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imagine.m
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imagine.m
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function hF = imagine(varargin)
% IMAGINE IMAGe visualization, analysis and evaluation engINE
%
% IMAGINE starts the IMAGINE user interface without initial data
%
% IMAGINE(DATA) Starts the IMAGINE user interface with one (DATA is 3D)
% or multiple panels (DATA is 4D).
%
% IMAGINE(DATA, PROPERTY1, VALUE1, ...)) Starts the IMAGINE user
% interface with data DATA plus supplying some additional information
% about the dataset in the usual property/value pair format. Possible
% combinations are:
% PROPERTY VALUE
% 'Name' String: A name for the dataset
% 'Voxelsize' [3x1] or [1x3] double: The voxel size of the first
% three dimensions of DATA.
% 'Units' String: The physical unit of the pixels (e.g. 'mm')
%
% IMAGINE(DATA1, DATA2, ...) Starts the IMAGINE user interface with
% multiple panels, where each input can be either a 3D- or 4D-array. Each
% dataset can be defined more detailedly with the properties above.
%
%
% Examples:
%
% 1. >> load mri % Gives variable D
% >> imagine(squeeze(D)); % squeeze because D is in rgb format
%
% 2. >> load mri % Gives variable D
% >> imagine(squeeze(D), 'Name', 'Head T1', 'Voxelsize', [1 1 2.7]);
% This syntax gives a more realistic aspect ration if you rotate the data.
%
% For more information about the IMAGINE functions refer to the user's
% guide file in the documentation folder supplied with the code.
%
% Copyright 2012-2015 Christian Wuerslin, University Hospital of Tübingen,
% Contact: [email protected]
%
% Extension 2014-2020 Thomas Küstner, University Hospital of Tübingen
% Contact: [email protected]
% =========================================================================
% Warp Zone! (using Cntl + D)
% -------------------------------------------------------------------------
% *** The callbacks ***
% fCloseGUI % On figure close
% fResizeFigure % On figure resize
% fIconClick % On clicking menubar or tool icons
% fWindowMouseHoverFcn % Standard figure mouse move callback
% fWindowButtonDownFcn % Figure mouse button down function
% fWindowMouseMoveFcn % Figure mouse move function when button is pressed or ROI drawing active
% fWindowButtonUpFcn % Figure mouse button up function: Starts most actions
% fKeyPressFcn % Keyboard callback
% fContextFcn % Context menu callback
% fSetWindow % Callback of the colorbars
%
% -------------------------------------------------------------------------
% *** IMAGINE Core ***
% fFillPanels
% fUpdateActivation
% fZoom
% fWindow
% fChangeImage
% fChangeNDim
% fEval
%
% -------------------------------------------------------------------------
% *** Lengthy subfunction ***
% fLoadFiles
% fParseInputs
% fAddImageToData
% fSaveToFiles
%
% -------------------------------------------------------------------------
% *** Helpers ***
% fCreatePanels
% fGetPanel
% fServesSizeCriterion
% fIsOn
% fGetNActiveVisibleSeries
% fGetNVisibleSeries
% fGetImg
% fGetData
% fPrintNumber
% fBackgroundImg
% fReplicate
%
% -------------------------------------------------------------------------
% *** GUIS ***
% fGridSelect
% fColormapSelect
% fSelectEvalFcns
% =========================================================================
% =========================================================================
% *** FUNCTION imagine
% ***
% *** Main GUI function. Creates the figure and all its contents and
% *** registers the callbacks.
% ***
% =========================================================================
% versioning (Thomas Kuestner)
% v2.1: added 4D/5D support and through-time ROI analysis
% v2.2: added quiver plots
% v2.3: improved rotation of flows and minor bugfixes
% -------------------------------------------------------------------------
% Control the figure's appearance
SAp.sVERSION = '2.3 - Belly Jeans';
SAp.sTITLE = ['IMAGINE ',SAp.sVERSION];% Title of the figure
SAp.iICONSIZE = 24; % Size if the icons
SAp.iICONPADDING = SAp.iICONSIZE/2; % Padding between icons
SAp.iMENUBARHEIGHT = SAp.iICONSIZE*2; % Height of the menubar (top)
SAp.iTOOLBARWIDTH = SAp.iICONSIZE*2; % Width of the toolbar (left)
SAp.iTITLEBARHEIGHT = 24; % Height of the titles (above each image)
SAp.iCOLORBARHEIGHT = 12; % Height of the colorbar
SAp.iCOLORBARPADDING = 60; % The space on the left and right of the colorbar for the min/max values
SAp.iEVALBARHEIGHT = 16; % Height of the evaluation bar
SAp.iDISABLED_SCALE = 0.3; % Brightness of disabled buttons (decrease to make darker)
SAp.iINACTIVE_SCALE = 0.6; % Brightness of inactive buttons (toggle buttons and radio groups)
SAp.dBGCOLOR = [0.15 0.25 0.35]; % Color scheme
SAp.dEmptyImg = 0; % The background image (is calculated in fResizeFigure);
% -------------------------------------------------------------------------
% -------------------------------------------------------------------------
% Set some paths.
SPref.sMFILEPATH = fileparts(mfilename('fullpath')); % This is the path of this m-file
SPref.sICONPATH = [SPref.sMFILEPATH, filesep, 'icons', filesep]; % That's where the icons are
configFolder = getenv('IMAGINE_CONFIG_PATH');
if isempty(configFolder) configFolder = SPref.sMFILEPATH, end;
SPref.sSaveFilename = [configFolder, filesep, 'imagineSave.mat']; % A .mat-file to save the GUI settings
addpath([SPref.sMFILEPATH, filesep, 'EvalFunctions'], ...
[SPref.sMFILEPATH, filesep, 'colormaps'], ...
[SPref.sMFILEPATH, filesep, 'import'], ...
[SPref.sMFILEPATH, filesep, 'tools']);
% -------------------------------------------------------------------------
% -------------------------------------------------------------------------
% Define some preferences
S = load('mylines.mat');
SPref.dCOLORMAP = S.mylines;% The color scheme of the overlays and lines
SPref.cMarkers = {'x', '+', 'o', '*', '.', 's', 'd', '^', 'v', '<', '>', 'p', 'h'}; % a list of markers used in ROI overlay plotting
SPref.dWINDOWSENSITIVITY = 0.02; % Defines mouse sensitivity for windowing operation
SPref.dZOOMSENSITIVITY = 0.02; % Defines mouse sensitivity for zooming operation
SPref.dROTATION_THRESHOLD = 50; % Defines the number of pixels the cursor has to move to rotate an image
SPref.dLWRADIUS = 200; % The radius in which the path maps are calculated in the livewire algorithm
SPref.lGERMANEXPORT = false; % Not a beer! Determines whether the data is exported with a period or a comma as decimal point
SPref.iQUIVERFACTOR = 8; % Defines quiver factor distance [px] for flow visualization
SPref.iQUIVERSTRENGTH = 100; % Defines quiver factor strength [%] for flow visualization
SPref.iQUIVERCOLOR = [1 1 0]; % Defines quiver color
% -------------------------------------------------------------------------
% -------------------------------------------------------------------------
% This is the definition of the menubar. If a radiobutton-like
% functionality is to implemented, the GroupIndex parameter of all
% icons within the group has to be set to the same positive integer
% value. Normal Buttons have group index -1, toggel switches have group
% index 0. The toolbar has the GroupIndex 255.
SIcons = struct( ...
'Name', {'folder_open', 'doc_import', 'save', 'doc_delete', 'print', 'exchange', 'grid', 'colormap', 'flow', 'link', 'link1', 'reset', 'phase', 'max', 'min', 'record', 'stop', 'rewind', 'clock', 'line1', 'cursor_arrow', 'rotate', 'line', 'roi', 'lw', 'rg', 'ic', 'tag'}, ...
'Spacer', { 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, ...
'GroupIndex', { -1, -1, -1, -1, -1, -1, -1, -1, -1, 0, 0, -1, 1, 1, 1, -1, -1, -1, 0, 0, 255, 255, 255, 255, 255, 255, 255, 255}, ...
'Enabled', { 1, 1, 0, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1}, ...
'Active', { 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 0, 0, 0, 1, 1, 1, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0}, ...
'Accelerator', { 'o', 'i', 's', 'delete', 'p', 'x', '', '', '', 'l', '', '0', '', '', '', 'r', 'r', 'z', 'c', 'w', 'm', 'r', 'l', 'o', 'w', 'g', 'i', 't'}, ...
'Modifier', { 'Cntl', 'Cntl', 'Cntl', '', '', 'Cntl', '', '', '', 'Cntl', '', 'Cntl', '', '', '', 'Cntl', 'Alt', 'Cntl', 'Cntl', 'Cntl', '', '', '', '', '', '', '', ''}, ...
'Tooltip', {'Open Files' , 'Import Workspace Variables', 'Save To Files', 'Delete', 'Print', 'Exchange', 'Change Layout', 'Colormap', 'Change Flow', 'Link Actions', 'Link Windowing','Reset View', 'Phase Image', 'Maximum Intensity Projection', 'Minimum Intensity Projection', 'Log Evaluation', 'Stop Logging Evaluation', 'Undo Last Evaluation', 'Eval Timeseries', 'Show Line/ROI Plots', 'Move/Zoom/Window', 'Rotate', 'Profile Evaluation', 'ROI Evaluation', 'Livewire ROI Evaluation', 'Region Growing Volume Evaluation', 'Isocontour Evaluation', 'Properties'});
% -------------------------------------------------------------------------
% ------------------------------------------------------------------------
% Reset the GUI's state variable
SState.iLastSeries = 0;
SState.iStartSeries = 1;
SState.sTool = 'cursor_arrow';
SState.sPath = [SPref.sMFILEPATH, filesep];
SState.csEvalLineFcns = {};
SState.csEvalROIFcns = {};
SState.csEvalVolFcns = {};
SState.sEvalFilename = [];
SState.iROIState = 0; % The ROI state machine
SState.dROILineX = [];
SState.dROILineY = [];
SState.iPanels = [0, 0];
SState.lShowColorbar = true;
SState.lShowEvalbar = true;
SState.dColormapBack = gray(256);
SState.dColormapMask = S.mylines;
SState.dMaskOpacity = 0.5;
SState.sDrawMode = 'mag';
SState.dTolerance = 1.0;
SState.hEvalFigure = 0.1;
% ------------------------------------------------------------------------
% ------------------------------------------------------------------------
% Create some globals
SData = []; % A struct for hoding the data (image data + visualization parameters)
SImg = []; % A struct for the image component handles
SLines = []; % A struct for the line component handles
SMouse = []; % A Struct to hold parameters of the mouse operations
SPanels = []; % A Struct to hold the panel data
% -------------------------------------------------------------------------
% -------------------------------------------------------------------------
% Read the preferences from the save file
iPosition = [100 100 1000 600];
if exist(SPref.sSaveFilename, 'file')
SSaveVar = [];
load(SPref.sSaveFilename);
SState.sPath = SSaveVar.sPath;
SState.csEvalLineFcns = SSaveVar.csEvalLineFcns;
SState.csEvalROIFcns = SSaveVar.csEvalROIFcns;
SState.csEvalVolFcns = SSaveVar.csEvalVolFcns;
iPosition = SSaveVar.iPosition;
SPref.lGERMANEXPORT = SSaveVar.lGermanExport;
clear SSaveVar; % <- no one needs you anymore! :((
else
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% First-time call: Do some setup
sAns = questdlg('Do you want to use periods (anglo-american) or commas (german) as decimal separator in the exported .csv spreadsheet files? This is important for a smooth Excel import.', 'IMAGINE First-Time Setup', 'Stick to the point', 'Use se commas', 'Stick to the point');
SPref.lGERMANEXPORT = strcmp(sAns, 'Use se commas');
fCompileMex;
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
end
% -------------------------------------------------------------------------
% -------------------------------------------------------------------------
% Make sure the figure fits on the screen
iScreenSize = get(0, 'ScreenSize');
if (iPosition(1) + iPosition(3) > iScreenSize(3)) || ...
(iPosition(2) + iPosition(4) > iScreenSize(4))
iPosition(1:2) = 50;
iPosition(3:4) = iScreenSize(3:4) - 100;
end
% -------------------------------------------------------------------------
% -------------------------------------------------------------------------
% Create the figure. Mouse scroll wheel is supported since Version 7.4 (I think).
hF = figure(...
'BusyAction' , 'cancel', ...
'Interruptible' , 'off', ...
'Position' , iPosition, ...
'Units' , 'pixels', ...
'Color' , SAp.dBGCOLOR, ...
'ResizeFcn' , @fResizeFigure, ...
'DockControls' , 'on', ...
'MenuBar' , 'none', ...
'Name' , SAp.sTITLE, ...
'NumberTitle' , 'off', ...
'KeyPressFcn' , @fKeyPressFcn, ...
'CloseRequestFcn' , @fCloseGUI, ...
'WindowButtonDownFcn' , @fWindowButtonDownFcn, ...
'WindowButtonMotionFcn', @fWindowMouseHoverFcn);
try
set(hF, 'WindowScrollWheelFcn' , @fChangeImage);
catch
warning('IMAGINE: No scroll wheel functionality!');
end
colormap(gray(256));
try % Try to apply a nice icon
warning('off','MATLAB:HandleGraphics:ObsoletedProperty:JavaFrame');
jframe = get(hF, 'javaframe');
jIcon = javax.swing.ImageIcon([SPref.sMFILEPATH, filesep, 'icons', filesep, 'icon.png']);
pause(0.001);
jframe.setFigureIcon(jIcon);
clear jframe jIcon
catch
warning('IMAGINE: Could not apply a nifty icon to the figure :(');
end
% -------------------------------------------------------------------------
% -------------------------------------------------------------------------
% Crate context menu for the region growing
hContextMenu = uicontextmenu;
uimenu(hContextMenu, 'Label', 'Tolerance +50%', 'Callback', @fContextFcn);
uimenu(hContextMenu, 'Label', 'Tolerance +10%', 'Callback', @fContextFcn);
uimenu(hContextMenu, 'Label', 'Tolerance -10%', 'Callback', @fContextFcn);
uimenu(hContextMenu, 'Label', 'Tolerance -50%', 'Callback', @fContextFcn);
% -------------------------------------------------------------------------
% -------------------------------------------------------------------------
% Create the menubar and the toolbar including their components
SPanels.hMenu = uipanel('Parent', hF, 'BackgroundColor', 'k', 'BorderWidth', 0, 'Units', 'pixels');
SPanels.hTools = uipanel('Parent', hF, 'BackgroundColor', 'k', 'BorderWidth', 0, 'Units', 'pixels');
SAxes.hIcons = zeros(length(SIcons), 1);
SImg .hIcons = zeros(length(SIcons), 1);
iStartPos = SAp.iTOOLBARWIDTH - SAp.iICONSIZE;
for iI = 1:length(SIcons)
if SIcons(iI).GroupIndex ~= 255, iStartPos = iStartPos + SAp.iICONPADDING + SAp.iICONSIZE; end
dImage = double(imread([SPref.sICONPATH, SIcons(iI).Name, '.png'])); % icon file name (.png) has to be equal to icon name
if size(dImage, 3) == 1, dImage = repmat(dImage, [1 1 3]); end
SIcons(iI).dImg = dImage./255;
if SIcons(iI).GroupIndex == 255, hParent = SPanels.hTools; else hParent = SPanels.hMenu; end
SAxes.hIcons(iI) = axes('Parent', hParent, 'Units', 'pixels', 'Position' , [iStartPos SAp.iICONPADDING SAp.iICONSIZE SAp.iICONSIZE]); %#ok<LAXES>
SImg.hIcons(iI) = image(SIcons(iI).dImg, 'Parent', SAxes.hIcons(iI),'ButtonDownFcn' , @fIconClick);
if SIcons(iI).Spacer, iStartPos = iStartPos + SAp.iICONSIZE; end
end
axis(SAxes.hIcons, 'off');
SState.dIconEnd = iStartPos + SAp.iICONPADDING + SAp.iICONSIZE;
STexts.hStatus = uicontrol(... % Create the text element
'Style' ,'Text', ...
'FontName' , 'Helvetica Neue', ...
'FontWeight' , 'light', ...
'Parent' , SPanels.hMenu, ...
'FontUnits' , 'normalized', ...
'FontSize' , 0.7, ...
'BackgroundColor' , 'k', ...
'ForegroundColor' , 'w', ...
'HorizontalAlignment' , 'right', ...
'Units' , 'pixels');
clear iStartPos hParent iI dImage
% -------------------------------------------------------------------------
% -------------------------------------------------------------------------
% Parse Inputs and determine and create the initial amount of panels
if ~isempty(varargin), fParseInputs(varargin); end
if ~prod(SState.iPanels), SState.iPanels = [1 1]; end
fCreatePanels;
clear varargin; % <- no one needs you anymore! :((
% -------------------------------------------------------------------------
% -------------------------------------------------------------------------
% Update the figure components
fUpdateActivation(); % Acitvate/deactivate some buttons according to the gui state
fResizeFigure(hF, []); % Call the resize function to allign all the gui elements
set(hF, 'UserData', @fGetData);
drawnow expose
% -------------------------------------------------------------------------
% The 'end' of the IMAGINE main function. The real end is, of course, after
% all the nested functions. Using the nested functions, shared varaiables
% (the variables of the IMAGINE function) can be used which makes the usage
% of the 'guidata' commands obsolete.
% =========================================================================
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * NESTED FUNCTION fCloseGUI (nested in imagine)
% * *
% * * Figure callback
% * *
% * * Closes the figure and saves the settings
% * *
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
function fCloseGUI(hObject, eventdata) %#ok<*INUSD> eventdata is repeatedly unused
% -----------------------------------------------------------------
% Save the settings
SSaveVar.sPath = SState.sPath;
SSaveVar.csEvalLineFcns = SState.csEvalLineFcns;
SSaveVar.csEvalROIFcns = SState.csEvalROIFcns;
SSaveVar.csEvalVolFcns = SState.csEvalVolFcns;
SSaveVar.iPosition = get(hObject, 'Position');
SSaveVar.lGermanExport = SPref.lGERMANEXPORT;
try
save(SPref.sSaveFilename, 'SSaveVar');
catch
warning('Could not save the settings! Is the IMAGINE folder protected?');
end
% -----------------------------------------------------------------
delete(hObject); % Bye-bye figure
end
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * END NESTED FUNCTION fCloseGUI
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * NESTED FUNCTION fResizeFigure (nested in imagine)
% * *
% * * Figure callback
% * *
% * * Re-arranges all the GUI elements after a figure resize
% * *
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
function fResizeFigure(hObject, eventdata)
% -----------------------------------------------------------------
% The resize callback is called very early, therefore we have to check
% if the GUI elements were already created and return if not
if ~isfield(SPanels, 'hImgFrame'), return, end
% -----------------------------------------------------------------
% -----------------------------------------------------------------
% Get figure dimensions
dFigureSize = get(hF, 'Position');
dFigureWidth = dFigureSize(3);
dFigureHeight = dFigureSize(4);
% -----------------------------------------------------------------
% -----------------------------------------------------------------
% Arrange the panels and all their contents
for iM = 1:SState.iPanels(1)
for iN = 1:SState.iPanels(2)
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% Determine the position of the panel
iLinInd = (iM - 1).*SState.iPanels(2) + iN;
dWidth = round((dFigureWidth - SAp.iTOOLBARWIDTH) / SState.iPanels(2)) - 1;
dHeight = round((dFigureHeight - SAp.iMENUBARHEIGHT) / SState.iPanels(1)) - 1;
dXStart = (iN - 1).*(dWidth + 1) + 2 + SAp.iTOOLBARWIDTH;
dYStart = (SState.iPanels(1) - iM).*(dHeight + 1) + 2;
if iN == SState.iPanels(2), dWidth = dFigureWidth - dXStart; end
if iM == 1 , dHeight = dFigureHeight - SAp.iMENUBARHEIGHT - dYStart; end
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% Arrange the panels
set(SPanels.hImgFrame(iLinInd), 'Position', [dXStart, dYStart, dWidth, dHeight]);
dImgYStart = 1 + SState.lShowEvalbar.*SAp.iEVALBARHEIGHT;
dImgHeight = dHeight - SAp.iTITLEBARHEIGHT - SState.lShowColorbar.*SAp.iCOLORBARHEIGHT - SState.lShowEvalbar.*SAp.iEVALBARHEIGHT;
set(SPanels.hImg(iLinInd), 'Position', [1, dImgYStart, dWidth, dImgHeight]);
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
set(STexts.hImg1(iLinInd), 'Position', [5, dHeight - SAp.iTITLEBARHEIGHT + 4, dWidth - 85, SAp.iTITLEBARHEIGHT - 4]);
set(STexts.hImg2(iLinInd), 'Position', [dWidth - 160, dHeight - SAp.iTITLEBARHEIGHT + 4, 155, SAp.iTITLEBARHEIGHT - 4]); % -80
set(SAxes.hColorbar(iLinInd), 'Position', [SAp.iCOLORBARPADDING, dHeight - SAp.iCOLORBARHEIGHT - SAp.iTITLEBARHEIGHT + 4, max([dWidth - 2*SAp.iCOLORBARPADDING, 1]), SAp.iCOLORBARHEIGHT - 3]);
set(STexts.hColorbarMin(iLinInd), 'Position', [5, dHeight - SAp.iTITLEBARHEIGHT - SAp.iCOLORBARHEIGHT + 3, SAp.iCOLORBARPADDING - 10, 12]);
set(STexts.hColorbarMax(iLinInd), 'Position', [dWidth - SAp.iCOLORBARPADDING + 5, dHeight - SAp.iTITLEBARHEIGHT - SAp.iCOLORBARHEIGHT + 3, SAp.iCOLORBARPADDING - 10, 12]);
set(STexts.hEval, 'Position', [5, 2, dWidth - 100, SAp.iEVALBARHEIGHT - 1]);
set(STexts.hVal, 'Position', [dWidth - 305, 2, 300, SAp.iEVALBARHEIGHT - 1]);
end
end
% -----------------------------------------------------------------
% -----------------------------------------------------------------
% Arrange the menubar
dTextWidth = max([dFigureWidth - SState.dIconEnd - 10, 1]);
set(SPanels.hMenu, 'Position', [1, dFigureHeight - SAp.iMENUBARHEIGHT + 1, dFigureWidth, SAp.iMENUBARHEIGHT]);
set(STexts.hStatus, 'Position', [SState.dIconEnd + 5, 10, dTextWidth, 28]);
% -----------------------------------------------------------------
% -----------------------------------------------------------------
% Arrange the toolbar
set(SPanels.hTools, 'Position', [1, 1, SAp.iTOOLBARWIDTH, dFigureHeight - SAp.iMENUBARHEIGHT]);
iStartPos = dFigureHeight - SAp.iMENUBARHEIGHT - SAp.iICONPADDING - SAp.iICONSIZE;
for i = 1:length(SIcons) % Unfortunately we have to rearrange all the icons to keep them on top :(
if SIcons(i).GroupIndex ~= 255, continue, end
set(SAxes.hIcons(i), 'Position', [SAp.iICONPADDING, iStartPos, SAp.iICONSIZE, SAp.iICONSIZE]);
iStartPos = iStartPos - SAp.iICONSIZE - SAp.iICONPADDING;
end
% -----------------------------------------------------------------
% -------------------------------------------------------------------------
% Create a beatuiful image for the empty axes
dWidth = ceil((dFigureWidth - SAp.iTOOLBARWIDTH) / SState.iPanels(2));
dHeight = ceil((dFigureHeight - SAp.iMENUBARHEIGHT) / SState.iPanels(1)) - SAp.iTITLEBARHEIGHT - SAp.iCOLORBARHEIGHT - SAp.iEVALBARHEIGHT;
SAp.dEmptyImg = fBackgroundImg(dHeight, dWidth);
% -------------------------------------------------------------------------
fFillPanels;
end
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * END NESTED FUNCTION fResizeFigure
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * NESTED FUNCTION fIconClick (nested in imagine)
% * *
% * * Common callback for all buttons in the menubar
% * *
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
function fIconClick(hObject, eventdata)
% -----------------------------------------------------------------
% Get the source's (pressed buttton) data and exit if disabled
iInd = find(SImg.hIcons == hObject);
if ~SIcons(iInd).Enabled, return, end;
% -----------------------------------------------------------------
sActivate = [];
% -----------------------------------------------------------------
% Distinguish the idfferent button types (normal, toggle, radio)
switch SIcons(iInd).GroupIndex
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% NORMAL pushbuttons
case -1
switch(SIcons(iInd).Name)
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% LOAD new FILES using file dialog
case 'folder_open'
if strcmp(get(hF, 'SelectionType'), 'normal')
% Load Files
[csFilenames, sPath] = uigetfile( ...
{'*.*', 'All Files'; ...
'*.dcm; *.DCM; *.mat; *.MAT; *.jpg; *.jpeg; *.JPG; *.JPEG; *.tif; *.tiff; *.TIF; *.TIFF; *.gif; *.GIF; *.bmp; *.BMP; *.png; *.PNG; *.nii; *.NII; *.gipl; *.GIPL', 'All images'; ...
'*.mat; *.MAT', 'Matlab File (*.mat)'; ...
'*.jpg; *.jpeg; *.JPG; *.JPEG', 'JPEG-Image (*.jpg)'; ...
'*.tif; *.tiff; *.TIF; *.TIFF;', 'TIFF-Image (*.tif)'; ...
'*.gif; *.GIF', 'Gif-Image (*.gif)'; ...
'*.bmp; *.BMP', 'Bitmaps (*.bmp)'; ...
'*.png; *.PNG', 'Portable Network Graphics (*.png)'; ...
'*.dcm; *.DCM', 'DICOM Files (*.dcm)'; ...
'*.nii; *.NII', 'NifTy Files (*.nii)'; ...
'*.gipl; *.GIPL', 'Guys Image Processing Lab Files (*.gipl)'}, ...
'OpenLocation' , SState.sPath, ...
'Multiselect' , 'on');
if isnumeric(sPath), return, end; % Dialog aborted
else
% Load a folder
sPath = uigetdir(SState.sPath);
if isnumeric(sPath), return, end;
sPath = [sPath, filesep];
SFiles = dir(sPath);
SFiles = SFiles(~[SFiles.isdir]);
csFilenames = cell(length(SFiles), 1);
for i = 1:length(SFiles), csFilenames{i} = SFiles(i).name; end
end
SState.sPath = sPath;
fLoadFiles(csFilenames);
fFillPanels();
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% IMPORT workspace (base) VARIABLE(S)
case 'doc_import'
csVars = fWSImport();
if isempty(csVars), return, end % Dialog aborted
for i = 1:length(csVars)
dVar = evalin('base', csVars{i});
fAddImageToData(dVar, csVars{i}, 'workspace');
end
fFillPanels();
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% SAVE panel data to file(s)
case 'save'
if strcmp(get(hF, 'SelectionType'), 'normal')
[sFilename, sPath] = uiputfile( ...
{'*.jpg', 'JPEG-Image (*.jpg)'; ...
'*.tif', 'TIFF-Image (*.tif)'; ...
'*.gif', 'Gif-Image (*.gif)'; ...
'*.bmp', 'Bitmaps (*.bmp)'; ...
'*.png', 'Portable Network Graphics (*.png)'}, ...
'Save selected series to files', ...
[SState.sPath, filesep, '%SeriesName%_%ImageNumber%']);
if isnumeric(sPath), return, end; % Dialog aborted
SState.sPath = sPath;
fSaveToFiles(sFilename, sPath);
else
[sFilename, sPath] = uiputfile( ...
{'*.jpg', 'JPEG-Image (*.jpg)'; ...
'*.tif', 'TIFF-Image (*.tif)'; ...
'*.gif', 'Gif-Image (*.gif)'; ...
'*.bmp', 'Bitmaps (*.bmp)'; ...
'*.png', 'Portable Network Graphics (*.png)'}, ...
'Save MASK of selected series to files', ...
[SState.sPath, filesep, '%SeriesName%_%ImageNumber%_Mask']);
if isnumeric(sPath), return, end; % Dialog aborted
SState.sPath = sPath;
fSaveMaskToFiles(sFilename, sPath);
end
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% SAVE panel data to file(s)
case 'print'
% if strcmp(get(hF, 'SelectionType'), 'normal')
[sFilename, sPath] = uiputfile( ...
{'*.tif', 'TIFF-Image (*.tif)'; ...
'*.gif', 'Gif-Image (*.gif)'; ...
'*.bmp', 'Bitmaps (*.bmp)'; ...
'*.jpg', 'JPEG-Image (*.jpg)'; ...
'*.png', 'Portable Network Graphics (*.png)'}, ...
'Save selected series to files', ...
[SState.sPath, filesep, '%SeriesName%_%ImageNumber%']);
if isnumeric(sPath), return, end; % Dialog aborted
SState.sPath = sPath;
fSaveToFiles(sFilename, sPath, true);
% else
% [sFilename, sPath] = uiputfile( ...
% {'*.tif', 'TIFF-Image (*.tif)'; ...
% '*.gif', 'Gif-Image (*.gif)'; ...
% '*.bmp', 'Bitmaps (*.bmp)'; ...
% '*.jpg', 'JPEG-Image (*.jpg)'; ...
% '*.png', 'Portable Network Graphics (*.png)'}, ...
% 'Save MASK of selected series to files', ...
% [SState.sPath, filesep, '%SeriesName%_%ImageNumber%_Mask']);
% if isnumeric(sPath), return, end; % Dialog aborted
%
% SState.sPath = sPath;
% fSaveToFiles(sFilename, sPath, true, true);
% end
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% DELETE DATA from structure
case 'doc_delete'
iSeriesInd = find([SData.lActive]); % Get indices of selected axes
iSeriesInd = iSeriesInd(iSeriesInd >= SState.iStartSeries);
SData(iSeriesInd) = []; % Delete the visible active data
fFillPanels();
fUpdateActivation(); % To make sure panels without data are not selected
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% EXCHANGE SERIES
case 'exchange'
iSeriesInd = find([SData.lActive]); % Get indices of selected axes
SData1 = SData(iSeriesInd(1));
SData(iSeriesInd(1)) = SData(iSeriesInd(2)); % Exchange the data
SData(iSeriesInd(2)) = SData1;
fFillPanels();
fUpdateActivation(); % To make sure panels without data are not selected
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% Determine the NUMBER OF PANELS and their LAYOUT
case 'grid'
iPanels = fGridSelect(4, 4);
if ~sum(iPanels), return, end % Dialog aborted
SState.iPanels = iPanels;
fCreatePanels; % also updates the SState.iPanels
fFillPanels;
fUpdateActivation;
fResizeFigure(hF, []);
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% Select the COLORMAP
case 'colormap'
dColormap = fColormapSelect(STexts.hStatus);
if ~isempty(dColormap)
SState.dColormapBack = dColormap;
fFillPanels;
colormap(dColormap);
set(SPanels.hImg, 'BackgroundColor', dColormap(1,:));
end
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% Select the FLOW
case 'flow'
[SPref.iQUIVERFACTOR, SPref.iQUIVERSTRENGTH, SPref.iQUIVERCOLOR] = fFlowSelect(STexts.hStatus, SPref.iQUIVERFACTOR, SPref.iQUIVERSTRENGTH, SPref.iQUIVERCOLOR);
fFillPanels();
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% RESET the view (zoom/window/center)
case 'reset' % Reset the view properties of all data
for i = 1:length(SData)
SData(i).dZoomFactor = 1;
SData(i).dWindowCenter = mean(SData(i).dDynamicRange);
SData(i).dWindowWidth = SData(i).dDynamicRange(2) - SData(i).dDynamicRange(1);
SData(i).dDrawCenter = [0.5 0.5];
end
fFillPanels();
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% RECORD Start recording data
case 'record'
[sName, sPath] = uiputfile( ...
{'*.csv', 'Comma-separated File (*.csv)'}, ...
'Chose Logfile', SState.sPath);
if isnumeric(sPath)
SState.sEvalFilename = '';
else
SState.sEvalFilename = [sPath, sName];
end
SState.sPath = sPath;
fUpdateActivation;
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% STOP logging data
case 'stop'
SState.sEvalFilename = '';
fUpdateActivation;
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% REWIND last measurement
case 'rewind'
iPosDel = fGetEvalFilePos;
if iPosDel < 0
fprintf('File ''%s''does not exist yet or is write-protexted!\n', SState.sEvalFilename);
return
end
if iPosDel == 0
fprintf('Log file ''%s'' is empty!\n', SState.sEvalFilename);
return
end
fid = fopen(SState.sEvalFilename, 'r');
sLine = fgets(fid);
i = 1;
lLast = false;
while ischar(sLine)
csText{i} = sLine;
i = i + 1;
sLine = fgets(fid);
csPos = textscan(sLine, '"%d"');
if isempty(csPos{1})
iPos = 0;
else
iPos = csPos{1};
end
if iPos == iPosDel - 1, lLast = true; end
if iPos ~= iPosDel - 1 && lLast, break, end
end
fclose(fid);
iEnd = length(csText);
if iPosDel == 1, iEnd = 3; end
fid = fopen(SState.sEvalFilename, 'w');
for i = 1:iEnd
fprintf(fid, '%s', csText{i});
end
fprintf('Removed entry %d from ''%s''!\n', iPosDel, SState.sEvalFilename);
fclose(fid);
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
otherwise
end
% End of NORMAL buttons
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% TOGGLE buttons: Invert the state
case 0
SIcons(iInd).Active = ~SIcons(iInd).Active;
fUpdateActivation();
fFillPanels; % Because of link button
% End of TOGGLE buttons
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% The render-mode group
case 1 % The render-mode group
if ~strcmp(SState.sDrawMode, SIcons(iInd).Name)
SState.sDrawMode = SIcons(iInd).Name;
sActivate = SIcons(iInd).Name;
else
SState.sDrawMode = 'mag';
end
fFillPanels;
case 255 % The toolbar
% - - - - - - - - - - - - -
% Right-click setup menus
if strcmp(get(hF, 'SelectionType'), 'alt') && ~isfield(eventdata, 'Character')% Right click, open tool settings in neccessary
switch SIcons(iInd).Name
case 'line',
csFcns = fSelectEvalFcns(SState.csEvalLineFcns, [SPref.sMFILEPATH, filesep, 'EvalFunctions']);
if iscell(csFcns), SState.csEvalLineFcns = csFcns; end
case {'roi', 'lw'},
csFcns = fSelectEvalFcns(SState.csEvalROIFcns, [SPref.sMFILEPATH, filesep, 'EvalFunctions']);
if iscell(csFcns), SState.csEvalROIFcns = csFcns; end
case 'rg'
csFcns = fSelectEvalFcns(SState.csEvalVolFcns, [SPref.sMFILEPATH, filesep, 'EvalFunctions']);
if iscell(csFcns), SState.csEvalVolFcns = csFcns; end
end
end
% - - - - - - - - - - - - -
% - - - - - - - - - - - - -
if ~strcmp(SState.sTool, SIcons(iInd).Name) % Tool change
% Try to delete the lines of the ROI and line eval tools
if isfield(SLines, 'hEval')
try delete(SLines.hEval); end %#ok<TRYNC>
SLines = rmfield(SLines, 'hEval');
end
% Set tool-specific context menus
switch SIcons(iInd).Name
case 'rg', set(SPanels.hImg, 'uicontextmenu', hContextMenu);
otherwise, set(SPanels.hImg, 'uicontextmenu', []);
end
% Remove the masks, if a new eval tool is selected
switch SIcons(iInd).Name
case {'line', 'roi', 'lw', 'rg', 'ic'}
for i = 1:length(SData), SData(i).lMask = []; end
fFillPanels;
end
% -----------------------------------------------------------------
% Reset the ROI painting state machine and Mouse callbacks
SState.iROIState = 0;
set(gcf, 'WindowButtonDownFcn' , @fWindowButtonDownFcn);
set(gcf, 'WindowButtonMotionFcn', @fWindowMouseHoverFcn);
set(gcf, 'WindowButtonUpFcn' , '');
% -----------------------------------------------------------------
end
SState.sTool = SIcons(iInd).Name;
sActivate = SIcons(iInd).Name;
% - - - - - - - - - - - - -
end
% - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - -
% Common code for all radio groups
if SIcons(iInd).GroupIndex > 0
for i = 1:length(SIcons)
if SIcons(i).GroupIndex == SIcons(iInd).GroupIndex
SIcons(i).Active = strcmp(SIcons(i).Name, sActivate);
end
end
end
fUpdateActivation();
% - - - - - - - - - - - - - - - - - - -
end
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * END NESTED FUNCTION fIconClick
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * NESTED FUNCTION fWindowMouseHoverFcn (nested in imagine)
% * *
% * * Figure callback
% * *
% * * The standard mouse move callback. Displays cursor coordinates and
% * * intensity value of corresponding pixel.
% * *
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
function fWindowMouseHoverFcn(hObject, eventdata)
if ~isfield(SPanels, 'hImgFrame'), return, end; % Return if called during GUI startup
iAxisInd = fGetPanel();
if iAxisInd
% -------------------------------------------------------------
% Cursor is over a panel -> show coordinates and intensity
iPos = uint16(get(SAxes.hImg(iAxisInd), 'CurrentPoint')); % Get cursor poition in axis coordinate system
for i = 1:length(SPanels.hImgFrame)
iSeriesInd = SState.iStartSeries + i - 1;
if iSeriesInd > length(SData), continue, end
if iPos(1, 1) > 0 && iPos(1, 2) > 0 && iPos(1, 1) <= size(SData(iSeriesInd).dImg, 2) && iPos(1, 2) <= size(SData(iSeriesInd).dImg, 1)
switch SState.sDrawMode
case {'mag', 'phase'}
dImg = fGetImg(iSeriesInd);
dVal = dImg(iPos(1, 2), iPos(1, 1));
case 'max'
if isreal(SData(iSeriesInd).dImg)
dVal = max(SData(iSeriesInd).dImg(iPos(1, 2), iPos(1, 1), :), [], 3);
else
dVal = max(abs(SData(iSeriesInd).dImg(iPos(1, 2), iPos(1, 1), :)), [], 3);
end
case 'min'
if isreal(SData(iSeriesInd).dImg)
dVal = min(SData(iSeriesInd).dImg(iPos(1, 2), iPos(1, 1), :), [], 3);
else
dVal = min(abs(SData(iSeriesInd).dImg(iPos(1, 2), iPos(1, 1), :)), [], 3);
end
end
if(~isempty(SData(iSeriesInd).dFlow))
iFlow = fGetFlow(iSeriesInd, SData(iSeriesInd).iActiveImage, SData(iSeriesInd).iActiveND(1), SData(iSeriesInd).iActiveND(2));
dValFlow = iFlow(iPos(1, 2), iPos(1, 1),:);
if(size(dValFlow,3) < 3)
dValFlow = cat(3,dValFlow,0);
end
end
if i == iAxisInd
if(~isempty(SData(iSeriesInd).dFlow))
set(STexts.hStatus, 'String', sprintf('I(%u,%u) = %s, F(%s,%s,%s) = [%s,%s,%s]', iPos(1, 1), iPos(1, 2), fPrintNumber(dVal), SData(iSeriesInd).sOri(1:2), SData(iSeriesInd).sOri(3:4), SData(iSeriesInd).sOri(5:6), fPrintNumber(dValFlow(:,:,1)), fPrintNumber(dValFlow(:,:,2)), fPrintNumber(dValFlow(:,:,3))));
else
set(STexts.hStatus, 'String', sprintf('I(%u,%u) = %s', iPos(1, 1), iPos(1, 2), fPrintNumber(dVal)));
end
end
if(~isempty(SData(iSeriesInd).dFlow))
set(STexts.hVal(i), 'String', sprintf('%s, (%s,%s,%s): [%s,%s,%s]', fPrintNumber(dVal), SData(iSeriesInd).sOri(1:2), SData(iSeriesInd).sOri(3:4), SData(iSeriesInd).sOri(5:6), fPrintNumber(dValFlow(:,:,1)), fPrintNumber(dValFlow(:,:,2)), fPrintNumber(dValFlow(:,:,3))));
else
set(STexts.hVal(i), 'String', sprintf('%s', fPrintNumber(dVal)));
end
else
if i == iAxisInd, set(STexts.hStatus, 'String', ''); end
set(STexts.hVal(i), 'String', '');
end
end
% -------------------------------------------------------------
else
% -------------------------------------------------------------
% Cursor is not over a panel -> Check if tooltip has to be shown
iCursorPos = get(hF, 'CurrentPoint');
iInd = 0;
for i = 1:length(SAxes.hIcons);
dPos = get(SAxes.hIcons(i), 'Position');
dParentPos = get(get(SAxes.hIcons(i), 'Parent'), 'Position');
dPos(1:2) = dPos(1:2) + dParentPos(1:2);
if ((iCursorPos(1) >= dPos(1)) && (iCursorPos(1) < dPos(1) + dPos(3)) && ...
(iCursorPos(2) >= dPos(2)) && (iCursorPos(2) < dPos(2) + dPos(4)))
iInd = i;
end
end
if iInd
sText = SIcons(iInd).Tooltip;
sAccelerator = SIcons(iInd).Accelerator;
if ~isempty(SIcons(iInd).Modifier), sAccelerator = sprintf('%s+%s', SIcons(iInd).Modifier, SIcons(iInd).Accelerator); end
if ~isempty(SIcons(iInd).Accelerator), sText = sprintf('%s [%s]', sText, sAccelerator); end
set(STexts.hStatus, 'String', sText);
else
set(STexts.hStatus, 'String', '');
end
% -------------------------------------------------------------
end
drawnow expose
end
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * END NESTED FUNCTION fWindowMouseHoverFcn
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * NESTED FUNCTION fWindowButtonDownFcn (nested in imagine)
% * *
% * * Figure callback
% * *
% * * Starting callback for mouse button actions.
% * *
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
function fWindowButtonDownFcn(hObject, eventdata)
iAxisInd = fGetPanel();
if ~iAxisInd, return, end % Exit if event didn't occurr in a panel
% -----------------------------------------------------------------
% Save starting parameters
dPos = get(SAxes.hImg(iAxisInd), 'CurrentPoint');
SMouse.iStartAxis = iAxisInd;
SMouse.iStartPos = get(hObject, 'CurrentPoint');
SMouse.dAxesStartPos = [dPos(1, 1), dPos(1, 2)];
% -----------------------------------------------------------------
% -----------------------------------------------------------------
% Backup the display settings of all data
SMouse.dDrawCenter = reshape([SData.dDrawCenter], [2, length(SData)]);
SMouse.dZoomFactor = [SData.dZoomFactor];
SMouse.dWindowCenter = [SData.dWindowCenter];
SMouse.dWindowWidth = [SData.dWindowWidth];
% -----------------------------------------------------------------
% -----------------------------------------------------------------
% Delete existing line objects, clear masks
if isfield(SLines, 'hEval')
try delete(SLines.hEval); end %#ok<TRYNC>
SLines = rmfield(SLines, 'hEval');
end
switch SState.sTool
case {'line', 'roi', 'lw', 'rg', 'ic'}
for i = 1:length(SData), SData(i).lMask = []; end
fFillPanels;
end
% -----------------------------------------------------------------
% -----------------------------------------------------------------
% Activate the callbacks for drag operations
set(hObject, 'WindowButtonUpFcn', @fWindowButtonUpFcn);
set(hObject, 'WindowButtonMotionFcn', @fWindowMouseMoveFcn);
% -----------------------------------------------------------------
drawnow expose
end
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * END NESTED FUNCTION fWindowButtonDownFcn
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * NESTED FUNCTION fWindowMouseMoveFcn (nested in imagine)
% * *
% * * Figure callback
% * *
% * * Callback for mouse movement while button is pressed.
% * *
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
function fWindowMouseMoveFcn(hObject, eventdata)
iAxesInd = fGetPanel();
% -----------------------------------------------------------------