text:
function varargout = panel_protocols(varargin)
% PANEL_PROTOCOLS: Create 'Protocols' panel of the main Brainstorm window.
%
% USAGE:  bstPanel = panel_protocols('CreatePanel');
%                    panel_protocols('SetExplorationMode',  ExplorationMode)
%         nodeRoot = panel_protocols('GetRootNode')
%                    panel_protocols('UpdateTree')
%                    panel_protocols('UpdateNode',          'Subject', iSubjects)
%                    panel_protocols('UpdateNode',          'Study',   iStudies, isExpandTrials)
%                    panel_protocols('ReloadNode',          bstNode)
%                    panel_protocols('CollapseAncestor',    nodeType, bstNodes )
%                    panel_protocols('ExpandPath',          bstNode, isSelected )
%        nodeFound = panel_protocols('SelectNode',          nodeRoot, nodeType, iStudy, iFile )
%        nodeFound = panel_protocols('SelectNode',          nodeRoot, FileName )
%        nodeFound = panel_protocols('GetNode',             nodeType, iStudy, iFile )
%        nodeFound = panel_protocols('GetNode',             FileName )
%        nodeStudy = panel_protocols('GetStudyNode',        nodeRoot, iStudy)
%        nodeStudy = panel_protocols('SelectStudyNode',     nodeStudy )  % Select given 'study' tree node
%        nodeStudy = panel_protocols('SelectStudyNode',     iStudy )     % Find 'study' tree node with studyIndex = iStudy and select it
%                    panel_protocols('SelectSubject',       SubjectName) % Select and expand subject node
%                    panel_protocols('MarkUniqueNode',      bstNode)
%      OutputFiles = panel_protocols('TreeHeadModel',       bstNode)
%      OutputFiles = panel_protocols('TreeInverse',         bstNodes, Version)

% @=============================================================================
% This function is part of the Brainstorm software:
% https://neuroimage.usc.edu/brainstorm
%
% Copyright (c) University of Southern California & McGill University
% This software is distributed under the terms of the GNU General Public License
% as published by the Free Software Foundation. Further details on the GPLv3
% license can be found at http://www.gnu.org/copyleft/gpl.html.
%
% FOR RESEARCH PURPOSES ONLY. THE SOFTWARE IS PROVIDED "AS IS," AND THE
% UNIVERSITY OF SOUTHERN CALIFORNIA AND ITS COLLABORATORS DO NOT MAKE ANY
% WARRANTY, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO WARRANTIES OF
% MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE, NOR DO THEY ASSUME ANY
% LIABILITY OR RESPONSIBILITY FOR THE USE OF THIS SOFTWARE.
%
% For more information type "brainstorm license" at command prompt.
% =============================================================================@
%
% Authors: Francois Tadel, 2008-2022
%          Martin Cousineau, 2019

eval(macro_method);
end

%% ===== CREATE PANEL =====
function bstPanelNew = CreatePanel() %#ok<DEFNU>
    panelName = 'Protocols';

    % Get scaling factor
    InterfaceScaling = bst_get('InterfaceScaling');
    % Get standard font
    stdFont = bst_get('Font');

    % Creation of the exploration tree
    jTreeProtocols = java_create('org.brainstorm.tree.BstTree', 'F', InterfaceScaling / 100, stdFont.getSize(), stdFont.getFontName());
    jTreeProtocols.setEditable(1);
    jTreeProtocols.setToggleClickCount(3);
    jTreeProtocols.setBorder(javax.swing.BorderFactory.createEmptyBorder(5,5,5,0));
    jTreeProtocols.setLoading(1);
    jTreeProtocols.setRowHeight(round(20 * InterfaceScaling / 100));
    % Configure selection model
    jTreeSelModel = jTreeProtocols.getSelectionModel();
    jTreeSelModel.setSelectionMode(jTreeSelModel.DISCONTIGUOUS_TREE_SELECTION);
    % Enable drag'n'drop
    jTreeProtocols.setDragEnabled(1);
    jTreeDragHandler = java_create('org.brainstorm.dnd.TreeDragTransferHandler');
    jTreeProtocols.setTransferHandler(jTreeDragHandler);

    % Add tree callbacks
    java_setcb(jTreeProtocols, 'MouseClickedCallback',   @(h,ev)bst_call(@protocolTreeClicked_Callback, h, ev), ...
                               'KeyPressedCallback',     @(h,ev)bst_call(@protocolTreeKeyPressed_Callback, h, ev), ...
                               'TreeWillExpandCallback', @(h,ev)bst_call(@protocolTreeExpand_Callback, h, ev));
    java_setcb(jTreeProtocols.getCellEditor(), 'EditingStoppedCallback', @protocolTreeEditingStopped_Callback);
    java_setcb(jTreeSelModel, 'ValueChangedCallback', @protocolTreeSelectionChanged_Callback);
    java_setcb(jTreeProtocols.getModel(), 'TreeNodesChangedCallback', @protocolTreeDrop_Callback);

    % Add tree to a scroll panel
    jScrollPaneNew = java_create('javax.swing.JScrollPane', 'Ljava.awt.Component;', jTreeProtocols);
    jScrollPaneNew.setBorder(javax.swing.BorderFactory.createMatteBorder(1,1,0,1, java.awt.Color(.5,.5,.5)));

    % Tabs for searches
    jTabpaneSearch = java_create('javax.swing.JTabbedPane', 'II', javax.swing.JTabbedPane.TOP, javax.swing.JTabbedPane.WRAP_TAB_LAYOUT);
    jTabpaneSearch.setFont(bst_get('Font', 11));
    java_setcb(jTabpaneSearch, 'StateChangedCallback', @DatabaseTabChanged_Callback, ...
        'MouseClickedCallback', @DatabaseTabClicked_Callback);

    % Overall container to switch between tabs
    jContainer = gui_component('Panel');
    jContainer.add(jScrollPaneNew);

    % Export panel to Brainstorm environment
    % Create the BstPanel object that is returned by the function
    % => constructor BstPanel(jHandle, panelName, sControls)
    bstPanelNew = BstPanel(panelName, ...
                           jContainer, ...
                           struct('jTreeProtocols', jTreeProtocols, ...
                           'jContainer', jContainer, ...
                           'jScrollPaneNew', jScrollPaneNew, ...
                           'jTabpaneSearch', jTabpaneSearch));

%% =================================================================================
%  === LOCAL CALLBACKS  ============================================================
%  =================================================================================
    %% ===== TREE CLICK CALLBACK ======
    function protocolTreeClicked_Callback( hObject, mouseEvent, varargin )
        % Get the path that was clicked
        pathClicked = jTreeProtocols.getPathForLocation(mouseEvent.getPoint.getX(), mouseEvent.getPoint.getY());
        % Return directly if no node were selected
        if isempty(pathClicked)
            return
        end
        % Get the button that was pressed
        switch (mouseEvent.getButton())
            % === LEFT CLICK ===
            case mouseEvent.BUTTON1
                % === DOUBLE LEFT CLICK ===
                if (mouseEvent.getClickCount() == 2)
                    % Process double click
                    bst_call(@tree_callbacks, pathClicked.getLastPathComponent, 'doubleclick');
                else
                    % Process click
                    bst_call(@tree_callbacks, pathClicked.getLastPathComponent, 'click');
                end

            % === MIDDLE CLICK ===
            case mouseEvent.BUTTON2
                % Nothing to do

            % === RIGHT CLICK ===
            % If clicked node is selected, display popup for all the selected nodes
            % Else select clicked node and display popup only for it
            case mouseEvent.BUTTON3
                % If path is selected
                if jTreeProtocols.isPathSelected(pathClicked)
                    % Get the list of all the selected nodes
                    selectedPaths = jTreeProtocols.getSelectionPaths();
                    targetNodes = javaArray('org.brainstorm.tree.BstNode', length(selectedPaths));
                    for iPath = 1:length(selectedPaths)
                        targetNodes(iPath) = selectedPaths(iPath).getLastPathComponent();
                    end
                % Else : clicked node is not selected
                else
                    % Select the path that was clicked
                    jTreeProtocols.setSelectionPath(pathClicked);
                    targetNodes = pathClicked.getLastPathComponent;
                end
                % Set mouse cursor to WAIT
                jTreeProtocols.setCursor(java_create('java.awt.Cursor', 'I', java.awt.Cursor.WAIT_CURSOR));
                % Create popup
                jPopup = bst_call(@tree_callbacks, targetNodes, 'popup');
                % Display popup menu
                if ~isempty(jPopup)
                    jPopup.pack();
                    jPopup.show(jTreeProtocols, mouseEvent.getPoint.getX(), mouseEvent.getPoint.getY());
                end
                % Restore default mouse cursor
                jTreeProtocols.setCursor([]);
        end
    end

    %% ===== TREE EXPAND =====
    function protocolTreeExpand_Callback( hObject, event, varargin )
        % Nothing selection: exit
        if isempty(event) || isempty(event.getSource())
            return;
        end
        % Get selected node
        nodeExpand = event.getPath().getLastPathComponent();
        nodeType = char(nodeExpand(1).getType());
        % If this is a study node, node created yet: create it
        if ismember(nodeType, {'condition', 'rawcondition', 'studysubject', 'study', 'defaultstudy'}) && (nodeExpand.getStudyIndex() ~= 0)
            panel_protocols('CreateStudyNode', nodeExpand);
        end
    end

    %% ===== TREE KEY PRESSED =====
    function protocolTreeKeyPressed_Callback( hObject, event, varargin )
        % Ignore CTRL press
        if (event.getKeyCode() == event.VK_CONTROL)
            return
        end
        % Get the list of all the selected nodes
        selectedPaths = jTreeProtocols.getSelectionPaths();
        if isempty(selectedPaths)
            return
        end
        targetNodes = javaArray('org.brainstorm.tree.BstNode', length(selectedPaths));
        if isempty(targetNodes)
            return
        end
        for iPath = 1:length(selectedPaths)
            targetNodes(iPath) = selectedPaths(iPath).getLastPathComponent();
        end
        % Switch between actions
        switch (event.getKeyCode())
            % ENTER/SPACE = MOUSE DOUBLECLICK
            case {event.VK_ENTER, event.VK_SPACE}
                bst_call(@tree_callbacks, targetNodes(1), 'doubleclick');
            % DELETE/BACKSPACE : DELETE NODE CALLBACK
            case {event.VK_DELETE, event.VK_BACK_SPACE}
                if ismember(char(targetNodes(1).getType()), {'subjectdb', 'studydbsubj', 'studydbcond'})
                    % Cancel action
                elseif ~bst_get('ReadOnly')
                    % Replace the "Link to raw file" nodes with their
                    % parent, except for spike-sorted raw files
                    if strcmpi(char(targetNodes(1).getType()), 'rawdata') ...
                            && strcmpi(char(targetNodes(1).getParent().getType()), 'rawcondition') ...
                            && isempty(strfind(targetNodes(1).getFileName(), '_0ephys'))
                        for iNode = 1:length(targetNodes)
                            targetNodes(iNode) = targetNodes(iNode).getParent();
                        end
                    end
                    % Delete nodes
                    bst_call(@node_delete, targetNodes);
                end
            % F5 : REFRESH
            case event.VK_F5
                UpdateTree();
            % CTRL+C: COPY
            case event.VK_C
                if event.isControlDown() && ~bst_get('ReadOnly')
                    CopyNode(targetNodes, 0);
                end
            % CTRL+X: CUT
            case event.VK_X
                if event.isControlDown() && ~bst_get('ReadOnly')
                    CopyNode(targetNodes, 1);
                end
            % CTRL+V: PASTE
            case event.VK_V
                if event.isControlDown() && ~bst_get('ReadOnly')
                    PasteNode(targetNodes);
                end
        end
    end

    %% ===== TREE SELECTION CALLBACK =====
    function protocolTreeSelectionChanged_Callback(hObject, event)
        % Get selected paths
        selectedPaths = event.getSource.getSelectionPaths();
        nbNodes = length(selectedPaths);
        % If one node is selected: Remember it
        if nbNodes == 1
            UpdateSearchSelNode(selectedPaths(nbNodes).getLastPathComponent());
        end
        % If less than two nodes selected: nothing else to do
        if (nbNodes < 2)
            return
        end
        % If the last node added in the selection is not of the same type
        % or have not the same 'StudyIndex' field
        % than all the previous nodes : select only the new node
        nodeNew = selectedPaths(nbNodes).getLastPathComponent();
        resetSelection = 0;
        iNode = 1;
        while ~resetSelection && (iNode < nbNodes)
            nodePrevious = selectedPaths(iNode).getLastPathComponent();
            if ~strcmpi(getNodeType(nodeNew), getNodeType(nodePrevious))
                % Reset selection
                event.getSource.setSelectionPath(selectedPaths(nbNodes));
                resetSelection = 1;
            else
                iNode = iNode + 1;
            end
        end

        function t = getNodeType(bstNode)
            switch lower(char(bstNode.getType()))
                case {'cortex', 'scalp', 'innerskull', 'outerskull', 'other'}
                    t = 'surface';
                case {'results', 'link'}
                    t = 'results';
                otherwise
                    t = lower(char(bstNode.getType()));
            end
        end
    end

    %% ===== TREE CELL EDITION STOP CALLBACK =====
    function protocolTreeEditingStopped_Callback(hObject, ev)
        % Get node handle (old node value)
        bstNode = jTreeProtocols.getSelectionPath.getLastPathComponent();
        % Get new node value
        newComment = char(ev.getSource.getCellEditorValue());
        % If the Comment field changed => need to update the DataBase and the node
        % Node: Cannot rename nodes starting with '(' => Special nodes
        if ~isempty(newComment) && ~strcmp(bstNode.getComment(), newComment) && (newComment(1) ~= '(') && ~bst_get('ReadOnly')
            % Rename node
            bst_call(@node_rename, bstNode, newComment);
        end
    end

    %% ===== TREE DROP =====
    function protocolTreeDrop_Callback(hObject, ev)
        % Get Brainstorm GUI structure
        if isempty(ev.getChildIndices()) && ~bst_get('ReadOnly')
            isCut = 1;
            if CopyNode(jTreeDragHandler.getSrcNodes(), isCut)
                PasteNode(jTreeDragHandler.getDestNode());
            end
        end
    end

    %% ===== SELECT TAB =====
    function DatabaseTabChanged_Callback(varargin)
        bst_progress('start', 'Database explorer', 'Applying search...');
        % Update database tree
        UpdateTree(0);
        % Move scrollbar to the left
        hScrollbar = jScrollPaneNew.getHorizontalScrollBar();
        hScrollbar.setValue(0);
        % Update process box count
        panel_nodelist('UpdatePanel', [], 1);
        bst_progress('stop');
    end

    %% ===== CLICK TAB =====
    function DatabaseTabClicked_Callback(jTabbedPane, ev)
        import org.brainstorm.icon.*;
        % Process right click
        if (ev.getButton() == ev.BUTTON3) && ev.getSource().isEnabled()
            % Do not add menu to default "Database" tab
            iSearch = jTabbedPane.getSelectedIndex();
            if iSearch > 0
                % Create popup menu
                jPopup = java_create('javax.swing.JPopupMenu');
                % Menu "Edit search"
                gui_component('MenuItem', jPopup, [], 'Edit search', IconLoader.ICON_EDIT, [], @(h,ev)PromptSearch(iSearch));
                % Menu "Copy search"
                gui_component('MenuItem', jPopup, [], 'Copy to clipboard', IconLoader.ICON_COPY, [], @(h,ev)CopySearch_Callback(iSearch));
                % Menu "Close search"
                gui_component('MenuItem', jPopup, [], 'Close search', IconLoader.ICON_DELETE, [], @(h,ev)CloseDatabaseTab(iSearch));
                % Show popup menu
                jPopup.pack();
                jPopup.show(jTabbedPane, ev.getPoint.getX(), ev.getPoint.getY());
            end
        end
    end
end

%% =================================================================================
%  === TREE FUNCTIONS ==============================================================
%  =================================================================================
%% ===== TREE: SET EXPLORATION MODE =====
% USAGE:  panel_protocols('SetExplorationMode', 'Subjects')
%         panel_protocols('SetExplorationMode', 'StudiesSubj')
%         panel_protocols('SetExplorationMode', 'StudiesCond')
function SetExplorationMode(ExplorationMode) %#ok<DEFNU>
    % Check if display mode changed
    if strcmpi(ExplorationMode, bst_get('Layout', 'ExplorationMode'))
        return
    end
    % Get Brainstorm GUI structure
    ctrl = bst_get('BstControls');
    % Select display mode
    switch (ExplorationMode)
        case 'Subjects',    ctrl.jToolButtonSubject.setSelected(1);
        case 'StudiesSubj', ctrl.jToolButtonStudiesSubj.setSelected(1);
        case 'StudiesCond', ctrl.jToolButtonStudiesCond.setSelected(1);
    end
    % Empty the clipboard
    bst_set('Clipboard', []);
end

%% ===== TREE: GET ROOT NODE =====
function nodeRoot = GetRootNode()
    % Get tree handle
    ctrl = bst_get('PanelControls', 'protocols');
    if isempty(ctrl) || isempty(ctrl.jTreeProtocols)
        nodeRoot = [];
        return;
    end
    % Get root node
    treeModel = ctrl.jTreeProtocols.getModel();
    nodeRoot = treeModel.getRoot();
end

%% ===== TREE: REPAINT =====
function RepaintTree()
    % Get tree handle
    ctrl = bst_get('PanelControls', 'protocols');
    if isempty(ctrl) || isempty(ctrl.jTreeProtocols)
        return;
    end
    % Repaint
    ctrl.jTreeProtocols.repaint();
end

%% ===== TREE: UPDATE =====
% USAGE: panel_protocols('UpdateTree')
function UpdateTree(resetNodes)
    % Parse inputs
    if nargin < 1
        resetNodes = 1;
    end

    % Get tree handle
    ctrl = bst_get('PanelControls', 'protocols');
    if isempty(ctrl) || isempty(ctrl.jTreeProtocols)
        return;
    end
    % Set tree as loading (remove all nodes and add a "Loading..." node)
    ctrl.jTreeProtocols.setLoading(1);
    % Get selected search tab
    iSearch = GetSelectedSearch();
    % Get root node
    nodeRoot = ctrl.jTreeProtocols.getModel.getRoot();
    % Reset existing nodes if required
    if resetNodes
        ResetSearchNodes();
    end
    % Switch according to the mode button that is checked
    explorationMode = bst_get('Layout', 'ExplorationMode');
    % Try to load the tree
    [dbNode, selNode, numNodes] = GetSearchNodes(iSearch, explorationMode);
    % Fill the tree if empty
    if isempty(dbNode)
        switch explorationMode
            case 'Subjects',     [selNode, dbNode, numNodes] = node_create_db_subjects(nodeRoot, iSearch);
            case 'StudiesSubj',  [selNode, dbNode, numNodes] = node_create_db_studies(nodeRoot, 'subject', iSearch);
            case 'StudiesCond',  [selNode, dbNode, numNodes] = node_create_db_studies(nodeRoot, 'condition', iSearch);
        end
        % Save node for quick tab changes
        SaveSearchNodes(iSearch, explorationMode, dbNode, selNode, numNodes);
    else
        nodeRoot.add(dbNode);
    end

    % When switching between exploration modes: Try to keep the same node selection
    prevExplorationMode = bst_get('Layout', 'PreviousExplorationMode');
    if ~isempty(selNode) && ~isempty(prevExplorationMode) && ~isequal(prevExplorationMode, explorationMode)
        [prevDbNode, prevSelNode] = GetSearchNodes(iSearch, prevExplorationMode);
        % If there was a previous node selection
        if ~isempty(prevSelNode)
            newSelNode = [];
            % Between functional views: keep the same file selected
            if ismember(prevExplorationMode, {'StudiesSubj', 'StudiesCond'}) && ismember(explorationMode, {'StudiesSubj', 'StudiesCond'})
                prevFileName = char(prevSelNode.getFileName());
                if ~isempty(prevFileName) && (length(prevFileName) > 4)
                    if isequal(prevFileName(end-3:end), '.mat') && ~strcmpi(char(prevSelNode.getType()), 'studysubject')
                        newSelNode = GetNode(dbNode, prevFileName);
                    else
                        iStudyOld = prevSelNode.getStudyIndex();
                        if iStudyOld > 0
                            newSelNode = GetStudyNode(dbNode, iStudyOld);
                        end
                    end
                end
            % From functional view to anatomy view: Keeps the same subject
            elseif ismember(prevExplorationMode, {'StudiesSubj', 'StudiesCond'}) && isequal(explorationMode, 'Subjects')
                % Get old subject index
                iStudyOld = prevSelNode.getStudyIndex();
                if (iStudyOld >= 1)
                    sStudyOld = bst_get('Study', iStudyOld);
                    if ~isempty(sStudyOld)
                        [sSubjectOld, iSubjectOld] = bst_get('Subject', sStudyOld.BrainStormSubject);
                        if ~isempty(sSubjectOld)
                            if sSubjectOld.UseDefaultAnat
                                iSubjectOld = 0;
                            end
                            % Get new subject index
                            iSubjectNew = selNode.getStudyIndex();
                            % If the subject changed: select the parent node for the new subject
                            if ~isequal(iSubjectNew, iSubjectOld)
                                newSelNode = dbNode.findChild('subject', iSubjectOld, -1, 0);
                            end
                        end
                    end
                end
            % From anatomy view to functional view: Keeps the same subject
            elseif isequal(prevExplorationMode, 'Subjects') && ismember(explorationMode, {'StudiesSubj', 'StudiesCond'})
                % Get old subject index
                iSubjectOld = prevSelNode.getStudyIndex();
                % If default anatomy is selected: nothing can be done
                if (iSubjectOld >= 1)
                    % Get new subject index
                    iStudyNew = selNode.getStudyIndex();
                    sStudyNew = bst_get('Study', iStudyNew);
                    if ~isempty(sStudyNew)
                        [sSubjectNew, iSubjectNew] = bst_get('Subject', sStudyNew.BrainStormSubject);
                        % If the subject changed: Select the parent node for the new subject
                        if ~isequal(iSubjectNew, iSubjectOld)
                            if isequal(explorationMode, 'StudiesSubj')
                                newSelNode = dbNode.findChild('studysubject', -1, iSubjectOld, 0);
                            elseif isequal(explorationMode, 'StudiesCond')
                                newSelNode = dbNode.findChild('studysubject', -1, iSubjectOld, 1);
                            end
                        end
                    end
                end
            end
            % Updated selected node
            if ~isempty(newSelNode)
                selNode = newSelNode;
                UpdateSearchSelNode(newSelNode, iSearch, explorationMode);
            end
        end
    end

    % Remove "Loading..." node, validate changes and redraw tree
    ctrl.jTreeProtocols.setLoading(0);
    drawnow;
    % Expand whole database if this is a search and we do not have too
    % many elements
    if iSearch > 0 && numNodes < 500
        ExpandAll(1);
    % If a default node is defined : select and expand it
    elseif ~isempty(selNode)
        % Expand default node
        ExpandPath(selNode, 1);
        % If default node is a study node
        if ismember(char(selNode.getType()), {'study', 'studysubject', 'condition', 'rawcondition'})
            % Select study node
            SelectStudyNode(selNode);
        end
    end

end

% Gets the ID of the search currently active (or 0 if no search active)
function iSearch = GetSelectedSearch()
    iSearch = 0;
    % Get tree handle
    ctrl = bst_get('PanelControls', 'protocols');
    if isempty(ctrl) || isempty(ctrl.jTreeProtocols)
        return;
    end
    % Get selected search tab
    iSearch = ctrl.jTabpaneSearch.getSelectedIndex();
    if isempty(iSearch) || iSearch < 0
        iSearch = 0;
    end
end

%% =================================================================================
%  === NODES FUNCTIONS =============================================================
%  =================================================================================
%% ===== NODE: CREATE STUDY NODE =====
function CreateStudyNode(nodeStudy) %#ok<DEFNU>
    % If node is already generated: return
    if isempty(nodeStudy.getUserObject())
        return;
    end
    % Remove existing nodes
    nodeStudy.removeAllChildren();
    % Get study and subject
    iStudy = nodeStudy.getStudyIndex();
    sStudy = bst_get('Study', iStudy);
    if isempty(sStudy)
        return;
    end
    % Get tree handle
    ctrl = bst_get('PanelControls', 'protocols');
    if isempty(ctrl) || isempty(ctrl.jTreeProtocols)
        return;
    end
    % Get subject
    sSubject = bst_get('Subject', sStudy.BrainStormSubject);
    % Get selected search tab
    iSearch = GetSelectedSearch();
    % Create node sub-tree
    UseDefaultChannel = ~isempty(sSubject) && (sSubject.UseDefaultChannel ~= 0);
    isExpandTrials = 1;
    node_create_study(nodeStudy, [], sStudy, iStudy, isExpandTrials, UseDefaultChannel, iSearch);
    % Mark as updated
    nodeStudy.setUserObject([]);
    ctrl.jTreeProtocols.getModel.reload(nodeStudy);
end

%% ===== NODE: UPDATE =====
% Update a set of tree nodes.
% USAGE:  panel_protocols('UpdateNode', 'Subject', iSubjects)
%         panel_protocols('UpdateNode', 'Study',   iStudies)
%         panel_protocols('UpdateNode', 'Study',   iStudies, isExpandTrials)
function UpdateNode(category, indices, isExpandTrials)
    % Parse inputs
    if (nargin < 2) || ~ischar(category) || ~isnumeric(indices) || isempty(indices)
        error('Invalid call to UpdateNode.');
    end
    if (nargin < 3) || isempty(isExpandTrials)
        isExpandTrials = 1;
    end
    % Get tree handle
    ctrl = bst_get('PanelControls', 'protocols');
    if isempty(ctrl) || isempty(ctrl.jTreeProtocols)
        return;
    end
    % Reset searches (otherwise the new nodes are added to one search tab only)
    ResetSearchNodes();
    % Get root of the exploration tree
    treeModel   = ctrl.jTreeProtocols.getModel();
    nodeRootTmp = treeModel.getRoot();
    if isempty(nodeRootTmp) || (nodeRootTmp.getChildCount() == 0)
        return
    end
    nodeRoot = nodeRootTmp.getChildAt(0);
    isUpdateWholeTree = 0;
    if isempty(nodeRoot)
        return
    end
    % Get selected search tab
    iSearch = GetSelectedSearch();
    % Switch between nodes type to update
    switch lower(category)
        case 'subject'
            % Get Protocol information
            ProtocolSubjects = bst_get('ProtocolSubjects');
            for i = 1:length(indices)
                iSubject = indices(i);
                % Exploration mode
                switch bst_get('Layout', 'ExplorationMode')
                    case 'Subjects'
                        % Find the target subject node
                        nodeSubject = nodeRoot.findChild('subject', iSubject, -1, 0);
                        % If subject node already exists : refresh it
                        if ~isempty(nodeSubject)
                            % Remove all children from this node
                            nodeSubject.removeAllChildren();
                            % Create new subject node (default node / normal node)
                            if (iSubject == 0)
                                node_create_subject(nodeSubject, nodeRoot, ProtocolSubjects.DefaultSubject, 0, 0);
                            else
                                node_create_subject(nodeSubject, nodeRoot, ProtocolSubjects.Subject(iSubject), iSubject, 0);
                            end
                            % Refresh node display
                            treeModel.reload(nodeSubject);
                        % Else: reload the whole tree
                        else
                            UpdateTree();
                        end
                    case {'StudiesSubj', 'StudiesCond'}
                        %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
                        %%%%%%%%%% INCORRECT : NEED TO PERFORM A SEARCH OF MULTIPLE NODES (ie. node.findChildren())
                        %%%%%%%%%% => THERE MIGHT BE MANY studysubject NODES FOR ONE GIVEN SUBJECT,
                        %%%%%%%%%%    (ONLY WHEN EXPLORATION MODE 'IS StudiesCond')
                        %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
                        % Find the target study/subject node
                        nodeStudy = nodeRoot.findChild('studysubject', -1, iSubject, 1);
                        % Node is found: update node
                        if ~isempty(nodeStudy)
                            % Update node name
                            nodeStudy.setComment(ProtocolSubjects.Subject(iSubject).Name);
                            % Refresh node display
                            treeModel.reload(nodeStudy);
                        % Node was not found: update whole tree
                        else
                            UpdateTree();
                        end
                end
            end

        case 'study'
            % For each study
            for i = 1:length(indices)
                iStudy = indices(i);
                % Get study
                sStudy  = bst_get('Study', iStudy);
                % Exploration mode
                switch bst_get('Layout', 'ExplorationMode')
                    case 'Subjects'
                        % NOTHING TO DO
                    case {'StudiesSubj', 'StudiesCond'}
                        % Find the target study node (possible types: studysubject, condition, study)
                        nodeStudy = GetStudyNode(nodeRoot, iStudy);
                        if ~isempty(nodeStudy)
                            % Do not update nodes are haven't been created yet ("Loading...")
                            if (nodeStudy.getChildCount() == 1) && strcmpi(char(nodeStudy.getChildAt(0).getType()), 'loading')
                                continue;
                            end
                            % Remove all children from this node
                            nodeStudy.removeAllChildren();
                            % Get associated subject
                            sSubject = bst_get('Subject', sStudy.BrainStormSubject);
                            % Create new study node (default node / normal node)
                            UseDefaultChannel = ~isempty(sSubject) && (sSubject.UseDefaultChannel ~= 0);
                            node_create_study(nodeStudy, [], sStudy, iStudy, isExpandTrials, UseDefaultChannel, iSearch);
                            % Refresh node display
                            ctrl.jTreeProtocols.getModel.reload(nodeStudy);
                            drawnow

                        % Node was not found: update whole tree
                        else
                            isUpdateWholeTree = 1;
                        end
                end
            end
    end
    if isUpdateWholeTree
        UpdateTree();
    end
end

%% ===== NODE: RELOAD =====
% Reload a tree node (parse again the underlying files).
% USAGE: panel_protocols('ReloadNode', bstNode)
function ReloadNode(bstNode) %#ok<DEFNU>
    nodeType = lower(char(bstNode.getType()));
    nodeFileName = char(bstNode.getFileName());
    iStudy = bstNode.getStudyIndex();
    iItem  = bstNode.getItemIndex();

    switch nodeType
        case {'subjectdb', 'studydbsubj', 'studydbcond'}
            bst_memory('UnloadAll', 'Forced');
            isError = db_reload_database('current');
            if isError
                gui_brainstorm('SetCurrentProtocol');
            end

        case 'subject'
            bst_memory('UnloadAll', 'Forced');
            % Reload current subject only
            db_reload_subjects(iStudy);

        case 'study'
            % Reload current study only
            if (iStudy ~= 0)
                db_reload_studies(iStudy);
            end

        case 'defaultstudy'
            bst_memory('UnloadAll', 'Forced');
            % Reload current study only
            db_reload_studies(iStudy);
            % Update whole tree display
            UpdateTree();

        case 'studysubject'
            % If StudySubject node is a Study node (datasets displayed in it)
            if (iStudy ~= 0)
                % Reload only study
                db_reload_studies(iStudy);
            % Else node is a directory node (only contains conditions)
            else
                % Reload subject
                db_reload_subjects(iItem);
                % Reload all conditions for the subject
                iNewStudies = db_reload_conditions(iItem);
            end

        case {'condition', 'rawcondition'}
            % If Condition node is a Study node (datasets displayed in it)
            if (iStudy ~= 0)
                % Reload only study
                db_reload_studies(iStudy);
            % Else node is a directory node (contains conditions/studysubject nodes)
            else
                % Reload all the studies that have this condition
                [sSubjects, iStudies] = bst_get('StudyWithCondition', nodeFileName);
                db_reload_studies(iStudies);
            end
    end
end

%% ===== NODE: COLLAPSE ANCESTOR =====
% Collapse parents of given nodes.
% USAGE:  panel_protocols('CollapseAncestor', nodeType, bstNodes )
%         panel_protocols('CollapseAncestor', nodeType )
function CollapseAncestor( nodeCategory, bstNodes ) %#ok<DEFNU>
    % Get tree handle
    ctrl = bst_get('PanelControls', 'protocols');
    if isempty(ctrl) || isempty(ctrl.jTreeProtocols)
        return;
    end
    % If nodes list is not specified : get selected nodes
    if (nargin < 2) || isempty(bstNodes)
        % Get nodes selected in tree
        selectedPaths = ctrl.jTreeProtocols.getSelectionPaths();
        if isempty(selectedPaths)
            return
        end
        bstNodes = javaArray('org.brainstorm.tree.BstNode', length(selectedPaths));
        for iPath = 1:length(selectedPaths)
            bstNodes(iPath) = selectedPaths(iPath).getLastPathComponent();
        end
    end
    if isempty(bstNodes)
        return
    end

    % For each node : find ancestor of the right type
    for i=1:length(bstNodes)
        % Find node
        switch lower(nodeCategory)
            case 'subject'
                nodeFound = [bstNodes(i).findAncestor('subject', -1, -1), ...
                             bstNodes(i).findAncestor('studysubject', -1, -1)];
            case 'study'
                nodeFound = [bstNodes(i).findAncestor('study', -1, -1), ...
                             bstNodes(i).findAncestor('condition', -1, -1), ...
                             bstNodes(i).findAncestor('rawcondition', -1, -1), ...
                             bstNodes(i).findAncestor('studysubject', -1, -1)];
            case 'data'
                nodeFound = bstNodes(i).findAncestor('data', -1, -1);
            case 'rawdata'
                nodeFound = bstNodes(i).findAncestor('rawdata', -1, -1);
            otherwise
                return
        end

        % Select node
        if ~isempty(nodeFound)
            % Get node path
            treeModel = ctrl.jTreeProtocols.getModel();
            nodes = treeModel.getPathToRoot(nodeFound(1));
            path_ = java_create('javax.swing.tree.TreePath', 'Ljava.lang.Object;', nodes);
            % Collapse tree
            ctrl.jTreeProtocols.collapsePath(path_);
        end
    end
end

%% ===== NODE: EXPAND PATH =====
% Expand a tree node, and optionally select it.
% USAGE:  panel_protocols('ExpandPath', bstNode, isSelected )
function ExpandPath(bstNode, isSelected)
    % Get tree handle
    ctrl = bst_get('PanelControls', 'protocols');
    if isempty(ctrl) || isempty(ctrl.jTreeProtocols)
        return;
    end
    % Get node path
    treeModel = ctrl.jTreeProtocols.getModel();
    nodes = treeModel.getPathToRoot(bstNode);
    % Create path
    jPath = java_create('javax.swing.tree.TreePath', 'Ljava.lang.Object;', nodes);
    % If node is not displayed: do nothing
    if (jPath.getPathCount() < 2)
        return
    end
    % Set path selected
    if isSelected
        ctrl.jTreeProtocols.setSelectionPath(jPath);
    end
    % Expand path
    ctrl.jTreeProtocols.expandPath(jPath);
    % Scroll to visible
    ctrl.jTreeProtocols.scrollPathToVisible(jPath);
end

%% ===== NODE: SELECT =====
% Find a node in the exploration tree and select it.
% USAGE:  nodeFound = panel_protocols('SelectNode', nodeRoot, nodeType, iStudy, iFile )
%         nodeFound = panel_protocols('SelectNode', nodeRoot, FileName )
% INPUT:
%    - nodeType   : {'subject', 'study', 'condition', 'data', 'channel', ...}, or '' to ignore node type from search
%    - iStudy : node's value of iStudy, or -1 to ignore this criteria
%    - iFile  : node's value of iFile, or -1 to ignore this criteria
function nodeFound = SelectNode(varargin)
    % Find node
    nodeFound = GetNode(varargin{:});
    % Select node
    if ~isempty(nodeFound)
        ExpandPath(nodeFound, 1);
    end
end

%% ===== NODE: SELECT STUDY =====
% Select and expand the input study in database tree.
% USAGE:   nodeStudy = panel_protocols('SelectStudyNode', nodeStudy ) % Select given 'study' tree node
%          nodeStudy = panel_protocols('SelectStudyNode', iStudy )    % Find 'study' tree node with studyIndex = iStudy and select it
function nodeStudy = SelectStudyNode( varargin )
    global TreeMarkedNode;
    % ===== PARSE INPUTS =====
    if isnumeric(varargin{1})
        iStudy = varargin{1};
        nodeStudy = SelectNode([], {'study','condition','rawcondition','studysubject'}, iStudy, -1);
    else
        nodeStudy = varargin{1};
    end
    if isempty(nodeStudy)
        return;
    else
        nodeStudy = nodeStudy(1);
    end
    % ===== UNMARK ALL OTHER NODES =====
    % Umark all marked nodes
    for i=1:length(TreeMarkedNode)
        if ishandle(TreeMarkedNode(i))
            TreeMarkedNode(i).setMarked(0);
        end
    end
    % ===== MARK SELECTED NODE =====
    % Mark current study node (parent node)
    nodeStudy.setMarked(1);
    TreeMarkedNode = nodeStudy;
    % Redraw tree
    RepaintTree();
    drawnow;
    % Update selected study in ProtocolInfo
    ProtocolInfo = bst_get('ProtocolInfo');
    if ~isempty(ProtocolInfo)
        ProtocolInfo.iStudy = nodeStudy.getStudyIndex();
        bst_set('ProtocolInfo', ProtocolInfo);
    end
end

%% ===== NODE: GET =====
% Find a node in the exploration tree.
% USAGE:  nodeFound = panel_protocols('GetNode', nodeRoot, nodeTypes, iStudy, iFile )
%         nodeFound = panel_protocols('GetNode', nodeRoot, FileName )
% INPUT:
%    - nodeType   : {'subject', 'study', 'condition', 'data', 'channel', ...}, or '' to ignore node type from search
%    - studyIndex : node's value of studyIndex, or -1 to ignore this criteria
%    - itemIndex  : node's value of itemIndex, or -1 to ignore this criteria
function nodeFound = GetNode( nodeRoot, nodeTypes, iStudy, iFile )
    nodeFound = [];
    % CALL: panel_protocols('GetNode', nodeRoot, FileName )
    if (nargin <= 2)
        % Find file in database
        FileName = nodeTypes;
        [sStudy, iStudy, iFile, nodeTypes] = bst_get('AnyFile', FileName);
        if isempty(sStudy)
            return
        end
        isExpand = 1;
    else
        isExpand = 0;
    end
    % Some files may have different types: make sure we are considering them all
    if ~iscell(nodeTypes)
        switch(nodeTypes)
            case 'data'
                nodeTypes = {'data','rawdata'};
            case 'results'
                nodeTypes = {'results','link','kernel'};
            case 'timefreq'
                nodeTypes = {'timefreq','spectrum','ptimefreq','pspectrum'};
            case 'ptimefreq'
                nodeTypes = {'ptimefreq','pspectrum'};
            case 'tess'
                nodeTypes = {'other'};
            otherwise
                nodeTypes = {nodeTypes};
        end
    end
    % Search node not specified, use tree root
    if isempty(nodeRoot)
        nodeRoot = GetRootNode();
        if isempty(nodeRoot)
            return;
        end
    end
    % Find node
    for i = 1:length(nodeTypes)
        nodeFound = nodeRoot.findChild(nodeTypes{i}, iStudy, iFile, 1);
        if ~isempty(nodeFound)
            return;
        end
    end
    % If nothing was found: expand the trials lists to look for the files
    if isExpand
        % Get study node
        nodeStudy = GetStudyNode(nodeRoot, iStudy);
        if isempty(nodeStudy)
            return;
        end
        % If this node is not rendered yet: render it
        if (nodeStudy.getChildCount() == 1) && strcmpi(char(nodeStudy.getChildAt(0).getType()), 'loading')
            CreateStudyNode(nodeStudy);
            % Find node again
            for i = 1:length(nodeTypes)
                nodeFound = nodeStudy.findChild(nodeTypes{i}, iStudy, iFile, 1);
                if ~isempty(nodeFound)
                    return;
                end
            end
        end
        % Look for trial lists in this study: expand them
        for i = 1:nodeStudy.getChildCount()
            % Get child node
            nodeChild = nodeStudy.getChildAt(i-1);
            % If child node is a trial list: expand it and look again for data file
            if ismember(char(nodeChild.getType()), {'datalist', 'matrixlist'})
                UpdateNode('Study', iStudy, 1);
                nodeFound = GetNode( nodeRoot, nodeTypes, iStudy, iFile );
                return;
            end
        end
    end
end

%% ===== NODE: GET STUDY NODE =====
function nodeStudy = GetStudyNode(nodeRoot, iStudy)
    nodeStudy = [nodeRoot.findChild('condition', iStudy, -1, 1), ...
                 nodeRoot.findChild('studysubject', iStudy, -1, 1), ...
                 nodeRoot.findChild('rawcondition', iStudy, -1, 1), ...
                 nodeRoot.findChild('study', iStudy, -1, 1), ...
                 nodeRoot.findChild('defaultstudy', iStudy, -1, 1)];
    if ~isempty(nodeStudy)
        nodeStudy = nodeStudy(1);
    end
end

%% ===== NODE: MARK UNIQUE =====
% Mark a given tree node, and unmark all the other nodes of the same type, in the same tree level.
% USAGE: panel_protocols('MarkUniqueNode', bstNode)
function MarkUniqueNode( bstNode ) %#ok<DEFNU>
    % Get parent node
    nodeParent = bstNode.getParent();
    % For each children node
    for iNode = 0:nodeParent.getChildCount()-1
        % If current node is target node : select it
        if (nodeParent.getChildAt(iNode) == bstNode)
            bstNode.setMarked(1);
        % If node type is target node type : unmark the node
        elseif nodeParent.getChildAt(iNode).getType.equalsIgnoreCase(bstNode.getType())
            nodeParent.getChildAt(iNode).setMarked(0);
        end
    end
end

%% ===== NODE: COPY =====
function isCopied = CopyNode( bstNodes, isCut )
    % Empty previous clipboard
    bst_set('Clipboard', []);
    isCopied = 0;
    % Get nodes types
    nodeType = {};
    for i = 1:length(bstNodes)
        nodeType{i} = lower(char(bstNodes(i).getType()));
    end
    % Cannot copy multiple unique nodes
    if ismember(nodeType{1}, {'channel', 'anatomy', 'volatlas', 'noisecov', 'ndatacov'}) && (length(bstNodes) > 1)
        bst_error(['Cannot copy multiple ' nodeType{1} ' nodes.'], 'Clipboard', 0);
        return;
    % Can only copy data files
    elseif ismember(nodeType{1}, {'defaultanat', 'subjectdb', 'studydbsubj', 'studydbcond', 'study', 'studysubject', 'defaultstudy', 'condition', 'rawcondition', 'subject', 'image'})
        bst_error(['Folders cannot be copied or moved.' 10 'To duplicate a subject or a condition, use the popup menu File > Duplicate.'], 'Clipboard', 0);
        return;
    % No links
    elseif any(ismember(nodeType, {'link', 'rawdata'}))
        bst_error('Links cannot be copied or moved.', 'Clipboard', 0);
        return;
%     % No stat
%     elseif any(ismember(nodeType, {'pdata', 'presults', 'ptimefreq', 'pspectrum', 'pmatrix'}))
%         bst_error('This type of file cannot be copied or moved.', 'Clipboard', 0);
%         return;
    % No filename
    elseif isempty(bstNodes(1).getFileName())
        bst_error('No file copied.', 'Clipboard', 0);
        return;
    % No kernel-based time-freq
    elseif any(ismember(nodeType, {'timefreq', 'spectrum'})) && ~isempty(strfind(char(bstNodes(1).getFileName()), '_KERNEL_'))
        bst_error('This type of file cannot be copied or moved.', 'Clipboard', 0);
        return;
    % Datalist/Matrixlist: copy all the child nodes
    elseif ismember(nodeType, {'datalist', 'matrixlist'})
        listNodes = bstNodes;
        bstNodes = repmat(bstNodes, 0);
        for iList = 1:length(listNodes)
            for iChild = 1:listNodes(iList).getChildCount()
                bstNodes = [bstNodes, listNodes(iList).getChildAt(iChild-1)];
            end
        end
    end
    % Copy nodes to the clipboard
    bst_set('Clipboard', bstNodes, isCut);
    isCopied = 1;
end

%% ===== NODE: PASTE =====
function destFile = PasteNode( targetNode )
    destFile = {};
    % Get copied nodes
    [srcNodes, isCut] = bst_get('Clipboard');
    if isempty(srcNodes)
        return
    end
    firstSrcType = lower(char(srcNodes(1).getType()));
    isAnatomy = ismember(firstSrcType, {'anatomy','volatlas','cortex','scalp','innerskull','outerskull','fibers','fem','other'});
    % Get all target studies/subjects
    iTarget = [];
    for i = 1:length(targetNode)
        iTarget(end+1) = targetNode(i).getStudyIndex();
    end
    % Can only copy towards one target
    iTarget = unique(iTarget);
    if (length(iTarget) > 1)
        bst_error('Cannot copy file towards multiple folders.', 'Clipboard', 0);
        return;
    end

    % Cannot copy anat files to a subject using default anatomy
    if isAnatomy
        sSubjectTarget = bst_get('Subject', iTarget);
        if (iTarget > 0) && sSubjectTarget.UseDefaultAnat
            bst_error('Destination subject uses the default anatomy.', 'Clipboard', 0);
            destFile = {};
            return;
        end
    % Non-anat files: requires a iStudy that is not zero
    elseif (iTarget == 0)
        destFile = {};
        return;
    else
        sStudyTarget = bst_get('Study', iTarget);
        [sSubjectTargetRaw, iSubjectTargetRaw] = bst_get('Subject', sStudyTarget.BrainStormSubject, 1);
    end
    % Channel/Headmodel/NoiseCov/Kernel: Make sure that target study is the right one
    if ismember(firstSrcType, {'channel', 'headmodel', 'noisecov', 'ndatacov', 'kernel'})
        % Get channel study for the target study
        [sChannel, iChanStudy] = bst_get('ChannelForStudy', iTarget);
        % If not the same: error
        if (iChanStudy ~= iTarget)
            bst_error('Invalid destination.', 'Clipboard', 0);
            destFile = {};
            return;
        end
    end

    % Progress bar
    if (length(srcNodes) > 1)
        bst_progress('start', 'Database explorer', 'Copying files...', 0, length(srcNodes));
    else
        bst_progress('start', 'Database explorer', 'Copying files...');
    end
    % Copy: Process file one by one
    for i = 1:length(srcNodes)
        % Get source filename
        srcFile = char(srcNodes(i).getFileName());
        srcType = lower(char(srcNodes(i).getType()));
        iSrcStudy = srcNodes(i).getStudyIndex();
        % Cannot copy (channel/noisecov/MRI) or move to the same folder
        if (isCut || ismember(srcType, {'channel', 'noisecov', 'ndatacov', 'anatomy', 'volatlas'})) && (iSrcStudy == iTarget)
            bst_error('Source and destination folders are the same.', 'Clipboard', 0);
            destFile = {};
            return;
        end
        % Copy file
        destFile{i} = CopyFile(iTarget, srcFile, srcType, iSrcStudy);
        if isempty(destFile{i})
            bst_progress('stop');
            return;
        end
        % Increment progress bar
        if (length(srcNodes) > 1)
            bst_progress('inc', 1);
        end
    end
    % Reloading the target study
    if isAnatomy
        db_reload_subjects(iTarget);
    else
        db_reload_studies(iTarget);
    end
    % If moving files instead of copying
    if isCut
        % Delete source file
        node_delete(srcNodes, 0);
        % Empty clipboard after moving
        bst_set('Clipboard', []);
    end
    % Select last copied file in the tree
    panel_protocols('SelectNode', [], destFile{end});
    % Close progress bar
    bst_progress('stop');
end

%% ===== COPY FILE =====
% USAGE:   destFile = CopyFile(iTarget, srcFile, srcType, iSrcStudy, sSubjectTargetRaw)
%          destFile = CopyFile(iTarget, srcFile)
function destFile = CopyFile(iTarget, srcFile, srcType, iSrcStudy, sSubjectTargetRaw)
    % File info is not passed in input
    if (nargin < 5)
        [sStudySrc, iSrcStudy, iSrcFile, srcType] = bst_get('AnyFile', srcFile);
        sStudyTarget = bst_get('Study', iTarget);
        [sSubjectTargetRaw, iSubjectTargetRaw] = bst_get('Subject', sStudyTarget.BrainStormSubject, 1);
    end
    isAnatomy = ismember(srcType, {'anatomy','volatlas','cortex','scalp','innerskull','outerskull','fibers','fem','other'});
    % Get source subject
    if ~isAnatomy
        sStudySrc   = bst_get('Study', iSrcStudy);
        [sSubjectSrcRaw, iSubjectSrcRaw] = bst_get('Subject', sStudySrc.BrainStormSubject, 1);
        % Check if the subject changes
        UseDefaultAnatSrc    = (sSubjectSrcRaw.UseDefaultAnat == 1)    || (iSubjectSrcRaw == 0);
        UseDefaultAnatTarget = (sSubjectTargetRaw.UseDefaultAnat == 1) || (iSubjectTargetRaw == 0);
        isSameSubjAnat = file_compare(sSubjectTargetRaw.FileName, sSubjectSrcRaw.FileName) || (UseDefaultAnatSrc && UseDefaultAnatTarget);
        % Check if the channel study changes
        UseDefaultChannelSrc    = (sSubjectSrcRaw.UseDefaultChannel == 2)    || (iSubjectSrcRaw == 0);
        UseDefaultChannelTarget = (sSubjectTargetRaw.UseDefaultChannel == 2) || (iSubjectTargetRaw == 0);
        isSameSubjChan = file_compare(sSubjectTargetRaw.FileName, sSubjectSrcRaw.FileName) || (UseDefaultChannelSrc && UseDefaultChannelTarget);
    else
        isSameSubjAnat = (iSrcStudy == iTarget);
        isSameSubjChan = (iSrcStudy == iTarget);
    end
    % Noise covariance: copy using db_set_noisecov
    if strcmpi(srcType, 'noisecov')
        destFile = db_set_noisecov(iSrcStudy, iTarget, 0);
        if ~isempty(destFile)
            destFile = destFile{1};
        end
        return;
    elseif strcmpi(srcType, 'ndatacov')
        destFile = db_set_noisecov(iSrcStudy, iTarget, 1);
        if ~isempty(destFile)
            destFile = destFile{1};
        end
        return;
    end
    % If reading a kernel file: Read full results, and save them again
    if strcmpi(srcType, 'results') && ~isempty(strfind(srcFile, '_KERNEL_'))
        src = in_bst_results(srcFile, 1);
        % Remove all the links (if not in the same study)
        if (iSrcStudy ~= iTarget)
            src.DataFile = '';
            if ~isSameSubjAnat
                src.SurfaceFile = '';
            end
            if ~isSameSubjChan
                src.HeadModelFile = '';
            end
        else
            src.DataFile = file_short(src.DataFile);
            if (src.DataFile(1) == '/')
                src.DataFile(1) = [];
            end
        end
    % Reading other files with references: remove references
    elseif ismember(srcType, {'results', 'headmodel', 'timefreq', 'spectrum', 'presults', 'ptimefreq', 'pspectrum', 'dipoles'})
        src = load(file_fullpath(srcFile));
        if (iSrcStudy ~= iTarget)
            if isfield(src, 'DataFile')
                src.DataFile = '';
            end
            if isfield(src, 'HeadModelFile') && ~isSameSubjChan
                src.HeadModelFile = '';
            end
            if isfield(src, 'SurfaceFile') && ~isSameSubjAnat
                src.SurfaceFile = '';
            end
        end
    else
        src = srcFile;
    end
    % Copy file
    destFile = db_add(iTarget, src, 0);
    if isempty(destFile)
        return
    end
    % If reading a surface file: ignore all the intermediate computations
    if ismember(srcType, {'cortex','scalp','innerskull','outerskull','other'})
        [tmpTessMat, TessFile] = in_tess_bst(destFile, 0);
        TessMat.Vertices = tmpTessMat.Vertices;
        TessMat.Faces    = tmpTessMat.Faces;
        TessMat.Comment  = tmpTessMat.Comment;
        TessMat.Atlas    = tmpTessMat.Atlas;
        TessMat.iAtlas   = tmpTessMat.iAtlas;
        if isfield(tmpTessMat, 'Reg')
            TessMat.Reg = tmpTessMat.Reg;
        end
        bst_save(TessFile, TessMat, 'v7');
    end
end

%% =================================================================================
%  === OTHER FUNCTIONS =============================================================
%  =================================================================================

%% ===== NODE: HEAD MODEL =====
% Call head modeler GUI for the given tree nodes.
% USAGE:  panel_protocols('TreeHeadModel', bstNode)
function OutputFiles = TreeHeadModel( bstNodes ) %#ok<DEFNU>
    OutputFiles = {};
    % Get selected channel studies
    iChanStudies = tree_channel_studies( bstNodes, 'NoIntra' );
    % Nothing to process: return
    if isempty(iChanStudies)
        bst_error('Missing channel information.', 'Compute head model', 0);
        return
    end
    % Get first study
    sStudy = bst_get('Study', iChanStudies(1));
    sSubject = bst_get('Subject', sStudy.BrainStormSubject);
    % DEFAULT ANAT: Check if the positions of the fiducials have been validated
    if ~isempty(sSubject.Anatomy)
        figure_mri('FiducialsValidation', sSubject.Anatomy(sSubject.iAnatomy).FileName);
    end
    % Check that the default cortex is not the high resolution one
    if ~isempty(sSubject.iCortex) && ~isempty(sSubject.Surface) && (sSubject.iCortex <= length(sSubject.Surface))
        nVertices = sscanf(sSubject.Surface(sSubject.iCortex).Comment, 'cortex_%dV');
        if (length(nVertices) == 1) && (nVertices > 100000) && ~java_dialog('confirm', sprintf([...
                    '<HTML>Warning: The selected cortex surface has <FONT COLOR="#FF0000">%d vertices</FONT>.\n' ...
                    'This resolution is very high and may cause memory issues in the source analysis.\n\n' ...
                    'To use a cortex surface with a lower resolution: Click "No", go to the anatomy view\n' ...
                    'and double-click on a surface with a lower resolution (eg. 15000V).\n\n' ...
                    'Proceed with the high-resolution cortex surface?'], nVertices), 'High-resolution cortex')
            return;
        end
    end
    % Call head modeler
    [OutputFiles, errMessage] = panel_headmodel('ComputeHeadModel', iChanStudies);
    % Error
    if isempty(OutputFiles) && ~isempty(errMessage)
        bst_error(errMessage, 'Compute head model', 0);
    elseif ~isempty(errMessage)
        java_dialog('warning', errMessage, 'Compute head model');
    end
end

%% ===== NODE: SOURCE GRID =====
% Just compute a source grid without the corresponding forward model.
% USAGE:  panel_protocols('TreeSourceGrid', bstNode)
function OutputFiles = TreeSourceGrid( bstNodes ) %#ok<DEFNU>
    % Get selected channel studies
    iChanStudies = tree_channel_studies( bstNodes, 'NoIntra' );
    iStudy = iChanStudies(1);
    % Get first study
    sStudy = bst_get('Study', iStudy);
    sSubject = bst_get('Subject', sStudy.BrainStormSubject);
    % DEFAULT ANAT: Check if the positions of the fiducials have been validated
    if ~isempty(sSubject.Anatomy)
        figure_mri('FiducialsValidation', sSubject.Anatomy(sSubject.iAnatomy).FileName);
    end
    % Call head modeler
    OutputFiles = panel_headmodel('GenerateSourceGrid', iStudy);
end

%% ===== NODE: INVERSE MODEL =====
function OutputFiles = TreeInverse(bstNodes, Version) %#ok<DEFNU>
    OutputFiles = {};
    % Get node type
    nodeType = lower(char(bstNodes(1).getType()));
    % Data file: gets "data file" dependence, else get channel studies
    if ismember(nodeType, {'rawdata', 'data'})
        [iStudies, iDatas] = tree_dependencies(bstNodes, 'data');
    else
        iStudies = tree_channel_studies( bstNodes, 'NoIntra' );
        iDatas = [];
    end
    % If no studies selected
    if isempty(iStudies)
        return;
    elseif isequal(iStudies, -10)
        bst_error('Error in file selection.', 'Compute sources', 0);
        return;
    end
    % Get studies structures
    sStudies = bst_get('Study', iStudies);
    % If all the studies have one and only one data file: switch to non-shared kernels
    if all(cellfun(@(c)isequal(length(c),1), {sStudies.Data}))
        % And if the files are not RAW
        sAllData = [sStudies.Data];
        if ~any(strcmpi({sAllData.DataType}, 'raw'))
            iDatas = ones(size(iStudies));
        end
    end
    % Call inverse function
    switch Version
        case '2009'
            [OutputFiles, errMessage] = process_inverse('Compute', iStudies, iDatas);
        case '2016'
            [OutputFiles, errMessage] = process_inverse_2016('Compute', iStudies, iDatas);
        case '2018'
            [OutputFiles, errMessage] = process_inverse_2018('Compute', iStudies, iDatas);
    end
    % Error
    if isempty(OutputFiles) && ~isempty(errMessage)
        bst_error(errMessage, 'Compute sources', 0);
    end
end

%% ===== SELECT SUBJECT =====
function SelectSubject(SubjectName) %#ok<DEFNU>
    % Check input subject name
    if ~ischar(SubjectName) || isempty(SubjectName)
        return;
    end
    % Get subject
    [sSubject, iSubject] = bst_get('Subject', SubjectName);
    if isempty(sSubject)
        return;
    end
    % Get exploration mode
    ExplorationMode = bst_get('Layout', 'ExplorationMode');
    % Select different nodes depending on the exploration mode
    switch (ExplorationMode)
        case 'Subjects'
            % Select first MRI
            if ~isempty(sSubject.Anatomy)
                SelectNode([], 'anatomy', iSubject, 1);
            else
                SelectNode([], 'subject', iSubject, -1);
            end
        case {'StudiesCond', 'StudiesSubj'}
            % Get all the studies for this subject
            [sStudies, iStudies] = bst_get('StudyWithSubject', sSubject.FileName);
            % Select first study
            if ~isempty(iStudies)
                SelectStudyNode(iStudies(1));
            else
                SelectNode([], 'studysubject', -1, iSubject);
            end
    end
end

%% ===== EXPAND/COLLAPSE ALL =====
function ExpandAll(isExpand) %#ok<DEFNU>
    % Get tree handle
    ctrl = bst_get('PanelControls', 'protocols');
    if isempty(ctrl) || isempty(ctrl.jTreeProtocols)
        return;
    end

    ExpandAllRecursive(isExpand, ctrl.jTreeProtocols, 1, ctrl.jTreeProtocols.getRowCount());
end
function ExpandAllRecursive(isExpand, tree, startingIndex, rowCount)
    for iRow = startingIndex:rowCount
        if isExpand
            tree.expandRow(iRow - 1);
        else
            tree.collapseRow(iRow - 1);
        end
    end

    if tree.getRowCount() ~= rowCount
        ExpandAllRecursive(isExpand, tree, rowCount, tree.getRowCount());
    end
end

%% ===== ADD DATABASE TAB =====
% Creates a search tab in the database tree
function AddDatabaseTab(tabName)
    import java.awt.GridBagConstraints;
    % Get tree handle
    ctrl = bst_get('PanelControls', 'protocols');
    if isempty(ctrl) || isempty(ctrl.jTreeProtocols)
        return;
    end

    % Add default Database tab if first tab
    if ctrl.jTabpaneSearch.getTabCount() == 0
        % Remove tab callback
        bakCallback = java_getcb(ctrl.jTabpaneSearch, 'StateChangedCallback');
        java_setcb(ctrl.jTabpaneSearch, 'StateChangedCallback', []);

        ctrl.jContainer.remove(ctrl.jScrollPaneNew);
        ctrl.jTabpaneSearch.addTab('Database', ctrl.jScrollPaneNew);
        ctrl.jContainer.add(ctrl.jTabpaneSearch);

        % Restore callback
        java_setcb(ctrl.jTabpaneSearch, 'StateChangedCallback', bakCallback);
    end

    % Create tab
    ctrl.jTabpaneSearch.addTab(tabName, []);
    index = ctrl.jTabpaneSearch.indexOfTab(tabName);
    jPanelTab = java_create('javax.swing.JPanel');
    jPanelTab.setLayout(java_create('java.awt.GridBagLayout'));
    % Make tabs transparent for better looking display, except on Linux
    % where it can cause weird behaviors on some environments
    if isempty(strfind(bst_get('OsType'), 'linux'))
        jPanelTab.setOpaque(0);
    end
    jLabel = gui_component('label', [], [], [tabName ' ']);
    jBtnClose = gui_component('button', [], [], ' x ');
    java_setcb(jBtnClose, 'ActionPerformedCallback', @(h,ev)CloseDatabaseTab(tabName));
    jBtnClose.setBorder([]);

    c = GridBagConstraints();
    c.gridx = 0;
    c.gridy = 0;
    c.weightx = 1;
    jPanelTab.add(jLabel, c);

    c.gridx = 1;
    c.weightx = 0;
    jPanelTab.add(jBtnClose, c);

    % Select new tab
    ctrl.jTabpaneSearch.setTabComponentAt(index, jPanelTab);
    index = ctrl.jTabpaneSearch.indexOfTab(tabName);
    ctrl.jTabpaneSearch.setSelectedIndex(index);
end

%% ===== CLOSE DATABASE TAB =====
% Closes the search tab of name or ID "tabName"
function CloseDatabaseTab(tabName)
    % Get tree handle
    ctrl = bst_get('PanelControls', 'protocols');
    if isempty(ctrl) || isempty(ctrl.jTreeProtocols)
        return;
    end

    % Parse inputs
    if isnumeric(tabName)
        index = tabName;
    else
        index = ctrl.jTabpaneSearch.indexOfTab(tabName);
    end
    if index == -1
        return
    end

    % Remove tab changed callback
    bakCallback = java_getcb(ctrl.jTabpaneSearch, 'StateChangedCallback');
    java_setcb(ctrl.jTabpaneSearch, 'StateChangedCallback', []);

    ctrl.jTabpaneSearch.removeTabAt(index);
    ActiveSearch('remove', index);
    CloseDefaultDbTab();

    % Restore callback and call it exactly once
    java_setcb(ctrl.jTabpaneSearch, 'StateChangedCallback', bakCallback);
    bakCallback();
end

% Iteratively closes all active database tabs
function CloseAllDatabaseTabs()
    % Get tree handle
    ctrl = bst_get('PanelControls', 'protocols');
    if isempty(ctrl) || isempty(ctrl.jTreeProtocols)
        return;
    end

    % Remove tab changed callback
    bakCallback = java_getcb(ctrl.jTabpaneSearch, 'StateChangedCallback');
    java_setcb(ctrl.jTabpaneSearch, 'StateChangedCallback', []);

    % Remove each tab one by one and release its Java objects
    while ctrl.jTabpaneSearch.getTabCount() > 1
        ctrl.jTabpaneSearch.removeTabAt(0);
        ActiveSearch('remove', 1);
    end

    % Close the default 'Database' tab since it's not needed without active
    % searches
    CloseDefaultDbTab();

    % Restore callback and call it exactly once
    java_setcb(ctrl.jTabpaneSearch, 'StateChangedCallback', bakCallback);
    bakCallback();
end

% Closes the 'Default' database tab, only if no search is active
function CloseDefaultDbTab()
    % Get tree handle
    ctrl = bst_get('PanelControls', 'protocols');
    if isempty(ctrl) || isempty(ctrl.jTreeProtocols)
        return;
    end

    % Do not close this default tab if searches are active
    if ctrl.jTabpaneSearch.getTabCount() ~= 1
        return;
    end

    ctrl.jContainer.remove(ctrl.jTabpaneSearch);
    ctrl.jTabpaneSearch.removeTabAt(0);
    ctrl.jContainer.add(ctrl.jScrollPaneNew);
end

% Prompts the user for a search query with the search panel
%
% Params:
%  - tabName: str, name of tab if we are modifying an existing one
%             Leave blank to create a new tab
%
% Returns: nothing
function PromptSearch(tabName)
    % Get tree handle
    ctrl = bst_get('PanelControls', 'protocols');
    if isempty(ctrl) || isempty(ctrl.jTreeProtocols)
        return;
    end

    % Parse inputs
    if nargin < 1 || isempty(tabName)
        iSearch = 0;
        searchRoot = [];
    else
        % Load active search
        if ~isnumeric(tabName)
            iSearch = ctrl.jTabpaneSearch.indexOfTab(tabName);
        else
            iSearch = tabName;
        end
        searchRoot = ActiveSearch('get', iSearch);
        % Make sure active search is compatible with the edit search GUI
        [res, errorMsg] = panel_search_database('SearchGUICompatible', searchRoot);
        if ~res
            java_dialog('error', ['Your search query cannot be edited using the GUI.' 10 errorMsg], 'Edit search');
            return;
        end
    end

    % Prompt user for search
    searchRoot = gui_show_dialog('Search Database', @panel_search_database, 0, [], searchRoot);
    if isempty(searchRoot)
        return;
    end

    % Apply search
    ApplySearch(searchRoot, iSearch);
end

function ApplySearch(searchRoot, iSearch)
    % Parse input
    if nargin < 2
        iSearch = 0;
    end

    % Get tree handle
    ctrl = bst_get('PanelControls', 'protocols');
    if isempty(ctrl) || isempty(ctrl.jTreeProtocols)
        return;
    end

    bst_progress('start', 'Database explorer', 'Applying search...');

    % Extract short and unique tab name
    [node, foundNot] = panel_search_database('GetFirstValueNode', searchRoot);
    if iscell(node.Value)
        shortName = node.Value{1};
    else
        shortName = node.Value;
    end
    % Add NOT operator prefix if applicable
    if foundNot
        shortName = ['NOT ' shortName];
    end
    shortName = shortName(1:min(length(shortName), 12));
    newTabName = shortName;
    id = 1;
    while ctrl.jTabpaneSearch.indexOfTab(newTabName) >= 0 ...
            && (iSearch == 0 || iSearch ~= ctrl.jTabpaneSearch.indexOfTab(newTabName))
        id = id + 1;
        newTabName = [shortName ' (' num2str(id) ')'];
    end

    % If this is a new tab, create it
    if iSearch == 0
        % Create tab
        AddDatabaseTab(newTabName);
        % Save to list of active searches
        ActiveSearch('add', newTabName, searchRoot);

    % If this is an existing tab, modify it
    else
        % Update list of active searches
        ActiveSearch('set', iSearch, searchRoot, newTabName);
        % Rename tab
        ctrl.jTabpaneSearch.setTitleAt(iSearch, newTabName);
        jPanelTab = ctrl.jTabpaneSearch.getTabComponentAt(iSearch);
        jLabel = jPanelTab.getComponent(0);
        jButton = jPanelTab.getComponent(1);
        jLabel.setText([newTabName ' '])
        java_setcb(jButton, 'ActionPerformedCallback', @(h,ev)CloseDatabaseTab(newTabName));
        % Update database
        UpdateTree(0);
        panel_nodelist('UpdatePanel', [], 1);
    end

    bst_progress('stop');
end

% Apply custom search
function ApplyCustomSearch(searchStr)
    % Try to convert to search structure
    try
        searchRoot = panel_search_database('StringToSearch', searchStr);
    catch e
        java_dialog('error', ['There is an error in your search query.' 10 e.message], 'Custom search');
        return;
    end
    % Apply converted search
    ApplySearch(searchRoot);
end

% Popup menu when 'Search' is clicked from the main Brainstorm GUI
function MainPopupMenu(jButton)
    global GlobalData;
    import org.brainstorm.icon.*;
    % Get active search
    iSearch = GetSelectedSearch();
    % Create popup menu
    jPopup = java_create('javax.swing.JPopupMenu');

    % New search
    gui_component('MenuItem', jPopup, [], 'New search', IconLoader.ICON_ZOOM, [], @(h,ev)PromptSearch());
    if iSearch > 0
        % Edit search
        gui_component('MenuItem', jPopup, [], 'Edit search', IconLoader.ICON_EDIT, [], @(h,ev)PromptSearch(iSearch));
    end
    jPopup.addSeparator();

    % === LOAD SEARCH ===
    % If some searches are defined
    if ~isempty(GlobalData.DataBase.Searches.All)
        jMenuLoad = gui_component('Menu', jPopup, [], 'Load', IconLoader.ICON_FOLDER_OPEN, [], []);
        % List all the searches
        for iSavedSearch = 1:length(GlobalData.DataBase.Searches.All)
            gui_component('MenuItem', jMenuLoad, [], GlobalData.DataBase.Searches.All(iSavedSearch).Name, IconLoader.ICON_ZOOM, [], @(h,ev)LoadSearch_Callback(iSavedSearch));
        end
    end

    % === SAVE SEARCH ===
    if iSearch > 0
        jMenuSave = gui_component('Menu', jPopup, [], 'Save', IconLoader.ICON_SAVE, [], []);
        % List all the searches
        for iSavedSearch = 1:length(GlobalData.DataBase.Searches.All)
            gui_component('MenuItem', jMenuSave, [], GlobalData.DataBase.Searches.All(iSavedSearch).Name, IconLoader.ICON_ZOOM, [], @(h,ev)SaveSearch_Callback(iSearch, iSavedSearch));
        end
        % Save new
        gui_component('MenuItem', jMenuSave, [], 'New...', IconLoader.ICON_SAVE, [], @(h,ev)SaveSearch_Callback(iSearch));
    end

    % === DELETE SEARCH ===
    % If some searches are defined
    if ~isempty(GlobalData.DataBase.Searches.All)
        jMenuDel = gui_component('Menu', jPopup, [], 'Delete', IconLoader.ICON_DELETE, [], []);
        % List all the searches
        for iSavedSearch = 1:length(GlobalData.DataBase.Searches.All)
            gui_component('MenuItem', jMenuDel, [], GlobalData.DataBase.Searches.All(iSavedSearch).Name, IconLoader.ICON_ZOOM, [], @(h,ev)DeleteSearch_Callback(iSavedSearch));
        end
    end

    if ~isempty(GlobalData.DataBase.Searches.All) || iSearch > 0
        jPopup.addSeparator();
    end

    % Copy to clipboard
    if iSearch > 0
        gui_component('MenuItem', jPopup, [], 'Copy to clipboard', IconLoader.ICON_COPY, [], @(h,ev)CopySearch_Callback(iSearch));
    end
    % Paste from clipboard
    gui_component('MenuItem', jPopup, [], 'Paste from clipboard', IconLoader.ICON_PASTE, [], @(h,ev)PasteSearch_Callback());
    % Type custom search
    gui_component('MenuItem', jPopup, [], 'Type search query', IconLoader.ICON_EDIT, [], @(h,ev)TypeSearch_Callback());
    % Generate pipeline
    if iSearch > 0
        gui_component('MenuItem', jPopup, [], 'Generate process call', IconLoader.ICON_CONDITION, [], @(h,ev)GenerateProcessCall_Callback(iSearch));
    end

    % Show popup menu
    jPopup.show(jButton, 0, jButton.getHeight());
end

%% Search menu callbacks
% Load search callback
function LoadSearch_Callback(iSearch)
    global GlobalData;
    ApplySearch(GlobalData.DataBase.Searches.All(iSearch).Search);
end

% Save search callback
function SaveSearch_Callback(iActiveSearch, iSavedSearch)
    global GlobalData;
    searchRoot = ActiveSearch('get', iActiveSearch);
    if isempty(searchRoot)
        return;
    end
    % Create new search
    if (nargin < 2) || isempty(iSavedSearch)
        % Ask user the name for the new search
        newName = java_dialog('input', 'Enter a name for the new search:', 'Save search');
        if isempty(newName)
            return;
        end
        % Check if search already exists
        if ~isempty(GlobalData.DataBase.Searches.All) && any(strcmpi({GlobalData.DataBase.Searches.All}, newName))
            bst_error('A search with this name already exists.', 'Save search', 0);
            return;
        end
        % Create new structure
        newSearch.Name = newName;
        newSearch.Search = searchRoot;
        % Add to list
        if isempty(GlobalData.DataBase.Searches.All)
            GlobalData.DataBase.Searches.All = newSearch;
        else
            GlobalData.DataBase.Searches.All(end+1) = newSearch;
        end
    % Update existing search
    else
        % Ask for confirmation
        isConfirm = java_dialog('confirm', ['Overwrite search "' GlobalData.DataBase.Searches.All(iSavedSearch).Name '"?'], 'Save search');
        % Overwrite existing entry
        if isConfirm
            GlobalData.DataBase.Searches.All(iSavedSearch).Search = searchRoot;
        end
    end
end

% Delete search callback
function DeleteSearch_Callback(iSearch)
    global GlobalData;
    % Ask confirmation
    if ~java_dialog('confirm', ['Delete search "' GlobalData.DataBase.Searches.All(iSearch).Name '"?'], 'Delete search')
        return;
    end
    GlobalData.DataBase.Searches.All(iSearch) = [];
end

% Let user type their own custom search
function TypeSearch_Callback()
    [searchStr, isCancel] = java_dialog('input', 'Type your query:', 'Search');
    if isCancel
        return;
    end

    ApplyCustomSearch(searchStr);
end

% Copy search to clipboard
function CopySearch_Callback(iSearch)
    searchRoot = panel_protocols('ActiveSearch', 'get', iSearch);
    if isempty(searchRoot)
        return;
    end
    searchStr = panel_search_database('SearchToString', searchRoot);
    disp(['BST> Copied the following search string to clipboard: ' searchStr]);
    clipboard('copy', searchStr);
end

% Paste from clipboard
function PasteSearch_Callback()
    searchStr = clipboard('paste');
    if isempty(searchStr)
        return;
    end

    ApplyCustomSearch(searchStr);
end

% Generate pipeline
function GenerateProcessCall_Callback(iSearch)
    % Get active search as string
    searchRoot = ActiveSearch('get', iSearch);
    % Generate process script
    panel_search_database('GenerateProcessScript', searchRoot);
end

% Function that lets you modify the Searches.Active structure
%
% Params:
%  - func: {'Get', 'Add', 'Remove'}, how to modify the search
%  - indexOrName: ID or name of the search to work with
%  - inNode: the db_template('searchnode') to save (for Add/Set only)
%  - newName: the new tab name, for 'Set' only
%
% Returns:
%  - Get: the requested db_template('searchnode') structure
%  - Other actions: nothing
function node = ActiveSearch(func, indexOrName, inNode, newName)
    global GlobalData

    node = [];
    numSearches = length(GlobalData.DataBase.Searches.Active);

    switch lower(func)
        % Get saved root node of requested search
        case 'get'
            if isnumeric(indexOrName)
                % Search IDs start at 2 since ID 1 is reserved for whole DB
                index = indexOrName + 1;
            else
                index = find(strcmp({GlobalData.DataBase.Searches.Active.Name}, indexOrName));
            end
            if isempty(index) || index > numSearches
                node = [];
            else
                node = GlobalData.DataBase.Searches.Active(index).SearchNode;
            end
        % Replace saved root node with new search
        case 'set'
            if isnumeric(indexOrName)
                % Search IDs start at 2 since ID 1 is reserved for whole DB
                index = indexOrName + 1;
            else
                index = find(strcmp({GlobalData.DataBase.Searches.Active.Name}, indexOrName));
            end
            if isempty(index) || index > numSearches
                node = [];
            else
                % Replace with new search values
                GlobalData.DataBase.Searches.Active(index).Name = newName;
                GlobalData.DataBase.Searches.Active(index).SearchNode = inNode;
                % Reset search nodes to force display refresh
                ResetSearchNodes(index);
            end
        % Add root node (inNode) of new search in memory
        case 'add'
            activeSearch = db_template('ActiveSearch');
            activeSearch.Name = indexOrName;
            activeSearch.SearchNode = inNode;
            GlobalData.DataBase.Searches.Active(end + 1) = activeSearch;
        % Remove nodes of requested search in memory
        case 'remove'
            if isnumeric(indexOrName)
                % Search IDs start at 2 since ID 1 is reserved for whole DB
                index = indexOrName + 1;
            else
                index = find(strcmp({GlobalData.DataBase.Searches.Active.Name}, indexOrName));
            end
            % Ensure we cannot remove search #1 (whole DB) from memory
            if ~isempty(index) && index > 1 && index <= numSearches
                iKeepNodes = 1:numSearches;
                iKeepNodes(index) = [];
                ResetSearchNodes(index);
                GlobalData.DataBase.Searches.Active = GlobalData.DataBase.Searches.Active(iKeepNodes);
            end
    end
end

% Return the database nodes of requested search, if in memory
%
% Params:
%  - iSearch: ID of the requested search
%  - explorationMode: how the database is organised in the tree
%       {'Subjects', 'StudiesSubj', 'StudiesCond'}
%
% Returns:
%  - rootNode: Root node of the requested search
%  - selNode: The node currently selected in the tree
function [rootNode, selNode, numNodes] = GetSearchNodes(iSearch, explorationMode)
    global GlobalData

    % Make sure the search ID exists
    if iSearch + 1 > length(GlobalData.DataBase.Searches.Active)
        rootNode = [];
        selNode  = [];
        numNodes = 0;
        return;
    end

    switch explorationMode
        case 'Subjects'
            % Anatomy view
            rootNode = GlobalData.DataBase.Searches.Active(iSearch+1).AnatRootNode;
            selNode  = GlobalData.DataBase.Searches.Active(iSearch+1).AnatSelNode;
            numNodes = GlobalData.DataBase.Searches.Active(iSearch+1).AnatNumNodes;
        case 'StudiesSubj'
            % Functional view, grouped by subjects
            rootNode = GlobalData.DataBase.Searches.Active(iSearch+1).FuncSubjRootNode;
            selNode  = GlobalData.DataBase.Searches.Active(iSearch+1).FuncSubjSelNode;
            numNodes = GlobalData.DataBase.Searches.Active(iSearch+1).FuncSubjNumNodes;
        case 'StudiesCond'
            % Functional view, grouped by conditions
            rootNode = GlobalData.DataBase.Searches.Active(iSearch+1).FuncCondRootNode;
            selNode  = GlobalData.DataBase.Searches.Active(iSearch+1).FuncCondSelNode;
            numNodes = GlobalData.DataBase.Searches.Active(iSearch+1).FuncCondNumNodes;
        otherwise
            error('Unsupported database view mode');
    end
end

% Save the results of a search in memory for a specific display mode
%
% Params:
%  - iSearch: ID of the requested search
%  - explorationMode: how the database is organised in the tree
%       {'Subjects', 'StudiesSubj', 'StudiesCond'}
%  - rootNode: root of the result database nodes
%  - selNode: the node currently selected in the tree
%
% Returns: nothing
function SaveSearchNodes(iSearch, explorationMode, rootNode, selNode, numNodes)
    global GlobalData

    switch explorationMode
        case 'Subjects'
            % Anatomy view
            GlobalData.DataBase.Searches.Active(iSearch+1).AnatRootNode = rootNode;
            GlobalData.DataBase.Searches.Active(iSearch+1).AnatSelNode  = selNode;
            GlobalData.DataBase.Searches.Active(iSearch+1).AnatNumNodes = numNodes;
        case 'StudiesSubj'
            % Functional view, grouped by subjects
            GlobalData.DataBase.Searches.Active(iSearch+1).FuncSubjRootNode = rootNode;
            GlobalData.DataBase.Searches.Active(iSearch+1).FuncSubjSelNode  = selNode;
            GlobalData.DataBase.Searches.Active(iSearch+1).FuncSubjNumNodes = numNodes;
        case 'StudiesCond'
            % Functional view, grouped by conditions
            GlobalData.DataBase.Searches.Active(iSearch+1).FuncCondRootNode = rootNode;
            GlobalData.DataBase.Searches.Active(iSearch+1).FuncCondSelNode  = selNode;
            GlobalData.DataBase.Searches.Active(iSearch+1).FuncCondNumNodes = numNodes;
        otherwise
            error('Unsupported database view mode');
    end
end

% Update the selected node in the current search node.
%
% Params:
%  - selNode: the node currently selected in the tree
%
% Returns: nothing
function UpdateSearchSelNode(selNode, iSearch, explorationMode)
    global GlobalData;

    % Get selected search tab
    if (nargin < 2) || isempty(iSearch)
        iSearch = GetSelectedSearch();
        if iSearch + 1 > length(GlobalData.DataBase.Searches.Active)
            return;
        end
    end
    % Get current exploration mode if not specified
    if (nargin < 3) || isempty(explorationMode)
        explorationMode = bst_get('Layout', 'ExplorationMode');
    end
    % Update selected node for current exploration mode
    switch explorationMode
        case 'Subjects'  % Anatomy view
            GlobalData.DataBase.Searches.Active(iSearch+1).AnatSelNode = selNode;
        case 'StudiesSubj'  % Functional view, grouped by subjects
            GlobalData.DataBase.Searches.Active(iSearch+1).FuncSubjSelNode = selNode;
        case 'StudiesCond'  % Functional view, grouped by conditions
            GlobalData.DataBase.Searches.Active(iSearch+1).FuncCondSelNode = selNode;
        otherwise
            error('Unsupported database view mode');
    end
end

% Clears all saved searches nodes from memory
%
% Params:
%  - iSearches: list of search IDs to remove
%       If empty, clear all searches
%
% Returns: nothing
function ResetSearchNodes(iSearches)
    global GlobalData

    % If no parameter: reset everything
    if nargin < 1 || isempty(iSearches)
        iSearches = 1:length(GlobalData.DataBase.Searches.Active);
    end

    for iSearch = iSearches
        GlobalData.DataBase.Searches.Active(iSearch).AnatRootNode = [];
        GlobalData.DataBase.Searches.Active(iSearch).AnatSelNode = [];
        GlobalData.DataBase.Searches.Active(iSearch).FuncSubjRootNode = [];
        GlobalData.DataBase.Searches.Active(iSearch).FuncSubjSelNode  = [];
        GlobalData.DataBase.Searches.Active(iSearch).FuncCondRootNode = [];
        GlobalData.DataBase.Searches.Active(iSearch).FuncCondSelNode  = [];
    end
end

author: brainstorm-tools


text:
function y = noise(varargin)
%  NOISE    Adds noise to an image.
%
%     NOISE creates a new image by adding noise to the original image.
%     NOISE can be used to any matrix (1D, 2D, 3D, nD)
%
%     Noisetypes are:
%       'ag' : additive gaussian (default)    'au' : additive uniform
%       'mg' : multiplicative gaussian        'mu' : multiplicative uniform
%       'sp' : salt and pepper
%
%     Additive noise sums an random value to the image value at each pixel,
%     Multiplicative noise replaces a pixel value with an random value,
%     Salt and Pepper noise replaces a pixel value with the maximum or minimum possible values.
%
%     For 'ag' noisetype use:  y = NOISE(x,'ag', variance, [incidence])
%       where 'variance' is the variance of the gaussian noise added and the optional parameter
%       'incidence' is the percetual of pixels affected be the noise (default for additive noise=1).
%       For a 50% incidence use 'incidence' = .5 and so on.
%
%     For 'au' noisetype use :  y = NOISE(x,'au', maximum, [incidence])
%       where 'maximum' is the maximum value the uniform noise can achieve
%
%     For 'mg' noisetype use :  y = NOISE(x,'mg', incidence)
%     For 'mu' noisetype use :  y = NOISE(x,'mu', incidence)
%       Multiplicative noisetypes require that the 'incidence' parameter. For this kind of noise
%       the variance or the maximum (respectivelly for gaussian and uniform noisetypes) are allways
%       set to the maximum image value.
%
%     For 'sp' noisetype use :  y = NOISE(x,'sp', incidence)
%
%     The 'maximum' and 'variance' parameters can be set as percentual of the maximum - minimum image
%     values by using these values as strings containg the percentual rate followed by the percent symbol.
%     The 'incidence' can also be expressed as a pecentual in this same way
%
%     Example:  y = NOISE(x,'ag', '25%')
%               y = NOISE(x,'mu', 10, .5) -> same as y = NOISE(x,'mu',10, '50%')
%

[u, noisetype,  scale, incid] = parse_inputs(varargin{:});

if ~isa(u,'double')
   u = double(u);
end

y = u;

n = zeros(size(u));
if incid == 1
   m_incid = logical(ones(size(u)));
else
   m_incid = rand(size(u));
   m_incid = find(m_incid <= incid);
end

if strcmp(noisetype, 'ag')
   n(m_incid) = scale*randn(size(m_incid));
   y = u + n;

elseif strcmp(noisetype, 'au')
   n(m_incid) = scale*rand(size(m_incid));
   y = u + n;

elseif strcmp(noisetype, 'mg')
   n(m_incid) = scale*randn(size(m_incid));
   y(m_incid) = n(m_incid);

elseif strcmp(noisetype, 'mu')
   n(m_incid) = scale*rand(size(m_incid));
   y(m_incid) = n(m_incid);

elseif strcmp(noisetype, 'sp')
   n(m_incid) = sign(randn(size(m_incid)));
   umax = max(u(:));
   umin = min(u(:));
   salt = find(n==-1);
   pepper = find(n==1);
   y(salt) = umax;
   y(pepper) = umin;
end

function [u, noisetype, scale, incid] = parse_inputs(varargin)
switch nargin
case 0
   error('Too few inputs')

case 1
   u = varargin{1};
   noisetype = 'ag';
   scale = double(max(u(:)));
   incid = 1;

case 2
   u = varargin{1};
   if strmatch(varargin{2},['ag';'au'])
      noisetype = varargin{2};
      scale = double(max(u(:)));
      incid = 1;
   elseif strmatch(varargin{2},['mg'; 'mu'; 'sp'])
      error('Incidence missing');
   else
      noisetype = 'ag';
      scale = varargin{2};
      incid = 1;
   end

case 3
   u = varargin{1};
   if strmatch(varargin{2},['ag';'au'])
      noisetype = varargin{2};
      scale = varargin{3};
      incid = 1;
   elseif strmatch(varargin{2},['mg'; 'mu'; 'sp'])
      noisetype = varargin{2};
      scale = double(max(u(:)));
      incid = varargin{3};
   else
      noisetype = 'ag';
      scale = varargin{2};
      incid = varargin{3};
   end

case 4
   u = varargin{1};
   if strmatch(varargin{2},['ag';'au'])
      noisetype = varargin{2};
      scale = varargin{3};
      incid = varargin{4};
   else
      error('Too many parameters')
   end

otherwise
   error('Too many parameters')
end

if findstr(scale,'%')
   scale = ( double(max(u(:))) - double(min(u(:))) )*str2num(scale(1:end-1))/100;
end
if findstr(incid,'%')
   incid = str2num(incid(1:end-1))/100;
end

author: Sable

repo: mcbench-benchmarks


text:
function [headername, dataname, fid] = write_text(D, varargin)
% "Flatten" dataset and write text files with header and data
% For all Event-level and Subject-level data.  Files are created in the
% current working directory.
%
% :Usage:
% ::
%
%    function [headername, dataname, fid] = write_text(D, [optional inputs])
%
% ..
%     Author and copyright information:
%
%     Copyright (C) 2013 Tor Wager
%
%     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 3 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.
%
%     You should have received a copy of the GNU General Public License
%     along with this program.  If not, see <http://www.gnu.org/licenses/>.
% ..
%
%
% :Inputs:
%
%   **D:**
%        a canlab_dataset object
%
% :Optional Inputs:
%    the first varargin parameter is the delimiter. Comma-delimited by default.
%    the second varargin parameter is a logical vector of subjects to use. All subjects by default.
%
%
% :Outputs:
%
%   **headername:**
%        filename of header output file
%
%   **dataname:**
%        filename of data output file
%
%   **fid:**
%        file ID (currently does not look to be used)
%

delim = ','; % flesh this out later as needed
wh_keep = true(size(D.Subj_Level.id));

if nargin > 1, delim = varargin{1}; end
if nargin > 2, wh_keep = varargin{2}; end

% Checks
% ----------------------------------------------------------------------
for i = 1:length(D.Subj_Level.names)

    if length(D.Subj_Level.descrip) < i
        D.Subj_Level.descrip{i} = 'No description provided';
    end

end

for i = 1:length(D.Event_Level.names)

    if length(D.Event_Level.descrip) < i
        D.Event_Level.descrip{i} = 'No description provided';
    end

end

if isempty(D.Event_Level.data)
    D.Event_Level.data = cell(1,length(D.Subj_Level.id));
end

if isempty(D.Event_Level.names)
    D.Event_Level.names = {};
end

% Open Files
% ----------------------------------------------------------------------
headername = [D.Description.Experiment_Name '_info_' scn_get_datetime '.txt'];
dataname = [D.Description.Experiment_Name '_data_' scn_get_datetime '.csv'];
fid = fopen(headername, 'w');

% Write Header
% ----------------------------------------------------------------------

u = '______________________________________________________________';

fprintf(fid, 'Experiment: %s\n', D.Description.Experiment_Name);

fprintf(fid, '\n%d subjects\n', length(D.Subj_Level.id));
fprintf(fid, 'Missing values coded with: %f\n', D.Description.Missing_Values);
fprintf(fid, '%s\n', u);

fprintf(fid, 'Subject Level\n\n');
fprintf(fid, 'Description:\n');

for i = 1:length(D.Description.Subj_Level)
    fprintf(fid, '\t%s\n', D.Description.Subj_Level{i});
end

fprintf(fid, 'Names:\n');
for i = 1:length(D.Subj_Level.names)
    fprintf(fid, '\t%s\t%s\n', D.Subj_Level.names{i}, D.Subj_Level.descrip{i});
end

fprintf(fid, '%s\n', u);

fprintf(fid, 'Event Level\n\n');
fprintf(fid, 'Description:\n');

for i = 1:length(D.Description.Event_Level)
    fprintf(fid, '\t%s\n', D.Description.Event_Level{i});
end

fprintf(fid, 'Names:\n');
for i = 1:length(D.Event_Level.names)
    fprintf(fid, '\t%s\t%s\n', D.Event_Level.names{i}, D.Event_Level.descrip{i});
end

fprintf(fid, '%s\n', u);

fclose(fid);

%% Write subj-level & event-level data
% -----------------------------------------------------------------------

fid = fopen(dataname, 'w');

if isempty(D.Event_Level.names)
    names = {'id' D.Subj_Level.names{:}};
else
    names = {'id' D.Subj_Level.names{:} 'Event_number' D.Event_Level.names{:}};
end

n = length(D.Subj_Level.id);

%slevels = length(D.Subj_Level.names);

printcell = @(x) fprintf(fid, ['%s' delim], x);
cellfun(printcell, names);
fprintf(fid, '\n');

for i = 1:n  % for each subject

    if ~wh_keep(i), continue; end % skip this subj

    e = size(D.Event_Level.data{i}, 1);

    if e==0 % no events
        fprintf(fid, ['%s' delim], D.Subj_Level.id{i});  % ID, can be char
        datarow = [D.Subj_Level.data(i, :)];
        printrow(fid, datarow, delim);
    else
        for j = 1:e  % for events within subject
            fprintf(fid, ['%s' delim], D.Subj_Level.id{i});  % ID, can be char
            datarow = [D.Subj_Level.data(i, :) j D.Event_Level.data{i}(j, :)];
            printrow(fid, datarow, delim);

        end  % events
    end
end  % subjects

fclose(fid);

end % function

function printrow(fid, datarow, delim)
    % Could switch by datatype in a better way here!!  need datatype codes in dataset.
    for k = 1:length(datarow)
        if datarow(k) == round(datarow(k))
            fprintf(fid, ['%d' delim], datarow(k));
        else
            fprintf(fid, ['%3.3f' delim], datarow(k));
        end
    end % row

    fprintf(fid, '\n');
end

author: canlab

repo: CanlabCore

save_path: github-repos/MATLAB/canlab-CanlabCore


text:
% std_renameclust()  - Commandline function, to rename clusters using specified (mnemonic) names.
% Usage:
%                   >> [STUDY] = std_renameclust(STUDY, ALLEEG, cluster, new_name);
% Inputs:
%   STUDY      - EEGLAB STUDY set comprising some or all of the EEG datasets in ALLEEG.
%   ALLEEG     - global EEGLAB vector of EEG structures for the dataset(s) included in the STUDY.
%                     ALLEEG for a STUDY set is typically created using load_ALLEEG().
%   cluster     - single cluster number.
%   new_name  - [string] mnemonic cluster name.
%
% Outputs:
%   STUDY    - the input STUDY set structure modified according to specified new cluster name.
%
%   Example:
%                         >> cluster = 7; new_name = 'artifacts';
%                         >> [STUDY] = std_renameclust(STUDY,ALLEEG, cluster, new_name);
%                    Cluster 7 name (i.e.: STUDY.cluster(7).name) will change to 'artifacts 7'.
%
%  See also  pop_clustedit
%
% Authors:  Hilit Serby, Arnaud Delorme, Scott Makeig, SCCN, INC, UCSD, June, 2005

% Copyright (C) Hilit Serby, SCCN, INC, UCSD, June 07, 2005, hilit@sccn.ucsd.edu
%
% 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.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA

function STUDY = std_renameclust(STUDY, ALLEEG, cls, new_name)

if ~exist('cls')
    error('std_renameclust: you must provide a cluster number to rename.');
end
if isempty(cls)
   error('std_renameclust: you must provide a cluster number to rename.');
end
if ~exist('new_name')
    error('std_renameclust: you must provide a new cluster name.');
end
if strncmpi('Notclust',STUDY.cluster(cls).name,8)  % Don't rename Notclust 'clusters'
    warndlg2('std_renameclust: Notclust cannot be renamed');
    return;
end

ti = strfind(STUDY.cluster(cls).name, ' ');
clus_id = STUDY.cluster(cls).name(ti(end) + 1:end);
new_name = sprintf('%s %s', new_name, clus_id);
% If the cluster have children cluster update their parent cluster name to the
% new cluster.
if ~isempty(STUDY.cluster(cls).child)
    for k = 1:length(STUDY.cluster(cls).child)
        child_cls = STUDY.cluster(cls).child{k};
        child_id = find(strcmp({STUDY.cluster.name},child_cls));
        parent_id = find(strcmp(STUDY.cluster(child_id).parent,STUDY.cluster(cls).name));
        STUDY.cluster(child_id).parent{parent_id} = new_name;
    end
end
% If the cluster has parent clusters, update the parent clusters with the
% new cluster name of child cluster.
if ~isempty(STUDY.cluster(cls).parent)
    for k = 1:length(STUDY.cluster(cls).parent)
        parent_cls = STUDY.cluster(cls).parent{k};
        parent_id = find(strcmp({STUDY.cluster.name},parent_cls));
        STUDY.cluster(parent_id).child{find(strcmp(STUDY.cluster(parent_id).child,STUDY.cluster(cls).name))} = new_name;
    end
end
% If the cluster have an Outlier cluster, update the Outlier cluster name.
outlier_clust = std_findoutlierclust(STUDY,cls); %find the outlier cluster for this cluster
if outlier_clust ~= 0
    ti = strfind(STUDY.cluster(outlier_clust).name, ' ');
    clus_id = STUDY.cluster(outlier_clust).name(ti(end) + 1:end);
    STUDY.cluster(outlier_clust).name = sprintf('Outliers %s %s', new_name, clus_id);
end

% Rename cluster
STUDY.cluster(cls).name = new_name;

author: PatternRecognition

repo: OpenBMI


text:
function cS = rotate_outer(cS,rot)
% rotate a crystal shape by an rotation or orientation
%
% Syntax
%
%    cS = rotate_outer(cS,rot)
%    cS = ori * cS
%
% Input
%  cS - @crystalShape
%  rot - @rotation
%  ori - @orientation
%
% Output
%  cS - @crystalShape

if size(cS.V,2) > 1, error('Not yet supported'); end

% duplicate the faces
shift = length(cS.V) * repmat((0:length(rot)-1),size(cS.F,1),1);
shift = repmat(shift(:),1,size(cS.F,2));

% shift faces indices
cS.F = repmat(cS.F,length(rot),1) + shift;

cS.V = (rotation(rot) * cS.V).';

end

author: mtex-toolbox

repo: mtex

save_path: github-repos/MATLAB/mtex-toolbox-mtex