%
%
%  Object Manager Function for Imaris
%
%  Copyright Bitplane AG 2006
%
%
%  Installation:
%
%  - Copy this file into the XTensions folder in the Imaris installation directory
%  - You will find this function in the Image Processing menu
%
%    <CustomTools>
%      <Menu>
%        <Item name="Open Object Manager" icon="Matlab" tooltip="Open object manager.">
%          <Command>Matlab::BPObjectManager(%i)</Command>
%        </Item>
%      </Menu>
%     <SurpassToolbar>
%        <Item name="Object Manager" icon="Matlab" tooltip="Open object manager.">
%          <Command>Matlab::BPObjectManager(%i)</Command>
%        </Item>
%     </SurpassToolbar>
%    </CustomTools>
% 
%
%  Description:
%   
%   Save/load/clear single imaris objects in .mat files.
%   Apply to Spots, Surface, Track, Filament and Groups.
%   Groups are saved with all their content.
%   Only first-level objects (mSurpassScene direct childs) can be saved.
%
%

function BPObjectManager(aImarisApplicationID)

global vImarisApplication vEditFileName;

% button callbacks
if aImarisApplicationID==-1
    clear global vImarisApplication vEditFileName;
    return;
elseif isa(aImarisApplicationID, 'numeric') && aImarisApplicationID==-5;
    Browse;
    return;
elseif isa(aImarisApplicationID, 'numeric') && aImarisApplicationID<-1;
    Execute(-aImarisApplicationID-1);
    return;
end

% connect to Imaris Com interface
if ~isa(aImarisApplicationID, 'COM.Imaris_Application')
  vImarisServer = actxserver('ImarisServer.Server');
  vImarisApplication = vImarisServer.GetObject(aImarisApplicationID);
else
  vImarisApplication = aImarisApplicationID;
end

% create the window
uicontrol('Style', 'text', 'String', 'Imaris Object Manager', ...
    'FontName', 'Times New Roman', 'FontSize', 10, ...
    'Position', [10,70,170,20], 'DeleteFcn', 'BPObjectManager(-1)');
uicontrol('Style', 'pushbutton', 'String', 'Browse...', ...
    'Position', [210,70,80,20], 'Callback', 'BPObjectManager(-5)');
uicontrol('Style', 'text', 'String', 'File Name:', ...
    'FontName', 'Times New Roman', 'FontSize', 10, ...
    'Position', [10,50,70,20]);
vEditFileName = uicontrol('Style', 'edit', 'String', 'ImarisObjects.mat', ...
    'FontName', 'Times New Roman', 'FontSize', 10, ...
    'Position', [80,50,210,20]);

uicontrol('Style', 'pushbutton', 'String', 'Save', ...
    'Position', [10,10,80,30], 'Callback', 'BPObjectManager(-2)');
uicontrol('Style', 'pushbutton', 'String', 'Load', ...
    'Position', [110,10,80,30], 'Callback', 'BPObjectManager(-3)');
uicontrol('Style', 'pushbutton', 'String', 'Clear', ...
    'Position', [210,10,80,30], 'Callback', 'BPObjectManager(-4)');

vWindow = get(vEditFileName, 'Parent');
vWindowPosition = get(vWindow, 'Position');
vWindowPosition(3:4) = [300, 100];
set(vWindow, 'Position', vWindowPosition);


%----------------------------------------------%

function Browse()

global vEditFileName;

vFileName = get(vEditFileName,'String');
[vFileName, vPathName] = uigetfile({'*.mat','MAT-files (*.mat)'}, ...
    'Select the file', vFileName);
if ~isequal(vFileName,0)
    set(vEditFileName,'String',fullfile(vPathName,vFileName));
end


%----------------------------------------------%

function Execute(aOperation, aParent, aParentName)
% aOperation = 1 save, 2 load, 3 clear

global vImarisApplication vEditFileName;

vStringOperations = {'save', 'load', 'clear'};
vStringTypes = {'Spots', 'Surface', 'Track', 'Filament', 'Group'};
vFileName = get(vEditFileName,'String');
vFactory = vImarisApplication.mFactory;
vDataSet = vImarisApplication.mDataSet;

if nargin==1
    vParent = vImarisApplication.mSurpassScene;
    vParentName = '';
else 
    vParent = aParent;
    vParentName = aParentName;
end

vObjectNameString = [vParentName,'vObjectsName'];
vObjectTypeString = [vParentName,'vObjectsType'];

vObjectsName = {};
vObjectsType = [];
vObjectsIndex = [];
vNumberOfObjects = 0;

if aOperation==1
    % search the scene objects - Spots, Surface, Track and Filament
    for vChildIndex = 1:vParent.GetNumberOfChildren
        vDataItem = vParent.GetChild(vChildIndex - 1);
        vFound = false;
        if vFactory.IsSpots(vDataItem)
            vObjectsType(vNumberOfObjects+1) = 1;
            vFound = true;
        elseif vFactory.IsSurface(vDataItem)
            vObjectsType(vNumberOfObjects+1) = 2;
            vFound = true;
        elseif vFactory.IsTrack(vDataItem)
            vObjectsType(vNumberOfObjects+1) = 3;
            vFound = true;
        elseif vFactory.IsFilament(vDataItem)
            vObjectsType(vNumberOfObjects+1) = 4;
            vFound = true;
        elseif vFactory.IsDataContainer(vDataItem)
            vObjectsType(vNumberOfObjects+1) = 5;
            vFound = true;
        end
        
        if vFound
            vNumberOfObjects = vNumberOfObjects + 1;
            vObjectsName(vNumberOfObjects) = cellstr(vDataItem.mName);
            vObjectsIndex(vNumberOfObjects) = vChildIndex;
        end
    end
else
    % load the list of the saved objects
    if exist(vFileName, 'file')
        load(vFileName,vObjectNameString,vObjectTypeString);
        vObjectsName = eval(vObjectNameString);
        vObjectsType = eval(vObjectTypeString);
        
        vNumberOfObjects = length(vObjectsName);
    else
        vNumberOfObjects = 0;
    end
end

if vNumberOfObjects==0
    if nargin==1
        msgbox(['There is no object to ', char(vStringOperations(aOperation)), '!']);
    end
    return;
end


vObjectsCaption = vObjectsName;

for vObject = 1:vNumberOfObjects
    % Name [Type]
    vObjectsCaption(vObject) = {[char(vObjectsName(vObject)), ' [', ...
        char(vStringTypes(vObjectsType(vObject))), ']']};
end

if nargin==1
    [vObjectList, vOk] = listdlg('ListString', vObjectsCaption, ...
                           'SelectionMode','single',...
                           'ListSize',[250 150],...
                           'Name','Imaris Object Manager',...
                           'PromptString',{['Please select the object to ', ...
                           char(vStringOperations(aOperation)), ':']});
    if vOk<1, return; end;
    
else
    vObjectList = 1:vNumberOfObjects;
end

vObjectsName_ = vObjectsName;
vObjectsType_ = vObjectsType;

for vSelectedObject = vObjectList

    vName = char(vObjectsName_(vSelectedObject));
    vType = vObjectsType_(vSelectedObject);

    % remove invalid characters
    vName_ = vName; 
    for vLetter = 1:length(vName)
        vChar = vName(vLetter);
        if (vChar<'0' || vChar>'9') && (vChar<'a' || vChar>'z') && (vChar<'A' || vChar>'Z')
            vName_(vLetter) = '_';
        end
    end

    % names (that should be unique) of the variables in the file.mat
    vPrefix = [vParentName,'v',vName_,'_','0'+vType,'_'];
    vNameColorVisible = [vPrefix,'ColorVisible'];
    vNamePosition = [vPrefix,'Position'];
    vNameTime = [vPrefix,'Time'];
    vNameRadius = [vPrefix,'Radius'];
    vNameNormals = [vPrefix,'Normals'];
    vNameTriangles = [vPrefix,'Triangles'];
    vNameVertices = [vPrefix,'Vertices'];
    vNameEdges = [vPrefix,'Edges'];


    if aOperation==1 % save
        vObject = vParent.GetChild(vObjectsIndex(vSelectedObject) - 1);

        if exist(vFileName, 'file')
            load(vFileName, vObjectNameString, vObjectTypeString);
            vObjectsName = eval(vObjectNameString);
            vObjectsType = eval(vObjectTypeString);

            % if the variable is already saved, their values are overwritten
            % but no new object is added
            vFound = false;
            vNumberOfObjects = length(vObjectsName);
            for vIndex = 1:vNumberOfObjects
                if strcmp(vName,char(vObjectsName(vIndex))) && vType==vObjectsType(vIndex)
                    vFound = true;
                    break;
                end
            end
            if vFound
                vAnswer = questdlg(['Overwrite ',char(vObjectsCaption(vSelectedObject)),'?'], ...
                    'Imaris Object Manager', 'Yes', 'No', 'Yes');
                if ~strcmp(vAnswer,'Yes')
                    return;
                elseif vType==5
                    % clear all the children of the group
                    Execute(3, vObject, vPrefix);
                end
            else
                vObjectsName(vNumberOfObjects+1) = {vName};
                vObjectsType(vNumberOfObjects+1) = vType;
            end
            eval([vObjectNameString,' = vObjectsName;']);
            eval([vObjectTypeString,' = vObjectsType;']);
            save(vFileName, vObjectNameString, vObjectTypeString, '-append');
        else
            vObjectsName = {vName};
            vObjectsType = vType;
            save(vFileName, 'vObjectsName', 'vObjectsType');   
        end

        [vR, vG, vB, vA] = vObject.GetColor;
        eval([vNameColorVisible, ' = [vR, vG, vB, vA, vObject.mVisible];']);
        save(vFileName, vNameColorVisible, '-append');

        if vType==1 % spots
            eval(['[',vNamePosition,',',vNameTime,',',vNameRadius,'] = vObject.Get;']);
            save(vFileName, vNamePosition, vNameRadius, '-append');
        elseif vType==2 % surface
            eval([vNameVertices,' = vObject.GetVertices;']);
            eval([vNameTriangles,' = vObject.GetTriangles;']);
            eval([vNameNormals,' = vObject.GetNormals;']);
            eval([vNameTime,' = vObject.GetTimeIndex;']);
            save(vFileName, vNameVertices, vNameTriangles, vNameNormals, '-append');
        elseif vType==3 % track
            vSpots = vObject.GetSpots;
            eval([vNameEdges,' = vObject.GetEdges;']);
            eval(['[',vNamePosition,',',vNameTime,',',vNameRadius,'] = vSpots.Get;']);
            save(vFileName, vNameEdges, vNamePosition, vNameRadius, '-append');
        elseif vType==4 % filament
            eval(['[',vNamePosition,',',vNameRadius,',',vNameEdges,'] = vObject.Get;']);
            eval([vNameTime,' = vObject.mIndexT;']);
            save(vFileName, vNamePosition, vNameRadius, vNameEdges, '-append');
        elseif vType==5 % data container
            eval([vNameTime,' = 0;']);
            % save all the childrens  
            eval([vPrefix,'vObjectsName',' = {};']);
            eval([vPrefix,'vObjectsType',' = [];']);
            save(vFileName,[vPrefix,'vObjectsName'],'-append');
            save(vFileName,[vPrefix,'vObjectsType'],'-append');
            Execute(1, vObject, vPrefix)
        end

        % time is required for all oject types (please set dummy 0 if not available)
        save(vFileName, vNameTime, '-append');

    elseif aOperation==2 % load

        load(vFileName, vNameTime);
        vTime = max(eval(vNameTime))+1;
        if vTime>vDataSet.mSizeT
            vAnswer = questdlg(sprintf(['%s is composited by %i frames. ', ...
                'Resizing the DataSet could cause memory problems. Procede anyway?'], ...
                char(vObjectsCaption(vSelectedObject)),vTime), ...
                'Imaris Object Manager', 'Yes', 'No', 'Yes');
            if ~strcmp(vAnswer,'Yes')
                return;
            end

           vDataSet.mSizeT = vTime;
        end

        if vType==1 % spots
            load(vFileName, vNamePosition, vNameRadius);        
            vObject = vFactory.CreateSpots;
            eval(['vObject.Set(',vNamePosition,',',vNameTime,',',vNameRadius,');']);
        elseif vType==2 % surface
            load(vFileName, vNameVertices, vNameTriangles, vNameNormals);
            vObject = vFactory.CreateSurface;
            eval(['vObject.SetSurface(',vNameVertices,',',vNameTriangles,',', ...
                vNameNormals,',',vNameTime,');']);
        elseif vType==3 % track
            load(vFileName, vNameEdges, vNamePosition, vNameRadius);        
            vObject = vFactory.CreateTrack;
            vSpots = vFactory.CreateSpots;
            eval(['vSpots.Set(',vNamePosition,',',vNameTime,',',vNameRadius,');']);
            vObject.SetSpots(vSpots);
            eval(['vObject.SetEdges(',vNameEdges,');']);
        elseif vType==4 % filament
            load(vFileName, vNamePosition, vNameRadius, vNameEdges);
            vObject = vFactory.CreateFilament;
            eval(['vObject.Set(',vNamePosition,',',vNameRadius,',',vNameEdges,');']);    
            eval(['vObject.mIndexT = ', vNameTime,';']);
        elseif vType==5 % data container
            vObject = vFactory.CreateDataContainer;
            
            Execute(2, vObject, vPrefix);
        end

        load(vFileName, vNameColorVisible);
        eval(['vObject.SetColor(',vNameColorVisible,'(1),',vNameColorVisible,'(2),', ...
            vNameColorVisible,'(3),',vNameColorVisible,'(4));']);
        eval(['vObject.mVisible = ',vNameColorVisible,'(5);']);

        vObject.mName = vName;
        vParent.AddChild(vObject);

    else % clear

        % copy the data into a struct
        % deletes the original file
        % rebuild the right file

        if nargin==1
            vAnswer = questdlg(['Remove ',char(vObjectsCaption(vSelectedObject)),' from the memory?'], ...
                'Imaris Object Manager', 'Yes', 'No', 'Yes');
            if ~strcmp(vAnswer,'Yes')
                return;
            end
        end

        vFile = load(vFileName);
        vFields = fieldnames(vFile);

        if nargin==1
            % remove the name and the type from the lists
            vRemaining = [1:vSelectedObject-1,vSelectedObject+1:vNumberOfObjects];
            vObjectsName = vObjectsName(vRemaining);
            vObjectsType = vObjectsType(vRemaining);
        end

        save(vFileName, 'vObjectsName', 'vObjectsType');

        vNumberOfLetters = length(vPrefix);

        for vVariable = 1:length(vFields)
            vString = char(vFields(vVariable));
            if ~strcmp(vString,'vObjectsName') && ~strcmp(vString,'vObjectsType') && ...
                    (length(vString)<vNumberOfLetters || ...
                    ~strcmp(vPrefix,vString(1:vNumberOfLetters)))
                eval([vString,' = vFile.(vString);']);
                save(vFileName,vString,'-append');
                clear(vString);
            end
        end
    end
end