Bugfix/sortfix (#84)

* Sort bugfix

Overall minor fixes to get Sort interface to work properly

- Recluster kmeans now is done on the feature space obtained by the wavelet decomposition. I'm planning to include some toggles to toggle between feature spaces.

SpikeImage Added some other shortcuts. Will add documentation in the wiki soon.

* Diskdata tweaks

Proposed diskdata  tweaks. Should improve performance a little. It is taking a really long time to save and load all the required data during sorting.

Major tweak: hd5write/read calls reduced by writing/loading files in chunks instead of column by column.

Old version is commented out instead of removing it to make it easily reversible.

* UImenuclick_sort fix

Modified uimenuclick to let the sortObj figure out what to do with the input arg.
Also added a small error if the user tries to sort more then one animal or the tank.

* Dashboard opening fix

Ported changes from multiAnimals branch to fix an issue with the dashboard not opening correctly

* fix nargout in diskdata

fixed weird bug that was causing subsref to crash due to a wrong number returned by nargout. This is not a definitive fix. Also, is happening only on my laptop (Matlab 2017a and b) but not on my workstation (2017a and 2019b). Will investigate further.

* Revert commit for demo

* various fixes

Various fixes.

the demo_nigelab now works to the end.

A small tweak in nigelObj to make sure that the data are correctly retrieved when moved.

Fixed a very rare fix in the artifact detection step.

getNigelPath was returning a hardcoded path to kumc internal directories when run in unix.

Author: Nabarb

+nigeLab/+libs/@DashBoard/DashBoard.m

@@ -653,16 +653,12 @@ function buildButtons(obj,nigelPanelObj)
             {@obj.toggleSplitMultiAnimalsUI,'start'})];
 
          % By default, buttons are enabled
-%          if obj.SelectionIndex(1,2) == 0
+         if ~any([obj.Tank.Children.MultiAnimals])
             setButton(obj.nigelButtons.Tree,'Split','Enable','off');
-%          end
-         
-%          obj.Listener = [obj.Listener, ...
-%             addlistener(obj,'SelectionIndex','PostSet',...
-%             @(~,~)obj.toggleSplitUIMenuEnable)];
-         
+         end   
       end
 
+      
       % Returns figure handle, with layout mediated by core nigelPanels
       function fig = buildGUI(obj)
          % LOADPANELS  Method to create all custom uipanels (nigelPanels)
@@ -1414,9 +1410,18 @@ function uiCMenuClick_Sort(obj,~,~)
          %  mitem.Callback = @(~,~)obj.uiCMenuClick_Sort;
          %
          %  Runs the spike sorting interface.
-         
-         blockObj = obj.getSelectedItems('obj');
-         Sort(blockObj); % Invoke sorting interface
+         nigelObj = obj.Tree.SelectedItems;
+         switch nigelObj.Type
+             case 'Block'
+                  Sort(nigelObj);
+             case 'Animal'
+                 if numel(nigelObj)>1
+                     error('You can only sort one aniaml at a time!');
+                 end
+                 Sort(nigelObj);
+             case 'Tank'
+                 error('Sort operation is not possible on the whole tank at once.\nPlease select an Animal or a Block.');
+         end
       end
 
       % LISTENER CALLBACK: Menu item toggle child mask on "Enable" click
@@ -1499,7 +1504,8 @@ function updateAfterSelectionChanged(obj,src,evt)
       end
 
 
-   end
+      end
+   
 
    % RESTRICTED: nigeLab.libs.splitMultiAnimalsUI
    methods (Access=?nigeLab.libs.splitMultiAnimalsUI)
@@ -1517,101 +1523,38 @@ function toggleSplitMultiAnimalsUI(obj,mode)
 
          switch mode
             case 'start'
-               bl = obj.getSelectedItems;
-               % if more than one block is selected, select the first
-               % one with a multiAnimal
-               indx = find([bl.MultiAnimals],1);
-               if isempty(indx)
-                   errordlg('This is not a multiAnimal!');
-                   return;
-               end % if ~MultiAnimals
-               bl = bl(indx);
-               Index = obj.selectedItems2Index(bl,obj.Tank);
-               obj.Tree.SelectedNodes = obj.Tree.Root.Children(Index(2)).Children(Index(3));
-               
-               
-               % Ensure that only 1 "child" object is selected at a time
-               obj.getChild('TreePanel').getChild('Tree').SelectionType = 'single';
-               if isvalid(obj.splitMultiAnimalsUI)
-                  obj.splitMultiAnimalsUI.toggleVisibility;
-                  return;
-               else
-                  % 'start' is only entered via button-click
-                  toggleSplitMultiAnimalsUI(obj,'init');
-                  drawnow;
-                  toggleSplitMultiAnimalsUI(obj,'start');
-                  return;
-               end % if isvalid
-               
-               % TODO disable nodes without multiAnimal flag!
-               %                    [obj.Tree.Root.Children(find([obj.Tank.Children.MultiAnimals])).Enable] = deal('off');
+                % pop multi aniamsl interface up
+                if ~isempty(obj.splitMultiAnimalsUI) && isvalid(obj.splitMultiAnimalsUI)
+                    obj.splitMultiAnimalsUI.toggleVisibility('on');
+                    obj.Tree.changeTreeSelection([])
+                else
+                    toggleSplitMultiAnimalsUI(obj,'init');
+                    toggleSplitMultiAnimalsUI(obj,'start');
+                end
+ 
             case 'stop'
-               obj.getChild('TreePanel').getChild('Tree').SelectionType = ...
-                  'discontiguous';
+               
                % TODO reenable nodes without multiAnimal flag!
                if any([obj.Tank.Children.MultiAnimals])
                   obj.splitMultiAnimalsUI.toggleVisibility;
                else
                   delete( obj.splitMultiAnimalsUI.Fig);
                   delete(obj.splitMultiAnimalsUI);
-                  listenerIndex = strcmp({obj.Listener.eventName},'SplitCompleted');
-                  delete(obj.Listener(listenerIndex));
-                  obj.Listener(listenerIndex) = [];
                end
 
             case 'init'
-               % First, make sure the selection is valid
-               
-               % The multiAnimalsUI must be opened
-               SelectedItems = cat(1,obj.Tree.SelectedNodes.UserData);
-               % Note that SelectedItems only contains nodes of a specific
-               % type, based on exclusion done in `treeSelectionFcn`.
-               % Therefore the vertical concatenation above is always valid
-               nCol = size(SelectedItems,2);
-               switch  nCol
-                  case 0  % tank
-                     % Cannot be invoked at "TANK" level
-                     error(['nigeLab:' mfilename ':badCase'],...
-                        'Should not be able to enter split UI from TANK level.');
-                  case 1  % animal
-                     % Gets all blocks of selected animals
-                     B = obj.Tank{SelectedItems(1),:};
-                     A = repmat(obj.Tank{SelectedItems(1)},1,numel(B));
-                     for i = 1:numel(SelectedItems)
-                        b = obj.Tank{SelectedItems(i),:};
-                        B = [B, b];
-                        A = [A, ...
-                           repmat(obj.Tank{SelectedItems(i)},1,numel(b))];
-                     end
-                     
-                  case 2  % block
-                     % Get specific subset of block or blocks
-                     A = obj.Tank{SelectedItems(:,1)};
-                     B = obj.Tank{SelectedItems};
-               end % switch nCol
+               % First, make sure the Tank contains multiAnimals
 
-               if ~all([A.MultiAnimals])
-                  return;
-               end
-               
-               if ~all([B.MultiAnimals])
-                  return;
-               end
+               an = obj.Tank.Children;
+               an = an([an.MultiAnimals]);
 
-               obj.toSplit = struct('Animal',cell(numel(A),1),...
-                  'Block',cell(numel(B),1));
-               for i = 1:numel(obj.toSplit)
-                  obj.toSplit(i).Animal = A(i);
-                  obj.toSplit(i).Block = B(i);
-               end
-               obj.toAdd = struct('Animal',{},'Block',{});
+               if isempty(an)
+                   errordlg('This is not a multiAnimal!');
+                   return;
+               end % if ~MultiAnimals
 
-               obj.splitMultiAnimalsUI = ...
-                  nigeLab.libs.splitMultiAnimalsUI(obj);
+               obj.splitMultiAnimalsUI = nigeLab.libs.splitMultiAnimalsUI(an);
 
-              obj.Listener = [obj.Listener,...
-            addlistener(obj.splitMultiAnimalsUI,'SplitCompleted',...
-               @(~,e)obj.addToTree(e.nigelObj))];
          end % switch mode
       end
 

+nigeLab/+libs/@DiskData/getEventsFromIndexing.m

@@ -36,12 +36,30 @@
    iCol = 1:obj.size_(2);
 end
 
-% First step: return full dataset using iCol
-varname_ = ['/' obj.name_];
-data = nan(obj.size_(1),numel(iCol));
-for i = 1:numel(iCol)
-   data(:,i)=h5read(obj.diskfile_,varname_,[1 iCol(i)],[N 1]);
-end
+%% optimized FB 2020/04/01
+%     % First step: return full dataset using iCol
+%     varname_ = ['/' obj.name_];
+%     data = nan(obj.size_(1),numel(iCol));
+%     for i = 1:numel(iCol)
+%         data(:,i)=h5read(obj.diskfile_,varname_,[1 iCol(i)],[N 1]);
+%     end
+
+    
+    % step 0. To speed up and avoid calling h5read too many times lets find
+    % adjacent chunks of iCol
+    iCol = iCol(:);
+    clustIdx = find([1;diff(iCol)-1]); % this is the starting index of clusters
+    stride = diff(clustIdx(:));
+    ColBlocks = [iCol(clustIdx(:)) [stride;numel(iCol)-sum(stride)]];
+    
+    % First step: return full dataset using iCol
+    varname_ = ['/' obj.name_];
+    data = nan(obj.size_(1),sum(ColBlocks(:,2)));
+    st = 0;
+    for i = 1:size(ColBlocks,1)
+        data(:,st+1:st+ColBlocks(i,2))=h5read(obj.diskfile_,varname_,[1 ColBlocks(i,1)],[N ColBlocks(i,2)]);
+        st = st + ColBlocks(i,2);
+    end
 
 % Second step: return reduced subset using iRow
 data = data(iRow,:);

+nigeLab/+libs/@DiskData/setEventsFromIndexing.m

@@ -39,19 +39,43 @@ function setEventsFromIndexing(obj,iRow,iCol,data)
    data = repmat(data,numel(iRow),numel(iCol));
 end
 
+% step 0. To speed up and avoid calling h5read too many times lets find
+% adjacent chunks of iCol
+iCol = iCol(:);
+clustIdx = find([1;diff(iCol)-1]); % this is the starting index of clusters
+strideCol = diff(clustIdx(:));
+ColBlocks = [iCol(clustIdx(:)) [strideCol;numel(iCol)-sum(strideCol)]];
+
+% same for iRow
+iRow = iRow(:);
+clustIdx = find([1;diff(iRow)-1]); % this is the starting index of clusters
+strideRow = diff(clustIdx(:));
+RowBlocks = [iRow(clustIdx(:)) [strideRow;numel(iRow)-sum(strideRow)]];
+
 % Do the H5 assignment
 varname_ = ['/' obj.name_];
 
 % Iterate on columns, reading in the full column and then overwriting the
 % relevant rows. There should in general be many fewer Columns than rows,
 % unless the number of rows is so small that it becomes a trivial tradeoff
-for i = 1:numel(iCol)
-   a = h5read(obj.diskfile_,varname_,[1 iCol(i)],[N 1]);
-   assigned_data = data(:,i);
-   a(iRow,1) = assigned_data;
-   h5write(obj.diskfile_,varname_,a,[1 iCol(i)],[N 1]);
-end
+% for i = 1:numel(iCol)
+%    a = h5read(obj.diskfile_,varname_,[1 iCol(i)],[N 1]);
+%    assigned_data = data(:,i);
+%    a(iRow,1) = assigned_data;
+%    h5write(obj.diskfile_,varname_,a,[1 iCol(i)],[N 1]);
+% end
 
+% write data to file
+stCol = 0;
+for ii = 1:size(ColBlocks,1)
+    stRow = 0;
+    for jj = 1:size(RowBlocks,1)
+        h5write(obj.diskfile_,varname_,data(stRow+1:stRow+RowBlocks(jj,2),stCol+1:stCol+ColBlocks(ii,2)),...
+            [RowBlocks(jj,1) ColBlocks(ii,1)],[RowBlocks(jj,2) ColBlocks(ii,2)]);
+        stRow = stRow + RowBlocks(jj,2);
+    end
+    stCol = stCol + ColBlocks(ii,2);
+end
 
 
 end

+nigeLab/+libs/@DiskData/subsref.m

@@ -17,7 +17,8 @@
       {'type','value','tag','ts','snippet','data'});
    mIdx = strcmp(diskMethods,S(1).subs);
    if any(mIdx) && ~any(strcmp(excludedPropNames,S(1).subs))
-      if nargout > 0
+       nOut = nargout;
+      if nOut > 0
          data = builtin('subsref',obj,S);
       else
          if numel(m(mIdx).OutputNames) > 0

+nigeLab/+libs/@FeaturesUI/FeaturesUI.m

@@ -331,7 +331,7 @@ function Init(obj)
          obj.rotateImg = imread(fullfile(fileparts(mfilename('fullpath')),'private','rotate.png'));
 
          obj.rotateButton = uicontrol(featureDisplayPanel,...
-            'Style','pushbutton',...
+            'Style','togglebutton',...
             'Units','Normalized',...
             'Position',[0.6 0 0.04 0.07],...
             'Callback',@obj.RotateBtnPress,...
@@ -575,9 +575,9 @@ function ChangeSize(obj,~,~)
       % Find subset of spikes to move based on convex-hull polygon
       function GetSpikesToMove(obj,ax)
          %GETSPIKESTOMOVE  Draw polygon, move spikes 
-         if ~obj.isVisible % If it's not visible, can't do cutting here
-            return;
-         end
+%          if ~obj.isVisible % If it's not visible, can't do cutting here
+%             return;
+%          end
 
          % Get the potential features to move clusters
          curCh = obj.ChannelSelector.Channel;

+nigeLab/+libs/@SpikeImage/Recluster.m

@@ -41,8 +41,9 @@ function Recluster(obj)
 
 % Perform clustering
 % Use PCA for reclustering, for the time-being
-[~,score,~,~,expl,~] = pca(spks);
-inspk=[inspk score(:,1:find(cumsum(expl)>95,1))];
+% [~,score,~,~,expl,~] = pca(spks);
+% inspk = score(:,1:find(cumsum(expl)>95,1));
+% inspk=spks;
 
 %     [classes,temp] = nigeLab.utils.SPC.DoSPC(par,inspk);
 try

+nigeLab/+libs/@SpikeImage/SpikeImage.m

@@ -316,7 +316,7 @@ function SetVisibleFeatures(obj,clus,val)
             return;
          end
 
-         if ~isfield(obj.Parent,'FeaturesUI')
+         if ~isprop(obj.Parent.UI,'FeaturesUI')
             return;
          end
 
@@ -757,9 +757,29 @@ function GetSpikesToMove(obj,curAxes)
       end
 
       % CALLBACK: Execute keyboard shortcut on keyboard button press
-      function WindowKeyPress(obj,~,evt)
+      function WindowKeyPress(obj,src,evt)
          %WINDOWKEYPRESS    Issue different events on keyboard presses
          switch evt.Key
+             case {'n','0'}
+                 if strcmpi(evt.Modifier,'control')
+                     thisClass =  obj.Spikes.CurClass;
+                     obj.Spikes.CurClass = 1;
+                     subsetIndex = find(obj.Spikes.Class == thisClass);
+                     evtData = nigeLab.evt.assignClus(subsetIndex,...
+                         obj.Spikes.CurClass,thisClass);
+                     obj.UpdateClusterAssignments(nan,evtData);
+                 else
+                 end
+             case {'1','2','3','4','5','6','7','8'}
+                 if strcmpi(evt.Modifier,'control')
+                     thisClass =  obj.Spikes.CurClass;
+                     obj.Spikes.CurClass = str2num(evt.Key)+1;
+                     subsetIndex = find(obj.Spikes.Class == thisClass);
+                     evtData = nigeLab.evt.assignClus(subsetIndex,...
+                         obj.Spikes.CurClass,thisClass);
+                     obj.UpdateClusterAssignments(nan,evtData);
+                 else
+                 end
             case 'space'
                obj.ConfirmChanges;
             case 'z'

+nigeLab/+utils/getNigelPath.m

@@ -35,10 +35,10 @@
 switch upper(pathMode)
    case 'UNC'
       if isunix
-         nigelPath = nigelPath_;
+         nigelPath = nigelPath;
       else
          nigelPath = getUNCPath(nigelPath);
-         nigelPath = strrep(nigelPath,'\','/');
+         nigelPath = strrep(nigelPath,'\','/'); 
       end
 
    case ''

+nigeLab/@Block/doSD.m

@@ -352,8 +352,9 @@
       if isempty(artifact)
          art = ones(0,5);
       else
-         iStart = artifact([true, diff(artifact) > 1]);
-         iStop = artifact(fliplr([true, diff(fliplr(artifact)) > 1]));
+          artifact = artifact(:); % make sure is column oriented
+         iStart = artifact([true, diff(artifact)' ~= 1]);
+         iStop = artifact(fliplr([true, diff(fliplr(artifact))' ~= 1]));
 
          artifact = reshape(artifact,numel(artifact),1);
 

+nigeLab/@Sort/Sort.m

@@ -9,9 +9,9 @@
 %    INPUTS
 %   --------
 %   nigelObj  :     (Optional) If not provided, a UI for generation or
-%                       loading of the correct orgExpObj pops up.
+%                       loading of the correct nigelObj pops up.
 %                       Otherwise, the Sort class object parses which
-%                       orgExpObj is given (based on object class), and
+%                       nigelObj is given (based on object class), and
 %                       presents the Sort interface based on that.
 %
 %   --------
@@ -219,7 +219,6 @@ function delete(sortObj)
       flag = parseBlocks(sortObj,nigelObj);  % Assigns Blocks property
       flag = parseAnimals(sortObj,nigelObj); % Assigns Blocks from Animals
 
-      flag = setAxesPositions(sortObj); % Draw axes positions
 
       channelName = parseChannelName(sortObj); % Get all channel names
    end
@@ -235,4 +234,10 @@ function delete(sortObj)
       end
    end   
    % % % % % % % % % % END METHODS% % %
+
+
+   methods (Access = ?nigeLab.libs.SortUI)
+       flag = setAxesPositions(sortObj); % Draw axes positions
+   end
+
 end