small improvements and updated db list

petersenpeter · Jul 31, 2019 · 6a3bac6 · 6a3bac6
1 parent b63d9ff
commit 6a3bac6
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Showing 7 changed files with 63 additions and 26 deletions.
diff --git a/CellExplorer.m b/CellExplorer.m
@@ -103,6 +103,7 @@
 fig2_axislimit_x = []; fig2_axislimit_y = []; fig3_axislimit_x = []; fig3_axislimit_y = []; groundTruthSelection = []; subsetGroundTruth = [];
 positionsTogglebutton = [[1 29 27 13];[29 29 27 13];[1 15 27 13];[29 15 27 13];[1 1 27 13];[29 1 27 13]]; dispTags = []; dispTags2 = [];
 incoming = []; outgoing = []; connections = []; plotName = ''; db = {}; plotConnections = [1 1 1]; tableDataOrder = []; 
+groundTruthCelltypesList = {''};
 set(groot, 'DefaultFigureVisible', 'on'), maxFigureSize = get(groot,'ScreenSize'); UI.settings.figureSize = [50, 50, min(1200,maxFigureSize(3)-50), min(800,maxFigureSize(4)-50)];
 
 if isempty(basename)
@@ -1784,7 +1785,7 @@ colormap hot(512), xlabel('Time (ms)'), title(['All ACGs (image)']), axis tight
                             end
                     end
                 end
-                plot(x_bins,rippleCorrelogram,'color', col,'linewidth',2, 'HitTest','off'), xlabel('time'),ylabel('Voltage')
+                plot(x_bins,rippleCorrelogram,'color', col,'linewidth',2, 'HitTest','off'), xlabel('time'),ylabel('')
                 axis tight, ax6 = axis; grid on
                 plot([0, 0], [ax6(3) ax6(4)],'color','k', 'HitTest','off');
                 set(gca, 'XTickMode', 'auto', 'XTickLabelMode', 'auto', 'YTickMode', 'auto', 'YTickLabelMode', 'auto', 'ZTickMode', 'auto', 'ZTickLabelMode', 'auto')
@@ -1817,7 +1818,7 @@ colormap hot(512), xlabel('Time (ms)'), title(['All ACGs (image)']), axis tight
                             end
                     end
                 end
-                plot(x_bins,rippleCorrelogram,'color', col,'linewidth',2, 'HitTest','off'), xlabel('time'),ylabel('Voltage')
+                plot(x_bins,rippleCorrelogram,'color', col,'linewidth',2, 'HitTest','off'), xlabel('time'),ylabel('')
                 axis tight, ax6 = axis; grid on
                 plot([0, 0], [ax6(3) ax6(4)],'color','k', 'HitTest','off');
                 set(gca, 'XTickMode', 'auto', 'XTickLabelMode', 'auto', 'YTickMode', 'auto', 'YTickLabelMode', 'auto', 'ZTickMode', 'auto', 'ZTickLabelMode', 'auto')
@@ -2280,7 +2281,7 @@ function tSNE_redefineMetrics(~,~)
             X(isnan(X) | isinf(X)) = 0;
             waitbar(0.1,f_waitbar,'Calculating tSNE space...')
 
-            tSNE_metrics.plot = tsne(X','Standardize',true,'Distance',UI.settings.tSNE_dDistanceMetric,'Exaggeration',10);            
+            tSNE_metrics.plot = tsne(X','Standardize',true,'Distance',UI.settings.tSNE_dDistanceMetric,'Exaggeration',15);            
 
             if size(tSNE_metrics.plot,2)==1
                 tSNE_metrics.plot = [tSNE_metrics.plot,tSNE_metrics.plot];
@@ -4679,7 +4680,7 @@ function saveMetrics(cell_metrics,file)
         cell_metrics = saveCellMetricsStruct(cell_metrics);
 
         if nargin > 1
-            save(file,'cell_metrics');
+            save(file,'cell_metrics','-v7.3','-nocompression');
             MsgLog(['Classification saved to ', file],[1,2]);
         elseif length(unique(cell_metrics.spikeSortingID)) > 1
             MsgLog('Saving cell metrics from batch',1);
@@ -4757,8 +4758,8 @@ function saveMetrics(cell_metrics,file)
             else
                 saveAs = 'cell_metrics';
             end
-            file = fullfile(clusteringpath,[saveAs,'.mat']);
-            save(file,'cell_metrics');
+            file = fullfile(cell_metrics.general.clusteringpath,[cell_metrics.general.basename, '.',saveAs,'.cellinfo.mat']);
+            save(file,'cell_metrics','-v7.3','-nocompression');
             classificationTrackChanges = [];
             UI.menu.file.save.ForegroundColor = 'k';
             MsgLog(['Classification saved to ', file],[1,2]);
@@ -5006,30 +5007,30 @@ function SignificanceMetricsMatrix(~,~)
 
         if UI.settings.tSNE_calcWideAcg && ~isfield(tSNE_metrics,'acg1')
             disp('Calculating tSNE space for wide ACGs')
-            tSNE_metrics.acg_wide = tsne([cell_metrics.acg.wide_zscored(ceil(size(cell_metrics.acg.wide_zscored,1)/2):end,:)]','Distance',UI.settings.tSNE_dDistanceMetric);
+            tSNE_metrics.acg_wide = tsne([cell_metrics.acg.wide_zscored(ceil(size(cell_metrics.acg.wide_zscored,1)/2):end,:)]','Distance',UI.settings.tSNE_dDistanceMetric,'Exaggeration',15);
         end
         if UI.settings.tSNE_calcNarrowAcg && ~isfield(tSNE_metrics,'acg2')
             disp('Calculating tSNE space for narrow ACGs')
-            tSNE_metrics.acg_narrow = tsne([cell_metrics.acg.narrow_zscored(ceil(size(cell_metrics.acg.narrow_zscored,1)/2):end,:)]','Distance',UI.settings.tSNE_dDistanceMetric);
+            tSNE_metrics.acg_narrow = tsne([cell_metrics.acg.narrow_zscored(ceil(size(cell_metrics.acg.narrow_zscored,1)/2):end,:)]','Distance',UI.settings.tSNE_dDistanceMetric,'Exaggeration',15);
         end
         if UI.settings.tSNE_calcFiltWaveform && ~isfield(tSNE_metrics,'filtWaveform')
             disp('Calculating tSNE space for filtered waveforms')
             X = cell_metrics.waveforms.filt_zscored';
-            tSNE_metrics.filtWaveform = tsne(X(:,find(~any(isnan(X)))),'Standardize',true,'Distance',UI.settings.tSNE_dDistanceMetric);
+            tSNE_metrics.filtWaveform = tsne(X(:,find(~any(isnan(X)))),'Standardize',true,'Distance',UI.settings.tSNE_dDistanceMetric,'Exaggeration',15);
         end
         if UI.settings.tSNE_calcRawWaveform && ~isfield(tSNE_metrics,'rawWaveform') && isfield(cell_metrics.waveforms,'raw')
             disp('Calculating tSNE space for raw waveforms')
             X = cell_metrics.waveforms.raw_zscored';
             if ~isempty(find(~any(isnan(X))))
-                tSNE_metrics.rawWaveform = tsne(X(:,find(~any(isnan(X)))),'Standardize',true,'Distance',UI.settings.tSNE_dDistanceMetric);
+                tSNE_metrics.rawWaveform = tsne(X(:,find(~any(isnan(X)))),'Standardize',true,'Distance',UI.settings.tSNE_dDistanceMetric,'Exaggeration',15);
             end
         end
         if ~isfield(tSNE_metrics,'plot')
             %             disp('Calculating tSNE space for combined metrics')
             UI.settings.tSNE_metrics = intersect(UI.settings.tSNE_metrics,fieldnames(cell_metrics));
             X = cell2mat(cellfun(@(X) cell_metrics.(X),UI.settings.tSNE_metrics,'UniformOutput',false));
             X(isnan(X) | isinf(X)) = 0;
-            tSNE_metrics.plot = tsne(X','Standardize',true,'Distance',UI.settings.tSNE_dDistanceMetric);
+            tSNE_metrics.plot = tsne(X','Standardize',true,'Distance',UI.settings.tSNE_dDistanceMetric,'Exaggeration',15);
         end
 
         % Setting initial settings for plots, popups and listboxes
@@ -5276,7 +5277,7 @@ function LoadDatabaseSession(~,~)
                 uicontrol('Parent',loadDB.dialog,'Style','pushbutton','Position',[700, 10, 90, 30],'String','OK','Callback',@(src,evnt)CloseDB_dialog);
                 uicontrol('Parent',loadDB.dialog,'Style','pushbutton','Position',[800, 10, 90, 30],'String','Cancel','Callback',@(src,evnt)CancelDB_dialog);
                 updateSummaryText
-                uiwait(loadDB.dialog)
+                uiwait(loadDB.popupmenu.filter)
 
         function reloadSessionlist
             loadDB_sessionlist
@@ -5339,7 +5340,7 @@ function LoadDatabaseSession(~,~)
                     db.dataTable(:,1) = {false};
                     [db_path,~,~] = fileparts(which('db_load_sessions.m'));
                     try
-                        save(fullfile(db_path,'db_cell_metrics_session_list.mat'),'db');
+                        save(fullfile(db_path,'db_cell_metrics_session_list.mat'),'db','-v7.3','-nocompression');
                     catch
                         warning('failed to save session list with metrics');
                     end
@@ -5602,7 +5603,7 @@ function editDBcredentials(~,~)
                     clusteringpath1 = cell_metrics.general.paths{batchIDsPrivate};
                     basename1 = cell_metrics.general.basenames{batchIDsPrivate};
                 else
-                    clusteringpath1 = clusteringpath;
+                    clusteringpath1 = cell_metrics.general.clusteringpath;
                     basename1 = cell_metrics.general.basename;
                 end
 
@@ -6187,8 +6188,10 @@ function buttonGroundTruthClassification(input)
     function [choice,dialog_canceled] = groundTruthDlg(groundTruthCelltypes,groundTruthSelectionIn)
         choice = '';
         dialog_canceled = 1;
+        updateGroundTruthCount;
+
         groundTruth_dialog = dialog('Position', [300, 300, 600, 350],'Name','Ground truth cell types'); movegui(groundTruth_dialog,'center')
-        groundTruthList = uicontrol('Parent',groundTruth_dialog,'Style', 'ListBox', 'String', groundTruthCelltypes, 'Position', [10, 50, 580, 220],'Min', 0, 'Max', 100,'Value',groundTruthSelectionIn);
+        groundTruthList = uicontrol('Parent',groundTruth_dialog,'Style', 'ListBox', 'String', groundTruthCelltypesList, 'Position', [10, 50, 580, 220],'Min', 0, 'Max', 100,'Value',groundTruthSelectionIn);
         groundTruthTextfield = uicontrol('Parent',groundTruth_dialog,'Style', 'Edit', 'String', '', 'Position', [10, 300, 580, 25],'Callback',@(src,evnt)UpdateGroundTruthList,'HorizontalAlignment','left');
         uicontrol('Parent',groundTruth_dialog,'Style','pushbutton','Position',[10, 10, 180, 30],'String','OK','Callback',@(src,evnt)CloseGroundTruth_dialog);
         uicontrol('Parent',groundTruth_dialog,'Style','pushbutton','Position',[200, 10, 190, 30],'String','Cancel','Callback',@(src,evnt)CancelGroundTruth_dialog);
@@ -6197,20 +6200,39 @@ function buttonGroundTruthClassification(input)
         uicontrol('Parent',groundTruth_dialog,'Style', 'text', 'String', 'Selct the cell types below', 'Position', [10, 270, 580, 20],'HorizontalAlignment','left');
         uicontrol(groundTruthTextfield)
         uiwait(groundTruth_dialog);
+
+        function updateGroundTruthCount
+            tagFilter2 = find(cellfun(@(X) ~isempty(X), cell_metrics.groundTruthClassification));
+            cellCount = zeros(1,length(groundTruthCelltypes));
+            if ~isempty(tagFilter2)
+                filter = [];
+                for i = 1:length(tagFilter2)
+                    filter(i,:) = strcmp(cell_metrics.groundTruthClassification{tagFilter2(i)},groundTruthCelltypes);
+                end
+
+                for j = 1:length({groundTruthCelltypes})
+                    cellCount = sum(filter);
+                end
+            end
+            cellCount = cellstr(num2str(cellCount'))';
+            groundTruthCelltypesList = strcat(groundTruthCelltypes,' (',cellCount,')');
+        end
+
         function UpdateGroundTruthList
-            temp = contains(groundTruthCelltypes,groundTruthTextfield.String,'IgnoreCase',true);
+            temp = find(contains(groundTruthCelltypes,groundTruthTextfield.String,'IgnoreCase',true));
+
             if ~isempty(groundTruthList.Value) && ~any(temp == groundTruthList.Value)
                 groundTruthList.Value = 1;
             end
             if ~isempty(temp)
-                groundTruthList.String = groundTruthCelltypes(temp);
+                groundTruthList.String = groundTruthCelltypesList(temp);
             else
                 groundTruthList.String = {''};
             end
         end
         function  CloseGroundTruth_dialog
             if length(groundTruthList.String)>=groundTruthList.Value
-                choice = groundTruthList.String(groundTruthList.Value);
+                choice = groundTruthCelltypes(groundTruthList.Value);
             end
             dialog_canceled = 0;
             delete(groundTruth_dialog);

diff --git a/CellExplorer_Preferences.m b/CellExplorer_Preferences.m
@@ -40,7 +40,7 @@
 UI.settings.deepSuperficial = {'Unknown','Cortical','Deep','Superficial'};
 UI.settings.tags = {'Good','Bad','Mua','Noise','InverseSpike','Other'};
 UI.settings.groundTruth = {'PV+','NOS1+','GAT1+','SST+','Axoaxonic','5HT3a'}; 
-UI.settings.groundTruthMarkers = {'ok','db','sm','*k','+k','+p'}; % Supports any Matlab marker symbols: https://www.mathworks.com/help/matlab/creating_plots/create-line-plot-with-markers.html
+UI.settings.groundTruthMarkers = {'om','dg','sm','*k','+k','+p'}; % Supports any Matlab marker symbols: https://www.mathworks.com/help/matlab/creating_plots/create-line-plot-with-markers.html
 
 % Cell type classification colors
 UI.settings.cellTypeColors = [[.5,.5,.5];[.8,.2,.2];[.2,.2,.8];[0.2,0.8,0.8];[0.8,0.2,0.8];[.2,.8,.2]];

diff --git a/LoadCellMetricBatch.m b/LoadCellMetricBatch.m
@@ -115,9 +115,11 @@
     end
     if exist(fullfile(clustering_paths{iii},[basenames{iii},'.',saveAs,'.cellinfo.mat']))
         cell_metrics2{iii} = load(fullfile(clustering_paths{iii},[basenames{iii},'.',saveAs,'.cellinfo.mat']));
-    else
+    elseif fullfile(clustering_paths{iii},[saveAs,'.mat'])
         warning('Loading legacy format')
         disp([fullfile(clustering_paths{iii},[basenames{iii},'.',saveAs,'.cellinfo.mat']), ' does not exist'])
+    else 
+        warning('session not found')
     end
     subfields2 = [subfields2(:);fieldnames(cell_metrics2{iii}.cell_metrics)];
     temp = struct2cell(structfun(@class,cell_metrics2{iii}.cell_metrics,'UniformOutput',false));

diff --git a/calc_CellMetrics/calc_CellMetrics.m b/calc_CellMetrics/calc_CellMetrics.m
@@ -724,6 +724,9 @@
 
 if any(contains(metrics,{'manipulation_metrics','all'})) && ~any(contains(excludeMetrics,{'manipulation_metrics'}))
     disp('* Calculating manipulaiton metrics');
+    field2remove = {'manipulations'};
+    test = isfield(cell_metrics,field2remove);
+    cell_metrics = rmfield(cell_metrics,field2remove(test));
     eventFiles = dir(fullfile(basepath,[basename,'.*.manipulation.mat']));
     eventFiles = {eventFiles.name};
     if ~isempty(eventFiles)

diff --git a/db/db_cell_metrics_session_list.mat b/db/db_cell_metrics_session_list.mat
diff --git a/db/db_update_session.m b/db/db_update_session.m
@@ -1,7 +1,7 @@
 function session = db_update_session(session,varargin)
 % Peter Petersen
 % [email protected]
-% Last edited: 17-06-2019
+% Last edited: 27-06-2019
 
 p = inputParser;
 addParameter(p,'forceReload',false,@islogical);
@@ -18,7 +18,7 @@
 %% % % % % % % % % % % % % % % % % % % %
 % Extracellular
 % % % % % % % % % % % % % % % % % % % %
-if session.general.duration == 0 | forceReload
+if ~isfield(session.general,'duration') | session.general.duration == 0 | forceReload
     sr = sessionInfo.rates.wideband;
     if exist(fullfile(session.general.basePath,'info.rhd'))
         Intan_rec_info = read_Intan_RHD2000_file_Peter(pwd);
@@ -52,7 +52,7 @@
 %% % % % % % % % % % % % % % % % % % % %
 % Epochs
 % % % % % % % % % % % % % % % % % % % %
-if any(session.epochs.duration == 0) | forceReload
+if isempty(session.epochs.duration) | any(session.epochs.duration == 0) | forceReload
     duration = [];
     for i = 1:size(session.epochs.name,2)
         fname = 'amplifier.dat';

diff --git a/get_CellMetrics.m b/get_CellMetrics.m
@@ -66,6 +66,7 @@
 addParameter(p,'deepSuperficial',[],@iscell);
 addParameter(p,'animal',[],@iscell);
 addParameter(p,'tags',[],@iscell);
+addParameter(p,'groundTruthClassification',[],@iscell);
 
 parse(p,varargin{:})
 
@@ -99,6 +100,7 @@
 deepSuperficial = p.Results.deepSuperficial;
 animal = p.Results.animal;
 tags = p.Results.tags;
+groundTruthClassification = p.Results.groundTruthClassification;
 
 if isempty(basename)
     s = regexp(basepath, filesep, 'split');
@@ -123,7 +125,7 @@
     cell_metrics = LoadCellMetricBatch('sessions',sessions);
 end
 
-filterIndx = ones(length(cell_metrics.UID),6);
+filterIndx = ones(length(cell_metrics.UID),7);
 if ~isempty(brainRegion)
     filterIndx(:,1) = strcmp(cell_metrics.brainRegion,brainRegion);
 end
@@ -148,6 +150,14 @@
         end
     end
 end
-
-cell_metrics_idxs = find(sum(filterIndx')==6);
+if ~isempty(groundTruthClassification)
+    for i = 1:length(cell_metrics.UID)
+        if ~isempty(cell_metrics.groundTruthClassification{i})
+            filterIndx(i,7) = any(strcmp(cell_metrics.groundTruthClassification{i},groundTruthClassification));
+        else
+            filterIndx(i,7) = 0;
+        end
+    end
+end
+cell_metrics_idxs = find(sum(filterIndx')==7);