Remove ReAx and GrainSpotter

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

1 files changed, 0 insertions, 500 deletions

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);
-}