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gui updates; predictData gets NT from rez
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@nsteinme
nsteinme committed Feb 22, 2019
1 parent 88e1733 commit 106f144
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Showing 2 changed files with 125 additions and 25 deletions.
148 changes: 124 additions & 24 deletions gui/ksGUI.m
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Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,7 @@
% - when re-loading old file and whitening matrix already exists, use
% it rather than re-compute
% - button to easily match folders to the source
% - why doesn't computeWhitening run on initial load?

properties
H % struct of handles to useful parts of the gui
Expand Down Expand Up @@ -147,7 +148,7 @@ function build(obj, f)
'Parent', obj.H.setRunVBox, ...
'Title', 'Run', 'FontSize', 18,...
'FontName', 'Myriad Pro');
obj.H.setRunVBox.Sizes = [-2 -1];
obj.H.setRunVBox.Sizes = [-4 -1];

obj.H.probePanel = uiextras.Panel(...
'Parent', obj.H.mainSection, ...
Expand Down Expand Up @@ -210,11 +211,34 @@ function build(obj, f)
'Style', 'text', 'HorizontalAlignment', 'right', ...
'String', 'Sampling frequency (Hz)');

% choose max number of clusters
obj.H.settings.setNfiltTxt = uicontrol(...
% choose threshold
obj.H.settings.setThTxt = uicontrol(...
'Parent', obj.H.settingsGrid,...
'Style', 'text', 'HorizontalAlignment', 'right', ...
'String', 'Number of templates');
'String', 'Threshold');

% good channels
obj.H.settings.setMinfrTxt = uicontrol(...
'Parent', obj.H.settingsGrid,...
'Style', 'text', 'HorizontalAlignment', 'right', ...
'String', 'Min. firing rate per chan (0=include all chans)');

% lambda
obj.H.settings.setLambdaTxt = uicontrol(...
'Parent', obj.H.settingsGrid,...
'Style', 'text', 'HorizontalAlignment', 'right', ...
'String', 'Lambda');

% ccsplit
obj.H.settings.setCcsplitTxt = uicontrol(...
'Parent', obj.H.settingsGrid,...
'Style', 'text', 'HorizontalAlignment', 'right', ...
'String', 'CC Split');

obj.H.settings.setTrangeTxt = uicontrol(...
'Parent', obj.H.settingsGrid,...
'Style', 'text', 'HorizontalAlignment', 'right', ...
'String', 'Time range (s)');

% advanced options
obj.H.settings.setAdvancedTxt = uicontrol(...
Expand Down Expand Up @@ -255,13 +279,31 @@ function build(obj, f)
'Parent', obj.H.settingsGrid,...
'Style', 'edit', 'HorizontalAlignment', 'left', ...
'String', '30000', 'Callback', @(~,~)obj.updateFileSettings());
obj.H.settings.setNfiltEdt = uicontrol(...
obj.H.settings.setThEdt = uicontrol(...
'Parent', obj.H.settingsGrid,...
'Style', 'edit', 'HorizontalAlignment', 'left', ...
'String', '');
obj.H.settings.setMinfrEdt = uicontrol(...
'Parent', obj.H.settingsGrid,...
'Style', 'edit', 'HorizontalAlignment', 'left', ...
'String', '');
obj.H.settings.setLambdaEdt = uicontrol(...
'Parent', obj.H.settingsGrid,...
'Style', 'edit', 'HorizontalAlignment', 'left', ...
'String', '');
obj.H.settings.setCcsplitEdt = uicontrol(...
'Parent', obj.H.settingsGrid,...
'Style', 'edit', 'HorizontalAlignment', 'left', ...
'String', '');
obj.H.settings.setTrangeEdt = uicontrol(...
'Parent', obj.H.settingsGrid,...
'Style', 'edit', 'HorizontalAlignment', 'left', ...
'String', '');



set( obj.H.settingsGrid, ...
'ColumnSizes', [-1 -1], 'RowSizes', -1*ones(1,8) );%
'ColumnSizes', [-1 -1], 'RowSizes', -1*ones(1,12) );%

obj.H.runVBox = uiextras.VBox(...
'Parent', obj.H.runPanel,...
Expand Down Expand Up @@ -304,20 +346,21 @@ function build(obj, f)
'Callback', @(~,~)obj.runSaveToPhy());

% button for write script
obj.H.settings.writeBtn = uicontrol(...
'Parent', obj.H.runVBox,...
'Style', 'pushbutton', 'HorizontalAlignment', 'left', ...
'String', 'Write this run to script', ...
'Callback', @(~,~)obj.writeScript());
% obj.H.settings.writeBtn = uicontrol(...
% 'Parent', obj.H.runVBox,...
% 'Style', 'pushbutton', 'HorizontalAlignment', 'left', ...
% 'String', 'Write this run to script', ...
% 'Callback', @(~,~)obj.writeScript());

% button for save defaults
obj.H.settings.saveBtn = uicontrol(...
'Parent', obj.H.runVBox,...
'Style', 'pushbutton', 'HorizontalAlignment', 'left', ...
'String', 'Save state', ...
'Callback', @(~,~)obj.saveGUIsettings());
% obj.H.settings.saveBtn = uicontrol(...
% 'Parent', obj.H.runVBox,...
% 'Style', 'pushbutton', 'HorizontalAlignment', 'left', ...
% 'String', 'Save state', ...
% 'Callback', @(~,~)obj.saveGUIsettings());

obj.H.runVBox.Sizes = [-3 -1 -1];
%obj.H.runVBox.Sizes = [-3 -1 -1];
obj.H.runVBox.Sizes = [-1];

% -- Probe view
obj.H.probeAx = axes(obj.H.probePanel);
Expand Down Expand Up @@ -537,14 +580,18 @@ function updateFileSettings(obj)
if obj.P.probeGood
set(obj.H.settings.runBtn, 'enable', 'on');
set(obj.H.settings.runPreprocBtn, 'enable', 'on');
end
end

obj.refocus(obj.H.settings.ChooseFileTxt);

end

function advancedPopup(obj)

% bring up popup window to set other ops
obj.log('setting advanced options not yet implemented.');
helpdlg({'To set advanced options, do this in the command window:','',...
'>> ks = get(gcf, ''UserData'');',...
'>> ks.ops.myOption = myValue;'})

end

Expand Down Expand Up @@ -585,17 +632,54 @@ function prepareForRun(obj)
chanMap.ycoords = obj.P.chanMap.ycoords(conn);
obj.ops.chanMap = chanMap;

obj.ops.Nfilt = str2double(obj.H.settings.setNfiltEdt.String);
% sanitize options set in the gui

%obj.ops.Nfilt = str2double(obj.H.settings.setNfiltEdt.String);
if isempty(obj.ops.Nfilt)||isnan(obj.ops.Nfilt)
obj.ops.Nfilt = numel(obj.ops.chanMap.chanMap)*2.5;
end
if mod(obj.ops.Nfilt,32)~=0
obj.ops.Nfilt = ceil(obj.ops.Nfilt/32)*32;
end
obj.H.settings.setNfiltEdt.String = num2str(obj.ops.Nfilt);
%obj.H.settings.setNfiltEdt.String = num2str(obj.ops.Nfilt);

obj.ops.NchanTOT = str2double(obj.H.settings.setnChanEdt.String);

obj.ops.minfr_goodchannels = str2double(obj.H.settings.setMinfrEdt.String);
if isempty(obj.ops.minfr_goodchannels)||isnan(obj.ops.minfr_goodchannels)
obj.ops.minfr_goodchannels = 0.1;
end
if obj.ops.minfr_goodchannels==0
obj.ops.throw_out_channels = false;
else
obj.ops.throw_out_channels = true;
end
obj.H.settings.setMinfrEdt.String = num2str(obj.ops.minfr_goodchannels);

obj.ops.Th = str2num(obj.H.settings.setThEdt.String);
if isempty(obj.ops.Th)||any(isnan(obj.ops.Th))
obj.ops.Th = [10 4];
end
obj.H.settings.setThEdt.String = num2str(obj.ops.Th);

obj.ops.lam = str2num(obj.H.settings.setLambdaEdt.String);
if isempty(obj.ops.lam)||isnan(obj.ops.lam)
obj.ops.lam = 100;
end
obj.H.settings.setLambdaEdt.String = num2str(obj.ops.lam);

obj.ops.ccsplit = str2double(obj.H.settings.setCcsplitEdt.String);
if isempty(obj.ops.ccsplit)||isnan(obj.ops.ccsplit)
obj.ops.ccsplit = 0.9;
end
obj.H.settings.setCcsplitEdt.String = num2str(obj.ops.ccsplit);

obj.ops.trange = str2num(obj.H.settings.setTrangeEdt.String);
if isempty(obj.ops.trange)||any(isnan(obj.ops.trange))
obj.ops.trange = [0 Inf];
end
obj.H.settings.setTrangeEdt.String = num2str(obj.ops.trange);

end

function runPreproc(obj)
Expand All @@ -608,10 +692,21 @@ function runPreproc(obj)
obj.log('Preprocessing...');
obj.rez = preprocessDataSub(obj.ops);

% update connected channels
igood = obj.rez.ops.igood;
previousGood = find(obj.P.chanMap.connected);
newGood = previousGood(igood);
obj.P.chanMap.connected = false(size(obj.P.chanMap.connected));
obj.P.chanMap.connected(newGood) = true;

% use the new whitening matrix, which can sometimes be
% quite different than the earlier estimated one
rW = obj.rez.Wrot;
pW = obj.P.Wrot;
if isfield(obj.P, 'Wrot')
pW = obj.P.Wrot;
else
pW = zeros(numel(obj.P.chanMap.connected));
end
cn = obj.P.chanMap.connected;
pW(cn,cn) = rW;
obj.P.Wrot = pW;
Expand All @@ -623,6 +718,7 @@ function runPreproc(obj)
obj.log('Done preprocessing.');
catch ex
obj.log(sprintf('Error preprocessing! %s', ex.message));
keyboard
end

end
Expand Down Expand Up @@ -679,6 +775,7 @@ function runSpikesort(obj)
obj.updateDataView();
catch ex
obj.log(sprintf('Error running kilosort! %s', ex.message));
keyboard
end

end
Expand Down Expand Up @@ -1297,7 +1394,10 @@ function saveGUIsettings(obj)
saveDat.settings.setProbeEdt.Value = obj.H.settings.setProbeEdt.Value;
saveDat.settings.setnChanEdt.String = obj.H.settings.setnChanEdt.String;
saveDat.settings.setFsEdt.String = obj.H.settings.setFsEdt.String;
saveDat.settings.setNfiltEdt.String = obj.H.settings.setNfiltEdt.String;
saveDat.settings.setThEdt.String = obj.H.settings.setThEdt.String;
saveDat.settings.setLambdaEdt.String = obj.H.settings.setLambdaEdt.String;
saveDat.settings.setCcsplitEdt.String = obj.H.settings.setCcsplitEdt.String;
saveDat.settings.setMinfrEdt.String = obj.H.settings.setMinfrEdt.String;

saveDat.ops = obj.ops;
saveDat.ops.gui = [];
Expand All @@ -1311,7 +1411,7 @@ function saveGUIsettings(obj)
savePath = fullfile(p, [fn '_ksSettings.mat']);

save(savePath, 'saveDat', '-v7.3');
obj.refocus(obj.H.settings.saveBtn);
%obj.refocus(obj.H.settings.saveBtn);
end

function restoreGUIsettings(obj)
Expand Down
2 changes: 1 addition & 1 deletion gui/predictData.m
View file
Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@
amplitudes = rez.st3(inclSpikes,3);

for s = 1:sum(inclSpikes)
ibatch = ceil(st(s)/NT); % this determines what batch the spike falls in
ibatch = ceil(st(s)/rez.ops.NT); % this determines what batch the spike falls in
ampi = rez.muA(inclTemps(s), ibatch);

% this is the reconstruction of the temporal part
Expand Down

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