FreqAnalysis now normalizes the whole sweep to on1 peak if normalizeFlag is on instead of just the mean stats, SinePowerSpec script added section to exclude sweeps based on PD trace and combine that info, selectSweeps simplified tVec calc

Author: sammykatta

Analysis/SK/GUIs/selectSweepsGUI.m

@@ -64,7 +64,7 @@
     case 'A'
         for iSweep = 1:nSweeps
             % Plot the sweep in its proper subplot against time
-            tVec = 0:1/sf:length(data(:,iSweep,1))/sf-(1/sf);
+            tVec = (0:length(data(:,iSweep,1))-1)/sf;
             handles.plt(iSweep) = subplot(nRows,nCols,iSweep,...
                 'Parent', handles.uip);
             plot(tVec,data(:,iSweep,1)*1E12);
@@ -92,7 +92,7 @@
         if isempty(strfind(protName,'Calib')) && channel == 1 % for non-PD calib traces, current clamp traces
             for iSweep = 1:nSweeps
                 % Plot the sweep in its proper subplot against time
-                tVec = 0:1/sf:length(data(:,iSweep,1))/sf-1/sf;
+                tVec = (0:length(data(:,iSweep,1))-1)/sf;
                 handles.plt(iSweep) = subplot(nRows,nCols,iSweep,...
                     'Parent', handles.uip);
                 plot(tVec,data(:,iSweep,1)*1E3);
@@ -112,7 +112,7 @@
         elseif isempty(strfind(protName,'Calib')) && channel == 3 % for PD signal for non-calib traces
             for iSweep = 1:nSweeps
                 % Plot the sweep in its proper subplot against time
-                tVec = 0:1/sf:length(data(:,iSweep,1))/sf-1/sf;
+                tVec = (0:length(data(:,iSweep,1))-1)/sf;
                 handles.plt(iSweep) = subplot(nRows,nCols,iSweep,...
                     'Parent', handles.uip);
                 plot(tVec,data(:,iSweep,2)); %leak-subtracted trace
@@ -132,7 +132,7 @@
         else % for PD calib traces
             for iSweep = 1:nSweeps
                 % Plot the sweep in its proper subplot against time
-                tVec = 0:1/sf:length(data(:,iSweep,1))/sf-1/sf;
+                tVec = (0:length(data(:,iSweep,1))-1)/sf;
                 handles.plt(iSweep) = subplot(nRows,nCols,iSweep,...
                     'Parent', handles.uip);
                 plot(tVec,data(:,iSweep,1));

Analysis/SK/Scripts-in-progress/FrequencyAnalysis.m

@@ -3,6 +3,9 @@
 % 
 % parameters in SinePeaks{:,3}:
 % [sineStart sineEnd sineFreq nReps steadyI sqOn1 sqOff1 sqOn2 sqOff2 sqOnRatio sqOffRatio]
+% 
+% normalize flag also normalizes the individual saved sweeps
+
 
 function sinePeaks = FrequencyAnalysis(ephysData, ephysMetaData, protList, varargin)
 
@@ -319,7 +322,8 @@
 
             stimMetaData(:,1:2) = sortedStim{1,iStim}(profileStartIdx,1:2);
             stimMetaData(:,3) = eachStimProfile(:,iStim);
-            stimMetaData(:,4) = nReps;
+            stimMetaData(:,4) = repmat(extFilterFreq{iCell},size(stimMetaData,1),1);
+            stimMetaData(:,5) = nReps;
 
             % Find mechanoreceptor current peaks and append to sinePeaks for
             % that stimulus number.
@@ -341,6 +345,8 @@
 
     if normalizeFlag
         steadyMeans = steadyMeans./squareMeans(:,1);
+        normMeans = num2cell(squareMeans(:,1)*1e-12);
+        theseSweeps = cellfun(@(x,y) x/y, theseSweeps,normMeans','un',0);
     end
 
     sinePeaks{iCell,1} = cellName;

Analysis/SK/Scripts-in-progress/SinePowerSpec.m

@@ -5,7 +5,7 @@
 stimPosition = {'anterior'};
 wormPrep = {'dissected'};
 cellDist = [40 150];
-extFilterFreq = 5;
+extFilterFreq = [2.5 5];
 includeFlag = 1;
 
 antSineCells = FilterRecordings(ephysData, ephysMetaData,...
@@ -16,14 +16,61 @@
 
 clear cellDist strainList internalList cellTypeList stimPosition resistCutoff ans wormPrep;
 
+%NEXT: check to see if there's a difference in the power spectrum (and
+%amplitude attenuation where applicable) for 2.5 vs. 5kHz photodiode
+%signals. If they look the same, combine the data.
+
 %%
+
 ExcludeSweeps(ephysData, protList, antSineCells, 'matchType', matchType, 'channel', 1);
 
 clear protList matchType;
 
+%% Check if the PD signal is useful/shows abnormalities
+% Make list of only sweeps with stable current AND good PD signal (lower
+% noise, high enough voltage for SNR, no weird movements during sine)
+
+% selectedSweeps_I = ExcludeSweeps(ephysData, protList, antSineCells, 'matchType', matchType, 'channel', 1);
+% selectedSweeps_PD = ExcludeSweeps(ephysData, protList, antSineCells, 'matchType', matchType, 'channel', 3);
+
+selectedSweeps_I = ImportMetaData();
+selectedSweeps_PD = ImportMetaData();
+
+
+% This method of comparing the two lists only works if there's only one
+% series/sweep per row. It simply concatenates cell ID, series, and sweep
+% number into a char row. For more sweeps per series, you will need to loop
+% (find matching cell/series combo, then check which sweeps are matching).
+a = selectedSweeps_I;
+b = selectedSweeps_PD;
+a(:,2) = cellfun(@num2str, a(:,2),'un',0);
+b(:,2) = cellfun(@num2str, b(:,2),'un',0);
+
+a = cellfun(@(x,y,z) [x y z], a(:,1),a(:,2),a(:,3),'un',0);
+b = cellfun(@(x,y,z) [x y z], b(:,1),b(:,2),b(:,3),'un',0);
+a = vertcat(a{:});
+b = vertcat(b{:});
+
+selectIdx = ismember(a,b,'rows');
+
+selectedSweeps = selectedSweeps_I(selectIdx,:);
+selectedSweeps(:,3) = cellfun(@(x) ['' x],selectedSweeps(:,3));
+
+% save the new selectedSweeps list to file
+[filename, pathname] = uiputfile(...
+    {'*.xls;*.xlsx', 'Excel files';
+    '*.*', 'All files'}, ...
+    'Save sweep list to .xls file:');
+fName = fullfile(pathname,filename);
+xlswrite(fName, selectedSweeps);
+
+clear fName filename pathname a b selectedSweeps_I selectedSweeps_PD selectedSweeps selectIdx
+
+
 %%
 sinePeaksNorm = FrequencyAnalysis(ephysData, ephysMetaData, protList, 'matchType', matchType, 'norm', 1);
 
+sinePeaks = FrequencyAnalysis(ephysData, ephysMetaData, protList, 'matchType', matchType, 'norm', 0);
 % okay we're just going to plot the power spectrum in the morning and
 % ignore the bode plot because I don't know what a "system" object really
 % is in matlab or if my data can be one, or what a linear time-invariant
@@ -97,13 +144,15 @@
 
 %% Plot steady state sine comparison
 
+whichPeaks = sinePeaksNorm;
+
 eachFreq = [0 10 30 100 200 500 1000];
 sf = 10000; %Hz
 allSteady = [];
 allSize = [];
 
-for iRec = 1:size(sinePeaksNorm,1)
-    theseSizes = sinePeaksNorm{iRec,3}(:,[1:3,5]);
+for iRec = 1:size(whichPeaks,1)
+    theseSizes = whichPeaks{iRec,3}(:,[1:3,6]);
 
     for iFreq = 1:size(theseSizes,1)
         allSteady = [allSteady; theseSizes(iFreq,4)];