Initial import

git-svn-id: svn://cook.msm.cam.ac.uk:745/diff-tomo/dtr@1 bf6ca9ba-c028-0410-8290-897cf20841d1

1 files changed, 254 insertions, 0 deletions

diff --git a/src/qdrp.c b/src/qdrp.c
new file mode 100644
index 0000000..42be13f
--- /dev/null
+++ b/src/qdrp.c
@@ -0,0 +1,254 @@
+/*
+ * qdrp.c
+ *
+ * Handle QDRP-style control files
+ *
+ * (c) 2007 Thomas White <taw27@cam.ac.uk>
+ *  dtr - Diffraction Tomography Reconstruction
+ *
+ */
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#define _GNU_SOURCE
+#include <stdlib.h>
+#include <string.h>
+#include <stdio.h>
+
+#include "readpng.h"
+#include "control.h"
+#include "reflections.h"
+
+static void qdrp_chomp(char *str) {
+
+	size_t i;
+	
+	for ( i=0; i<strlen(str); i++ ) {
+		if ( str[i] == '\r' ) {
+			str[i] = '\0';
+			return;
+		}
+		if ( str[i] == '\n' ) {
+			str[i] = '\0';
+			return;
+		}
+	}
+}
+
+#define skip_whitespace										\
+	while ( (( line[pos] == ' ' ) || ( line[pos] == '\t' )) && ( pos < strlen(line) ) ) {	\
+		pos++;										\
+	}
+
+#define skip_chars										\
+	while ( ( line[pos] != ' ' ) && ( line[pos] != '\t' ) && ( pos < strlen(line) ) ) {	\
+		pos++;										\
+	}
+
+static int qdrp_parsefileline(ControlContext *ctx, const char *line) {
+
+	size_t pos = 0;
+	size_t mark = 0;
+	char *tilt_s;
+	char *file;
+	double tilt;
+					
+	skip_whitespace;
+	mark = pos;
+	skip_chars;
+	tilt_s = strndup(line+mark, pos-mark);
+	
+	skip_whitespace;
+	mark = pos;
+	skip_chars;
+	file = strndup(line+mark, pos-mark);
+					
+	tilt = strtod(tilt_s, NULL);
+	free(tilt_s);
+	printf("QD: Reading file: Tilt = %f deg, File='%s'\n", tilt, file);
+	
+	if ( readpng_read(file, tilt, ctx) ) {
+		printf("Reconstruction failed.\n");
+		return 1;
+	}
+	
+	return 0;
+	
+}
+
+static int qdrp_parseline(ControlContext *ctx, const char *line) {
+
+	if ( ctx->started ) {
+		return qdrp_parsefileline(ctx, line);						
+	}
+
+	if ( ( line[0] == '-' ) && ( line[1] == '-') ) {
+		
+		if ( !ctx->camera_length_set ) {
+			printf("QD: Parameter 'camera-length' not specified!\n");
+			return 1;
+		}
+					
+		if ( !ctx->lambda_set ) {
+			printf("QD: Parameter 'lambda' not specified!\n");
+			return 1;
+		}
+					
+		if ( !ctx->resolution_set ) {
+			printf("QD: Parameter 'resolution' not specified!\n");
+			return 1;
+		}
+					
+		if ( !ctx->omega_set ) {
+			printf("QD: Parameter 'omega' not specified, and not using tilt-axis-search.\n");
+			return 1;
+		}
+				
+		ctx->started = 1;
+		ctx->reflectionctx = reflection_init();
+						
+	}
+					
+	if ( !ctx->started ) {
+						
+		size_t pos = 0;
+		size_t mark = 0;
+						
+		skip_whitespace;
+						
+		if ( strncasecmp(line+pos, "resolution", 10) == 0 ) {
+			
+			char *resolution_s;
+						
+			skip_chars;
+			skip_whitespace;
+			mark = pos;
+			skip_chars;
+			resolution_s = strndup(line+mark, pos-mark);
+			ctx->resolution = strtod(resolution_s, NULL);
+			free(resolution_s);
+			ctx->resolution_set = 1;
+			printf("QD: resolution = %f pixels/m\n", ctx->resolution);	
+			
+		}
+		
+		if ( strncasecmp(line+pos, "lambda", 6) == 0 ) {
+			
+			char *lambda_s;
+						
+			skip_chars;
+			skip_whitespace;
+			mark = pos;
+			skip_chars;
+			lambda_s = strndup(line+mark, pos-mark);
+			ctx->lambda = strtod(lambda_s, NULL);
+			free(lambda_s);
+			ctx->lambda_set = 1;
+			printf("QD: lambda = %e m\n", ctx->lambda);	
+			
+		}
+		
+		if ( strncasecmp(line+pos, "camera-length", 13) == 0 ) {
+			
+			char *camera_length_s;
+						
+			skip_chars;
+			skip_whitespace;
+			mark = pos;
+			skip_chars;
+			camera_length_s = strndup(line+mark, pos-mark);
+			ctx->camera_length = strtod(camera_length_s, NULL);
+			free(camera_length_s);
+			ctx->camera_length_set = 1;
+			printf("QD: camera-length = %f m\n", ctx->camera_length);	
+			
+		}
+		
+		if ( strncasecmp(line+pos, "max_d", 5) == 0 ) {
+			
+			char *max_d_s;
+			
+			skip_chars;
+			skip_whitespace;
+			mark = pos;
+			skip_chars;
+			max_d_s = strndup(line+mark, pos-mark);
+			ctx->max_d = strtod(max_d_s, NULL);
+			free(max_d_s);
+			ctx->max_d_set = 1;
+			if ( ctx->max_d == 0 ) {
+				printf("QD: max_d=0 is Not Allowed!\n");
+				return 1;
+			}
+			printf("QD: max_d = %i pixels\n", ctx->max_d);	
+			
+		}
+		
+		if ( strncasecmp(line+pos, "omega", 5) == 0 ) {
+			
+			char *omega_s;
+			
+			skip_chars;
+			skip_whitespace;
+			mark = pos;
+			skip_chars;
+			omega_s = strndup(line+mark, pos-mark);
+			ctx->omega = strtod(omega_s, NULL);
+			free(omega_s);
+			ctx->omega_set = 1;
+			printf("CO: omega = %f deg\n", ctx->omega);
+				
+		}
+		
+	}
+
+	return 0;
+
+}
+
+int qdrp_read(ControlContext *ctx) {
+	
+	char *line;
+	
+	line = malloc(256);
+
+	ctx->camera_length_set = 0;
+	ctx->omega_set = 0;
+	ctx->max_d_set = 0;
+	ctx->resolution_set = 0;
+	ctx->lambda_set = 0;
+	ctx->max_d = 0;
+	ctx->started = 0;
+	ctx->first_image = 1;
+	
+	FILE *fh;
+	
+	fh = fopen(ctx->filename, "r");
+	if ( !fh ) {
+		printf("QD: Couldn't open control file '%s'\n", ctx->filename);
+		return -1;
+	}
+	
+	while ( !feof(fh) ) {			
+		fgets(line, 256, fh);			
+		if ( !feof(fh) ) {				
+			qdrp_chomp(line);				
+			if ( line[0] != '#' ) {					
+				if ( qdrp_parseline(ctx, line) ) {
+					fclose(fh);
+					free(line);
+					return -1;
+				}			
+			}			
+		}
+	}
+	
+	fclose(fh);
+	
+	free(line);
+	
+	return 0;	/* Success */
+	
+}