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Drop down stores and apply to all channels #2

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Binary file modified neural_data_processing/SimpleSpikeDataProcessor.fig
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232 changes: 178 additions & 54 deletions neural_data_processing/SimpleSpikeDataProcessor.m
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@

% Edit the above text to modify the response to help SimpleSpikeDataProcessor

% Last Modified by GUIDE v2.5 27-May-2019 17:41:12
% Last Modified by GUIDE v2.5 12-Aug-2019 11:16:45

% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
Expand Down Expand Up @@ -74,7 +74,10 @@ function SimpleSpikeDataProcessor_OpeningFcn(hObject, eventdata, handles, vararg
handles.numsnips = 1000; % plot 1000 snips max

handles.data = [];
handles.store = 'spik';

handles.store = {'-- Select storage --'};

handles.all_channels_checkbox_value = get(handles.all_channels_checkbox,'Value');

% Update handles structure
guidata(hObject, handles);
Expand Down Expand Up @@ -111,20 +114,14 @@ function loadTDT_button_Callback(hObject, eventdata, handles)
% get block info
heads = TDTbin2mat(BLOCKPATH, 'HEADERS', 1);

% Find spikes store -- always 'spik'? make user specify that? use 'type' from TDTbin2mat to extract 'snips' only?
if ~isfield(heads.stores, handles.store)
warning('no ''spik'' store in specified file, sadly this is hardcoded in this function for now... sorry!');
return;
end

handles.chanlist = sort(unique(heads.stores.spik.chan));
handles.numchan = length(handles.chanlist);
handles.chan = handles.chanlist(1);
handles.stream_t0 = 0; % start at beginning of data (first 60 sec);

% read data from first channel
handles = read_chan(handles);
heads_fieldnames = fieldnames(heads.stores);

for i = 1:length(fieldnames(heads.stores))
handles.store{i+1,1} = heads_fieldnames{i,1};
end
% stream_snip = heads.stores
% handles.store = stream_snip(handles.store);
set(handles.list_popup,'String',string(handles.store));
end
end

Expand All @@ -136,7 +133,7 @@ function thresh_button_Callback(hObject, eventdata, handles)
update_snips(handles);

num_snips = size(handles.data.snips.Snip.data,1);
fprintf('Extracted %d snips\n',num_snips);
fprintf('Extracted %d snips from ch %d\n',num_snips,handles.chan);

% Update handles structure
guidata(hObject, handles);
Expand Down Expand Up @@ -222,32 +219,70 @@ function post_snip_wind_button_Callback(hObject, eventdata, handles)
guidata(hObject, handles);

function apply_all_button_Callback(hObject, eventdata, handles)
% thresholding
handles = extract_snips(handles);
num_snips = size(handles.data.snips.Snip.data,1);
fprintf('Extracted %d snips\n',num_snips);

% remove snips above reject line
rem_idx = find(any(abs(handles.data.snips.Snip.data') > handles.reject));

% remove snips when outside presnip window
rem_idx = [rem_idx find(any(abs(handles.data.snips.Snip.data(:,handles.presnipT(1):handles.presnipT(2)))' > handles.presnip))];

% remove snips when below postsnip threshold
rem_idx = [rem_idx find(any(handles.data.snips.Snip.data(:,handles.postsnipT(1):handles.postsnipT(2))' < handles.postsnip))];

% remove snips when outside postsnip window
rem_idx = [rem_idx find(any(abs(handles.data.snips.Snip.data(:,handles.postwindT(1):handles.postwindT(2)))' > handles.postwind))];

rem_idx = unique(rem_idx);

% actually remove all relevant snips
handles.data.snips.Snip.data(rem_idx,:) = [];
handles.data.snips.Snip.sortcode(rem_idx,:) = [];
handles.data.snips.Snip.ts(rem_idx,:) = [];

fprintf('Removed %d of %d snips\n',length(rem_idx),num_snips);
update_snips(handles);
if handles.all_channels_checkbox_value == 1
for i = 1:length(handles.chanlist)
handles.chan = handles.chanlist(i);
handles.stream_t0 = 0;
handles = read_chan(handles);

% thresholding
handles = extract_snips(handles);
num_snips = size(handles.data.snips.Snip.data,1);
fprintf('Extracted %d snips from ch %d\n',num_snips,handles.chan);

% remove snips above reject line
rem_idx = find(any(abs(handles.data.snips.Snip.data') > handles.reject));

% remove snips when outside presnip window
rem_idx = [rem_idx find(any(abs(handles.data.snips.Snip.data(:,handles.presnipT(1):handles.presnipT(2)))' > handles.presnip))];

% remove snips when below postsnip threshold
rem_idx = [rem_idx find(any(handles.data.snips.Snip.data(:,handles.postsnipT(1):handles.postsnipT(2))' < handles.postsnip))];

% remove snips when outside postsnip window
rem_idx = [rem_idx find(any(abs(handles.data.snips.Snip.data(:,handles.postwindT(1):handles.postwindT(2)))' > handles.postwind))];

rem_idx = unique(rem_idx);

% actually remove all relevant snips
handles.data.snips.Snip.data(rem_idx,:) = [];
handles.data.snips.Snip.sortcode(rem_idx,:) = [];
handles.data.snips.Snip.ts(rem_idx,:) = [];

fprintf('Removed %d of %d snips from ch %d\n',length(rem_idx),num_snips,handles.chan);
update_snips(handles);
save_chan(handles);
set(handles.all_channels_checkbox,'Value',0);
end
else
% thresholding
handles = extract_snips(handles);
num_snips = size(handles.data.snips.Snip.data,1);
fprintf('Extracted %d snips from ch %d\n',num_snips,handles.chan);

% remove snips above reject line
rem_idx = find(any(abs(handles.data.snips.Snip.data') > handles.reject));

% remove snips when outside presnip window
rem_idx = [rem_idx find(any(abs(handles.data.snips.Snip.data(:,handles.presnipT(1):handles.presnipT(2)))' > handles.presnip))];

% remove snips when below postsnip threshold
rem_idx = [rem_idx find(any(handles.data.snips.Snip.data(:,handles.postsnipT(1):handles.postsnipT(2))' < handles.postsnip))];

% remove snips when outside postsnip window
rem_idx = [rem_idx find(any(abs(handles.data.snips.Snip.data(:,handles.postwindT(1):handles.postwindT(2)))' > handles.postwind))];

rem_idx = unique(rem_idx);

% actually remove all relevant snips
handles.data.snips.Snip.data(rem_idx,:) = [];
handles.data.snips.Snip.sortcode(rem_idx,:) = [];
handles.data.snips.Snip.ts(rem_idx,:) = [];

fprintf('Removed %d of %d snips from ch %d\n',length(rem_idx),num_snips,handles.chan);
update_snips(handles);
end

% Update handles structure
guidata(hObject, handles);
Expand Down Expand Up @@ -293,8 +328,6 @@ function save_button_Callback(hObject, eventdata, handles)

end

function done_button_Callback(hObject, eventdata, handles)

function prev_chan_button_Callback(hObject, eventdata, handles)

% save snips from current channel
Expand Down Expand Up @@ -334,7 +367,7 @@ function update_stream(handles)
set(handles.figure1,'CurrentAxes',handles.stream_axes);

% select and plot relevant data and timeframe
yvals = handles.data.streams.(handles.store).data( handles.stream_timeframe >= handles.stream_t0 & handles.stream_timeframe < handles.stream_t0 + handles.stream_width);
yvals = handles.data.streams.(handles.list_choice).data( handles.stream_timeframe >= handles.stream_t0 & handles.stream_timeframe < handles.stream_t0 + handles.stream_width);
xvals = handles.stream_timeframe( handles.stream_timeframe >= handles.stream_t0 & handles.stream_timeframe < handles.stream_t0 + handles.stream_width);

cla(handles.stream_axes);
Expand Down Expand Up @@ -371,7 +404,7 @@ function update_snips(handles)
end
hold on; axis manual
xlim([handles.snips_timeframe(1) handles.snips_timeframe(end)]);
ylabel('uV'); xlabel('ms'); title(sprintf('first %d snips',numsnips));
ylabel('uV'); xlabel('ms'); title(sprintf('First %d snips',numsnips));

% if big artifacts, auto scale zooms out too much to see real data. Set a max yrange of +- 500 uV
yy = ylim; ylim([max(-500,yy(1)) min(500,yy(2))]);
Expand All @@ -397,22 +430,22 @@ function update_snips(handles)
function handles = read_chan(handles)

% read the specified data from our block into a Matlab structure
handles.data = TDTbin2mat(handles.blockpath_edit.String, 'STORE', handles.store, 'CHANNEL', handles.chan);
handles.data = TDTbin2mat(handles.blockpath_edit.String, 'STORE', handles.list_choice, 'CHANNEL', handles.chan);

% filter data 300-5000 Hz
handles.data = TDTdigitalfilter(handles.data, handles.store, [300 5000]);
handles.data = TDTdigitalfilter(handles.data, handles.list_choice, [300 5000]);

% convert to uV
handles.data.streams.(handles.store).data = handles.data.streams.(handles.store).data *1e6;
handles.data.streams.(handles.list_choice).data = handles.data.streams.(handles.list_choice).data *1e6;

handles.stream_timeframe = ((1:length(handles.data.streams.(handles.store).data))-1)/handles.data.streams.(handles.store).fs;
handles.stream_timeframe = ((1:length(handles.data.streams.(handles.list_choice).data))-1)/handles.data.streams.(handles.list_choice).fs;

% per TDTthresh:
%pre_wave = floor(NPTS/4)-1;
%post_wave = NPTS - pre_wave-1;
pre_wave = floor(handles.snip_width/4);
post_wave = handles.snip_width-pre_wave-1;
handles.snips_timeframe = (-pre_wave:post_wave)/handles.data.streams.(handles.store).fs*1e3; % in ms
handles.snips_timeframe = (-pre_wave:post_wave)/handles.data.streams.(handles.list_choice).fs*1e3; % in ms

% enable/disable buttons
if handles.chan == handles.chanlist(1)
Expand All @@ -426,15 +459,15 @@ function update_snips(handles)
handles.next_chan_button.Enable = 'on';
end

saved_snips = ~isempty(dir([handles.blockpath_edit.String filesep 'chandata' filesep 'ch' num2str(handles.chan) '_snips.mat']));
saved_snips = ~isempty(dir([handles.blockpath_edit.String filesep 'chandata' filesep 'ch' num2str(handles.chan) '_snips.mat']));

% load saved snips if already processed
if saved_snips
handles.data.snips.Snip = load([handles.blockpath_edit.String filesep 'chandata' filesep 'ch' num2str(handles.chan) '_snips.mat']);
else
handles = extract_snips(handles);
num_snips = size(handles.data.snips.Snip.data,1);
fprintf('Extracted %d snips\n',num_snips);
fprintf('Extracted %d snips from ch %d\n',num_snips,handles.chan);
end

snips_compat = length(handles.snips_timeframe) == size(handles.data.snips.Snip.data,2);
Expand All @@ -450,10 +483,10 @@ function update_snips(handles)
function handles = extract_snips(handles)

% extract snips using specified parameters
handles.data = TDTthresh(handles.data, handles.store, 'MODE', 'manual', 'THRESH', handles.thresh, 'NPTS', handles.snip_width, 'OVERLAP', 0,'VERBOSE',0);
handles.data = TDTthresh(handles.data, handles.list_choice, 'MODE', 'manual', 'THRESH', handles.thresh, 'NPTS', handles.snip_width, 'OVERLAP', 0,'VERBOSE',0);

%TDT thresh simply writes '1' in Snip.chan when only one channel at a time. We want that to reflect the real channel number
handles.data.snips.Snip.chan = handles.data.streams.(handles.store).channel;
handles.data.snips.Snip.chan = handles.data.streams.(handles.list_choice).channel;

function Snip = mergeSnips(s,Snip)
if isempty(Snip)
Expand Down Expand Up @@ -502,6 +535,7 @@ function thresh_edit_Callback(hObject, eventdata, handles)

% Update handles structure
guidata(hObject, handles);

function thresh_edit_CreateFcn(hObject, eventdata, handles)
% hObject handle to thresh_edit (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
Expand All @@ -521,6 +555,7 @@ function reject_edit_Callback(hObject, eventdata, handles)

% Update handles structure
guidata(hObject, handles);

function reject_edit_CreateFcn(hObject, eventdata, handles)
% hObject handle to reject_edit (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
Expand All @@ -540,6 +575,7 @@ function pre_snip_edit_Callback(hObject, eventdata, handles)

% Update handles structure
guidata(hObject, handles);

function pre_snip_edit_CreateFcn(hObject, eventdata, handles)

if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
Expand Down Expand Up @@ -573,6 +609,7 @@ function post_snip_thresh_edit_Callback(hObject, eventdata, handles)

% Update handles structure
guidata(hObject, handles);

function post_snip_thresh_edit_CreateFcn(hObject, eventdata, handles)
% hObject handle to post_snip_thresh_edit (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
Expand All @@ -595,3 +632,90 @@ function blockpath_edit_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end


% --- Executes on button press in raw_data_radio.
function raw_data_radio_Callback(hObject, eventdata, handles)
% hObject handle to raw_data_radio (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)

% Hint: get(hObject,'Value') returns toggle state of raw_data_radio


% --- Executes on button press in snips_only_radio.
function snips_only_radio_Callback(hObject, eventdata, handles)
% hObject handle to snips_only_radio (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)

% Hint: get(hObject,'Value') returns toggle state of snips_only_radio


%% Added -VK 11/08/2019
% Adds popup menu with drop down list of available stores and load
% selected option

% --- Executes on selection change in list_popup.
function list_popup_Callback(hObject, eventdata, handles)
% hObject handle to list_popup (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)

% Hints: contents = cellstr(get(hObject,'String')) returns list_popup contents as cell array
% contents{get(hObject,'Value')} returns selected item from list_popup

list_contents = get(handles.list_popup,'String');
handles.list_choice = list_contents{get(handles.list_popup,'Value')};

heads = TDTbin2mat(handles.blockpath_edit.String, 'HEADERS', 1);

handles.chanlist = sort(unique(heads.stores.(handles.list_choice).chan));
handles.numchan = length(handles.chanlist);
handles.chan = handles.chanlist(1);
handles.stream_t0 = 0; % start at beginning of data (first 60 sec);

% read data from first channel
fprintf('Loading %s...\n', handles.list_choice)

try
handles = read_chan(handles);
catch
warning('Failed to load %s. Select a different storage.\n', handles.list_choice)
return
end

fprintf('%s loaded successfully.\n', handles.list_choice)

% Update handles structure
guidata(hObject, handles);

% --- Executes during object creation, after setting all properties.
function list_popup_CreateFcn(hObject, eventdata, handles)
% hObject handle to list_popup (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called

% Hint: popupmenu controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end

% Checkbox for applying settings to all channels
% --- Executes on button press in all_channels_checkbox.
function all_channels_checkbox_Callback(hObject, eventdata, handles)
% hObject handle to all_channels_checkbox (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)

% Hint: get(hObject,'Value') returns toggle state of all_channels_checkbox

handles.all_channels_checkbox_value = get(handles.all_channels_checkbox,'Value');

% Update handles structure
guidata(hObject, handles);

%% End of code %%