view_nii.m

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%  VIEW_NII: Create or update a 3-View (Front, Top, Side) of the 
%	brain data that is specified by nii structure
%
%  Usage:  	status = view_nii([h], nii, [option])	or
%		status = view_nii(h, [option])
%
%  Where, h is the figure on which the 3-View will be plotted;
%	nii is the brain data in NIFTI format;
%	option is a struct that configures the view plotted, can be:
%
%		option.command = 'init'
%		option.command = 'update'
%		option.command = 'clearnii'
%		option.command = 'updatenii'
%		option.command = 'updateimg' (nii is nii.img here)
%
%		option.usecolorbar = 0 | [1]
%		option.usepanel = 0 | [1]
%		option.usecrosshair = 0 | [1]
%		option.usestretch = 0 | [1]
%		option.useimagesc = 0 | [1]
%		option.useinterp = [0] | 1
%
%		option.setarea = [x y w h] | [0.05 0.05 0.9 0.9]
%		option.setunit = ['vox'] | 'mm'
%		option.setviewpoint = [x y z] | [origin]
%		option.setscanid = [t] | [1]
%		option.setcrosshaircolor = [r g b] | [1 0 0]
%		option.setcolorindex = From 1 to 9 (default is 2 or 3)
%		option.setcolormap = (Mx3 matrix, 0 <= val <= 1)
%		option.setcolorlevel = No more than 256 (default 256)
%		option.sethighcolor = []
%		option.setcbarminmax = []
%		option.setvalue = []
%		option.glblocminmax = []
%		option.setbuttondown = ''
%		option.setcomplex = [0] | 1 | 2
%
%	Options description in detail:
%	==============================
%
%	1. command: A char string that can control program.
%
%		init: If option.command='init', the program will display
%			a 3-View plot on the figure specified by figure h
%			or on a new figure. If there is already a 3-View
%			plot on the figure, please use option.command = 
%			'updatenii' (see detail below); otherwise, the
%			new 3-View plot will superimpose on the old one.
%			If there is no option provided, the program will
%			assume that this is an initial plot. If the figure
%			handle is omitted, the program knows that it is
%			an initial plot.
%
%		update: If there is no command specified, and a figure
%			handle of the existing 3-View plot is provided,
%			the program will choose option.command='update'
%			to update the 3-View plot with some new option 
%			items.
%
%		clearnii: Clear 3-View plot on specific figure
%
%		updatenii: If a new nii is going to be loaded on a fig
%			that has already 3-View plot on it, use this
%			command to clear existing 3-View plot, and then
%			display with new nii. So, the new nii will not
%			superimpose on the existing one. All options
%			for 'init' can be used for 'updatenii'.
%
%		updateimg: If a new 3D matrix with the same dimension
%			is going to be loaded, option.command='updateimg'
%			can be used as a light-weighted 'updatenii, since
%			it only updates the 3 slices with new values.
%			inputing argument nii should be a 3D matrix
%			(nii.img) instead of nii struct. No other option
%			should be used together with 'updateimg' to keep
%			this command as simple as possible.
%
%
%	2. usecolorbar: If specified and usecolorbar=0, the program
%		will not include the colorbar in plot area; otherwise,
%		a colorbar will be included in plot area.
%
%	3. usepanel: If specified and usepanel=0, the control panel
%		at lower right cornor will be invisible; otherwise,
%		it will be visible.
%
%	4. usecrosshair: If specified and usecrosshair=0, the crosshair
%		will be invisible; otherwise, it will be visible.
%
%	5. usestretch: If specified and usestretch=0, the 3 slices will
%		not be stretched, and will be displayed according to
%		the actual voxel size; otherwise, the 3 slices will be 
%		stretched to the edge.
%
%	6. useimagesc: If specified and useimagesc=0, images data will
%		be used directly to match the colormap (like 'image'
%		command); otherwise, image data will be scaled to full
%		colormap with 'imagesc' command in Matlab.
%
%	7. useinterp: If specified and useinterp=1, the image will be
%		displayed using interpolation. Otherwise, it will be
%		displayed like mosaic, and each tile stands for a
%		pixel. This option does not apply to 'setvalue' option
%		is set.
%
%
%	8. setarea: 3-View plot will be displayed on this specific 
%		region. If it is not specified, program will set the
%		plot area to [0.05 0.05 0.9 0.9].
%
%	9. setunit: It can be specified to setunit='voxel' or 'mm'
%		and the view will change the axes unit of [X Y Z]
%		accordingly.
%
%	10. setviewpoint: If specified, [X Y Z] values will be used
%		to set the viewpoint of 3-View plot.
%
%	11. setscanid: If specified, [t] value will be used to display
%		the specified image scan in NIFTI data.
%
%	12. setcrosshaircolor: If specified, [r g b] value will be used
%		for Crosshair Color. Otherwise, red will be the default.
%
%	13. setcolorindex: If specified, the 3-View will choose the
%		following colormap:  2 - Bipolar; 3 - Gray; 4 - Jet;
%		5 - Cool; 6 - Bone; 7 - Hot; 8 - Copper; 9 - Pink;
%		If not specified, it will choose 3 - Gray if all data
%		values are not less than 0; otherwise, it will choose
%		2 - Bipolar if there is value less than 0. (Contrast
%		control can only apply to 3 - Gray colormap.
%
%	14. setcolormap: 3-View plot will use it as a customized colormap.
%		It is a 3-column matrix with value between 0 and 1. If
%		using MS-Windows version of Matlab, the number of rows
%		can not be more than 256, because of Matlab limitation.
%		When colormap is used, setcolorlevel option will be
%		disabled automatically.
%
%	15. setcolorlevel: If specified (must be no more than 256, and
%		cannot be used for customized colormap), row number of
%		colormap will be squeezed down to this level; otherwise,
%		it will assume that setcolorlevel=256.
%
%	16. sethighcolor: If specified, program will squeeze down the
%		colormap, and allocate sethighcolor (an Mx3 matrix)
%		to high-end portion of the colormap. The sum of M and
%		setcolorlevel should be less than 256. If setcolormap
%		option is used, sethighcolor will be inserted on top 
%		of the setcolormap, and the setcolorlevel option will
%		be disabled automatically.
%
%	17. setcbarminmax: if specified, the [min max] will be used to
%		set the min and max of the colorbar, which does not
%		include any data for highcolor.
%
%	18. setvalue: If specified, setvalue.val (with the same size as
%		the source data on solution points) in the source area
%		setvalue.idx will be superimposed on the current nii 
%		image. So, the size of setvalue.val should be equal to
%		the size of setvalue.idx. To use this feature, it needs
%		single or double nii structure for background image.
%
%	19. glblocminmax: If specified, pgm will use glblocminmax to
%		calculate the colormap, instead of minmax of image.
%
%	20. setbuttondown: If specified, pgm will evaluate the command
%		after a click or slide action is invoked to the new
%		view point.
%
%	21. setcomplex: This option will decide how complex data to be
%		displayed:  0 - Real part of complex data; 1 - Imaginary
%		part of complex data; 2 - Modulus (magnitude) of complex
%		data;  If not specified, it will be set to 0 (Real part
%		of complex data as default option. This option only apply
%		when option.command is set to 'init or 'updatenii'.
%
%
%	Additional Options for 'update' command:
%	=======================================
%
%		option.enablecursormove = [1] | 0
%		option.enableviewpoint = 0 | [1]
%		option.enableorigin = 0 | [1]
%		option.enableunit = 0 | [1]
%		option.enablecrosshair = 0 | [1]
%		option.enablehistogram = 0 | [1]
%		option.enablecolormap = 0 | [1]
%		option.enablecontrast = 0 | [1]
%		option.enablebrightness = 0 | [1]
%		option.enableslider = 0 | [1]
%		option.enabledirlabel = 0 | [1]
%
%
%  e.g.:
%	nii = load_nii('T1');		% T1.img/hdr
%	view_nii(nii);
%
%	or
%
%	h = figure('unit','normal','pos', [0.18 0.08 0.64 0.85]);
%	opt.setarea = [0.05 0.05 0.9 0.9];
%	view_nii(h, nii, opt);
%
%
%  Part of this file is copied and modified under GNU license from
%  MRI_TOOLBOX developed by CNSP in Flinders University, Australia
%
%  NIFTI data format can be found on: http://nifti.nimh.nih.gov
%
%  - Jimmy Shen ([e-mail])
%
function status = view_nii(varargin)

   if nargin < 1
      error('Please check inputs using ''help view_nii''');
   end;

   nii = '';
   opt = '';
   command = '';

   usecolorbar = [];
   usepanel = [];
   usecrosshair = '';
   usestretch = [];
   useimagesc = [];
   useinterp = [];

   setarea = [];
   setunit = '';
   setviewpoint = [];
   setscanid = [];
   setcrosshaircolor = [];
   setcolorindex = '';
   setcolormap = 'NA';
   setcolorlevel = [];
   sethighcolor = 'NA';
   setcbarminmax = [];
   setvalue = [];
   glblocminmax = [];
   setbuttondown = '';
   setcomplex = 0;

   status = [];

   if ishandle(varargin{1})		% plot on top of this figure

      fig = varargin{1};

      if nargin < 2
         command = 'update';		% just to get 3-View status
      end

      if nargin == 2
         if ~isstruct(varargin{2})
            error('2nd parameter should be either nii struct or option struct');
         end

         opt = varargin{2};

         if isfield(opt,'hdr') & isfield(opt,'img')
            nii = opt;
         elseif isfield(opt, 'command') & (strcmpi(opt.command,'init') ...
		| strcmpi(opt.command,'updatenii') ...
		| strcmpi(opt.command,'updateimg') )

            error('Option here cannot contain "init", "updatenii", or "updateimg" comand');
         end
      end

      if nargin == 3
         nii = varargin{2};
         opt = varargin{3};

         if ~isstruct(opt)
            error('3rd parameter should be option struct');
         end

         if ~isfield(opt,'command') | ~strcmpi(opt.command,'updateimg')
            if ~isstruct(nii) | ~isfield(nii,'hdr') | ~isfield(nii,'img')
               error('2nd parameter should be nii struct');
            end

            if isfield(nii,'untouch') & nii.untouch == 1
               error('Usage: please use ''load_nii.m'' to load the structure.');
            end
         end
      end

      set(fig, 'menubar', 'none');

   elseif ischar(varargin{1})		% call back by event

      command = lower(varargin{1});
      fig = gcbf;

   else					% start nii with a new figure

      nii = varargin{1};

      if ~isstruct(nii) | ~isfield(nii,'hdr') | ~isfield(nii,'img')
         error('1st parameter should be either a figure handle or nii struct');
      end

      if isfield(nii,'untouch') & nii.untouch == 1
         error('Usage: please use ''load_nii.m'' to load the structure.');
      end

      if nargin > 1
         opt = varargin{2};

         if isfield(opt, 'command') & ~strcmpi(opt.command,'init')
            error('Option here must use "init" comand');
         end
      end

      command = 'init';
      fig = figure('unit','normal','position',[0.15 0.08 0.70 0.85]);
      view_nii_menu(fig);
      rri_file_menu(fig);

   end

   if ~isempty(opt)

      if isfield(opt,'command')
         command = lower(opt.command);
      end

      if isempty(command)
         command = 'update';
      end

      if isfield(opt,'usecolorbar')
         usecolorbar = opt.usecolorbar;
      end

      if isfield(opt,'usepanel')
         usepanel = opt.usepanel;
      end

      if isfield(opt,'usecrosshair')
         usecrosshair = opt.usecrosshair;
      end

      if isfield(opt,'usestretch')
         usestretch = opt.usestretch;
      end

      if isfield(opt,'useimagesc')
         useimagesc = opt.useimagesc;
      end

      if isfield(opt,'useinterp')
         useinterp = opt.useinterp;
      end

      if isfield(opt,'setarea')
         setarea = opt.setarea;
      end

      if isfield(opt,'setunit')
         setunit = opt.setunit;
      end

      if isfield(opt,'setviewpoint')
         setviewpoint = opt.setviewpoint;
      end

      if isfield(opt,'setscanid')
         setscanid = opt.setscanid;
      end

      if isfield(opt,'setcrosshaircolor')
         setcrosshaircolor = opt.setcrosshaircolor;

         if ~isempty(setcrosshaircolor) & (~isnumeric(setcrosshaircolor) | ~isequal(size(setcrosshaircolor),[1 3]) | min(setcrosshaircolor(:))<0 | max(setcrosshaircolor(:))>1)
            error('Crosshair Color should be a 1x3 matrix with value between 0 and 1');
         end
      end

      if isfield(opt,'setcolorindex')
         setcolorindex = round(opt.setcolorindex);

         if ~isnumeric(setcolorindex) | setcolorindex < 1 | setcolorindex > 9
            error('Colorindex should be a number between 1 and 9');
         end
      end

      if isfield(opt,'setcolormap')
         setcolormap = opt.setcolormap;

         if ~isempty(setcolormap) & (~isnumeric(setcolormap) | size(setcolormap,2) ~= 3 | min(setcolormap(:))<0 | max(setcolormap(:))>1)
            error('Colormap should be a Mx3 matrix with value between 0 and 1');
         end
      end

      if isfield(opt,'setcolorlevel')
         setcolorlevel = round(opt.setcolorlevel);

         if ~isnumeric(setcolorlevel) | setcolorlevel > 256 | setcolorlevel < 1
            error('Colorlevel should be a number between 1 and 256');
         end
      end

      if isfield(opt,'sethighcolor')
         sethighcolor = opt.sethighcolor;

         if ~isempty(sethighcolor) & (~isnumeric(sethighcolor) | size(sethighcolor,2) ~= 3 | min(sethighcolor(:))<0 | max(sethighcolor(:))>1)
            error('Highcolor should be a Mx3 matrix with value between 0 and 1');
         end
      end

      if isfield(opt,'setcbarminmax')
         setcbarminmax = opt.setcbarminmax;

         if isempty(setcbarminmax) | ~isnumeric(setcbarminmax) | length(setcbarminmax) ~= 2
            error('Colorbar MinMax should contain 2 values: [min max]');
         end
      end

      if isfield(opt,'setvalue')
         setvalue = opt.setvalue;

         if isempty(setvalue) | ~isstruct(setvalue) | ...
		~isfield(opt.setvalue,'idx') | ~isfield(opt.setvalue,'val')
            error('setvalue should be a struct contains idx and val');
         end