_dir; i++ ) {
-
-		double new_fom;
-
-		new_fom = check_dir(&p->directions[i], image->features,
-		                    p->nel, pmax, fft_in, fft_out, p->plan,
-		                    smin, smax, NULL, NULL);
-		if ( new_fom > fom ) {
-			fom = new_fom;
-			th = p->directions[i].th;
-			ph = p->directions[i].ph;
-		}
-
-	}
-	fine_search(p, image->features, p->nel, pmax, fft_in, fft_out,
-	            p->plan, smin, smax, th, ph, &ax, &ay, &az);
-
-	/* Search for b */
-	smin = 2.0*pmax * bmin;
-	smax = 2.0*pmax * bmax;
-	fom = 0.0;  th = 0.0;  ph = 0.0;
-	for ( i=0; i<p->n_dir; i++ ) {
-
-		double new_fom, ang;
-
-		ang = angle_between(p->directions[i].x, p->directions[i].y,
-		                    p->directions[i].z, ax, ay, az);
-		if ( fabs(ang-ga) > angtol ) continue;
-
-		new_fom = check_dir(&p->directions[i], image->features,
-		                    p->nel, pmax, fft_in, fft_out, p->plan,
-		                    smin, smax, NULL, NULL);
-		if ( new_fom > fom ) {
-			fom = new_fom;
-			th = p->directions[i].th;
-			ph = p->directions[i].ph;
-		}
-
-	}
-	fine_search(p, image->features, p->nel, pmax, fft_in, fft_out,
-	            p->plan, smin, smax, th, ph, &bx, &by, &bz);
-
-	/* Search for c */
-	smin = 2.0*pmax * cmin;
-	smax = 2.0*pmax * cmax;
-	fom = 0.0;  th = 0.0;  ph = 0.0;
-	for ( i=0; i<p->n_dir; i++ ) {
-
-		double new_fom, ang;
-
-		ang = angle_between(p->directions[i].x, p->directions[i].y,
-		                    p->directions[i].z, ax, ay, az);
-		if ( fabs(ang-be) > angtol ) continue;
-
-		ang = angle_between(p->directions[i].x, p->directions[i].y,
-		                    p->directions[i].z, bx, by, bz);
-		if ( fabs(ang-al) > angtol ) continue;
-
-		new_fom = check_dir(&p->directions[i], image->features,
-		                    p->nel, pmax, fft_in, fft_out, p->plan,
-		                    smin, smax, NULL, NULL);
-		if ( new_fom > fom ) {
-			fom = new_fom;
-			th = p->directions[i].th;
-			ph = p->directions[i].ph;
-		}
-
-	}
-	fine_search(p, image->features, p->nel, pmax, fft_in, fft_out,
-	            p->plan, smin, smax, th, ph, &cx, &cy, &cz);
-
-	image->candidate_cells[0] = cell_new();
-	cell_set_cartesian(image->candidate_cells[0],
-	                   ax, ay, az, bx, by, bz, cx, cy, cz);
-
-	refine_all_rigid_groups(image, image->candidate_cells[0], p->nel, pmax,
-	                        fft_in, fft_out, p->plan, smin, smax,
-	                        image->det, p);
-	map_all_peaks(image);
-	refine_cell(image, image->candidate_cells[0], image->features);
-
-	fftw_free(fft_in);
-	fftw_free(fft_out);
-
-	image->ncells = 1;
-}
-
-
-IndexingPrivate *reax_prepare()
-{
-	struct reax_private *p;
-	int samp;
-	double th;
-
-	p = calloc(1, sizeof(*p));
-	if ( p == NULL ) return NULL;
-
-	p->base.indm = INDEXING_REAX;
-
-	p->angular_inc = deg2rad(1.7);  /* From Steller (1997) */
-
-	/* 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);
-
-	return (IndexingPrivate *)p;
-}
-
-
-void reax_cleanup(IndexingPrivate *pp)
-{
-	struct reax_private *p;
-
-	assert(pp->indm == INDEXING_REAX);
-	p = (struct reax_private *)pp;
-
-	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/src/reax.h b/src/reax.h
deleted file mode 100644
index 543cd0d5..00000000
--- a/src/reax.h
+++ /dev/null
@@ -1,27 +0,0 @@
-/*
- * reax.h
- *
- * A new auto-indexer
- *
- * (c) 2011 Thomas White <taw@physics.org>
- *
- * Part of CrystFEL - crystallography with a FEL
- *
- */
-
-
-#ifndef REAX_H
-#define REAX_H
-
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include "cell.h"
-
-extern IndexingPrivate *reax_prepare(void);
-extern void reax_cleanup(IndexingPrivate *pp);
-
-extern void reax_index(IndexingPrivate *p, struct image *image, UnitCell *cell);
-
-#endif	/* REAX_H */
diff --git a/src/render.c b/src/render.c
deleted file mode 100644
index dbaca2fd..00000000
--- a/src/render.c
+++ /dev/null
@@ -1,442 +0,0 @@
-/*
- * render.c
- *
- * Render a high dynamic range buffer in some sensible way
- *
- * (c) 2006-2011 Thomas White <taw@physics.org>
- *
- * Part of CrystFEL - crystallography with a FEL
- *
- */
-
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-
-#ifdef HAVE_GTK
-#include <gdk-pixbuf/gdk-pixbuf.h>
-#endif
-
-#include <stdlib.h>
-#include <math.h>
-#include <stdint.h>
-
-#ifdef HAVE_TIFF
-#include <tiffio.h>
-#endif
-
-
-#include "hdf5-file.h"
-#include "render.h"
-#include "peaks.h"
-#include "filters.h"
-#include "utils.h"
-
-
-static void render_rgb(double val, double max,
-                       double *rp, double *gp, double *bp)
-{
-	int s;
-	double p;
-	double r, g, b;
-
-	s = val / (max/6);
-	p = fmod(val, max/6.0);
-	p /= (max/6.0);
-
-	r = 0.0;  g = 0.0;  b = 0.0;
-
-	if ( (val < 0.0) ) {
-		s = 0;
-		p = 0;
-	}
-	if ( (val > max) ) {
-		s = 6;
-	}
-	switch ( s ) {
-		case 0 : {	/* Black to blue */
-			r = 0;  g = 0;  b = p;
-			break;
-		}
-		case 1 : {	/* Blue to pink */
-			r = p;  g = 0;  b = 1.0;
-			break;
-		}
-		case 2 : {	/* Pink to red */
-			r = 1.0;  g = 0;  b = (1.0-p)*1.0;
-			break;
-		}
-		case 3 : {	/* Red to Orange */
-			r = 1.0;  g = 0.5*p;  b = 0;
-			break;
-		}
-		case 4 : {	/* Orange to Yellow */
-			r = 1.0;  g = 0.5 + 0.5*p;  b = 0;
-			break;
-		}
-		case 5 : {	/* Yellow to White */
-			r = 1.0;  g = 1.0;  b = 1.0*p;
-			break;
-		}
-		case 6 : {	/* Pixel has hit the maximum value */
-			r = 1.0;  g = 1.0;  b = 1.0;
-			break;
-		}
-	}
-
-	*rp = r;
-	*gp = g;
-	*bp = b;
-}
-
-
-static void render_ratio(double val, double max,
-                         double *rp, double *gp, double *bp)
-{
-	if ( val <= 1.0 ) {
-		render_rgb(val, 2.0, rp, gp, bp);
-	} else {
-		/* Your homework is to simplify this expression */
-		val = ((val-1.0)/(max-1.0)) * (max/2.0) + max/2.0;
-		render_rgb(val, max, rp, gp, bp);
-	}
-}
-
-
-static void render_mono(double val, double max,
-                        double *rp, double *gp, double *bp)
-{
-	double p;
-	p = val / max;
-	if ( val < 0.0 ) p = 0.0;
-	if ( val > max ) p = 1.0;
-	*rp = p;
-	*gp = p;
-	*bp = p;
-}
-
-
-static void render_invmono(double val, double max,
-                           double *rp, double *gp, double *bp)
-{
-	double p;
-	p = val / max;
-	p = 1.0 - p;
-	if ( val < 0.0 ) p = 1.0;
-	if ( val > max ) p = 0.0;
-	*rp = p;
-	*gp = p;
-	*bp = p;
-}
-
-
-void render_scale(double val, double max, int scale,
-                  double *rp, double *gp, double *bp)
-{
-	switch ( scale ) {
-	case SCALE_COLOUR :
-		render_rgb(val, max, rp, gp, bp);
-		break;
-	case SCALE_MONO :
-		render_mono(val, max, rp, gp, bp);
-		break;
-	case SCALE_INVMONO :
-		render_invmono(val, max, rp, gp, bp);
-		break;
-	case SCALE_RATIO :
-		render_ratio(val, max, rp, gp, bp);
-		break;
-	}
-}
-
-
-#ifdef HAVE_GTK
-
-static float *get_binned_panel(struct image *image, int binning,
-                               int min_fs, int max_fs, int min_ss, int max_ss)
-{
-	float *data;
-	int x, y;
-	int w, h;
-	int fw;
-	float *in;
-
-	fw = image->width;
-	in = image->data;
-
-	/* Some pixels might get discarded */
-	w = (max_fs - min_fs + 1) / binning;
-	h = (max_ss - min_ss + 1) / binning;
-
-	data = malloc(w*h*sizeof(float));
-
-	for ( x=0; x<w; x++ ) {
-	for ( y=0; y<h; y++ ) {
-
-		double total;
-		size_t xb, yb;
-
-		total = 0;
-		for ( xb=0; xb<binning; xb++ ) {
-		for ( yb=0; yb<binning; yb++ ) {
-
-			double v;
-			v = in[binning*x+xb+min_fs + (binning*y+yb+min_ss)*fw];
-			total += v;
-
-		}
-		}
-
-		data[x+w*y] = total / ((double)binning * (double)binning);
-
-	}
-	}
-
-	return data;
-}
-
-
-/* NB This function is shared between render_get_image() and
- * render_get_colour_scale() */
-static void render_free_data(guchar *data, gpointer p)
-{
-	free(data);
-}
-
-
-static GdkPixbuf *render_panel(struct image *image,
-                               int binning, int scale, double boost,
-                               int min_fs, int max_fs, int min_ss, int max_ss)
-{
-	int w, h;
-	guchar *data;
-	float *hdr;
-	int x, y;
-	double max;
-	int pw, ph;
-	int i;
-
-	/* Calculate panel width and height
-	 * (add one because min and max are inclusive) */
-	pw = max_fs - min_fs + 1;
-	ph = max_ss - min_ss + 1;
-	w = pw / binning;
-	h = ph / binning;
-
-	/* High dynamic range version */
-	max = 0.0;
-	for ( i=0; i<image->width*image->height; i++ ) {
-		if ( image->data[i] > max ) max = image->data[i];
-	}
-	hdr = get_binned_panel(image, binning, min_fs, max_fs, min_ss, max_ss);
-	if ( hdr == NULL ) return NULL;
-
-	/* Rendered (colourful) version */
-	data = malloc(3*w*h);
-	if ( data == NULL ) {
-		free(hdr);
-		return NULL;
-	}
-
-	max /= boost;
-	if ( max <= 6 ) { max = 10; }
-	/* These x,y coordinates are measured relative to the bottom-left
-	 * corner */
-	for ( y=0; y<h; y++ ) {
-	for ( x=0; x<w; x++ ) {
-
-		double val;
-		double r, g, b;
-
-		val = hdr[x+w*y];
-		render_scale(val, max, scale, &r, &g, &b);
-
-		/* Stuff inside square brackets makes this pixel go to
-		 * the expected location in the pixbuf (which measures
-		 * from the top-left corner */
-		data[3*( x+w*y )+0] = 255*r;
-		data[3*( x+w*y )+1] = 255*g;
-		data[3*( x+w*y )+2] = 255*b;
-
-	}
-	}
-
-	/* Finished with this */
-	free(hdr);
-
-	/* Create the pixbuf from the 8-bit display data */
-	return gdk_pixbuf_new_from_data(data, GDK_COLORSPACE_RGB, FALSE, 8,
-					w, h, w*3, render_free_data, NULL);
-
-}
-
-
-/* Render an image into multiple pixbufs according to geometry */
-GdkPixbuf **render_panels(struct image *image,
-                          int binning, int scale, double boost,
-                          int *n_pixbufs)
-{
-	int i;
-	int np = image->det->n_panels;
-	GdkPixbuf **pixbufs;
-
-	pixbufs = calloc(np, sizeof(GdkPixbuf*));
-	if ( pixbufs == NULL ) {
-		*n_pixbufs = 0;
-		return NULL;
-	}
-
-	for ( i=0; i<np; i++ ) {
-
-		pixbufs[i] = render_panel(image, binning, scale, boost,
-		                          image->det->panels[i].min_fs,
-		                          image->det->panels[i].max_fs,
-		                          image->det->panels[i].min_ss,
-		                          image->det->panels[i].max_ss);
-
-	}
-
-	*n_pixbufs = np;
-
-	return pixbufs;
-}
-
-
-GdkPixbuf *render_get_colour_scale(size_t w, size_t h, int scale)
-{
-	guchar *data;
-	size_t x, y;
-	int max;
-
-	data = malloc(3*w*h);
-	if ( data == NULL ) return NULL;
-
-	max = h;
-
-	for ( y=0; y<h; y++ ) {
-
-		double r, g, b;
-		int val;
-
-		val = y;
-
-		render_scale(val, max, scale, &r, &g, &b);
-
-		data[3*( 0+w*(h-1-y) )+0] = 0;
-		data[3*( 0+w*(h-1-y) )+1] = 0;
-		data[3*( 0+w*(h-1-y) )+2] = 0;
-		for ( x=1; x<w; x++ ) {
-			data[3*( x+w*(h-1-y) )+0] = 255*r;
-			data[3*( x+w*(h-1-y) )+1] = 255*g;
-			data[3*( x+w*(h-1-y) )+2] = 255*b;
-		}
-
-	}
-
-	return gdk_pixbuf_new_from_data(data, GDK_COLORSPACE_RGB, FALSE, 8,
-					w, h, w*3, render_free_data, NULL);
-}
-
-
-int render_tiff_fp(struct image *image, const char *filename)
-{
-#ifdef HAVE_TIFF
-	TIFF *th;
-	float *line;
-	int y;
-
-	th = TIFFOpen(filename, "w");
-	if ( th == NULL ) return 1;
-
-	TIFFSetField(th, TIFFTAG_IMAGEWIDTH, image->width);
-	TIFFSetField(th, TIFFTAG_IMAGELENGTH, image->height);
-	TIFFSetField(th, TIFFTAG_SAMPLESPERPIXEL, 1);
-	TIFFSetField(th, TIFFTAG_SAMPLEFORMAT, SAMPLEFORMAT_IEEEFP);
-	TIFFSetField(th, TIFFTAG_BITSPERSAMPLE, 32);
-	TIFFSetField(th, TIFFTAG_PHOTOMETRIC, PHOTOMETRIC_MINISBLACK);
-	TIFFSetField(th, TIFFTAG_ORIENTATION, ORIENTATION_TOPLEFT);
-	TIFFSetField(th, TIFFTAG_PLANARCONFIG, PLANARCONFIG_CONTIG);
-	TIFFSetField(th, TIFFTAG_ROWSPERSTRIP,
-	             TIFFDefaultStripSize(th, image->width*4));
-
-	line = _TIFFmalloc(TIFFScanlineSize(th));
-	for ( y=0; y<image->height; y++ ) {
-		memcpy(line, &image->data[(image->height-1-y)*image->width],
-		       image->width*4);
-		TIFFWriteScanline(th, line, y, 0);
-	}
-	_TIFFfree(line);
-
-	TIFFClose(th);
-
-#else
-	STATUS("No TIFF support.\n");
-#endif
-	return 0;
-}
-
-
-int render_tiff_int16(struct image *image, const char *filename, double boost)
-{
-#ifdef HAVE_TIFF
-	TIFF *th;
-	int16_t *line;
-	int x, y;
-	double max;
-
-	th = TIFFOpen(filename, "w");
-	if ( th == NULL ) return 1;
-
-	TIFFSetField(th, TIFFTAG_IMAGEWIDTH, image->width);
-	TIFFSetField(th, TIFFTAG_IMAGELENGTH, image->height);
-	TIFFSetField(th, TIFFTAG_SAMPLESPERPIXEL, 1);
-	TIFFSetField(th, TIFFTAG_SAMPLEFORMAT, SAMPLEFORMAT_INT); /* (signed) */
-	TIFFSetField(th, TIFFTAG_BITSPERSAMPLE, 16);
-	TIFFSetField(th, TIFFTAG_PHOTOMETRIC, PHOTOMETRIC_MINISBLACK);
-	TIFFSetField(th, TIFFTAG_ORIENTATION, ORIENTATION_TOPLEFT);
-	TIFFSetField(th, TIFFTAG_PLANARCONFIG, PLANARCONFIG_CONTIG);
-	TIFFSetField(th, TIFFTAG_ROWSPERSTRIP,
-	             TIFFDefaultStripSize(th, image->width*4));
-
-	line = _TIFFmalloc(TIFFScanlineSize(th));
-	max = 0.0;
-	for ( y=0; y<image->height; y++ ) {
-	for ( x=0;x<image->width; x++ ) {
-		double val;
-		val = image->data[x+image->height*y];
-		if ( val > max ) max = val;
-	}
-	}
-	max /= 32767.0;
-
-	for ( y=0; y<image->height; y++ ) {
-		for ( x=0;x<image->width; x++ ) {
-
-			double val;
-
-			val = image->data[x+(image->height-1-y)*image->width];
-			val *= ((double)boost/max);
-
-			/* Clamp to 16-bit range,
-			 * and work round inability of most readers to deal
-			 * with signed integers. */
-			val += 1000.0;
-			if ( val > 32767.0 ) val = 32767.0;
-			if ( val < 0.0 ) val = 0.0;
-
-			line[x] = val;
-		}
-
-		TIFFWriteScanline(th, line, y, 0);
-	}
-	_TIFFfree(line);
-
-	TIFFClose(th);
-#else
-	STATUS("No TIFF support.\n");
-#endif
-	return 0;
-}
-
-#endif /* HAVE_GTK */
diff --git a/src/render.h b/src/render.h
deleted file mode 100644
index fbfbbdb2..00000000
--- a/src/render.h
+++ /dev/null
@@ -1,55 +0,0 @@
-/*
- * render.h
- *
- * Render a high dynamic range buffer in some sensible way
- *
- * (c) 2006-2011 Thomas White <taw@physics.org>
- *
- * Part of CrystFEL - crystallography with a FEL
- *
- */
-
-
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#ifndef RENDER_H
-#define RENDER_H
-
-
-#include <stddef.h>
-
-#include "image.h"
-
-enum {
-	SCALE_COLOUR,
-	SCALE_MONO,
-	SCALE_INVMONO,
-	SCALE_RATIO
-};
-
-/* Colour scale lookup */
-extern void render_scale(double val, double max, int scale,
-                         double *rp, double *gp, double *bp);
-
-
-#ifdef HAVE_GTK
-
-#include <gdk-pixbuf/gdk-pixbuf.h>
-
-extern GdkPixbuf **render_panels(struct image *image,
-                                 int binning, int scale, double boost,
-                                 int *n_pixbufs);
-
-extern GdkPixbuf *render_get_colour_scale(size_t w, size_t h, int scale);
-
-extern int render_tiff_fp(struct image *image, const char *filename);
-extern int render_tiff_int16(struct image *image, const char *filename,
-                             double boost);
-
-#endif /* HAVE_GTK */
-
-
-
-#endif	/* RENDER_H */