mosflm works!

2 files changed, 34 insertions, 415 deletions

diff --git a/src/mosflm.c b/src/mosflm.c
index 1a2beb7b..0470a19a 100644
--- a/src/mosflm.c
+++ b/src/mosflm.c
@@ -3,8 +3,6 @@
  *
  * Invoke the DPS auto-indexing algorithm through MOSFLM
  *
- * This will actuaully run DirAx for now... will be fixed soon...
- *
  * (c) 2006-2010 Thomas White <taw@physics.org>
  *
  * Part of CrystFEL - crystallography with a FEL
@@ -42,353 +40,37 @@
 
 
 
+/*
 
+todo
 
+** properly read the newmat file (don't use fscanf-- spaces between numers
+   are not guaranteed)
 
-#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;
-
-
-static void dirax_parseline(const char *line, struct image *image)
-{
-	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 ) {
-			image->dirax_read_cell = 1;
-			image->candidate_cells[image->ncells] = cell_new();
-			return;
-		}
-		i++;
-	}
-
-	/* Parse unit cell vectors as appropriate */
-	if ( image->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");
-			image->dirax_read_cell = 0;
-			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);
-		image->dirax_read_cell++;
-		return;
-	} else if ( image->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");
-			image->dirax_read_cell = 0;
-			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);
-		image->dirax_read_cell++;
-		return;
-	} else if ( image->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");
-			image->dirax_read_cell = 0;
-			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);
-		image->dirax_read_cell = 0;
-		return;
-	}
-
-	image->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 > image->best_acl_nh ) {
-
-			int i, found = 0;
-
-			for ( i=0; i<image->n_acls_tried; i++ ) {
-				if ( image->acls_tried[i] == acl ) found = 1;
-			}
-
-			if ( !found ) {
-				image->best_acl_nh = acl_nh;
-				image->best_acl = acl;
-			}
-
-		}
-	}
-}
-
-
-static void dirax_sendline(const char *line, struct image *image)
-{
-	#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(image->dirax_pty, line, strlen(line));
-}
-
-
-static void dirax_send_next(struct image *image)
-{
-	char tmp[32];
-
-	switch ( image->dirax_step ) {
-
-	case 1 :
-		dirax_sendline("\\echo off\n", image);
-		break;
-
-	case 2 :
-		snprintf(tmp, 31, "read xfel-%i.drx\n", image->id);
-		dirax_sendline(tmp, image);
-		break;
-
-	case 3 :
-		dirax_sendline("dmax 1000\n", image);
-		break;
-
-	case 4 :
-		dirax_sendline("indexfit 2\n", image);
-		break;
-
-	case 5 :
-		dirax_sendline("levelfit 1000\n", image);
-		break;
-
-	case 6 :
-		dirax_sendline("go\n", image);
-		break;
-
-	case 7 :
-		dirax_sendline("acl\n", image);
-		break;
-
-	case 8 :
-		if ( image->best_acl_nh == 0 ) {
-			STATUS("No more cells to try.\n");
-			/* 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", image);
-			break;
-		}
-		snprintf(tmp, 31, "%i\n", image->best_acl);
-		image->acls_tried[image->n_acls_tried++] = image->best_acl;
-		dirax_sendline(tmp, image);
-		break;
-
-	case 9 :
-		dirax_sendline("cell\n", image);
-		break;
-
-	case 10 :
-		if ( image->n_acls_tried == MAX_DIRAX_CELL_CANDIDATES ) {
-			dirax_sendline("exit\n", image);
-		} else {
-			/* Go back round for another cell */
-			image->best_acl_nh = 0;
-			image->dirax_step = 7;
-			dirax_sendline("acl\n", image);
-		}
-		break;
-
-	default:
-		dirax_sendline("exit\n", image);
-		return;
-
-	}
-
-	image->dirax_step++;
-}
-
-
-static int dirax_readable(struct image *image)
-{
-	int rval;
-	int no_string = 0;
-
-	rval = read(image->dirax_pty, image->dirax_rbuffer+image->dirax_rbufpos,
-	            image->dirax_rbuflen-image->dirax_rbufpos);
-
-	if ( (rval == -1) || (rval == 0) ) return 1;
-
-	image->dirax_rbufpos += rval;
-	assert(image->dirax_rbufpos <= image->dirax_rbuflen);
-
-	while ( (!no_string) && (image->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<image->dirax_rbufpos-1; i++ ) {
-			/* Means the last value looked at is rbufpos-2 */
-
-			/* Is there a prompt in the buffer? */
-			if ( (i+7 <= image->dirax_rbufpos)
-			  && (!strncmp(image->dirax_rbuffer+i, "Dirax> ", 7)) ) {
-				block_ready = 1;
-				type = DIRAX_INPUT_PROMPT;
-				break;
-			}
-
-			/* How about an ACL prompt? */
-			if ( (i+10 <= image->dirax_rbufpos)
-			  && (!strncmp(image->dirax_rbuffer+i, "acl/auto [", 10)) ) {
-				block_ready = 1;
-				type = DIRAX_INPUT_ACL;
-				break;
-			}
-
-			if ( (image->dirax_rbuffer[i] == '\r')
-			  && (image->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, image->dirax_rbuffer, i);
-				block_buffer[i] = '\0';
-
-				if ( block_buffer[0] == '\r' ) {
-					memmove(block_buffer, block_buffer+1, i);
-				}
-
-				dirax_parseline(block_buffer, image);
-				free(block_buffer);
-				endbit_length = i+2;
-				break;
-
-			case DIRAX_INPUT_PROMPT :
-
-				dirax_send_next(image);
-				endbit_length = i+7;
-				break;
-
-			case DIRAX_INPUT_ACL :
-
-				dirax_send_next(image);
-				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(image->dirax_rbuffer,
-			        image->dirax_rbuffer + endbit_length,
-			        image->dirax_rbuflen - endbit_length);
-
-			/* Subtract the number of bytes removed */
-			image->dirax_rbufpos = image->dirax_rbufpos
-			                       - endbit_length;
-			new_rbuflen = image->dirax_rbuflen - endbit_length;
-			if ( new_rbuflen == 0 ) new_rbuflen = 256;
-			image->dirax_rbuffer = realloc(image->dirax_rbuffer,
-			                               new_rbuflen);
-			image->dirax_rbuflen = new_rbuflen;
-
-		} else {
-
-			if ( image->dirax_rbufpos==image->dirax_rbuflen ) {
-
-				/* More buffer space is needed */
-				image->dirax_rbuffer = realloc(
-				                    image->dirax_rbuffer,
-				                    image->dirax_rbuflen + 256);
-				image->dirax_rbuflen = image->dirax_rbuflen
-				                                          + 256;
-				/* The new space gets used at the next
-				 * read, shortly... */
+** "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.
 
-			}
-			no_string = 1;
+*/
 
-		}
 
-	}
 
-	return 0;
-}
+#define MOSFLM_VERBOSE 0
 
 
 static int read_newmat(const char * filename, struct image *image)
@@ -401,25 +83,29 @@ static int read_newmat(const char * filename, struct image *image)
 	double c;
 	
 	fh = fopen(filename,"r");
-	if (fh == NULL){ 
+	if (fh == NULL){
+		STATUS("found newmat.\n"); 
 		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("<9 parameters.\n");
 		return 1;
 	}
 	fclose(fh);
 	
 	/* mosflm A matrix is multiplied by lambda, so fix this */
-	c = 1e-10/image->lambda;
+	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;
@@ -440,8 +126,6 @@ void run_mosflm(struct image *image, UnitCell *cell)
 	const char newmatfile[128];
 	int fail;
 	
-	printf("Mosflm is not fully implemented.  Using DirAx for now.\n");
-	
 	wavelength = image->lambda*1e10;
 	cell_get_parameters(cell, &a, &b, &c, &alpha, &beta, &gamma);
 	sg = cell_get_spacegroup(cell);
@@ -460,7 +144,7 @@ void run_mosflm(struct image *image, UnitCell *cell)
 	
 	
 	/* build a script to run mosflm */
-	sprintf(mos_cmd,"%s","ipmosflm << eof-mosflm >> /dev/null\n");
+	sprintf(mos_cmd,"%s","ipmosflm << eof-mosflm > /dev/null\n");
 	sprintf(mos_cmd,"%s%s",mos_cmd,
 	                     "DETECTOR ROTATION HORIZONTAL ANTICLOCKWISE"
 	                     " ORIGIN LL FAST HORIZONTAL RECTANGULAR\n");
@@ -495,71 +179,8 @@ void run_mosflm(struct image *image, UnitCell *cell)
 	}
 
 	/* remove the mosflm NEWMAT file */
-	remove(newmatfile);
+	//remove(newmatfile);
 	
-	image->dirax_pid = forkpty(&image->dirax_pty, NULL, NULL, NULL);
-	if ( image->dirax_pid == -1 ) {
-		ERROR("Failed to fork for DirAx\n");
-		return;
-	}
-	if ( image->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);
-
-	}
-
-	image->dirax_rbuffer = malloc(256);
-	image->dirax_rbuflen = 256;
-	image->dirax_rbufpos = 0;
-
-	/* Set non-blocking */
-	opts = fcntl(image->dirax_pty, F_GETFL);
-	fcntl(image->dirax_pty, F_SETFL, opts | O_NONBLOCK);
-
-	image->dirax_step = 1;	/* This starts the "initialisation" procedure */
-	image->dirax_read_cell = 0;
-	image->n_acls_tried = 0;
-	image->best_acl_nh = 0;
-
-	do {
-
-		fd_set fds;
-		struct timeval tv;
-		int sval;
-
-		FD_ZERO(&fds);
-		FD_SET(image->dirax_pty, &fds);
-
-		tv.tv_sec = 10;
-		tv.tv_usec = 0;
-
-		sval = select(image->dirax_pty+1, &fds, NULL, NULL, &tv);
-
-		if ( sval == -1 ) {
-			ERROR("select() failed.\n");
-			rval = 1;
-		} else if ( sval != 0 ) {
-			rval = dirax_readable(image);
-		} else {
-			ERROR("No response from DirAx..\n");
-			rval = 1;
-		}
-
-	} while ( !rval );
-
-	close(image->dirax_pty);
-	free(image->dirax_rbuffer);
-	wait(&status);
-
 	return;
 }
+
diff --git a/src/mosflm.h b/src/mosflm.h
index 53939902..5f6bc128 100644
--- a/src/mosflm.h
+++ b/src/mosflm.h
@@ -3,8 +3,6 @@
  *
  * Invoke the DPS auto-indexing algorithm through MOSFLM
  *
- * This will actuaully run DirAx for now... will be fixed soon...
- *
  * (c) 2006-2010 Thomas White <taw@physics.org>
  *
  * Part of CrystFEL - crystallography with a FEL