/*
 * main.c
 *
 * The Top Level Source File
 *
 * (c) 2007 Thomas White <taw27@cam.ac.uk>
 *	    Gordon Ball <gfb21@cam.ac.uk>
 *
 *  dtr - Diffraction Tomography Reconstruction
 *
 */

#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#define _GNU_SOURCE
#include <string.h>
#include <stdarg.h>
#include <stdlib.h>
#include <gtk/gtk.h>
#include <math.h>
#include <gdk/gdkgl.h>
#include <gtk/gtkgl.h>
#include <sys/stat.h>

#include "displaywindow.h"
#include "reflections.h"
#include "mrc.h"
#include "qdrp.h"
#include "ipr.h"
#include "cache.h"
#include "mapping.h"
#include "prealign.h"
#include "control.h"

void main_do_reconstruction(ControlContext *ctx) {

	int val = 0;
	
	if ( ctx->inputfiletype != INPUT_CACHE ) {
		prealign_sum_stack(ctx);
		mapping_create(ctx);
	}
	
	if ( (ctx->inputfiletype != INPUT_CACHE) && !val && ctx->reflectionlist && ctx->savecache ) {
		cache_save(ctx->filename, ctx->reflectionlist);			
	}
	
	if ( (ctx->rmode == RECONSTRUCTION_PREDICTION) && (ctx->reflectionlist) ) {
		val = ipr_refine(ctx);
	}
	
	if ( !val && (ctx->reflectionlist) ) {
		ctx->dw = displaywindow_open(ctx);
	} else {
		fprintf(stderr, "Reconstruction failed.\n");
		gtk_exit(0);
	}
	
}

static gint main_method_window_response(GtkWidget *method_window, gint response, ControlContext *ctx) {

	if ( response == GTK_RESPONSE_OK ) {
	
		int val = -1;
		
		switch ( gtk_combo_box_get_active(GTK_COMBO_BOX(ctx->combo_algorithm)) ) {
			case 0 : ctx->rmode = RECONSTRUCTION_MAPPING; break;
			case 1 : ctx->rmode = RECONSTRUCTION_PREDICTION; break;
			default: abort();
		}
		
		switch ( gtk_combo_box_get_active(GTK_COMBO_BOX(ctx->combo_peaksearch)) ) {
			case 0 : ctx->psmode = PEAKSEARCH_THRESHOLD; break;
			case 1 : ctx->psmode = PEAKSEARCH_ADAPTIVE_THRESHOLD; break;
			case 2 : ctx->psmode = PEAKSEARCH_LSQ; break;
			case 3 : ctx->psmode = PEAKSEARCH_ZAEFFERER; break;
			case 4 : ctx->psmode = PEAKSEARCH_STAT; break;
			default: ctx->psmode = PEAKSEARCH_NONE; break;	/* This happens when reading from a cache file */
		}
		
		if ( gtk_toggle_button_get_active(GTK_TOGGLE_BUTTON(ctx->checkbox_prealign)) ) {
			ctx->prealign = TRUE;
		} else {
			ctx->prealign = FALSE;
		}
		
		if ( gtk_toggle_button_get_active(GTK_TOGGLE_BUTTON(ctx->checkbox_savecache)) ) {
			ctx->savecache = TRUE;
		} else {
			ctx->savecache = FALSE;
		}
		
		gtk_widget_destroy(method_window);
		while ( gtk_events_pending() ) gtk_main_iteration();
		
		/* Load the input */
		if ( ctx->inputfiletype == INPUT_QDRP ) {
			val = qdrp_read(ctx);
		} else if ( ctx->inputfiletype == INPUT_MRC ) {
			val = mrc_read(ctx);
		} else if ( ctx->inputfiletype == INPUT_CACHE ) {
			ctx->reflectionlist = cache_load(ctx->filename);
			val=0;
		}
		
		if ( val ) {
			fprintf(stderr, "Reconstruction failed.\n");
			gtk_exit(0);
		}
		
		if ( ctx->prealign ) {
			prealign_do_series(ctx);
		} else {
			main_do_reconstruction(ctx);
		}
		
	} else {
		gtk_exit(0);
	}
	
	return 0;

}

void main_method_dialog_open(ControlContext *ctx) {

	GtkWidget *method_window;
	GtkWidget *vbox;
	GtkWidget *hbox;
	GtkWidget *table;
	GtkWidget *method_label;
	GtkWidget *peaksearch_label;
	
	method_window = gtk_dialog_new_with_buttons("Reconstruction Parameters", NULL,
		GTK_DIALOG_DESTROY_WITH_PARENT,	GTK_STOCK_CANCEL, GTK_RESPONSE_CLOSE, GTK_STOCK_OK, GTK_RESPONSE_OK, NULL);
	
	vbox = gtk_vbox_new(FALSE, 0);
	hbox = gtk_hbox_new(TRUE, 0);
	gtk_box_pack_start(GTK_BOX(GTK_DIALOG(method_window)->vbox), GTK_WIDGET(hbox), FALSE, FALSE, 7);
	gtk_box_pack_start(GTK_BOX(hbox), GTK_WIDGET(vbox), FALSE, FALSE, 10);
	
	table = gtk_table_new(4, 2, FALSE);
	gtk_table_set_row_spacings(GTK_TABLE(table), 5);

	method_label = gtk_label_new("Reconstruction Algorithm: ");
	gtk_table_attach_defaults(GTK_TABLE(table), method_label, 1, 2, 1, 2);
	gtk_misc_set_alignment(GTK_MISC(method_label), 1, 0.5);
	ctx->combo_algorithm = gtk_combo_box_new_text();
	gtk_combo_box_append_text(GTK_COMBO_BOX(ctx->combo_algorithm), "Feature Detection and Mapping");
	gtk_combo_box_append_text(GTK_COMBO_BOX(ctx->combo_algorithm), "Iterative Prediction and Refinement");
	gtk_combo_box_set_active(GTK_COMBO_BOX(ctx->combo_algorithm), 1);
	gtk_table_attach_defaults(GTK_TABLE(table), ctx->combo_algorithm, 2, 3, 1, 2);
	gtk_table_set_row_spacing(GTK_TABLE(table), 1, 5);
	
	peaksearch_label = gtk_label_new("Peak Search: ");
	gtk_table_attach_defaults(GTK_TABLE(table), peaksearch_label, 1, 2, 2, 3);
	gtk_misc_set_alignment(GTK_MISC(peaksearch_label), 1, 0.5);
	ctx->combo_peaksearch = gtk_combo_box_new_text();
	gtk_combo_box_append_text(GTK_COMBO_BOX(ctx->combo_peaksearch), "Simple Thresholding");
	gtk_combo_box_append_text(GTK_COMBO_BOX(ctx->combo_peaksearch), "Adaptive Thresholding");
	gtk_combo_box_append_text(GTK_COMBO_BOX(ctx->combo_peaksearch), "Least-Squares Fit");
	gtk_combo_box_append_text(GTK_COMBO_BOX(ctx->combo_peaksearch), "Zaefferer Gradient Search");
	gtk_combo_box_append_text(GTK_COMBO_BOX(ctx->combo_peaksearch), "Iterative Statistical Analysis");
	gtk_combo_box_set_active(GTK_COMBO_BOX(ctx->combo_peaksearch), 3);
	gtk_table_attach_defaults(GTK_TABLE(table), ctx->combo_peaksearch, 2, 3, 2, 3);
	
	ctx->checkbox_prealign = gtk_check_button_new_with_label("Pre-align image stack");
	gtk_table_attach_defaults(GTK_TABLE(table), ctx->checkbox_prealign, 1, 3, 3, 4);
	
	ctx->checkbox_savecache = gtk_check_button_new_with_label("Save 3D mapping cache file");
	gtk_table_attach_defaults(GTK_TABLE(table), ctx->checkbox_savecache, 1, 3, 4, 5);
	
	if ( ctx->inputfiletype == INPUT_CACHE ) {
		gtk_combo_box_append_text(GTK_COMBO_BOX(ctx->combo_peaksearch), "Get from cache file");
		gtk_widget_set_sensitive(GTK_WIDGET(ctx->combo_peaksearch), FALSE);
		gtk_combo_box_set_active(GTK_COMBO_BOX(ctx->combo_peaksearch), 5);
	}

	gtk_box_pack_start(GTK_BOX(vbox), GTK_WIDGET(table), TRUE, TRUE, 5);
	
	g_signal_connect(G_OBJECT(method_window), "response", G_CALLBACK(main_method_window_response), ctx);
	
	gtk_widget_show_all(method_window);

}


int main(int argc, char *argv[]) {

	char *filename;
	ControlContext *ctx;
	InputFileType type;
	struct stat stat_buffer;

	gtk_init(&argc, &argv);
	
	if ( gtk_gl_init_check(&argc, &argv) == FALSE ) {
		fprintf(stderr, "Could not initialise gtkglext\n");
		return 1;
	}
	
	if ( gdk_gl_query_extension() == FALSE ) {
		fprintf(stderr, "OpenGL not supported\n");
		return 1;
	}
	
	if ( argc != 2 ) {
		fprintf(stderr, "Syntax: %s [<MRC file> | qdrp.rc | reflect.cache]\n", argv[0]);
		return 1;
	}
	
	filename = basename(argv[1]);
	ctx = control_ctx_new();
	type = INPUT_NONE;
	
	if ( qdrp_is_qdrprc(filename) ) {
		printf("QDRP input file detected.\n");
		ctx->inputfiletype = INPUT_QDRP;
	} else if ( mrc_is_mrcfile(filename) ) {
		printf("MRC tomography file detected.\n");
		ctx->inputfiletype = INPUT_MRC;
	} else if ( cache_is_cachefile(filename) ) {
		printf("Cached reflection file detected.\n");
		ctx->inputfiletype = INPUT_CACHE;
	} else {
		fprintf(stderr, "Unrecognised input file type\n");
		return 1;
	}
	
	ctx->filename = strdup(argv[1]);
	ctx->n_images = 0;
	
	if ( stat(argv[1], &stat_buffer) == -1 ) {
		fprintf(stderr, "File '%s' not found\n", argv[1]);
		return 1;
	}
	
	main_method_dialog_open(ctx);
		
	gtk_main();
	
	free(ctx->filename);
	free(ctx);
	
	return 0;
	
}