Linewrap, copyright and brackets in dirax.c

1 files changed, 188 insertions, 150 deletions

diff --git a/src/dirax.c b/src/dirax.c
index e58983a..439d03b 100644
--- a/src/dirax.c
+++ b/src/dirax.c
@@ -4,7 +4,7 @@
  * Invoke the DirAx auto-indexing program
  * also: handle DirAx input files
  *
- * (c) 2007 Thomas White <taw27@cam.ac.uk>
+ * (c) 2007-2009 Thomas White <taw27@cam.ac.uk>
  *
  *  dtr - Diffraction Tomography Reconstruction
  *
@@ -26,7 +26,7 @@
 #include <assert.h>
 #include <sys/ioctl.h>
 #include <termio.h>
-#include <sgtty.h>	
+#include <sgtty.h>
 
 #include "control.h"
 #include "reflections.h"
@@ -41,11 +41,11 @@ typedef enum {
 	DIRAX_INPUT_PROMPT
 } DirAxInputType;
 
-static void dirax_parseline(const char *line, ControlContext *ctx) {
-	
+static void dirax_parseline(const char *line, ControlContext *ctx)
+{
 	int i, rf;
 	char *copy;
-	
+
 	copy = strdup(line);
 	for ( i=0; i<strlen(copy); i++ ) {
 		if ( copy[i] == '\r' ) copy[i]='r';
@@ -53,15 +53,17 @@ static void dirax_parseline(const char *line, ControlContext *ctx) {
 	}
 	printf("DX: DirAx: %s\n", copy);
 	free(copy);
-	
+
 	if ( strstr(line, "reflections from file") ) {
-		displaywindow_error("DirAx can't understand this data.", ctx->dw);
+		displaywindow_error("DirAx can't understand this data.",
+					ctx->dw);
 		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] == ' ')) ) {
+	while ( (i<strlen(line)) && ((line[i] == 'R')
+		|| (line[i] == 'D') || (line[i] == ' ')) ) {
 		if ( line[i] == 'R' ) rf = 1;
 		if ( (line[i] == 'D') && rf ) {
 			ctx->dirax_read_cell = 1;
@@ -69,52 +71,63 @@ static void dirax_parseline(const char *line, ControlContext *ctx) {
 				free(ctx->cell);
 			}
 			ctx->cell = malloc(sizeof(Basis));
-			ctx->cell->a.x = 0.0;  ctx->cell->a.y = 0.0;  ctx->cell->a.z = 0.0;
-			ctx->cell->b.x = 0.0;  ctx->cell->b.y = 0.0;  ctx->cell->b.z = 0.0;
-			ctx->cell->c.x = 0.0;  ctx->cell->c.y = 0.0;  ctx->cell->c.z = 0.0;
+			ctx->cell->a.x = 0.0;
+			ctx->cell->a.y = 0.0;
+			ctx->cell->a.z = 0.0;
+			ctx->cell->b.x = 0.0;
+			ctx->cell->b.y = 0.0;
+			ctx->cell->b.z = 0.0;
+			ctx->cell->c.x = 0.0;
+			ctx->cell->c.y = 0.0;
+			ctx->cell->c.z = 0.0;
 			return;
 		}
 		i++;
 	}
-	
+
 	/* Parse unit cell vectors as appropriate */
 	if ( ctx->dirax_read_cell == 1 ) {
 		/* First row of unit cell values */
 		float x1, x2, x3;
 		sscanf(line, "%f %f %f", &x1, &x2, &x3);
-		ctx->cell->a.x = x1*1e10;  ctx->cell->b.x = x2*1e10;  ctx->cell->c.x = x3*1e10;
+		ctx->cell->a.x = x1*1e10;
+		ctx->cell->b.x = x2*1e10;
+		ctx->cell->c.x = x3*1e10;
 		ctx->dirax_read_cell++;
 		return;
 	} else if ( ctx->dirax_read_cell == 2 ) {
 		/* First row of unit cell values */
 		float y1, y2, y3;
 		sscanf(line, "%f %f %f", &y1, &y2, &y3);
-		ctx->cell->a.y = y1*1e10;  ctx->cell->b.y = y2*1e10;  ctx->cell->c.y = y3*1e10;
+		ctx->cell->a.y = y1*1e10;
+		ctx->cell->b.y = y2*1e10;
+		ctx->cell->c.y = y3*1e10;
 		ctx->dirax_read_cell++;
 		return;
 	} else if ( ctx->dirax_read_cell == 3 ) {
 		/* First row of unit cell values */
 		float z1, z2, z3;
 		sscanf(line, "%f %f %f", &z1, &z2, &z3);
-		ctx->cell->a.z = z1*1e10;  ctx->cell->b.z = z2*1e10;  ctx->cell->c.z = z3*1e10;
+		ctx->cell->a.z = z1*1e10;
+		ctx->cell->b.z = z2*1e10;
+		ctx->cell->c.z = z3*1e10;
 		printf("DX: Read a reciprocal unit cell\n");
 		displaywindow_update(ctx->dw);
 		reproject_lattice_changed(ctx);
 		ctx->dirax_read_cell = 0;
 		return;
 	}
-	
-	ctx->dirax_read_cell = 0;
 
+	ctx->dirax_read_cell = 0;
 }
 
-static void dirax_sendline(const char *line, ControlContext *ctx) {
-	
+static void dirax_sendline(const char *line, ControlContext *ctx)
+{
 	char *copy;
 	int i;
-	
+
 	write(ctx->dirax_pty, line, strlen(line));
-	
+
 	copy = strdup(line);
 	for ( i=0; i<strlen(copy); i++ ) {
 		if ( copy[i] == '\r' ) copy[i]='\0';
@@ -122,236 +135,256 @@ static void dirax_sendline(const char *line, ControlContext *ctx) {
 	}
 	printf("DX: Sent '%s'\n", copy);	/* No newline here */
 	free(copy);
-	
 }
 /* Send a "user" command to DirAx, failing if DirAx is not idle */
-static void dirax_sendline_if_idle(const char *line, ControlContext *ctx) {
-
+static void dirax_sendline_if_idle(const char *line, ControlContext *ctx)
+{
 	if ( ctx->dirax_step != 0 ) {
 		printf("DX: DirAx not idle\n");
 		return;
 	}
-	
-	dirax_sendline(line, ctx);
 
+	dirax_sendline(line, ctx);
 }
 
-static void dirax_send_next(ControlContext *ctx) {
-
+static void dirax_send_next(ControlContext *ctx)
+{
 	switch ( ctx->dirax_step ) {
-	
+
 		case 1 : {
 			dirax_sendline("\\echo off\n", ctx);
 			ctx->dirax_step++;
 			break;
 		}
-		
+
 		case 2 : {
 			dirax_sendline("read dtr.drx\n", ctx);
 			ctx->dirax_step++;
 			break;
 		}
-		
+
 		case 3 : {
 			dirax_sendline("dmax 10\n", ctx);
 			ctx->dirax_step++;
 			break;
 		}
-		
+
 		case 4 : {
 			dirax_sendline("indexfit 6\n", ctx);
 			ctx->dirax_step++;
 			break;
 		}
-		
+
 		case 5 : {
 			dirax_sendline("levelfit 300\n", ctx);
 			ctx->dirax_step++;
 			break;
 		}
-		
+
 		case 6 : {
 			dirax_sendline("go\n", ctx);
 			ctx->dirax_step++;
 			break;
 		}
-		
+
 		case 7 : {
 			dirax_sendline("cell\n", ctx);
 			ctx->dirax_step++;
 			break;
 		}
-				
+
 		default: {
 			ctx->dirax_step = 0;
 			printf("DX: Prompt.  DirAx is idle\n");
 		}
-		
+
 	}
-	
 }
 
-static gboolean dirax_readable(GIOChannel *dirax, GIOCondition condition, ControlContext *ctx) {
-	
+static gboolean dirax_readable(GIOChannel *dirax, GIOCondition condition,
+				ControlContext *ctx)
+{
 	int rval;
-	
-	rval = read(ctx->dirax_pty, ctx->dirax_rbuffer+ctx->dirax_rbufpos, ctx->dirax_rbuflen-ctx->dirax_rbufpos);
-	
+
+	rval = read(ctx->dirax_pty, ctx->dirax_rbuffer+ctx->dirax_rbufpos,
+			ctx->dirax_rbuflen-ctx->dirax_rbufpos);
+
 	if ( (rval == -1) || (rval == 0) ) {
-	
+
 		printf("DX: Lost connection to DirAx\n");
 		waitpid(ctx->dirax_pid, NULL, 0);
 		g_io_channel_shutdown(ctx->dirax, FALSE, NULL);
 		ctx->dirax = NULL;
 		displaywindow_update_dirax(ctx, ctx->dw);
 		return FALSE;
-		
+
 	} else {
-	
+
 		int no_string = 0;
-		
+
 		ctx->dirax_rbufpos += rval;
 		assert(ctx->dirax_rbufpos <= ctx->dirax_rbuflen);
-		
+
 		while ( (!no_string) && (ctx->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<ctx->dirax_rbufpos-1; i++ ) {	/* Means the last value looked at is rbufpos-2 */
-			
+			for ( i=0; i<ctx->dirax_rbufpos-1; i++ ) {
+			/* Means the last value looked at is rbufpos-2 */
+
 				/* Is there a prompt in the buffer? */
 				if ( i+7 <= ctx->dirax_rbufpos ) {
-					if ( (strncmp(ctx->dirax_rbuffer+i, "Dirax> ", 7) == 0)
-					  || (strncmp(ctx->dirax_rbuffer+i, "PROMPT:", 7) == 0) ) {
+					if ( (strncmp(ctx->dirax_rbuffer+i,
+							"Dirax> ", 7) == 0)
+					  || (strncmp(ctx->dirax_rbuffer+i,
+					  		"PROMPT:", 7) == 0) ) {
 						block_ready = 1;
 						type = DIRAX_INPUT_PROMPT;
 						break;
 					}
 				}
-				
-				if ( (ctx->dirax_rbuffer[i] == '\r') && (ctx->dirax_rbuffer[i+1] == '\n') ) { 
+
+				if ( (ctx->dirax_rbuffer[i] == '\r')
+					&& (ctx->dirax_rbuffer[i+1] == '\n') ) {
 					block_ready = 1;
 					type = DIRAX_INPUT_LINE;
 					break;
 				}
-				
+
 			}
-			
+
 			if ( block_ready ) {
-			
+
 				unsigned int new_rbuflen;
 				unsigned int endbit_length;
-				
+
 				switch ( type ) {
-				
+
 					case DIRAX_INPUT_LINE : {
-					
+
 						char *block_buffer = NULL;
-						
+
 						block_buffer = malloc(i+1);
-						memcpy(block_buffer, ctx->dirax_rbuffer, i);
+						memcpy(block_buffer,
+							ctx->dirax_rbuffer, i);
 						block_buffer[i] = '\0';
-						
+
 						if ( block_buffer[0] == '\r' ) {
-							memmove(block_buffer, block_buffer+1, i);
+							memmove(block_buffer,
+							 block_buffer+1, i);
 						}
-						
-						dirax_parseline(block_buffer, ctx);
+
+						dirax_parseline(block_buffer,
+								ctx);
 						free(block_buffer);
 						endbit_length = i+2;
-						
+
 						break;
-						
+
 					}
-					
+
 					case DIRAX_INPUT_PROMPT : {
-						
+
 						dirax_send_next(ctx);
 						endbit_length = i+7;
 						break;
-					
+
 					}
-					
+
 					default : {
-						printf("DX: Unrecognised input mode (this never happens!)\n");
+						printf("DX: Unrecognised input "
+						"mode (this never happens!)\n");
 						abort();
 					}
-				
+
 				}
-			
-				/* Now the block's been parsed, it should be forgotten about */
-				memmove(ctx->dirax_rbuffer, ctx->dirax_rbuffer + endbit_length, ctx->dirax_rbuflen - endbit_length);
-				
+
+				/* Now the block's been parsed, it should
+				 * be forgotten about */
+				memmove(ctx->dirax_rbuffer, ctx->dirax_rbuffer
+					+ endbit_length, ctx->dirax_rbuflen
+					- endbit_length);
+
 				/* Subtract the number of bytes removed */
-				ctx->dirax_rbufpos = ctx->dirax_rbufpos - endbit_length;
-				new_rbuflen = ctx->dirax_rbuflen - endbit_length;
+				ctx->dirax_rbufpos = ctx->dirax_rbufpos
+							- endbit_length;
+				new_rbuflen = ctx->dirax_rbuflen-endbit_length;
 				if ( new_rbuflen == 0 ) {
 					new_rbuflen = 256;
 				}
-				ctx->dirax_rbuffer = realloc(ctx->dirax_rbuffer, new_rbuflen);
+				ctx->dirax_rbuffer = realloc(ctx->dirax_rbuffer,
+							new_rbuflen);
 				ctx->dirax_rbuflen = new_rbuflen;
-				
+
 			} else {
-			
-				if ( ctx->dirax_rbufpos == ctx->dirax_rbuflen ) {
-			
+
+				if ( ctx->dirax_rbufpos==ctx->dirax_rbuflen ) {
+
 					/* More buffer space is needed */
-					ctx->dirax_rbuffer = realloc(ctx->dirax_rbuffer, ctx->dirax_rbuflen + 256);
-					ctx->dirax_rbuflen = ctx->dirax_rbuflen + 256;
-					/* The new space gets used at the next read, shortly... */
-			
+					ctx->dirax_rbuffer = realloc(
+					ctx->dirax_rbuffer,
+					ctx->dirax_rbuflen + 256);
+					ctx->dirax_rbuflen = ctx->dirax_rbuflen
+							+ 256;
+					/* The new space gets used at the next
+					 * read, shortly... */
+
 				}
 				no_string = 1;
-			
+
 			}
-			
+
 		}
-		
+
 	}
-	
+
 	return TRUE;
-	
+
 }
 
-void dirax_stop(ControlContext *ctx) {
+void dirax_stop(ControlContext *ctx)
+{
 	dirax_sendline_if_idle("end\n", ctx);
 }
 
-void dirax_rerun(ControlContext *ctx) {
+void dirax_rerun(ControlContext *ctx)
+{
 	dirax_sendline_if_idle("go\n", ctx);
 	ctx->dirax_step = 7;
 }
 
-void dirax_invoke(ControlContext *ctx) {
-
+void dirax_invoke(ControlContext *ctx)
+{
 	FILE *fh;
 	Reflection *ref;
 	unsigned int opts;
 	int saved_stderr;
-	
+
 	if ( ctx->dirax ) {
 		dirax_rerun(ctx);
 		return;
 	}
-	
+
 	printf("DX: Starting DirAx...\n");
-	
+
 	fh = fopen("dtr.drx", "w");
 	if ( !fh ) {
 		printf("DX: Couldn't open temporary file dtr.drx\n");
 		return;
 	}
-	fprintf(fh, "%f\n", 0.5);  /* Lie about the wavelength.  DirAx can't handle the truth. */
+	fprintf(fh, "%f\n", 0.5);  /* Lie about the wavelength.  DirAx can't
+				    *  handle the truth. */
 	ref = ctx->reflectionlist->reflections;
 	while ( ref ) {
-		fprintf(fh, "%10f %10f %10f %8f\n", ref->x/1e10, ref->y/1e10, ref->z/1e10, ref->intensity);
+		fprintf(fh, "%10f %10f %10f %8f\n", ref->x/1e10, ref->y/1e10,
+						ref->z/1e10, ref->intensity);
 		ref = ref->next;
 	}
 	fclose(fh);
-	
+
 	saved_stderr = dup(STDERR_FILENO);
 	ctx->dirax_pid = forkpty(&ctx->dirax_pty, NULL, NULL, NULL);
 	if ( ctx->dirax_pid == -1 ) {
@@ -359,28 +392,28 @@ void dirax_invoke(ControlContext *ctx) {
 		return;
 	}
 	if ( ctx->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);
-		
+
 		/* Reconnect stderr */
 		dup2(saved_stderr, STDERR_FILENO);
-		
+
 		execlp("dirax", "", (char *)NULL);
 		printf("(from the Other Side) Failed to invoke DirAx.\n");
 		_exit(0);
-		
+
 	}
-		
+
 	ctx->dirax_rbuffer = malloc(256);
 	ctx->dirax_rbuflen = 256;
 	ctx->dirax_rbufpos = 0;
-	
+
 	/* Set non-blocking */
 	opts = fcntl(ctx->dirax_pty, F_GETFL);
 	fcntl(ctx->dirax_pty, F_SETFL, opts | O_NONBLOCK);
@@ -388,55 +421,60 @@ void dirax_invoke(ControlContext *ctx) {
 	ctx->dirax_step = 1;	/* This starts the "initialisation" procedure */
 	ctx->dirax_read_cell = 0;
 	ctx->dirax = g_io_channel_unix_new(ctx->dirax_pty);
-	g_io_add_watch(ctx->dirax, G_IO_IN | G_IO_HUP, (GIOFunc)dirax_readable, ctx);
-	
+	g_io_add_watch(ctx->dirax, G_IO_IN | G_IO_HUP, (GIOFunc)dirax_readable,
+					ctx);
+
 	displaywindow_update_dirax(ctx, ctx->dw);
-	
+
 	return;
-	
-}
 
-/* Despite being part of the same module, this has very little to do with invoking DirAx */
-ReflectionList *dirax_load(const char *filename) {
+}
 
+/* Despite being part of the same module, this has very little to do with
+ * invoking DirAx */
+ReflectionList *dirax_load(const char *filename)
+{
 	FILE *fh;
 	char line[256];
 	ReflectionList *list;
 	int lambda_set = 0;
-	
+
 	fh = fopen(filename, "r");
 	if ( !fh ) {
 		printf("Couldn't open file '%s'\n", filename);
 		return 0;
 	}
-	
+
 	list = reflectionlist_new();
-	
+
 	while ( !feof(fh) ) {
-	
+
 		size_t ptr;
 		float lambda, theta, chib, phib;
-		
+
 		fgets(line, 255, fh);
 		ptr = skipspace(line);
 		if ( line[ptr] == '!' ) continue;
 		if ( line[ptr] == '\n' ) continue;
 		if ( line[ptr] == '\r' ) continue;
-		if ( sscanf(line+ptr, "%f %f %f\n", &theta, &phib, &chib) == 3 ) {
-			
+		if ( sscanf(line+ptr, "%f %f %f\n",
+				&theta, &phib, &chib) == 3 ) {
+
 			double s, x, y, z;
 			float blah, intensity;
-			
-			/* Try to find an intensity value. Use dummy value if it fails */
-			if ( sscanf(line+ptr, "%f %f %f %f\n", &blah, &blah, &blah, &intensity) != 4 ) {
+
+			/* Try to find an intensity value. Use dummy value if
+			 * it fails */
+			if ( sscanf(line+ptr, "%f %f %f %f\n", &blah, &blah,
+					&blah, &intensity) != 4 ) {
 				intensity = 1.0;
 			}
-				
+
 			if ( !lambda_set ) {
 				printf("DX: Wavelength not specified\n");
 				continue;
 			}
-			
+
 			chib = deg2rad(chib);
 			phib = deg2rad(phib);
 			theta = deg2rad(theta);
@@ -445,42 +483,43 @@ ReflectionList *dirax_load(const char *filename) {
 			y = +s*cos(chib)*cos(phib);
 			z = +s*sin(chib);
 			reflection_add(list, x, y, z, 1.0, REFLECTION_NORMAL);
-			
+
 			continue;
-			
+
 		}
 		if ( sscanf(line+ptr, "%f\n", &lambda) == 1 ) {
 			if ( lambda_set ) {
-				printf("DX: Warning: Found something which looks like a second wavelength\n");
+				printf("DX: Warning: Found something which "
+					"looks like a second wavelength\n");
 			}
 			lambda /= 1e10; /* Convert from A to m */
 			lambda_set = 1;
 		}
-		
+
 	}
-	
+
 	fclose(fh);
-	
+
 	return list;
-	
 }
 
-int dirax_is_drxfile(const char *filename) {
+int dirax_is_drxfile(const char *filename)
+{
 
 	FILE *fh;
 	float lambda;
 	char line[256];
-	
+
 	fh = fopen(filename, "r");
 	if ( !fh ) {
 		printf("Couldn't open file '%s'\n", filename);
 		return 0;
 	}
-	
+
 	while ( !feof(fh) ) {
-	
+
 		size_t ptr;
-		
+
 		fgets(line, 255, fh);
 		ptr = skipspace(line);
 		if ( line[ptr] == '!' ) continue;
@@ -493,12 +532,11 @@ int dirax_is_drxfile(const char *filename) {
 		} else {
 			return 0;
 		}
-		
+
 	}
-	
+
 	fclose(fh);
-	
+
 	return 0;
-	
+
 }
-