minor changes to some old notebooks;

DFFunctions/Iterators/singleDayAnal.m

@@ -5,7 +5,6 @@
 % f().function.loadvariables{:}.  Also the function call appends any
 % options in the f().function.options{} cell array.
 %
-%                 Cerulean City
 %                        .|
 %                        | |
 %                        |'|            ._____
@@ -17,7 +16,6 @@
 
 %{
 % Notes:
-%   - city.alien
 % Each function call is for all epochs in a day, and it is assumed that
 % the function's first input is the index to the day, then all epochs ([day ep1 ep2..]).  
 % The second input is a list of exclusion periods [starttime endtime].
@@ -51,7 +49,7 @@
     end
     % iterate through the days within each data group
     g = 1; % this was intended for multiple epoch filter groups, but isn't currently used?
-    fprintf(':::::::: single Day iterator (Cerulean City):::::::: \n');
+    fprintf(':::::::: single Day iterator :::::::: \n');
     tmp = [];
     fout = cell(numel(unqDays),1);
     for d = 1:numel(unqDays) % can use parfor

DFFunctions/getLickBout.m

@@ -25,9 +25,9 @@
 @DKR
 %}
 output_intervals = 0;
-maxILIthresh = .25; % max burst ili threshold in seconds
+maxILIthresh = 1; % max burst ili threshold in seconds
 minILIthresh = .06; % min burst ili threshold in seconds
-minBoutLicks = 3; %filter out bouts with less than boutNum licks
+minBoutLicks = 2; %filter out bouts with less than boutNum licks
 lick = [];
 if ~isempty(varargin)
     assign(varargin{:})

DFFunctions/load_filter_params.m

@@ -20,7 +20,20 @@
 for s = Fp.params
 fprintf('* %s\n', s{1})
 switch s{1}
-% common
+
+%% ========= rewTrigSWRXP =========
+case 'rewTrigSWRXP'
+    win = [-4 10];
+    bin = .001;
+    eventType = 'ca1rippleskons';
+
+case 'dfa_rewTrigSWRXP'
+    iterator = 'singleDayAnal'; %'singleepochanal';
+    filtfunction = 'dfa_rewTrigSWRXP';
+    datatypes = {'ca1rippleskons', 'lick', 'DIO', 'task'};
+    options = {'win', win, 'bin', bin, 'eventType', eventType};     
+
+%% ========= common =========    
 case 'valid_ntrodes'
     %             ntAreas = {'ca1', 'mec', 'ref'}; %, 'por', 'v2l', 'sub'};
     areas = {{'ca1', 'd'}, {'mec', 'deep'}, {'mec', 'supf'}};
@@ -72,7 +85,34 @@
         'minBoutLicks', minBoutLicks, 'cellfilter', cellFilter, ...
         'rippleFilter', rippleFilter};
 
-%% ========= XP-SWR mod 'city.alien' =========
+%% ========= SWR iLB vs eLB =========
+case 'pctILB'
+    eventType = 'ca1rippleskons';
+        % lick burst filter
+    maxILIthresh = 1; % max burst ili threshold in seconds
+    minBoutLicks = 2; % filter out bouts with less than boutNum licks
+    minILIthresh = .06; 
+    stdthresh = [2 3 4];
+
+case 'dfa_pctILB'   
+    iterator = 'singleDayAnal'; %'singleepochanal';
+    filtfunction = 'dfa_pctILB';
+    datatypes = {'ca1rippleskons','task', 'lick', 'DIO'};
+    options = {'eventType', eventType, 'maxILIthresh', maxILIthresh,...
+        'minBoutLicks', minBoutLicks, 'stdthresh', stdthresh, 'minILIthresh', minILIthresh};
+
+%% ========= XP-SWR mod =========
+case 'XPtrigAvgRip'
+    win = [-4 4];
+    eventType = 'ca1rippleskons';
+
+case 'dfa_XPtrigAvgRip'
+    iterator = 'singleDayAnal'; %'singleepochanal';
+    filtfunction = 'dfa_XPtrigAvgRip';
+    datatypes = {'ca1rippleskons','task', 'lick', 'DIO'};
+    options = {'win', win, 'eventType', eventType};     
+
+
 case 'wXPTrigSWR'
     %     maxTimeSinceRew = 5;
     bin = .01;
@@ -90,20 +130,53 @@
     compute_shuffle = 1;
     numshuffs = 1000;
     maxShift = tmax/2; %ms integer. timemod shift
-
+
+
 case 'dfa_lickswrcorr'
     % make sure to include a 'ripples' timefilter in the paramset
     % func
     iterator = 'singleDayAnal'; %'singleepochanal';
     filtfunction = 'dfa_lickswrcorr';
     datatypes = {'ca1rippleskons','task', 'lick', 'DIO'};
+    options = {'bin', bin, 'tmax', tmax, 'eventType', eventType, ...
+        'excShortBin', excShortBin, 'excLongBin', excLongBin, ...
+        'minILIthresh', minILIthresh, 'maxILIthresh', maxILIthresh, ...
+        'rmsmincounts', rmsmincounts, 'rmstmax', rmstmax, 'compute_shuffle', ...
+        compute_shuffle, 'numshuffs', numshuffs, 'shuffOffset', maxShift, ...
+        'minBoutLicks', minBoutLicks};         
+
+case 'XPprepostSWR'    
+        %     maxTimeSinceRew = 5;
+    bin = .01;
+    tmax = .5;
+    eventType = 'ca1rippleskons';
+    minILIthresh = .06; % seconds
+    maxILIthresh = 1; % seconds
+    minBoutLicks = 2;
+    % xcorr / excorr
+    excShortBin = bin; 
+    excLongBin = .500;
+    rmsmincounts = 1; % min bin count within rmstamax. otherwise nan
+    rmstmax = .25; % seconds
+    % shuf
+    compute_shuffle = 1;
+    numshuffs = 1000;
+    maxShift = tmax/2; %ms integer. timemod shift
+
+case 'dfa_XPprepostSWR'
+    % make sure to include a 'ripples' timefilter in the paramset
+    % func
+    iterator = 'singleDayAnal'; %'singleepochanal';
+    filtfunction = 'dfa_XPprepostSWR';
+    datatypes = {'ca1rippleskons','task', 'lick', 'DIO'};
     options = {'bin', bin, 'tmax', tmax, 'eventType', eventType, ...
         'excShortBin', excShortBin, 'excLongBin', excLongBin, ...
         'minILIthresh', minILIthresh, 'maxILIthresh', maxILIthresh, ...
         'rmsmincounts', rmsmincounts, 'rmstmax', rmstmax, 'compute_shuffle', ...
         compute_shuffle, 'numshuffs', numshuffs, 'shuffOffset', maxShift, ...
         'minBoutLicks', minBoutLicks};     
 
+
 %% ========= 'dfa_eventTrigSpiking'=========
 case 'lickboutlicks'
 %     minILIthresh = .06; % seconds
@@ -164,6 +237,17 @@
     win = [1.5 1.5];
     LFPtypes = {'eeg'};
 
+%% ========= ripPos    
+case 'ripPos'    
+    eventType = 'ca1rippleskons';
+
+case 'dfa_ripPos'
+    iterator = 'singleDayAnal'; %'singleepochanal';
+    filtfunction = 'dfa_ripPos';
+    datatypes = {'ca1rippleskons','pos', 'lick'};
+    options = {'eventType', eventType};     
+
+
 %% ========= EPOCH TETRODE CELL RIPPLE filters
 case 'ripples'
     eventType = 'ca1rippleskons';
@@ -177,11 +261,24 @@
         'minstdthresh', minstdthresh,'exclusion_dur',exclusion_dur, ...
         'minvelocity', minvelocity,'maxvelocity',maxvelocity};
 
+case 'ripples>5'
+    eventType = 'ca1rippleskons';
+    consensus_numtets = 2;   % minimum # of tets for consensus event detection
+    minstdthresh = 5;        % STD. how big your ripples are
+    exclusion_dur = .5;  % seconds within which consecutive events are eliminated / ignored
+    minvelocity = 0;
+    maxvelocity = 4;
+    timefilter{end+1} = {'getconstimes', '($cons == 1)', ...
+        'ca1rippleskons', 1,'consensus_numtets',consensus_numtets, ...
+        'minstdthresh', minstdthresh,'exclusion_dur',exclusion_dur, ...
+        'minvelocity', minvelocity,'maxvelocity',maxvelocity};    
+
+
 case 'ripples>2'
     eventType = 'ca1rippleskons';
     consensus_numtets = 2;   % minimum # of tets for consensus event detection
     minstdthresh = 2;        % STD. how big your ripples are
-    exclusion_dur = .5;  % seconds within which consecutive events are eliminated / ignored
+    exclusion_dur = 0;  % seconds within which consecutive events are eliminated / ignored
     minvelocity = 0;
     maxvelocity = 4;
     timefilter{end+1} = {'getconstimes', '($cons == 1)', ...

DFFunctions/load_plotting_params.m

@@ -17,6 +17,12 @@
 end
 for s = param_set
 switch s{1}
+case 'rewTrigSWRXP'    
+    position = [.1 .1 .3 .4];
+    spikeSz = 10;
+    spikeAlpha = .5;
+    win = [-4 10];
+    Pp.bin = .2;
 case 'defaults'
     position = [.1 .1 .4 .4];
     pwin = [1 1];
@@ -38,7 +44,45 @@
 case 'phaseXcorr'
     position = [.1 .1 .5 .5];    
 
+
+%% ========= SWR iLB vs eLB =========
+case 'pctILB-pAn-pDay'
+    position = [.1 .1 .4 .4];
+case 'pctILB'
+    position = [.1 .1 .2 .4];
+
+
 %% ========= XPmod-SWR=========
+case 'XPprepostSWR-pAn-pDay'
+    position = [.1 .1 .2 .8];
+    hbins = 50;
+    preClr = [0.4660 0.6740 0.1880];
+    postClr = [0.4940 0.1840 0.5560];
+case 'XPprepostSWR-pAn'
+    position = [.1 .1 .4 .3];
+    hbins = 50;
+    preClr = [0.4660 0.6740 0.1880];
+    postClr = [0.4940 0.1840 0.5560];
+case 'XPprepostSWR'
+    position = [.1 .1 .4 .3];
+    hbins = 50;
+    preClr = [0.4660 0.6740 0.1880];
+    postClr = [0.4940 0.1840 0.5560];
+
+case 'XPtrigAvgRip-pAn-pDay'
+    position = [.1 .1 .3 .8];
+    win = [-2 2];
+case 'XPtrigAvgRip-pAn'
+    position = [.1 .1 .4 .3];
+    win = [-2 2];
+case 'XPtrigAvgRip'
+    position = [.1 .1 .4 .3];
+    win = [-2 2];
+
+case 'ripPos'
+    position = [.1 .1 .3 .4];
+    size = 80;
+
 case 'wRxnFullAllAn'
     position = [.1 .1 .5 .5];
     winSE = [-.5 .5];

Functions/check_required.m

@@ -0,0 +1,8 @@
+
+function check_required(reqData, vararg)
+
+for s = 1:length(reqData)
+    if ~any(cellfun(@(x) strcmp(x,reqData{s}), vararg(1:2:end), 'un', 1))
+        error(sprintf('missing data: %s ', reqData{~ismember(reqData,vararg(1:2:end))}));
+    end
+end

Functions/getLickBoutLicks.m

@@ -14,9 +14,9 @@
 FFPhy
 @DR
 %}
-maxILIthresh = .25; % max burst ili threshold in seconds
+maxILIthresh = 1; % max burst ili threshold in seconds
 minILIthresh = .06; % min burst ili threshold in seconds
-minBoutLicks = 3; %filter out bouts with less than boutNum licks
+minBoutLicks = 2; %filter out bouts with less than boutNum licks
 lick = [];
 if ~isempty(varargin)
     assign(varargin{:});

Functions/get_dio_output.m

@@ -0,0 +1,34 @@
+function [dioOut, dioOutfields] = get_dio_output(DIO, task, day, eps);
+
+dioOutfields = {'day', 'epoch', 'dioNum', 'dioNumOrig', 'startTime', 'endTime'};
+dioOut = [];
+for e = 1:length(eps)
+    epoch = eps(e);
+    isinput = cellfun(@(x) isequal(x.input,1), DIO{day}{epoch}, 'un', 1);
+    dioID = cellfun(@(x) str2double(regexp(x.original_id,'\d*','Match')), ...
+        DIO{day}{epoch}, 'un', 1);
+    outputdios = task{day}{epoch}.outputdio;
+    outdioIdx = find(all([ismember(dioID, outputdios)' ~isinput'],2));
+    for c = 1:length(outdioIdx)
+        ch = outdioIdx(c);
+        dioTimeCh = double(DIO{day}{epoch}{ch}.times);
+        dioValsCh = double(DIO{day}{epoch}{ch}.values);
+        % dios are Up (1) to Down (0)
+        while ~isempty(dioValsCh) && dioValsCh(1) == 0
+            dioValsCh(1) = []; dioTimeCh(1) = [];
+        end
+        while ~isempty(dioValsCh) && dioValsCh(end) == 1
+            dioValsCh(end) = []; dioTimeCh(end) = [];
+        end
+        if ~isempty(dioValsCh)
+            dioVd = [1; find(abs(diff(dioValsCh)))+1];
+            diotimes = dioTimeCh(dioVd);
+            dioStEnd = [diotimes(1:2:end) diotimes(2:2:end)];
+            numDIO = length(dioStEnd(:,1));
+            dioOut = [dioOut; repmat(day,numDIO,1) repmat(epoch,numDIO,1) ...
+                repmat(ch,numDIO,1) repmat(outputdios(c),numDIO,1) dioStEnd];
+        else
+            continue
+        end
+    end
+end

notebooks/eventtrig_20191117.m

@@ -1,4 +1,6 @@
 %{
+statsfig_20190812: notebook with original spect quantifications
+
 NB 20191117
 finalize swr-trig and lick trig results all animals combined
 .. continuation of suresplickvsswr_20191116

notebooks/xpswrAll_20191105.m

@@ -6,7 +6,7 @@
 
 eventType = 'lick'; %lick swr
 % run FF
-create_filter = 1;
+create_filter = 1;k
 run_ff = 1;
 load_ffdata = 0;
 
@@ -59,7 +59,7 @@
             ifig = init_plot(showfigs, Pp.position);
             days = cell2mat([{F(a).output{1}.index}']);
             ndays = size(days,1);
-            nc = 3;
+            ncols = 3;
             dNormxcZ = {};
             for d = 1:ndays
                 day = days(d,1);
@@ -71,15 +71,15 @@
                     nSWRsN = 0;
                 end
                 g = [nSWRsN nSWRsN nSWRsN];
-                sf1 = subaxis(ndays+1, nc, (d-1)*(nc)+1, Pp.posparams{:});
+                sf1 = subaxis(ndays+1, ncols, (d-1)*(ncols)+1, Pp.posparams{:});
                 bar(idata.time, idata.normxc, 'FaceColor', g)
                 xticks([])
 %                 yticks([])
                 ylim([0 .025])
                 title(sprintf('%d Bouts %d XP. %d swr', size(idata.boutTimes, 1), length(idata.licks), nSWRs));
                 ylabel(sprintf('%d', day));
               %% z-scored
-                sf1 = subaxis(ndays+1, nc, (d-1)*(nc)+2, Pp.posparams{:});
+                sf1 = subaxis(ndays+1, ncols, (d-1)*(ncols)+2, Pp.posparams{:});
                 dNormxc = idata.smthxc;
                 dNormxcSh = idata.smthxcSh;
                 dNormxcZ{d} = (dNormxc - nanmean(dNormxcSh,1)) ./ nanstd(dNormxcSh,[],1);
@@ -89,7 +89,7 @@
                 ylim([-10 10])
                 title(sprintf('%d Bouts %d XP. %d swr', size(idata.boutTimes, 1), length(idata.licks), length(idata.swrLickPhase)));
               %% phase
-                sf2 = subaxis(ndays+1, nc, (d-1)*(nc)+3, Pp.posparams{:});
+                sf2 = subaxis(ndays+1, ncols, (d-1)*(ncols)+3, Pp.posparams{:});
                 polarhistogram(idata.swrLickPhase, 20, 'Normalization', 'pdf', 'facecolor', g)
 %                 rticks([])
                 thetaticks([])
@@ -100,7 +100,7 @@
 
             end
             %% all days normx
-            subaxis(ndays+1, nc, (nc*(d-1))+4, Pp.posparams{:});
+            subaxis(ndays+1, ncols, (ncols*(d-1))+4, Pp.posparams{:});
             swrXPxc = nanmean(cell2mat({F(a).output{1}.smthxc}'));
             bar(idata.time, swrXPxc, 'facecolor', 'b')
             ylabel('all');
@@ -110,14 +110,14 @@
             NormxcZsem = sem(NormxcZ,1);
             NormxcZmean = mean(NormxcZ,1);
 
-            subaxis(ndays+1, nc, (nc*(d-1))+5, Pp.posparams{:});
+            subaxis(ndays+1, ncols, (ncols*(d-1))+5, Pp.posparams{:});
             plot(idata.time, NormxcZmean, 'b')
             hold on
             fill([idata.time'; flipud(idata.time')],[NormxcZmean'-NormxcZsem';flipud(NormxcZmean'+NormxcZsem')],'k',...
                 'linestyle','none', 'facealpha', .2);
             ylim([-10 10])
              %% all days polar
-            subaxis(ndays+1, nc, (nc*(d-1))+6, Pp.posparams{:});
+            subaxis(ndays+1, ncols, (ncols*(d-1))+6, Pp.posparams{:});
             swrXPph = cell2mat({idata.swrLickPhase}');
             polarhistogram(swrXPph, 20, 'Normalization', 'pdf', 'facecolor', 'b')
             rlim([0 .8])