avw_view.m

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function [ varargout ] = avw_view(avw,parent,command),

% avw_view - create and navigate ortho views of Analyze 7.5 volume
% 
% [ avw ] = avw_view([avw], [parent], [command])
% 
% avw - a struct, created by avw_read; if omitted, a gui file locator will
% prompt for a .hdr file.
% 
% parent  - an optional handle to the gui that calls this gui, useful for
% updating the UserData field of the parent. The avw structure may be
% returned to the parent, if possible.
% 
% command - an optional string, such as 'init' or various callback
% commands, 'init' is the default.
% 
% The navigation is by sliders, mouse clicks and arrow keys.  Right mouse
% clicks on any ortho-view will show a command menu, for simple block
% region of interest (ROI) calculations, image zoom, and save image.  The
% ROI calculations are returned into avw.stats.
% 
% Fiducial points can be selected, which are returned into 'avw.fiducials'
% in the base workspace. These points are given in several coordinate
% frameworks (voxels, mm, and meters), with values given relative to an
% origin located at the "center" of the MRI volume (see avw_center, which
% returns abs and corner values, abs used here).
% 
% The AC location can be selected and the values are returned into 'avw.ac'
% in the base workspace. These points are given in voxels, mm & meters; for
% the latter, the values are given as offsets from the "center" of the MRI
% volume (see avw_center).
% 
% +X is left (L), +Y is anterior (A), +Z is superior (S), the default LAS
% orientation of the Analyze 7.5 format.  The coordinate system is left
% handed.  This is the radiological convention, as opposed to the
% neurological convention (RAS).  The latter can be emulated by using the
% 'Flip L/R' button.
% 
% Example of loading and viewing the SPM T1 template:
% avw = avw_read('T1')
% avw = avw_view(avw);
% 
% Similarly, just 'avw_view' can be typed at the command prompt and you can
% use the gui file locator to select any .hdr file.
%
% See also, avw_read, avw_img_read, avw_hdr_read
% 

% $Revision: 1.12 $ $Date: 2004/04/08 20:09:34 $

% Licence:  GNU GPL, no express or implied warranties
% History:  06/2002, Darren.Weber_at_flinders.edu.au
%           10/2002, Darren.Weber_at_flinders.edu.au
%                    added fiducial point determination
%                    changed plots from surf to imagesc commands
%                    added handling of datatype for avw.img
%                    altered daspect to use avw.hdr.dime.pixdim
%                    altered color scheme
%           01/2003, Darren.Weber_at_flinders.edu.au
%                    added parent GUI handling
%           10/2003, Darren.Weber_at_radiology.ucsf.edu
%                    added right click options, including simple block ROI
%                    functions, zoom and save image
%           11/2003, Darren.Weber_at_radiology.ucsf.edu
%                    added arrow key navigation
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

if gcbf,
    AVWVIEW = get(gcbf,'Userdata');
end

if ~exist('command','var'), command = 'init'; end

command = lower(command);

% Check for specific keys and assign command
if strcmp(command, 'keypress'),
  
  cc = get(AVWVIEW.gui,'CurrentCharacter');
  cc = double(cc);
  if cc,
    switch cc,
      case 27, command = 'quit';  % ESC
      case 28, command = 'left';  % left
      case 29, command = 'right'; % right
      case 30, command = 'up';    % up
      case 31, command = 'down';  % down
      otherwise, return;  % all other keys
    end
  end
end

switch command,
    
  case 'init',
    
    if ~exist('avw','var'),
      avw = avw_read;
    end
    
    if nargin == 0,
      AVWVIEW = init(avw);
    elseif isempty(inputname(1)),
      AVWVIEW = init(avw);
    else
      AVWVIEW = init(avw,inputname(1));
    end
    
    AVWVIEW = set_coordinates(AVWVIEW);
    
    
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    
  case 'coordinates',
    
    AVWVIEW = set_coordinates(AVWVIEW);
    
    
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    
  case 'crosshairs',
    
    AVWVIEW = set_crosshairs(AVWVIEW);
    
    
  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
  
  case {'axial_image','coronal_image','sagittal_image'},
    
    switch command,
      case 'axial_image',    AVWVIEW.view = 'axi'; axi_update = 0; cor_update = 1; sag_update = 1;
      case 'coronal_image',  AVWVIEW.view = 'cor'; axi_update = 1; cor_update = 0; sag_update = 1;
      case 'sagittal_image', AVWVIEW.view = 'sag'; axi_update = 1; cor_update = 1; sag_update = 0;
    end
    
    AVWVIEW = get_current_position(AVWVIEW);
    
    if axi_update,
        axial_update(AVWVIEW);
    end
    if cor_update,
        coronal_update(AVWVIEW);
    end;
    if sag_update,
        sagittal_update(AVWVIEW);
    end;
    
    set_display_values(AVWVIEW);
    
    AVWVIEW = set_crosshairs(AVWVIEW);
    
    
    
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    
  case {'axial_slider','coronal_slider','sagittal_slider'},
    
    switch command,
      
      case 'axial_slider',
        AVWVIEW.view = 'axi';
        AVWVIEW = get_slider_position(AVWVIEW);
        axial_update(AVWVIEW);
        
      case 'coronal_slider',
        AVWVIEW.view = 'cor';
        AVWVIEW = get_slider_position(AVWVIEW);
        coronal_update(AVWVIEW);
        
      case 'sagittal_slider',
        AVWVIEW.view = 'sag';
        AVWVIEW = get_slider_position(AVWVIEW);
        sagittal_update(AVWVIEW);
    end
    
    set_display_values(AVWVIEW);
    
    AVWVIEW = set_crosshairs(AVWVIEW);
    
    
    
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    
  case {'left','right','up','down'},
    
    AVWVIEW = get_slider_position(AVWVIEW);
    
    % what axes are we in?
    if isequal(gca, AVWVIEW.handles.axial_axes),
      switch command,
        case 'left',
          % decrease sagittal slice
          if AVWVIEW.slices.sag > 1,
            AVWVIEW.slices.sag = AVWVIEW.slices.sag - 1;
          end
        case 'right',
          % increase sagittal slice
          if AVWVIEW.slices.sag < AVWVIEW.xdim,
            AVWVIEW.slices.sag = AVWVIEW.slices.sag + 1;
          end
        case 'up',
          % increase coronal slice
          if AVWVIEW.slices.cor < AVWVIEW.ydim,
            AVWVIEW.slices.cor = AVWVIEW.slices.cor + 1;
          end
        case 'down',
          % decrease coronal slice
          if AVWVIEW.slices.cor > 1,
            AVWVIEW.slices.cor = AVWVIEW.slices.cor - 1;
          end
      end
      switch command,
        case {'left','right'}
          set(AVWVIEW.handles.sagittal_slider,'Value',AVWVIEW.slices.sag);
          Ssag = squeeze(AVWVIEW.avw.img(AVWVIEW.slices.sag,:,:));
          set(AVWVIEW.handles.sagittal_image,'CData',Ssag');
          set(AVWVIEW.handles.sagittal_sliderN,'String',num2str(AVWVIEW.slices.sag));
          set(AVWVIEW.handles.sagittal_sliderN,'Value',AVWVIEW.slices.sag);
        case {'up','down'},
          set(AVWVIEW.handles.coronal_slider,'Value',AVWVIEW.slices.cor);
          Scor = squeeze(AVWVIEW.avw.img(:,AVWVIEW.slices.cor,:));
          set(AVWVIEW.handles.coronal_image,'CData',Scor');
          set(AVWVIEW.handles.coronal_sliderN,'String',num2str(AVWVIEW.slices.cor));
          set(AVWVIEW.handles.coronal_sliderN,'Value',AVWVIEW.slices.cor);
      end
    end
    
    if isequal(gca, AVWVIEW.handles.coronal_axes),
      switch command,
        case 'left',
          % decrease sagittal slice
          if AVWVIEW.slices.sag > 1,
            AVWVIEW.slices.sag = AVWVIEW.slices.sag - 1;
          end
        case 'right',
          % increase sagittal slice
          if AVWVIEW.slices.sag < AVWVIEW.xdim,
            AVWVIEW.slices.sag = AVWVIEW.slices.sag + 1;
          end
        case 'up',
          % increase axial slice
          if AVWVIEW.slices.axi < AVWVIEW.zdim,
            AVWVIEW.slices.axi = AVWVIEW.slices.axi + 1;
          end
        case 'down',
          % decrease axial slice
          if AVWVIEW.slices.axi > 1,
            AVWVIEW.slices.axi = AVWVIEW.slices.axi - 1;
          end
      end
      switch command,
        case {'left','right'}
          set(AVWVIEW.handles.sagittal_slider,'Value',AVWVIEW.slices.sag);
          Ssag = squeeze(AVWVIEW.avw.img(AVWVIEW.slices.sag,:,:));
          set(AVWVIEW.handles.sagittal_image,'CData',Ssag');
          set(AVWVIEW.handles.sagittal_sliderN,'String',num2str(AVWVIEW.slices.sag));
          set(AVWVIEW.handles.sagittal_sliderN,'Value',AVWVIEW.slices.sag);
        case {'up','down'},
          set(AVWVIEW.handles.axial_slider,'Value',AVWVIEW.slices.axi);
          Saxi = squeeze(AVWVIEW.avw.img(:,:,AVWVIEW.slices.axi));
          set(AVWVIEW.handles.axial_image,'CData',Saxi');
          set(AVWVIEW.handles.axial_sliderN,'String',num2str(AVWVIEW.slices.axi));
          set(AVWVIEW.handles.axial_sliderN,'Value',AVWVIEW.slices.axi);
      end
    end
    
    if isequal(gca, AVWVIEW.handles.sagittal_axes),
      switch command,
        case 'left',
          % decrease sagittal slice
          if AVWVIEW.slices.cor > 1,
            AVWVIEW.slices.cor = AVWVIEW.slices.cor - 1;
          end
        case 'right',
          % increase sagittal slice
          if AVWVIEW.slices.cor < AVWVIEW.ydim,
            AVWVIEW.slices.cor = AVWVIEW.slices.cor + 1;
          end
        case 'up',
          % increase axial slice
          if AVWVIEW.slices.axi < AVWVIEW.zdim,
            AVWVIEW.slices.axi = AVWVIEW.slices.axi + 1;
          end
        case 'down',
          % decrease axial slice
          if AVWVIEW.slices.axi > 1,
            AVWVIEW.slices.axi = AVWVIEW.slices.axi - 1;
          end
      end
      switch command,
        case {'left','right'}
          set(AVWVIEW.handles.coronal_slider,'Value',AVWVIEW.slices.cor);
          Scor = squeeze(AVWVIEW.avw.img(:,AVWVIEW.slices.cor,:));
          set(AVWVIEW.handles.coronal_image,'CData',Scor');
          set(AVWVIEW.handles.coronal_sliderN,'String',num2str(AVWVIEW.slices.cor));
          set(AVWVIEW.handles.coronal_sliderN,'Value',AVWVIEW.slices.cor);
        case {'up','down'},
          set(AVWVIEW.handles.axial_slider,'Value',AVWVIEW.slices.axi);
          Saxi = squeeze(AVWVIEW.avw.img(:,:,AVWVIEW.slices.axi));
          set(AVWVIEW.handles.axial_image,'CData',Saxi');
          set(AVWVIEW.handles.axial_sliderN,'String',num2str(AVWVIEW.slices.axi));
          set(AVWVIEW.handles.axial_sliderN,'Value',AVWVIEW.slices.axi);
      end
    end
    
    AVWVIEW = set_crosshairs(AVWVIEW);
    
    
    
    
    
    
    
    
    
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    
  case {'roi_9','roi_7','roi_5','roi_3'},
    
    position = [ AVWVIEW.slices.sag, AVWVIEW.slices.cor, AVWVIEW.slices.axi ];
    
    shape.type = 'block';
    if findstr(command,'9'), shape.size = [9,9,9]; end
    if findstr(command,'7'), shape.size = [7,7,7]; end
    if findstr(command,'5'), shape.size = [5,5,5]; end
    if findstr(command,'3'), shape.size = [3,3,3]; end
    
    stats.roi = avw_roi(AVWVIEW.avw,position,shape);
    
    AVWVIEW.avw.stats = avw_stats(stats);
    
    
    
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    
  case {'nasion','rpa','lpa','ac'},
    
    % return voxel coordinates into AVWVIEW.imgXYZ
    AVWVIEW = slices2metric(AVWVIEW);
    
    if get(AVWVIEW.handles.coord,'value') == 2,
      format = '%7.3f %7.3f %7.3f';
      imgXYZ = AVWVIEW.imgXYZ.mm;
      string = sprintf('%7.3f %7.3f %7.3f',imgXYZ);
    elseif get(AVWVIEW.handles.coord,'value') == 3,
      format = '%7.3f %7.3f %7.3f';
      imgXYZ = AVWVIEW.imgXYZ.meters;
      string = sprintf('%7.3f %7.3f %7.3f',imgXYZ);
    else
      imgXYZ = AVWVIEW.imgXYZ.voxels;
      string = sprintf('%7.0f %7.0f %7.0f',imgXYZ);
    end;
    
    switch command,
      case 'nasion',