updated classifiers in sigInspectAutoLabel

ebakstein · Dec 9, 2016 · e799144 · e799144
1 parent 80fb877
commit e799144
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Showing 8 changed files with 448 additions and 61 deletions.
diff --git a/README.md b/README.md
@@ -1,2 +1,2 @@
 # sigInspect
-Matlab GUI tool for inspection and automatic artifact detection in microelectrode EEG
+Matlab GUI tool for inspection and automatic artifact detection in microelectrode EEG
diff --git a/manual/sigInspectExploratory.png b/manual/sigInspectExploratory.png
diff --git a/sigInspect.m b/sigInspect.m
@@ -71,12 +71,14 @@ function sigInspect_OpeningFcn(hObject, eventdata, handles, varargin)
 
 % overview window
 handles.settings.OVERVIEW_DECIMATE_FACTOR = 20;                             % decimate signals by this factor before view in the overview window - this is multipliet with the basic DECIMATE_FACTOR
-handles.settings.OVERVIEW_GAIN = 10;                                        % increase gain in overview window (to adapt for decimation)
+handles.settings.OVERVIEW_GAIN = 5;                                         % increase gain in overview window (to adapt for decimation)
 handles.settings.OVERVIEW_ALWAYS_ON_TOP = 0;                                % keeps overview window always on top
+handles.settings.OVERVIEW_CHANNEL_COLOR = [0,0.447,0.741];                  % signal color in overview window
+handles.settings.OVERVIEW_ARTIFACT_COLOR='r';                               % color to plot artifacts (shown in overview only)
 
 % automatic artifact type buttons - TODO:
 handles.settings.ARTIFACT_TYPES={'ARTIF','UNSURE'};                         % cell array with artifact type abbreviations (max TODO types)
-handles.settings.ARTIFACT_COLOR='r';                                        % NOT IMPLEMENTED YET color to plot artifacts (shown in overview only), cycled if more artifact types than colors
+handles.settings.ARTIFACT_AUTOLABEL_WHICH=1;                                % which artifact type shall be use in sigInspectAutoLabel (just for compatibility)
 
 % spectrogram
 handles.settings.SPECTROGRAM_NFFT = 1024;                                   % points to be used in spectrogram FFT
@@ -91,7 +93,9 @@ function sigInspect_OpeningFcn(hObject, eventdata, handles, varargin)
 handles.settings.PLOT_STEP = 150;                                           % distance on the y axis between channels
 handles.settings.PLOT_CHANNELS = 5;                                         % max. number of prallel channels to plot (max. 9)
 handles.settings.REVERSE_CHANNEL_ORDER = 1;                                 % 0: first channel at the top, last at the bottom 1: first channel at the bottom
-
+handles.settings.CHANNELS_SAME_COLOR = 0;                                   % 0: use different color for each channel (see CHANNEL_COLORS) 1: use same color for all channels (first color from CHANNEL_COLORS)
+handles.settings.CHANNEL_COLORS = {[0,0.447,0.741],...                      % cell array of channel colors in time series plot, if there are more channels than colors, colors are repeated. First color used if CHANNELS_SAME_COLOR=1
+    [0.85,0.325,0.098],[0.929,0.694,0.125],[0.494,0.184,0.556],[0.466,0.674,0.188],[0.301,0.745,0.933],[0.635,0.078,0.184]};
 
 % audio
 handles.settings.START_WITH_SOUND_ON = 0;                                   % start with sound turned on
@@ -148,10 +152,10 @@ function sigInspect_OpeningFcn(hObject, eventdata, handles, varargin)
             [fileName, pathName, fileIndex] = uigetfile('*.mat','sigInspect: Select *.mat file with signal(s)');
             filePath = [pathName fileName];
 
-            if(~ischar(fileName))
+            if(~ischar(fileName))            
                 h=errordlg(['sigInspect can not start without a signal - please select mat file with signals or provide signals or interface as an input parameter'],'can not start without signals', 'modal');
                 waitfor(h)
-                continue
+                return
             end
 
             try
@@ -253,6 +257,19 @@ function sigInspect_OpeningFcn(hObject, eventdata, handles, varargin)
     handles.curSigInfo=''; % current signal info, provided by interface
     handles.spectroWholePatch=[]; % handle to second-showing patch in whole spectrogram
 
+    % color settings
+    if(isempty(handles.settings.CHANNEL_COLORS) || ~iscell(handles.settings.CHANNEL_COLORS))
+        warning('Invalid color format in handles.settings.CHANNEL_COLORS. Should be a nonempty cell array of color specifiers compatible with plot function (RGB triples or character shortcuts). Using default (blue)')
+        handles.settings.CHANNEL_COLORS = {[0,0.447,0.741]};
+    end
+    if(handles.settings.CHANNELS_SAME_COLOR)
+        handles.internal.channelColors = handles.settings.CHANNEL_COLORS(1);
+    else
+        handles.internal.channelColors = handles.settings.CHANNEL_COLORS(:);
+    end
+    %           repeat for all possible channels
+    handles.internal.channelColors = repmat(handles.internal.channelColors,ceil(handles.internal.MaxChannels/length(handles.internal.channelColors)),1);
+    handles.internal.channelColors = handles.internal.channelColors(1:handles.internal.MaxChannels);
 
     % for overview window
     handles.overviewFig = []; % overview window figure handle
@@ -362,15 +379,16 @@ function sigInspect_OpeningFcn(hObject, eventdata, handles, varargin)
     if(~isempty(fld))
         for fi=1:length(fld)            
             fName=fld{fi};
-            intVal=interface.settings.(fName);
-            setVal=handles.settings.(fName);
 
             % check if settings field exists
             if(~isfield(handles.settings, fName))
                 warning('nonexistent settings field in interface: %s - skipping',fName)
                 continue;
-            end                
-
+            end
+
+            intVal=interface.settings.(fName);
+            setVal=handles.settings.(fName);
+
             % check if new field is not empty
             if(isempty(intVal))
                 warning('empty interface settings field: %s - skipping',fName)
@@ -501,8 +519,8 @@ function redraw(handles,adaptGainToSignal)
         % amplify
         sig = sig*get(handles.gainEdit,'Value');        
 
-        % plot
-        plot(t,sig+yShift)
+        % plot        
+        plot(t,sig+yShift,'color',handles.internal.channelColors{ci});
 
         % constant samples
         if(handles.settings.CHECK_CONST_SAMPLES)
@@ -570,14 +588,14 @@ function redrawOverview(handles, justPatch)
                    % amplify
                    sig = sig*get(handles.gainEdit,'Value')*handles.settings.OVERVIEW_GAIN;        
                    % plot
-                   plot(handles.overviewSigAxes,t,sig+yShift);
+                   plot(handles.overviewSigAxes,t,sig+yShift,'color',handles.settings.OVERVIEW_CHANNEL_COLOR);
 
                    % overplot annotation
                    plotInds = getOverviewAnnotInds(handles, ii);
                    if(any(plotInds))
                        sigTmp = sig;
                        sigTmp(~plotInds)= nan;
-                       plot(handles.overviewSigAxes,t,sigTmp+yShift,'Color',handles.settings.ARTIFACT_COLOR)
+                       plot(handles.overviewSigAxes,t,sigTmp+yShift,'Color',handles.settings.OVERVIEW_ARTIFACT_COLOR)
                    end
                 end                  
                 ylim(handles.overviewSigAxes,[0 (Nch+1)*handles.settings.PLOT_STEP]);
@@ -633,7 +651,7 @@ function redrawOverview(handles, justPatch)
 
     anT = (1:size(annot,2))-.5;
     sigT=(0:sigN-1)/handles.samplingFreqOverview;
-    plotInds = logical(interp1(anT,annot,sigT,'nearest','extrap'));
+    plotInds = logical(interp1(anT,double(annot),sigT,'nearest','extrap'));
 
 
 

diff --git a/sigInspectAutoLabel.m b/sigInspectAutoLabel.m
@@ -1,5 +1,5 @@
-function annotation = sigInspectAutoLabel(interfSignalOrPath, pathToSave, method)
-% annot = sigInspectAutoLabel(iterfSignalOrPath, pathToSave, method...)  
+function annotation = sigInspectAutoLabel(interfSignalOrPath, pathToSave, method, varargin)
+% annot = sigInspectAutoLabel(iterfSignalOrPath, pathToSave, method, params)  
 %   label all signals from provided cell array or interface using pre-learned 
 %   classifier, return/save annot
 %
@@ -24,18 +24,23 @@
 %   pathToSave - file path to save *.mat file with generated annotation
 %                to.(only if no output parameters are set
 %                default: sigInspectAutoAnnotationyyyy-mm-dd-HHMMSS.mat.
+%   params     - one or more parameters for the selected method. See
+%                sigInspectClassify for details.
+% 
 % OUT
 %   annot - annotation structure (optional)
 % 
 % E. Bakstein 2015-06-26
+% UPDATES: 20161010 - reworked, additional classifiers (tree, cov)
 % 
 
-if(nargin<2)
-    method=[]; % use default of sigInspectClassify
-end
 
 
 fprintf('----------- sigInspectAutoLabel -------------\n')
+if(nargin<3)
+    method=[]; % use default of sigInspectClassify
+    fprintf('Classification method unspecified, using psd(default)\n')
+end
 fprintf('initialization ')
 
 interface = initInterface(interfSignalOrPath);
@@ -65,10 +70,20 @@
 end
 Nartif = length(artifactTypes);
 
+% default field to store automatic artifact in
+if(isprop(interface,'settings') && isfield(interface.settings,'ARTIFACT_AUTOLABEL_WHICH'))
+    artifactAutoWhich =interface.settings.ARTIFACT_AUTOLABEL_WHICH;
+    fprintf('auto artifact will be stored at position %d (%s)(from interface)\n',artifactAutoWhich,artifactTypes{artifactAutoWhich});
+else
+    artifactAutoWhich = 1;
+    fprintf('auto artifact will be stored at position %d (%s)(DEFAULT)\n',artifactAutoWhich,artifactTypes{artifactAutoWhich});
+end
+
+
 % init empty annotation array
 annotation=cell(length(signalIds),1);
 
-fprintf(' ... DONE\n');
+fprintf(' ... ihitialization done\n');
 
 % go through all signals
 tic
@@ -77,29 +92,40 @@
     sigId=signalIds{ii};
     [curSignals ~]=interface.getSignalsById(sigId);
     [Nr,Nc] = size(curSignals);
-    fprintf('   > signal %s (%d/%d)',sigId, ii,N)
     Nsec=ceil(Nc/samplingFreq);
+    fprintf('   > signal %s (%d/%d), %ds',sigId, ii,N,Nsec)
 
     % init empty annot
     % annotation matrix - rows=channels, columns=seconds, slices=artifact types
-    allAn = false(Nr,Nsec,Nartif); 
+%     allAn = false(Nr,Nsec,Nartif); 
+%     
+%     artSec=[];
+%     % process all channels
+%     for ci=1:Nr
+%         
+%         curAn = sigInspectClassify(curSignals(ci,:),samplingFreq, method);
+%         
+%         allAn(ci,:,1)=curAn;
+%         artSec(ci) = sum(curAn>0);
+%     end
+
+    % all channels at once
 
-    artSec=[];
-    % process all channels
-    for ci=1:Nr
-
-        curAn = sigInspectClassify(curSignals(ci,:),samplingFreq, method);
-
-        allAn(ci,:,1)=curAn;
-        artSec(ci) = sum(curAn>0);
-    end
+    allAn = false(Nr,Nsec,Nartif); 
+    curAn = sigInspectClassify(curSignals,samplingFreq, method,varargin{:});        
+    allAn(:,:,artifactAutoWhich)=curAn; % channel, second, artif. type
 
-    fprintf(' > (%s) artifact seconds in channels \n',num2str(artSec))
+    % annot summary
+    artSec = sum(any(curAn,3),2);
+    fprintf(' > %s artifact seconds in channels \n',sprintf('%d,',artSec))
 
+    % store 
+    annotation{ii} = allAn;
     % pad to artifact type count Nartif
-    annotation{ii} = padarray(allAn,[0 0 (Nartif-size(allAn,3))],0,'post');
+    % annotation{ii} = padarray(allAn,[0 0 (Nartif-size(allAn,3))],0,'post');
 
 end
+
 fprintf('DONE: signals labelled in %.2f seconds----\n',toc)
 
 % save annotation to *.mat file