fixed ExcludeSweeps to include cell id in output. AnalyzePatchData import cleans up the messed up names

Author: sammykatta

Analysis/SK/AnalyzePatchData.m

@@ -19,7 +19,13 @@
 projects = {'FAT';'SYM'};
 % projects = {'SAR','FAT'};
 
+%fix a couple messed up names
+ephysData.FAT029 = ephysData.FAT029s;
+ephysData.FAT017 = ephysData.FAT017e001;
+ephysData.FAT164 = ephysData.FAT164001;
+ephysData = rmfield(ephysData,{'FAT017e001';'FAT029s';'FAT164001'});
 
+%get rid of the crap/unrelated recordings
 ephysData = FilterProjectData(ephysData, projects);
 
 clear projects;

Analysis/SK/ExcludeSweeps.m

@@ -202,7 +202,7 @@
             sweepsTxt = sweepsTxt(1:end-1); % trim last comma
             sweepsTxt = horzcat('''',sweepsTxt); % prepend ' to force xls text format
 
-            selectedSweeps{totSeries,1}=keepCells(iCell);
+            selectedSweeps{totSeries,1}=keepCells{iCell};
             selectedSweeps{totSeries,2}=keepProts{iCell}(iSeries);
             selectedSweeps{totSeries,3}=sweepsTxt;
 

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

@@ -0,0 +1,89 @@
+%PreIndentNoiseAnalysis.m
+
+
+strainList = {'TU2769'};
+internalList = {'IC6'};
+stimPosition = {'anterior'};
+
+wormPrep = {'dissected'};
+cellDist = [40 100];
+resistCutoff = '<251';
+extFilterFreq = [2.5 5];
+
+noisePreCells = FilterRecordings(ephysData, ephysMetaData,...
+    'strain', strainList, 'internal', internalList, ...
+    'stimLocation', stimPosition, 'wormPrep', wormPrep, ...
+    'cellStimDistUm',cellDist, 'RsM', resistCutoff, ...
+    'stimFilterFrequencykHz', extFilterFreq);
+
+noisePreCells = {'FAT231','FAT232','FAT233','FAT234','FAT235'};
+
+%% Exclusion 
+protList ={'NoisePre','WC_Probe'};
+
+matchType = 'first';
+
+ExcludeSweeps(ephysData, protList, testCell,'matchType',matchType);
+%TODO: Upgrade ExcludeSweeps to allow passing in an existing list, then
+%check recording name/series number against it and skip (if overWriteFlag)
+%if it's already been vetted. Add new recordings to the end of the list,
+%sortrows (and maybe check unique/warn which rows have multiple) and save
+%as new file.
+
+%% Running analysis
+
+noisePre = NonStatNoiseAnalysis(ephysData,protList,noisePreCells,'matchType',matchType);
+clear protList matchType
+
+%% Turn data into tables for Igor
+
+%Get protocol name parts and means/variances for each recording
+preRecs = fieldnames(noisePre);
+recNames = cell(0); % name of cell
+protNames = cell(0); % name of protocol
+stimNames = cell(0); % number of stim (e.g., 1=on, 2=off) as string
+totMeans = cell(0);
+totVars = cell(0);
+
+for iRec = 1:length(preRecs);
+    %get rid of empty rows, which mess with sorting strings later
+    clearEmpty = arrayfun(@(s) isempty(s.protocol),noisePre.(preRecs{iRec}));
+    noisePre.(preRecs{iRec})(clearEmpty)=[];
+    
+    theseStim = cellfun(@(x) sprintf('stim%d',x),...
+        num2cell([noisePre.(preRecs{iRec})(:).stimNum]),'un',0);
+
+    stimNames = [stimNames theseStim];
+    protNames = [protNames vertcat({noisePre.(preRecs{iRec})(:).protocol})];
+    totMeans = [totMeans vertcat({noisePre.(preRecs{iRec})(:).totalMean})];
+    totVars = [totVars vertcat({noisePre.(preRecs{iRec})(:).totalVar})];
+    recNames = [recNames repmat(preRecs(iRec),1,length(noisePre.(preRecs{iRec})))];
+end
+
+[protNames, protIdx] = sort(protNames);
+totMeans = totMeans(protIdx);
+totVars = totVars(protIdx);
+recNames = recNames(protIdx);
+stimNames = stimNames(protIdx);
+
+% Pad with nans and turn means/vars into arrays
+meanLengths = cellfun('length',totMeans);
+maxLength = max(meanLengths);
+totMeans = cellfun(@(x)cat(1,x,NaN(maxLength-length(x),1)),totMeans,'UniformOutput',false);
+totMeans = cell2mat(totMeans);
+totVars = cellfun(@(x)cat(1,x,NaN(maxLength-length(x),1)),totVars,'UniformOutput',false);
+totVars = cell2mat(totVars);
+
+protTimes = cellfun(@(x) sprintf('%sms',x(isstrprop(x,'digit'))), protNames,'un',0);
+
+% Create identifying wave names for Igor
+waveMeanNames = cellfun(@(x,y,z) sprintf('mean_%s_%s_%s', x, y,z), protTimes, stimNames, recNames, 'un',0);
+waveVarNames = cellfun(@(x,y,z) sprintf('var_%s_%s_%s', x, y,z), protTimes, stimNames, recNames, 'un',0);
+
+
+% write into Excel file for loading into Igor
+xlswrite('PatchData/testTrap.xls',waveMeanNames,'means');
+xlswrite('PatchData/testTrap.xls',totMeans,'means','A2');
+
+xlswrite('PatchData/testTrap.xls',waveVarNames,'vars');
+xlswrite('PatchData/testTrap.xls',totVars,'vars','A2');