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Merge pull request #350 from buzsakilab/dev
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Pulling dev to master before we do all this new stuff
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@dlevenstein
dlevenstein authored Oct 28, 2019
2 parents d74d373 + db1c43a commit 05a8bd5
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Showing 70 changed files with 2,835 additions and 1,012 deletions.
15 changes: 14 additions & 1 deletion GUITools/EventExplorer/EEhelpers/EventVewPlot.m
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Original file line number Diff line number Diff line change
Expand Up @@ -24,9 +24,12 @@
%viewwin = subplot(3,1,2,'ButtonDownFcn',@MouseClick);
%set(gca,'ButtonDownFcn', @MouseClick)
hold(FO.viewwin,'off')
bz_MultiLFPPlot(FO.data.lfp,'timewin',thiseventwin,'spikes',FO.data.spikes,...
%Plot The LFP
ywinrange = bz_MultiLFPPlot(FO.data.lfp,'timewin',thiseventwin,'spikes',FO.data.spikes,...
'axhandle',FO.viewwin,'scaleLFP',FO.scaleLFP)
hold on

%Plot the events
if size(FO.EventTimes,2) == 1 %Single timepoint events
inwinevents = FO.EventTimes>=thiseventwin(1) & FO.EventTimes<=thiseventwin(2);
inwineventtimes = FO.EventTimes(inwinevents);
Expand All @@ -50,6 +53,16 @@
error('EventTimes error, call in the big guns!')
end

%Plot the behavior
if isfield(FO,'behavior')
numbeh = length(FO.behavior);
for bb = 1:numbeh
inwinbehavior = InIntervals(FO.behavior{bb}.timestamps,thiseventwin);
behnorm = bz_NormToRange(FO.behavior{bb}.data,ywinrange);
plot(FO.behavior{bb}.timestamps(inwinbehavior),behnorm(inwinbehavior))
end
end

%Passthrough info from the plot
viewinfo.thiseventwin = thiseventwin;
viewinfo.inwinevents = inwineventtimes;
Expand Down
23 changes: 23 additions & 0 deletions GUITools/EventExplorer/EventExplorer.m
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Original file line number Diff line number Diff line change
Expand Up @@ -210,6 +210,9 @@
winsizetext = uicontrol('Parent',FO.SignalPanel,...
'Position',[150 70 80 18],'style','text',...
'string','LFP Channel:','HorizontalAlignment','left');
loadbehavior = uicontrol('Parent',FO.SignalPanel,...
'Position',[230 90 50 25],'String','Load Behavior',...
'Callback',@LoadBeh);


%Set up the navigation panel
Expand Down Expand Up @@ -540,6 +543,26 @@ function ChangeLFPChan(obj,event)
EventVewPlot;
end

function LoadBeh(obj,event)
FO = guidata(obj);
FO.lookatchannel=str2num(obj.String);
if isfield(FO,'behavior')
numbeh = length(FO.behavior);
FO.behavior{numbeh+1} = bz_LoadBehavior(FO.basePath);
else
numbeh = 0;
FO.behavior{1} = bz_LoadBehavior(FO.basePath);
end
if ~isfield(FO.behavior{numbeh+1},'data')
hasfields = fieldnames(FO.behavior{numbeh+1});
[s,v] = listdlg('PromptString','Which field is your data?',...
'ListString',hasfields,'SelectionMode','single');
FO.behavior{numbeh+1}.data = FO.behavior{numbeh+1}.(hasfields{s});
end
guidata(FO.fig, FO);
EventVewPlot;
end

function CloseDialog(obj,event)
FO = guidata(obj);
if isfield(FO,'eventsfilename') && isfield(FO,'FlagsAndComments')
Expand Down
137 changes: 97 additions & 40 deletions GUITools/TheStateEditor/TheStateEditor.m
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Original file line number Diff line number Diff line change
Expand Up @@ -323,13 +323,19 @@ function TheStateEditor(baseName, inputData, supressGUI, makePortable)
e = [];
end
catch
try
%First try Anton's LoadBinary - this is not in buzcode
eeg = LoadBinary([baseName, suffix], Chs+1, nCh, [], 'int16', 'single');
disp('No eeg in your eegstates.mat. Loading from .lfp/.eeg file...');
try %first try bz_getLFP
eeg = bz_GetLFP(Chs,'basepath',FO.basePath,'noPrompts',true);
eeg = single(eeg.data)';
catch
%Otherwise try to use Micheal Zugaro
eeg = LoadBinaryIn([baseName, suffix], 'channels', Chs+1, 'nChannels', nCh)';
eeg = double(eeg);
try
% try Anton's LoadBinary
eeg = LoadBinary([baseName, suffix], Chs+1, nCh, [], 'int16', 'single');
catch
%Otherwise try to use Micheal Zugaro
eeg = LoadBinaryIn([baseName, suffix], 'channels', Chs+1, 'nChannels', nCh)';
eeg = single(eeg);
end
end

end
Expand Down Expand Up @@ -357,7 +363,7 @@ function TheStateEditor(baseName, inputData, supressGUI, makePortable)

if exist([baseName '.SleepScoreLFP.LFP.mat'],'file')
load([baseName '.SleepScoreLFP.LFP.mat'])
defaultchans = unique([SleepScoreLFP.SWchanID SleepScoreLFP.THchanID]);
defaultchans = ([SleepScoreLFP.SWchanID SleepScoreLFP.THchanID]);
if length(defaultchans)<2
defaultchans = num2str(defaultchans);
elseif length(defaultchans)>=2
Expand Down Expand Up @@ -1509,8 +1515,8 @@ function DefKey(fig, e)
eeg = getappdata(FO.fig,'eeg');
eegX = (1:length(eeg{1}))/(FO.eegFS/FO.downsample);
% catch
% eeg = F0.eeg;
% eegX = F0
% eeg = FO.eeg;
% eegX = FO
% end

if isempty(varargin)
Expand Down Expand Up @@ -2478,14 +2484,15 @@ function ToggleStateAxisActive(obj,~)
basePath = FO.basePath;

%Load baseName.SleepState.states.mat
SleepState = bz_LoadStates(basePath,'SleepState');
[SleepState,sleepstatefilename] = bz_LoadStates(basePath,'SleepState');

%Check if the SleepState file is new, manually detected, or auto-detected
if isempty(SleepState)
STATESFILETYPE = 'new';
SleepState.detectorinfo.detectorname = 'TheStateEditor';
SleepState.detectorinfo.detectiondate = datestr(now,'yyyy-mm-dd');
SleepState.idx.statenames = {'','','','',''};
SleepState.idx.timestamps = FO.to;
elseif isfield(FO,'AutoScore')
STATESFILETYPE = 'auto';
elseif isfield(SleepState,'detectorinfo')
Expand All @@ -2511,13 +2518,13 @@ function ToggleStateAxisActive(obj,~)
else
idx.statenames = {'WAKE','','NREM','','REM'}; %assume...
end
idx.states = FO.States';
idx.timestamps = FO.to;
%note: FO.to is 0-indexed... does not line up with F0.states. issue with
%loading. to fix.
%Interpolate back to the scoring timestamps
idx.timestamps = SleepState.idx.timestamps;
idx.states = interp1(FO.to,FO.States,idx.timestamps,'nearest');


%Make a buzcode-style ints structure (should wrap this into IDXtoINT.mat)
ints = bz_IDXtoINT(idx,'nameStates',true); %2:end to deal with 0-indexing
ints = bz_IDXtoINT(idx,'nameStates',true);


switch STATESFILETYPE
Expand Down Expand Up @@ -2563,7 +2570,7 @@ function ToggleStateAxisActive(obj,~)
SleepState.detectorinfo.LastManualUpdate = datestr(now,'yyyy-mm-dd');

%Save the results!
save([baseName '.SleepState.states.mat'],'SleepState')
save(sleepstatefilename,'SleepState')


%Make a new figure
Expand Down Expand Up @@ -3797,6 +3804,7 @@ function leftScreenOver(obj,event)
states = FO.States;
ds = logical(abs(diff(states)));%find state switches with 1's
ds = cat(2,ds(:)',0);%pad

%find start
spanstart = find(ds(1:pointTo)>0,1,'last')+1;
if isempty(spanstart)
Expand Down Expand Up @@ -5302,9 +5310,9 @@ function EventNumber(e, src)
if paramsAvailBool
%DL: this seems weird to me...
%why do we assume the detectionparms in SleepState are auto?
F0.AutoScore.detectionparms = detectionparms;
FO.AutoScore.detectionparms = detectionparms;
else
F0.AutoScore.detectionparms = [];
FO.AutoScore.detectionparms = [];
end


Expand Down Expand Up @@ -5350,55 +5358,80 @@ function EventNumber(e, src)


% start figure
h = figure('position',[940 5 480 720]);
h = figure('position',[940 5 960 720]);
set(h, 'MenuBar', 'none');
set(h, 'ToolBar', 'none');

%top plot: Slow wave power
ax1 = subplot(3,1,1,'ButtonDownFcn',@ClickSetsLineXIn);hold on;
ax1 = subplot(3,2,2,'ButtonDownFcn',@ClickSetsLineXIn);hold on;
bar(histsandthreshs.swhistbins,histsandthreshs.swhist)
swline = plot(ax1,[histsandthreshs.swthresh histsandthreshs.swthresh],ylim(ax1),'tag','bw');
swline = plot(ax1,[histsandthreshs.swthresh histsandthreshs.swthresh],ylim(ax1),'r','tag','bw');
xlabel('SWS Band Power (NREM vs other)')
ylabel('Counts (sec)')
ResetToInitButton_sw = uicontrol('style', 'pushbutton', 'String', 'Init', 'Units', 'normalized', 'Position', [0.85, 0.95, 0.15, 0.05]);
ResetToInitButton_sw = uicontrol('style', 'pushbutton', 'String', 'Init', 'Units', 'normalized', 'Position', [0.92, 0.87, 0.08, 0.05]);
set(ResetToInitButton_sw,'Callback',@ResetToInitSw);
ResetToOrigButton_sw = uicontrol('style', 'pushbutton', 'String', 'Orig', 'Units', 'normalized', 'Position', [0.85, 0.9, 0.15, 0.05]);
ResetToOrigButton_sw = uicontrol('style', 'pushbutton', 'String', 'Orig', 'Units', 'normalized', 'Position', [0.92, 0.82, 0.08, 0.05]);
set(ResetToOrigButton_sw,'Callback',@ResetToOrigSw);
StickyThreshCheck_sw = uicontrol('style', 'checkbox', 'String', 'Sticky', 'Units', 'normalized', 'Position', [0.85, 0.85, 0.15, 0.05],...
StickyThreshCheck_sw = uicontrol('style', 'checkbox', 'String', 'Sticky', 'Units', 'normalized', 'Position', [0.92, 0.77, 0.08, 0.05],...
'Value',histsandthreshs.stickySW);
%set(StickyThreshCheck_sw,'Callback',@SetStickySw);

title({'Click in plots to reset X value of thresholds',...
'Setting thresholds to ''Sticky'' will reduce noise'})

%middle plot: EMG amplitude
ax2 = subplot(3,1,2,'ButtonDownFcn',@ClickSetsLineXIn);hold on;
ax2 = subplot(3,2,4,'ButtonDownFcn',@ClickSetsLineXIn);hold on;
bar(histsandthreshs.EMGhistbins,histsandthreshs.EMGhist)
EMGline = plot(ax2,[histsandthreshs.EMGthresh histsandthreshs.EMGthresh],ylim(ax2),'tag','bw');
EMGline = plot(ax2,[histsandthreshs.EMGthresh histsandthreshs.EMGthresh],ylim(ax2),'r','tag','bw');
xlabel('EMG (300-600Hz Correlation, active WAKE vs REM/inactive)')
ylabel('Counts (sec)')
ResetToInitButton_EMG = uicontrol('style', 'pushbutton', 'String', 'Init', 'Units', 'normalized', 'Position', [0.85, 0.62, 0.15, 0.05]);
ResetToInitButton_EMG = uicontrol('style', 'pushbutton', 'String', 'Init', 'Units', 'normalized', 'Position', [0.92, 0.58, 0.08, 0.05]);
set(ResetToInitButton_EMG,'Callback',@ResetToInitEMG);
ResetToOrigButton_EMG = uicontrol('style', 'pushbutton', 'String', 'Orig', 'Units', 'normalized', 'Position', [0.85, 0.57, 0.15, 0.05]);
ResetToOrigButton_EMG = uicontrol('style', 'pushbutton', 'String', 'Orig', 'Units', 'normalized', 'Position', [0.92, 0.53, 0.08, 0.05]);
set(ResetToOrigButton_EMG,'Callback',@ResetToOrigEMG);
StickyThreshCheck_EMG = uicontrol('style', 'checkbox', 'String', 'Sticky', 'Units', 'normalized', 'Position', [0.85, 0.52, 0.15, 0.05],...
StickyThreshCheck_EMG = uicontrol('style', 'checkbox', 'String', 'Sticky', 'Units', 'normalized', 'Position', [0.92, 0.48, 0.08, 0.05],...
'Value',histsandthreshs.stickyEMG);
%set(StickyThreshCheck_EMG,'Callback',@SetStickyEMG);

%bottom plot: Theta power
ax3 = subplot(3,1,3,'ButtonDownFcn',@ClickSetsLineXIn);hold on;
ax3 = subplot(3,2,6,'ButtonDownFcn',@ClickSetsLineXIn);hold on;
bar(histsandthreshs.THhistbins,histsandthreshs.THhist)
THline = plot(ax3,[histsandthreshs.THthresh histsandthreshs.THthresh],ylim(ax3),'tag','bw');
THline = plot(ax3,[histsandthreshs.THthresh histsandthreshs.THthresh],ylim(ax3),'r','tag','bw');
xlabel('Theta ratio (5-10Hz/2-15Hz, REM vs inactive WAKE)')
ylabel('Counts (sec)')
ResetToInitButton_TH = uicontrol('style', 'pushbutton', 'String', 'Init', 'Units', 'normalized', 'Position', [0.85, 0.29, 0.15, 0.05]);
ResetToInitButton_TH = uicontrol('style', 'pushbutton', 'String', 'Init', 'Units', 'normalized', 'Position', [0.92, 0.28, 0.08, 0.05]);
set(ResetToInitButton_TH,'Callback',@ResetToInitTH);
ResetToOrigButton_TH = uicontrol('style', 'pushbutton', 'String', 'Orig', 'Units', 'normalized', 'Position', [0.85, 0.24, 0.15, 0.05]);
ResetToOrigButton_TH = uicontrol('style', 'pushbutton', 'String', 'Orig', 'Units', 'normalized', 'Position', [0.92, 0.23, 0.08, 0.05]);
set(ResetToOrigButton_TH,'Callback',@ResetToOrigTH);
StickyThreshCheck_TH = uicontrol('style', 'checkbox', 'String', 'Sticky', 'Units', 'normalized', 'Position', [0.85, 0.19, 0.15, 0.05],...
StickyThreshCheck_TH = uicontrol('style', 'checkbox', 'String', 'Sticky', 'Units', 'normalized', 'Position', [0.92, 0.18, 0.08, 0.05],...
'Value',histsandthreshs.stickyTH);
%set(StickyThreshCheck_TH,'Callback',@SetStickyTH);

%For 2d cluster plots
broadbandSlowWave = SleepState.detectorinfo.detectionparms.SleepScoreMetrics.broadbandSlowWave;
thratio = SleepState.detectorinfo.detectionparms.SleepScoreMetrics.thratio;
EMG = SleepState.detectorinfo.detectionparms.SleepScoreMetrics.EMG;
plotstates = interp1(FO.to,FO.States,SleepState.detectorinfo.detectionparms.SleepScoreMetrics.t_clus,'nearest');
%right plot
ax4 = subplot(2,2,1);hold on;
for ss = 1:5
plot(ax4,broadbandSlowWave(plotstates==ss),EMG(plotstates==ss),'.','color',FO.colors.states{ss},'markersize',1)
end
swline2 = plot(histsandthreshs.swthresh*[1 1],ylim(ax4),'r','LineWidth',1);
EMGline2 = plot(histsandthreshs.swthresh*[0 1],histsandthreshs.EMGthresh*[1 1],'r','LineWidth',1);
xlabel('Broadband SW');ylabel('EMG')
title('Isolate NREM')


ax5 = subplot(2,2,3);hold on;
for ss = [1 2 4 5]
plot(ax5,thratio(plotstates==ss),EMG(plotstates==ss),'.','color',FO.colors.states{ss},'markersize',1)
end
xlabel('Narrowband Theta');ylabel('EMG')
thline2 = plot(histsandthreshs.THthresh*[1 1],histsandthreshs.EMGthresh*[0 1],'r','LineWidth',1);
EMGline3 = plot([0 1],histsandthreshs.EMGthresh*[1 1],'r','LineWidth',1);
title('Isolate REM from WAKE')

%RESCORE!
ReScoreButton = uicontrol('style', 'pushbutton', 'String', 'Re-Score', 'Units', 'normalized', 'Position', [0.4, 0.01, 0.2, 0.05]);
set(ReScoreButton,'Callback',@ReClusterStates_In);
Expand All @@ -5408,9 +5441,15 @@ function EventNumber(e, src)
AutoClusterFig.ax1 = ax1;
AutoClusterFig.ax2 = ax2;
AutoClusterFig.ax3 = ax3;
AutoClusterFig.ax4 = ax4;
AutoClusterFig.ax5 = ax5;
AutoClusterFig.swline = swline;
AutoClusterFig.EMGline = EMGline;
AutoClusterFig.THline = THline;
AutoClusterFig.swline2 = swline2;
AutoClusterFig.EMGline2 = EMGline2;
AutoClusterFig.thline2 = thline2;
AutoClusterFig.EMGline3 = EMGline3;
AutoClusterFig.stickySWbox = StickyThreshCheck_sw;
AutoClusterFig.stickyEMGbox = StickyThreshCheck_EMG;
AutoClusterFig.stickyTHbox = StickyThreshCheck_TH;
Expand Down Expand Up @@ -5536,7 +5575,7 @@ function ClickSetsLineXIn(obj,ev)
% load detectionparameters if not loaded when user pressed "a" in ViewAutoScoreThresholds
if isfield(FO,'AutoScore')
if isfield(FO.AutoScore,'detectionparms')
dp = F0.AutoScore.detectionparms;
dp = FO.AutoScore.detectionparms;
end
end
if ~exist('dp','var')
Expand Down Expand Up @@ -5568,12 +5607,29 @@ function ClickSetsLineXIn(obj,ev)
% Execute scoring - USE SleepScore toolbox functions
[stateintervals,stateidx,~] = ClusterStates_DetermineStates(...
dp.SleepScoreMetrics,dp.MinTimeWindowParms,FO.AutoScore.histsandthreshs);
%May want to re-make figure here using CluterStates_MakeFigure....
%Pad the beginning and end to match fspec{1}.to
states = stateidx.states';
states = cat(2,zeros(1,stateidx.timestamps(1)-(FO.to(1))),states);
states = cat(2,states,zeros(1,length(FO.to)-length(states)));

plotstates = interp1(stateidx.timestamps,stateidx.states,dp.SleepScoreMetrics.t_clus,'nearest');
%Redraw 2d cluster plots
cla(FO.AutoClusterFig.ax4)
for ss = 1:5
plot(FO.AutoClusterFig.ax4,dp.SleepScoreMetrics.broadbandSlowWave(plotstates==ss),...
dp.SleepScoreMetrics.EMG(plotstates==ss),'.','color',FO.colors.states{ss},'markersize',1)
end
plot(FO.AutoClusterFig.ax4,swthresh.*[1 1],ylim(FO.AutoClusterFig.ax4),'r','LineWidth',1);
plot(FO.AutoClusterFig.ax4,[0 swthresh],EMGthresh.*[1 1],'r','LineWidth',1);

cla(FO.AutoClusterFig.ax5)
for ss = [1 2 4 5]
plot(FO.AutoClusterFig.ax5,dp.SleepScoreMetrics.thratio(plotstates==ss),...
dp.SleepScoreMetrics.EMG(plotstates==ss),'.','color',FO.colors.states{ss},'markersize',1)
end
plot(FO.AutoClusterFig.ax5,THthresh.*[1 1],[0 EMGthresh],'r','LineWidth',1);
plot(FO.AutoClusterFig.ax5,[0 1],EMGthresh.*[1 1],'r','LineWidth',1);

%Interpolate to match fspec{1}.to
states = interp1(stateidx.timestamps,stateidx.states,FO.to,'nearest');
states(isnan(states)) = 0; %Bug fix DL - FO.to starts at time 0....

FO.States = states;
guidata(FO.fig,FO);
modifyStates(1, states, 0);
Expand Down Expand Up @@ -6699,6 +6755,7 @@ function chkinputdatatype_In(varargin)
error('Your SleepState is broken.')
end

states(isnan(states)) = 0; %Bug fix DL

%% END for TheStateEditor
end
12 changes: 8 additions & 4 deletions analysis/lfp/SpectralAnalyses/bz_WaveSpec.m
View file
Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,7 @@
% 'showprogress' true/false (default:false)
% 'saveMat ' put the basePath to save an LFP file
% 'MatNameExtraText' text(X) to add to name as in: 'basename.wavespec(text).lfp.mat'
% 'downsampleout' factor by which to downsample output (default: 1)
% =========================================================================
%
%OUTPUT
Expand Down Expand Up @@ -79,6 +80,7 @@
addParameter(parms,'fvector',[]);
addParameter(parms,'intervals',[-Inf Inf])
addParameter(parms,'chanID',[])
addParameter(parms,'downsampleout',1)

parse(parms,varargin{:})
frange = parms.Results.frange;
Expand All @@ -93,6 +95,7 @@
fvector = parms.Results.fvector;
intervals = parms.Results.intervals;
chanID = parms.Results.chanID;
downsampleout = parms.Results.downsampleout;


%Channel restrict
Expand Down Expand Up @@ -153,16 +156,17 @@
%Filter with wavelets
nfreqs = size(freqs,2);
nchan = size(lfp.data,2);
ntime = size(lfp.data,1);
ntime = ceil(size(lfp.data,1)./downsampleout);
wavespec.data = nan(ntime,nfreqs,nchan);
wavespec.timestamps = lfp.timestamps;
wavespec.timestamps = downsample(lfp.timestamps,downsampleout);
for cidx = 1:nchan
for f_i = 1:nfreqs
if showprogress
bz_Counter(f_i,nfreqs,'Wavelet Frequency')
end
wavelet = MorletWavelet(freqs(f_i),ncyc,si);
wavespec.data(:,f_i,cidx) = FConv(wavelet',lfp.data(:,cidx));
wavespec.data(:,f_i,cidx) = ...
downsample(FConv(wavelet',lfp.data(:,cidx)),downsampleout);
end
end

Expand All @@ -174,7 +178,7 @@

wavespec.freqs = freqs;
wavespec.nfreqs = nfreqs;
wavespec.samplingRate = samplingRate;
wavespec.samplingRate = samplingRate./downsampleout;
if isstruct(lfp) && isfield(lfp,'channels')
wavespec.channels = lfp.channels;
end
Expand Down
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