More flexible splitting options

JaneliaSciComp · Mar 29, 2019 · 7df290a · 7df290a
1 parent 923c12c
commit 7df290a
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Showing 7 changed files with 147 additions and 52 deletions.
diff --git a/+jrclust/+curate/@CurateController/autoSplit.m b/+jrclust/+curate/@CurateController/autoSplit.m
@@ -33,19 +33,69 @@ function autoSplit(obj, multisite)
 
     clusterTimes = obj.hClust.spikeTimes(iSpikes);
 
-    nSplits = jrclust.utils.inputdlgNum('Number of clusters:', '', 2);
-    if isnan(nSplits)
-        return;
-    elseif nSplits < 2 || nSplits ~= round(nSplits)
-        jrclust.utils.qMsgBox('Please enter an integer >= 2');
+    % create split figure
+    hFigSplit = jrclust.views.Figure('FigSplit', [0.05 0.05 0.8 0.8], sprintf('Split cluster %d', iCluster), 0, 0);
+    hFigSplit.figApply(@set, 'Visible', 'off');
+    hFigSplit.figData.nSplits = 0;
+
+    % create a dialog
+    splitDlg = dialog('Name', 'Split cluster', ...
+                      'Units', 'Normalized', ...
+                      'Position', [0.4, 0.5, 0.2, 0.15]);
+
+    uicontrol('Parent', splitDlg, 'Style', 'text', ...
+              'String', 'Number of splits', ...
+              'Units', 'Normalized', ...
+              'Position', [0.4 0.4 0.2 0.07]);
+
+    nsplit = uicontrol('Parent', splitDlg, 'Style', 'edit', ...
+                       'String', 2, ...
+                       'Units', 'Normalized', ...
+                       'Position', [0.4 0.25 0.2 0.15]);
+
+    % button group: K-means, K-medoids, Hierarchical clustering
+    btngrp = uibuttongroup('Parent', splitDlg, 'Units', 'Normalized', ...
+                           'Position', [0.1 0.1 0.3 0.8]);
+    uicontrol('Parent', btngrp, 'Style', 'radiobutton', 'String', 'Hierarchical (Ward)', ...
+              'Units', 'Normalized', 'Position', [0.1, 0.1, 1, 0.15]);
+    uicontrol('Parent', btngrp, 'Style', 'radiobutton', 'String', 'K-means', ...
+              'Units', 'Normalized', 'Position', [0.1, 0.7, 1, 0.15]);
+    uicontrol('Parent', btngrp, 'Style', 'radiobutton', 'String', 'K-medoids', ...
+              'Units', 'Normalized', 'Position', [0.1, 0.4, 1, 0.15]);
+
+    uicontrol('Parent', splitDlg, 'Style', 'pushbutton', ...
+              'String', 'Split', ...
+              'Units', 'Normalized', ...
+              'Position', [0.4 0.1 0.2 0.15], ...
+              'Callback', @(hO, hE) preSplit(splitDlg, nsplit.String, btngrp, hFigSplit));
+    uicontrol('Parent', splitDlg, 'Style', 'pushbutton', ...
+              'String', 'Cancel', ...
+              'Units', 'Normalized', ...
+              'Position', [0.6 0.1 0.2 0.15], ...
+              'Callback', @(hO, hE) doCancel(splitDlg, hFigSplit));
+    uicontrol('Parent', splitDlg, 'Style', 'text', ...
+              'String', 'How to recluster this unit?', ...
+              'Units', 'Normalized', ...
+              'Position', [0.1 0.9 0.3 0.07]);
+
+    uiwait(splitDlg);
+
+%     nSplits = jrclust.utils.inputdlgNum('Number of clusters:', '', 2);
+%     if isnan(nSplits)
+%         return;
+%     elseif nSplits < 2 || nSplits ~= round(nSplits)
+%         jrclust.utils.qMsgBox('Please enter an integer >= 2');
+%         return;
+%     end
+
+    if hFigSplit.figData.nSplits <= 1
         return;
+    else
+        nSplits = hFigSplit.figData.nSplits;
     end
 
     hBox = jrclust.utils.qMsgBox('Splitting... (this closes automatically)', 0, 1);
 
-    % create split figure
-    hFigSplit = jrclust.views.Figure('FigSplit', [0.05 0.05 0.8 0.8], 'Split', 0, 0);
-
     % add plots
     hFigSplit.addAxes('vppTime', 'Units', 'Normalized', 'OuterPosition', [0 0 0.7 0.5]);
     hFigSplit.addAxes('pc12', 'Units', 'Normalized', 'OuterPosition', [0 0.5 0.2333 0.5]);
@@ -106,7 +156,7 @@ function autoSplit(obj, multisite)
     hFigSplit.figData.iSite = iSite;
     hFigSplit.figData.refracInt = obj.hCfg.refracInt/1000;
     while 1
-        [assigns, pcaFeatures] = doAutoSplit(sampledTraces, [double(clusterTimes) double(localVpp')], nSplits); %TW
+        [assigns, pcaFeatures] = doAutoSplit(sampledTraces, [double(clusterTimes) double(localVpp')], hFigSplit); %TW
         hFigSplit.figData.pcaFeatures = pcaFeatures;
         hFigSplit.figData.clusterTimes = double(clusterTimes)/obj.hCfg.sampleRate;
         hFigSplit.figData.localVpp = double(localVpp');
@@ -135,7 +185,7 @@ function autoSplit(obj, multisite)
 end
 
 %% LOCAL FUNCTIONS
-function [assigns, pcaFeatures] = doAutoSplit(sampledSpikes, spikeFeatures, nSplits)
+function [assigns, pcaFeatures] = doAutoSplit(sampledSpikes, spikeFeatures, hFigSplit)
     %DOAUTOSPLIT
     % TODO: ask users number of clusters and split multi-way
     %Make automatic split of clusters using PCA + hierarchical clustering
@@ -146,14 +196,44 @@ function autoSplit(obj, multisite)
     % ask how many clusters there are
     try
         combinedFeatures = (combinedFeatures - mean(combinedFeatures, 1)) ./ std(combinedFeatures, 1);
-        assigns = clusterdata(combinedFeatures, 'linkage', 'ward', ...
-                              'distance', 'euclidean', ...
-                              'maxclust', nSplits, 'savememory', 'on');
-    catch % not enough features to automatically split
+        assigns = hFigSplit.figData.hFunSplit(combinedFeatures);
+    catch % not enough features to automatically split or some other failure
         assigns = ones(nSpikes, 1);
     end
 end
 
+function doCancel(splitDlg, hFigSplit)
+    delete(splitDlg);
+    hFigSplit.figData.nSplits = 0;
+end
+
+function preSplit(splitDlg, nsplit, btngrp, hFigSplit)
+    whichSelected = logical(arrayfun(@(child) child.Value, btngrp.Children));
+    selected = btngrp.Children(whichSelected);
+
+    nsplit = floor(str2double(nsplit));
+    if isnan(nsplit)
+        nsplit = 2;
+    end
+
+    switch selected.String
+        case 'K-means'
+            hFigSplit.figData.hFunSplit = @(X) kmeans(X, nsplit);
+        case 'K-medoids'
+            hFigSplit.figData.hFunSplit = @(X) kmedoids(X, nsplit);
+        otherwise
+            hFigSplit.figData.hFunSplit = @(X) clusterdata(X, ...
+                                                           'maxclust', nsplit, ...
+                                                           'linkage', 'ward', ...
+                                                           'distance', 'euclidean', ...
+                                                           'savememory', 'on');
+    end
+
+    delete(splitDlg)
+
+    hFigSplit.figData.nSplits = nsplit;
+end
+
 function updateSplitPlots(hFigSplit)
     clustList = hFigSplit.figData.clustList;
 

diff --git a/+jrclust/+curate/@CurateController/keyPressFigProj.m b/+jrclust/+curate/@CurateController/keyPressFigProj.m
@@ -62,34 +62,36 @@ function keyPressFigProj(obj, ~, hEvent)
             obj.updateFigProj(1);
 
         case 's' %split
-            disp('Split: not implemented yet');
-%             if numel(obj.selected) == 1
-%                 iCluster = obj.selected(1);
-% 
-%                 hFigProj.addPlot('hPoly', @impoly)
-%                 polyPos = hFigProj.plotApply('hPoly', @getPosition);
-% 
-%                 XData = hFigProj.plotApply('foreground', @get, 'XData');
-%                 YData = hFigProj.plotApply('foreground', @get, 'YData');
-% 
-%                 retained = inpolygon(XData, YData, polyPos(:,1), polyPos(:,2));
-%                 jSites = unique(floor(XData(retained))) + 1;
-%                 iSites = unique(floor(YData(retained))) + 1;
-% 
-%                 % return here
-%                 hFigProj.addPlot('hSplit', @line, XData(retained), YData(retained), ...
-%                                  'Color', obj.hCfg.colorMap(3, :), ...
-%                                  'Marker', '.', 'LineStyle', 'none');
-% 
-%                 dlgAns = questdlg('Split?', 'Confirmation', 'No');
-% 
-%                 hFigProj.rmPlot('hPoly');
-%                 hFigProj.rmPlot('hSplit');
-% 
-%                 if strcmp(dlgAns, 'Yes')
-%                     obj.splitCluster(iCluster, retained);
-%                 end
-%             end
+            if numel(obj.selected) == 1
+                iCluster = obj.selected(1);
+
+                hFigProj.addPlot('hPoly', @impoly)
+                polyPos = hFigProj.plotApply('hPoly', @getPosition);
+                if isempty(polyPos)
+                    return;
+                end
+
+                XData = hFigProj.plotApply('foreground', @get, 'XData');
+                YData = hFigProj.plotApply('foreground', @get, 'YData');
+
+                retained = inpolygon(XData, YData, polyPos(:,1), polyPos(:,2));
+
+                % return here
+                hFigProj.addPlot('hSplit', @line, XData(retained), YData(retained), ...
+                                 'Color', obj.hCfg.colorMap(3, :), ...
+                                 'Marker', '.', 'LineStyle', 'none');
+
+                dlgAns = questdlg('Split?', 'Confirmation', 'No');
+
+                hFigProj.rmPlot('hPoly');
+                hFigProj.rmPlot('hSplit');
+
+                if strcmp(dlgAns, 'Yes')
+                    iSpikes = obj.hClust.spikesByCluster{iCluster};
+                    retained = ismember(hFigProj.figData.dispFeatures.fgSpikes(retained), iSpikes);
+                    obj.splitCluster(iCluster, retained);
+                end
+            end
 
     end % switch
 end
diff --git a/+jrclust/+views/plotFigProj.m b/+jrclust/+views/plotFigProj.m
@@ -54,7 +54,9 @@
     plotFeatures(hFigProj, 'background', bgYData, bgXData, boundScale, hCfg);
 
     % plot foreground spikes
-    plotFeatures(hFigProj, 'foreground', fgYData, fgXData, boundScale, hCfg);
+    assigns = plotFeatures(hFigProj, 'foreground', fgYData, fgXData, boundScale, hCfg);
+    hFigProj.figData.dispFeatures.fgSpikes = hFigProj.figData.dispFeatures.fgSpikes(assigns);
+
     % plot secondary foreground spikes
     if numel(selected) == 2
         plotFeatures(hFigProj, 'foreground2', fg2YData, fg2XData, boundScale, hCfg);
@@ -82,14 +84,14 @@
 end
 
 %% LOCAL FUNCTIONS
-function plotFeatures(hFigProj, plotKey, featY, featX, boundScale, hCfg)
+function assigns = plotFeatures(hFigProj, plotKey, featY, featX, boundScale, hCfg)
     %PLOTFEATURES Plot features in a grid
     if strcmp(hCfg.dispFeature, 'vpp')
         bounds = boundScale*[0 1];
     else
         bounds = boundScale*[-1 1];
     end
 
-    [XData, YData] = ampToProj(featY, featX, bounds, hCfg.nSiteDir, hCfg);
+    [XData, YData, assigns] = ampToProj(featY, featX, bounds, hCfg.nSiteDir, hCfg);
     hFigProj.updatePlot(plotKey, XData, YData);
 end
diff --git a/+jrclust/+views/private/ampToProj.m b/+jrclust/+views/private/ampToProj.m
@@ -1,4 +1,4 @@
-function [XData, YData, validXY, boxShape] = ampToProj(YData, XData, bounds, maxPair, hCfg)
+function [XData, YData, assigns] = ampToProj(YData, XData, bounds, maxPair, hCfg)
     %AMPTOPROJ Reshape feature data from nSpikes x nSites to display in an
     %nSites x nSites grid
     %   input: YData, nSpikes x nSites, y-values for feature projection
@@ -13,12 +13,15 @@
 
     % spike features translated into site-site boxes
     [boxedX, boxedY] = deal(nan([nSpikes, nSites, nSites], 'single'));
+    assigns = zeros([nSpikes, nSites, nSites]);
 
     for jSite = 1:nSites
         jSiteY = YData(:, jSite);
         yMask = jSiteY > 0  & jSiteY < 1; % get points away from the boundaries
 
         for iSite = 1:nSites
+            assigns(:, jSite, iSite) = 1:nSpikes;
+
             if abs(iSite - jSite) > maxPair
                 continue;
             end
@@ -46,7 +49,8 @@
     YData = boxedY(validXY);
     YData = YData(:);
 
-    boxShape = [nSpikes, nSites, nSites];
+    assigns = assigns(validXY);
+    assigns = assigns(:);
 end
 
 %% LOCAL FUNCTIONS

diff --git a/+jrclust/+views/private/getFigProjFeatures.m b/+jrclust/+views/private/getFigProjFeatures.m
@@ -131,7 +131,7 @@
                           'bgXData', bgXData, ...
                           'fgYData', fgYData, ...
                           'fgXData', fgXData, ...
-                          'fgSpikes', fgSpikes, ...
+                          'fgSpikes', fgSpikes, ... % for finding spikes to split off
                           'fg2YData', fg2YData, ...
                           'fg2XData', fg2XData, ...
                           'fg2Spikes', fg2Spikes);

diff --git a/CHANGELOG.TXT b/CHANGELOG.TXT
@@ -1,9 +1,16 @@
+29 Mar 2019 (4.0.0-beta release)
+
+- Allow user to select exploratory clustering algorithm in main split.
+- Allow user to split in FigProj.
+
+
 27 Mar 2019
 
-Export results in phy-compatible format with jrc export-phy /path/to/your/config.prm
-Display summaries after detect and sort, also added an option to display a summary in UI.
+- Bugfix: non-integral sample rates are supported to full precision.
+- Export results in phy-compatible format with jrc export-phy /path/to/your/config.prm.
+- Display summaries after detect and sort, also added an option to display a summary in UI.
 
-20 Mar 2019 (4.0.0-beta release)
+20 Mar 2019
 
 - Bugfix: import-ksort didn't use the correct sites for imported spikes; this has been fixed.
 

diff --git a/json/jrc.json b/json/jrc.json
@@ -7,7 +7,7 @@
         "tag": "beta",
         "codename": "Edward"
     },
-    "changeDate": "27 March 2019",
+    "changeDate": "29 March 2019",
     "authors": [
         "James Jun"
     ],