librelion-dev-common 1.3+dfsg-2 / usr / include / relion-1.3 / src / displayer.h

/***************************************************************************
 *
 * Author: "Sjors H.W. Scheres"
 * MRC Laboratory of Molecular Biology
 *
 * This program is free software; you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation; either version 2 of the License, or
 * (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * This complete copyright notice must be included in any revised version of the
 * source code. Additional authorship citations may be added, but existing
 * author citations must be preserved.
 ***************************************************************************/

#ifndef DISPLAYER_H_
#define DISPLAYER_H_

#include "src/image.h"
#include "src/metadata_label.h"
#include "src/metadata_table.h"
#include <src/matrix2d.h>
#include <src/fftw.h>
#include <src/time.h>
#include <src/args.h>

#include <Fl/Fl.H>
#include <Fl/Fl_Shared_Image.H>
#include <Fl/Fl_Double_Window.H>
#include <Fl/Fl_Scroll.H>
#include <Fl/Fl_Image.H>
#include <Fl/Fl_JPEG_Image.H>
#include <Fl/Fl_Box.H>
#include <Fl/fl_draw.H>
#include <Fl/Fl_Menu_Bar.H>
#include <Fl/Fl_File_Chooser.H>
#include <Fl/Fl_Float_Input.H>
#include <Fl/Fl_Text_Display.H>

#define GUI_BACKGROUND_COLOR (fl_rgb_color(240,240,240))
#define GUI_INPUT_COLOR (fl_rgb_color(255,255,230))
#define GUI_RUNBUTTON_COLOR (fl_rgb_color(255,80,80))

#define SELECTED true
#define NOTSELECTED false
#define MULTIVIEW_WINDOW_WIDTH  720
#define MULTIVIEW_WINDOW_HEIGHT 486

#define BOX_OFFSET 4

#define MULTIVIEWER 0
#define SINGLEVIEWER 1
#define BLACK 0
#define WHITE 1

static bool has_dragged;
static int predrag_xc;
static int predrag_yc;
static bool has_shift;
static int preshift_ipos;

class DisplayBox : public Fl_Box
{
protected:

	// Draw the actual box on the screen (this function is used by redraw())
	void draw();

public:

	int xsize_data;
	int ysize_data;
	int xoff;
	int yoff;

	// The box's selection status
	bool selected;

	// The box's original position in the input MetaDataTable
	int ipos;

	// The metadata fir this image
	MetaDataTable MDimg;

	// The actual image data array
	char * img_data;

	// For getting back close the original image values from the uchar ones...
	double minval;
	double maxval;
	double scale;

	// Constructor with an image and its metadata
	DisplayBox(int X, int Y, int W, int H, const char *L=0) : Fl_Box(X,Y,W,H,L) { img_data = NULL; MDimg.clear(); }

	void setData(MultidimArray<double> &img, MetaDataContainer *MDCin, int ipos, double minval, double maxval,
			double _scale, bool do_relion_scale = false);

	// Destructor
	~DisplayBox()
	{
		MDimg.clear();
		if (img_data)
			delete [] img_data;
	};

	// Change selected status, redraw and return new status
	bool toggleSelect();
	// Select, redraw and return new selected status
	bool select();
	// unSelect, redraw and return new selected status
	bool unSelect();

};


// This class only puts scrollbars around the resizable canvas
class basisViewerWindow : public Fl_Window
{

public:

	// Constructor with w x h size of the window and a title
	basisViewerWindow(int W, int H, const char* title=0): Fl_Window(W, H, title){}

	int fillCanvas(int viewer_type, MetaDataTable &MDin, EMDLabel display_label, bool _do_read_whole_stacks, bool _do_apply_orient,
			double _minval, double _maxval, double _sigma_contrast,
			double _scale, double _ori_scale, int _ncol, bool do_class = false, MetaDataTable *MDdata = NULL,
			int _nr_regroup = -1, bool _is_data = false, MetaDataTable *MDgroups = NULL);
	int fillSingleViewerCanvas(MultidimArray<double> image, double _minval, double _maxval, double _sigma_contrast, double _scale);
	int fillPickerViewerCanvas(MultidimArray<double> image, double _minval, double _maxval, double _sigma_contrast, double _scale,
			int _particle_radius, FileName _fn_coords = "",
			FileName _fn_color = "", FileName _fn_mic= "", FileName _color_label = "", double _color_blue_value = 0., double _color_red_value = 1.);


};

class basisViewerCanvas : public Fl_Widget
{
protected:

	void draw();

public:

	int ncol;
	int nrow;
	int xsize_box;
	int ysize_box;
	int xoff;
	int yoff;

	// To get positions in scrolled canvas...
	Fl_Scroll *scroll;

	// All the individual image display boxes
	std::vector<DisplayBox*> boxes;

	// Read stacks at once to speed up?
	bool do_read_whole_stacks;

	// Constructor with w x h size of the window and a title
	basisViewerCanvas(int X,int Y, int W, int H, const char* title=0) : Fl_Widget(X,Y,W, H, title) { }

	void SetScroll(Fl_Scroll *val) { scroll = val; }

	int fill(MetaDataTable &MDin, EMDLabel display_label, bool _do_apply_orient, double _minval, double _maxval,
			double _sigma_contrast, double _scale, int _ncol);
	int fill(MultidimArray<double> &image, double _minval, double _maxval, double _sigma_contrast, double _scale = 1.);

private:
	void getImageContrast(MultidimArray<double> &image, double &minval, double &maxval, double &sigma_contrast);

};

class multiViewerCanvas : public basisViewerCanvas
{
protected:

	int handle(int ev);

public:

	// Flag to indicate whether this is a viewer for class averages from 2D/3D relion_refine classification runs
	bool do_class;

	// Flag to indicate whether this is a viewer for a data.star (to also allow regrouping)
	bool is_data;

	// Number of groups for regrouping the selected particles (for model.star)
	int nr_regroups;

	// pointer to the MetaDataTable for the individually aligned particles when do_class (the data.star file)
	MetaDataTable *MDdata;

	// pointer to the MetaDataTable for the groups when do_class and do_regroup (the data.star file)
	MetaDataTable *MDgroups;

	// Scale for showing the original image
	double ori_scale;

	// To know which original image to display
	EMDLabel display_label;

	// To know which contrast to apply to original image display
	double sigma_contrast;

	// Constructor with w x h size of the window and a title
	multiViewerCanvas(int X,int Y, int W, int H, const char* title=0): basisViewerCanvas(X,Y,W, H, title) { }

private:

	// Functionalities for  popup menu
	void clearSelection();
	void invertSelection();
	void selectFromHereBelow(int ipos);
	void selectFromHereAbove(int ipos);
	void printMetaData(int ipos);
	void showAverage(bool selected, bool show_stddev=false);
	void showOriginalImage(int ipos);
	void makeStarFileSelectedParticles(bool save_selected, MetaDataTable &MDpart);
	void saveSelectedParticles(bool save_selected);
	void showSelectedParticles(bool save_selected);
	void saveSelected(bool save_selected);
	void saveBackupSelection();
	void loadBackupSelection();

};

// Generally accessible function
void regroupSelectedParticles(MetaDataTable &MDdata, MetaDataTable &MDgroups, int nr_regroups);

class singleViewerCanvas : public basisViewerCanvas
{

protected:
	int handle(int ev);

public:

	// Constructor with w x h size of the window and a title
	singleViewerCanvas(int X, int Y, int W, int H, const char* title=0): basisViewerCanvas(X,Y,W, H, title) { }
private:

	// Functionalities for  popup menu
	void printMetaData();

	// explain functionality of clicks
	void printHelp();


};

class pickerViewerCanvas : public basisViewerCanvas
{

protected:
	int handle(int ev);
	void draw();

public:
	// MetaDataTable with all picked coordinates
	MetaDataTable MDcoords;

	int particle_radius;

	// Filename of the picked coordinate files
	FileName fn_coords;

	// FileName of the STAR file that contains the color-based column
	FileName fn_color;

	// Label to base coloring on
	EMDLabel color_label;

	// Blue value for coloring
	double smallest_color_value;

	// Red value for coloring
	double biggest_color_value;

	// Red->Blue is true; blue->red is false
	bool do_blue_to_red;

	// Micrograph name (useful to search relevant particles in fn_color)
	FileName fn_mic;

	// Constructor with w x h size of the window and a title
	pickerViewerCanvas(int X, int Y, int W, int H, const char* title=0): basisViewerCanvas(X,Y,W, H, title) { }

	void loadCoordinates(bool ask_filename = false);

	// if a fn_zscore is given, then match the coordinates to the Zscores in the corresponding MDtable
	void findColorColumnForCoordinates();

private:

	// Functionalities for  popup menu
	void saveCoordinates(bool ask_filename = false);
	void clearCoordinates();
	void printHelp();
	void viewExtractedParticles();
};

class popupInputWindow : Fl_Window
{
	Fl_Input * input;
	double result;
public:

	// Constructor with w x h size of the window and a title
	popupInputWindow(int W, int H, const char* title=0): Fl_Window(W, H, title){}

	int fill(std::string label, double &_result)
	{
		input = new Fl_Input(x() + 200, 0, 100, 30, "black value: ") ;
		Fl_Button * done = new Fl_Button(x()+350, 0, 30, 30, "go!");
		//*result = atof(input->value());
		done->callback( cb_done, this);
		result = _result;
		show();
	}

	static void cb_done(Fl_Widget* o, void* v)
	{
		popupInputWindow* T=(popupInputWindow*)v;
	    T->cb_done_i();
	}
	inline void cb_done_i()
	{
		std::cerr << " input->value()= " << input->value() << std::endl;
		result =  atof(input->value());
	}

};
// This class only puts scrollbars around the resizable canvas
class displayerGuiWindow : public Fl_Window
{
public:

	FileName fn_in, fn_data;

	// Some general settings for different types
	bool is_class;

	bool is_multi;

	bool is_star;

	// Allow regrouping from _data.star
	bool is_data;

	// Label option to display or to sort on
	std::vector<std::string> display_labels;
	std::vector<std::string> sort_labels;

	// Input for the display parameters
	Fl_Input *black_input, *white_input, *sigma_contrast_input, *scale_input, *lowpass_input, *angpix_input;
	Fl_Input *col_input, *ori_scale_input, *particle_radius_input, *pick_rootname_input, *nr_groups_input;
	Fl_Check_Button *sort_button, *reverse_sort_button, *pick_button, *apply_orient_button, *read_whole_stack_button, *regroup_button;
	Fl_Choice *display_choice, *sort_choice;

	// Constructor with w x h size of the window and a title
	displayerGuiWindow(int W, int H, const char* title=0): Fl_Window(W, H, title){}

	// Fill all except for the browser
	int fill(FileName &fn_in);

private:

	static void cb_display(Fl_Widget*, void*);
    inline void cb_display_i();
    void readLastSettings();
    void writeLastSettings();

};

class Displayer
{
public:

	// I/O Parser
	IOParser parser;

	// Launch the GUI for parameter input
	bool do_gui;

	// Verbosity
	int verb;

	// Which metadatalabel to display
	EMDLabel display_label, sort_label;

	// use reverse order for sorting?
	bool reverse_sort;

	// Scale factor for displaying
	double scale;

	// Number of rows for tiled view
	int nrow, ncol;

	// Apply orientations stored in metadatatable
	bool do_apply_orient;

	// Scale for showing the original image
	double ori_scale;

	// Black and white values
	double minval, maxval;

	// For setting black and white contrast to a specified times the image standard deviation from the mean
	double sigma_contrast;

	// Particle diameter
	int particle_radius;

	// Input & Output rootname
	FileName fn_in;

	// Filename for coordinates star file
	FileName fn_coords;

	// FileName of the STAR file that contains the color label
	FileName fn_color;

	// Which column to color on?
	FileName color_label;

	// Values for blue and red coloring
	double color_blue_value, color_red_value;

	// Tablename to read from in the input STAR file
	FileName table_name;

	// Flag to pick
	bool do_pick;

	// Flag for looking at classes
	bool do_class;

	// Number of groups for regrouping (negative number is no regrouping)
	int nr_regroups;

	// Flag for reading whole stacks instead of individual images
	bool do_read_whole_stacks;

	// data.star metadata (for do_class)
	MetaDataTable MDdata;

	// model_groups  metadata (for do_class and regrouping)
	MetaDataTable MDgroups;

	// Input metadata
	MetaDataTable MDin;

	// For the multiviewer
	std::vector<DisplayBox*> boxes;

	// Lowpass filter for picker images
	double lowpass;

	// Pixel size to calculate lowpass filter in Angstroms
	double angpix;

public:
	// Read command line arguments
	void read(int argc, char **argv);

	// Print usage instructions
	void usage();

	// Initialise some general stuff after reading
	void initialise();

	// Decide what to do
	int run();

	// run the GUI
	int runGui();

};


#endif /* DISPLAYER_H_ */