Move indexing and rendering to libcrystfel

1 files changed, 0 insertions, 609 deletions

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);
-}