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kushaanguptakushaangupta
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Make cross-platform compatible
1 parent f78cdbe commit 693a4f4

38 files changed

Lines changed: 206 additions & 151 deletions

‎.gitignore‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -11,3 +11,4 @@ preProcessing/FilterM/FilterX.exp
1111
preProcessing/FilterM/FilterX.mexw64
1212
preProcessing/FilterM/FilterX.lib
1313
preProcessing/FilterM/FilterX.exp
14+
spikeSorting/KiloSort1/CUDA/CUDA.xml

‎BARRs/BARR_N2.m‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -24,7 +24,7 @@ function BARR_N2(basepath)
2424
%% Create Neuroscope2 file for barrage events
2525
basename = basenameFromBasepath(basepath);
2626

27-
savePath = strcat(basepath, '\Barrage_Files\', basename, '.');
27+
savePath = strcat(basepath, filesep, 'Barrage_Files', filesep, basename, '.');
2828
load([savePath 'HSE.mat']);
2929

3030
HSEn2.timestamps = HSE.timestamps(HSE.keep(HSE.NREM),:);

‎BARRs/BARR_PSTH.m‎

Lines changed: 40 additions & 40 deletions
Original file line numberDiff line numberDiff line change
@@ -15,68 +15,68 @@ function BARR_PSTH(plotSave,useState)
1515
HSE = loadBarrage(basepath);
1616
if ~isempty(HSE.NREM)
1717
load(strcat(basename,'.cell_metrics.cellinfo.mat'));
18-
load(strcat(basepath,'\',basename,'.SleepState.states.mat'));
18+
load(strcat(basepath,filesep,basename,'.SleepState.states.mat'));
1919
switch useState
2020
case "nonTheta"
21-
if ~exist([basepath '\Barrage_Files\nonTheta'])
22-
mkdir([basepath '\Barrage_Files\nonTheta']);
21+
if ~exist([basepath filesep 'Barrage_Files' filesep 'nonTheta'])
22+
mkdir([basepath filesep 'Barrage_Files' filesep 'nonTheta']);
2323
end
2424
if contains(plotSave,'clean')
25-
plotSave = [basepath '\Barrage_Files\nonTheta\' basename '.clean.'];
25+
plotSave = [basepath filesep 'Barrage_Files' filesep 'nonTheta' filesep basename '.clean.'];
2626
else
27-
plotSave = [basepath '\Barrage_Files\nonTheta\' basename '.'];
27+
plotSave = [basepath filesep 'Barrage_Files' filesep 'nonTheta' filesep basename '.'];
2828
end
2929
case "imm"
30-
if ~exist([basepath '\Barrage_Files\imm'])
31-
mkdir([basepath '\Barrage_Files\imm']);
30+
if ~exist([basepath filesep 'Barrage_Files' filesep 'imm'])
31+
mkdir([basepath filesep 'Barrage_Files' filesep 'imm']);
3232
end
3333
if contains(plotSave,'clean')
34-
plotSave = [basepath '\Barrage_Files\imm\' basename '.clean.'];
34+
plotSave = [basepath filesep 'Barrage_Files' filesep 'imm' filesep basename '.clean.'];
3535
else
36-
plotSave = [basepath '\Barrage_Files\imm\' basename '.'];
36+
plotSave = [basepath filesep 'Barrage_Files' filesep 'imm' filesep basename '.'];
3737
end
3838
case "theta"
39-
if ~exist([basepath '\Barrage_Files\theta'])
40-
mkdir([basepath '\Barrage_Files\theta']);
39+
if ~exist([basepath filesep 'Barrage_Files' filesep 'theta'])
40+
mkdir([basepath filesep 'Barrage_Files' filesep 'theta']);
4141
end
4242
if contains(plotSave,'clean')
43-
plotSave = [basepath '\Barrage_Files\theta\' basename '.clean.'];
43+
plotSave = [basepath filesep 'Barrage_Files' filesep 'theta' filesep basename '.clean.'];
4444
else
45-
plotSave = [basepath '\Barrage_Files\theta\' basename '.'];
45+
plotSave = [basepath filesep 'Barrage_Files' filesep 'theta' filesep basename '.'];
4646
end
4747
case "REM"
48-
if ~exist([basepath '\Barrage_Files\REM'])
49-
mkdir([basepath '\Barrage_Files\REM']);
48+
if ~exist([basepath filesep 'Barrage_Files' filesep 'REM'])
49+
mkdir([basepath filesep 'Barrage_Files' filesep 'REM']);
5050
end
5151
if contains(plotSave,'clean')
52-
plotSave = [basepath '\Barrage_Files\REM\' basename '.clean.'];
52+
plotSave = [basepath filesep 'Barrage_Files' filesep 'REM' filesep basename '.clean.'];
5353
else
54-
plotSave = [basepath '\Barrage_Files\REM\' basename '.'];
54+
plotSave = [basepath filesep 'Barrage_Files' filesep 'REM' filesep basename '.'];
5555
end
5656
otherwise
5757
useState = "NREM";
5858
end
5959

60-
if ~exist(strcat(basepath,'\Barrage_Files\PSTHmet\'))
61-
mkdir(strcat(basepath,'\Barrage_Files\PSTHmet\'));
60+
if ~exist([basepath filesep 'Barrage_Files' filesep 'PSTHmet'])
61+
mkdir([basepath filesep 'Barrage_Files' filesep 'PSTHmet']);
6262
end
63-
if ~exist(strcat(basepath,'\',basename,'.ripples.events.mat'))
64-
if exist(strcat(basepath,'\',basename,'SWR.events.mat'))
65-
load(strcat(basepath,'\',basename,'SWR.events.mat'));
63+
if ~exist(strcat(basepath,filesep,basename,'.ripples.events.mat'))
64+
if exist(strcat(basepath,filesep,basename,'SWR.events.mat'))
65+
load(strcat(basepath,filesep,basename,'SWR.events.mat'));
6666
ripples = SWR;
6767
if isfield(ripples,'peaktimes')
6868
ripples.peaks = ripples.peaktimes;
6969
end
7070
plotRips = 1;
71-
elseif exist(strcat(basepath,'\old files\SWR.mat'))
72-
load(strcat(basepath,'\old files\SWR.mat'));
71+
elseif exist(strcat(basepath, filesep, 'old files', filesep, 'SWR.mat'))
72+
load(strcat(basepath, filesep, 'old files', filesep, 'SWR.mat'));
7373
ripples = SWR;
7474
if isfield(ripples,'peaktimes')
7575
ripples.peaks = ripples.peaktimes;
7676
end
7777
plotRips = 1;
78-
elseif exist(strcat(basepath,'\oldfiles\SWR.mat'))
79-
load(strcat(basepath,'\oldfiles\SWR.mat'));
78+
elseif exist(strcat(basepath, filesep, 'old files', filesep, 'SWR.mat'))
79+
load(strcat(basepath, filesep, 'old files', filesep, 'SWR.mat'));
8080
ripples = SWR;
8181
if isfield(ripples,'peaktimes')
8282
ripples.peaks = ripples.peaktimes;
@@ -215,11 +215,11 @@ function BARR_PSTH(plotSave,useState)
215215
regCheck = regions{j};
216216
if contains(regCheck, check(i))
217217
br = convertStringsToChars(check(i));
218-
if ~exist([basepath '\Barrage_Files\' basename '.' br 'pyr.cellinfo.mat'])
218+
if ~exist([basepath filesep 'Barrage_Files' filesep basename '.' br 'pyr.cellinfo.mat'])
219219
spikes = importSpikes('brainRegion', check(i), 'cellType', "Pyramidal Cell");
220-
save([basepath '\Barrage_Files\' basename '.' br 'pyr.cellinfo.mat'], 'spikes');
220+
save([basepath filesep 'Barrage_Files' filesep basename '.' br 'pyr.cellinfo.mat'], 'spikes');
221221
else
222-
load([basepath '\Barrage_Files\' basename '.' br 'pyr.cellinfo.mat']);
222+
load([basepath filesep 'Barrage_Files' filesep basename '.' br 'pyr.cellinfo.mat']);
223223
end
224224
if ~isempty(spikes.times)
225225
if plotRips
@@ -268,15 +268,15 @@ function BARR_PSTH(plotSave,useState)
268268

269269
if useState == "NREM"
270270
if contains(plotSave, 'clean')
271-
save([basepath '\Barrage_Files\PSTHmet\' basename '.clean.' br 'PSTHmets.mat'], 'PSTHmets');
271+
save([basepath filesep 'Barrage_Files' filesep 'PSTHmet' filesep basename '.clean.' br 'PSTHmets.mat'], 'PSTHmets');
272272
else
273-
save([basepath '\Barrage_Files\PSTHmet\' basename '.' br 'PSTHmets.mat'], 'PSTHmets');
273+
save([basepath filesep 'Barrage_Files' filesep 'PSTHmet' filesep basename '.' br 'PSTHmets.mat'], 'PSTHmets');
274274
end
275275
else
276276
if contains(plotSave, 'clean')
277-
save(strcat(basepath, '\Barrage_Files\', useState,'\', basename, '.clean.', br, 'PSTHmets.mat'), 'PSTHmets');
277+
save(strcat(basepath, filesep, 'Barrage_Files', filesep, useState, filesep, basename, '.clean.', br, 'PSTHmets.mat'), 'PSTHmets');
278278
else
279-
save(strcat(basepath, '\Barrage_Files\', useState,'\', basename, '.', br, 'PSTHmets.mat'), 'PSTHmets');
279+
save(strcat(basepath, filesep, 'Barrage_Files', filesep, useState, filesep, basename, '.', br, 'PSTHmets.mat'), 'PSTHmets');
280280
end
281281
end
282282

@@ -298,11 +298,11 @@ function BARR_PSTH(plotSave,useState)
298298
if contains(regCheck, check(i))
299299
br = convertStringsToChars(check(i));
300300
spikes = [];
301-
if ~exist([basepath '\Barrage_Files\' basename '.' br 'int.cellinfo.mat'])
301+
if ~exist([basepath filesep 'Barrage_Files' filesep basename '.' br 'int.cellinfo.mat'])
302302
spikes = importSpikes('brainRegion', check(i), 'cellType', ["Wide Interneuron"; "Narrow Interneuron"]);
303-
save([basepath '\Barrage_Files\' basename '.' br 'int.cellinfo.mat'], 'spikes');
303+
save([basepath filesep 'Barrage_Files' filesep basename '.' br 'int.cellinfo.mat'], 'spikes');
304304
else
305-
load([basepath '\Barrage_Files\' basename '.' br 'int.cellinfo.mat']);
305+
load([basepath filesep 'Barrage_Files' filesep basename '.' br 'int.cellinfo.mat']);
306306
end
307307
if ~isempty(spikes.times)
308308
if plotRips
@@ -351,15 +351,15 @@ function BARR_PSTH(plotSave,useState)
351351

352352
if useState == "NREM"
353353
if contains(plotSave, 'clean')
354-
save([basepath '\Barrage_Files\PSTHmet\' basename '.clean.' br 'PSTHmetsINT.mat'], 'PSTHmetsINT');
354+
save([basepath filesep 'Barrage_Files' filesep 'PSTHmet' filesep basename '.clean.' br 'PSTHmetsINT.mat'], 'PSTHmetsINT');
355355
else
356-
save([basepath '\Barrage_Files\PSTHmet\' basename '.' br 'PSTHmetsINT.mat'], 'PSTHmetsINT');
356+
save([basepath filesep 'Barrage_Files' filesep 'PSTHmet' filesep basename '.' br 'PSTHmetsINT.mat'], 'PSTHmetsINT');
357357
end
358358
else
359359
if contains(plotSave, 'clean')
360-
save(strcat(basepath, '\Barrage_Files\', useState,'\', basename, '.clean.', br, 'PSTHmetsINT.mat'), 'PSTHmetsINT');
360+
save(strcat(basepath, filesep, 'Barrage_Files', filesep, useState, filesep, basename, '.clean.', br, 'PSTHmetsINT.mat'), 'PSTHmetsINT');
361361
else
362-
save(strcat(basepath, '\Barrage_Files\', useState,'\', basename, '.', br, 'PSTHmetsINT.mat'), 'PSTHmetsINT');
362+
save(strcat(basepath, filesep, 'Barrage_Files', filesep, useState, filesep, basename, '.', br, 'PSTHmetsINT.mat'), 'PSTHmetsINT');
363363
end
364364
end
365365

‎BARRs/detectBARR.m‎

Lines changed: 10 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -123,32 +123,32 @@
123123
basename = basenameFromBasepath(basepath);
124124
animal = animalFromBasepath(basepath);
125125

126-
if exist([basepath '\Barrage_Files\' basename '.HSE.mat'])&&~force
126+
if exist([basepath filesep 'Barrage_Files' filesep basename '.HSE.mat'])&&~force
127127
disp('BARRs already detected! Loading file...');
128-
load([basepath '\Barrage_Files\' basename '.HSE.mat']);
128+
load([basepath filesep 'Barrage_Files' filesep basename '.HSE.mat']);
129129
return
130130
end
131131

132132
%% Prep for detection
133-
savePath = convertStringsToChars(strcat(basepath, '\Barrage_Files\', basename, '.'));
134-
if ~exist([basepath '\Barrage_Files'])
135-
mkdir('Barrage_Files');
133+
savePath = convertStringsToChars(strcat(basepath, filesep, 'Barrage_Files', filesep, basename, '.'));
134+
if ~exist([basepath filesep 'Barrage_Files'])
135+
mkdir([basepath filesep 'Barrage_Files']);
136136
end
137137

138-
pullSpikes('basepath', basepath, 'savePath', [basepath '\Barrage_Files'], 'force', true); %Get region/cell type spike files
138+
pullSpikes('basepath', basepath, 'savePath', [basepath filesep 'Barrage_Files'], 'force', true); %Get region/cell type spike files
139139

140-
if ~exist(strcat(basepath,'\Barrage_Files\',basename,'.CA2pyr.cellinfo.mat'))
140+
if ~exist(strcat(basepath,filesep,'Barrage_Files',filesep,basename,'.CA2pyr.cellinfo.mat'))
141141
disp('No CA2 pyramidal cells detected, exiting');
142142
return
143143
end
144144

145-
if ~exist(strcat(basepath,'\',basename,'.SleepState.states.mat'))
145+
if ~exist(strcat(basepath,filesep,basename,'.SleepState.states.mat'))
146146
disp('SleepScore not detected, calculating');
147-
load([basepath '\' basename '.session.mat']);
147+
load([basepath filesep basename '.session.mat']);
148148
SleepState = SleepScoreMaster(basepath,'rejectChannels',session.channelTags.Bad.channels);
149149
clear session
150150
else
151-
load(strcat(basepath,'\',basename,'.SleepState.states.mat'));
151+
load(strcat(basepath,filesep,basename,'.SleepState.states.mat'));
152152
end
153153

154154
%% Detect good candidate units

‎BARRs/find_HSE_BARR.m‎

Lines changed: 7 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -145,16 +145,16 @@
145145
basename = basenameFromBasepath(basepath);
146146

147147
if isempty(spikes)&&(~loadspkhist) %if we don't plan to load spikes but they weren't inputted
148-
load(strcat(basepath, '\', basename, '.spikes.cellinfo.mat'));
148+
load(strcat(basepath, filesep, basename, '.spikes.cellinfo.mat'));
149149
end
150150

151-
if ~exist(strcat(basepath,'\','Barrage_Files'))
151+
if ~exist(strcat(basepath,filesep,'Barrage_Files'))
152152
mkdir('Barrage_Files');
153153
end
154154
if cleanest
155-
savePath = strcat(basepath, '\Barrage_Files\', basename, '.clean.');
155+
savePath = strcat(basepath, filesep, 'Barrage_Files', filesep, basename, '.clean.');
156156
else
157-
savePath = strcat(basepath, '\Barrage_Files\', basename, '.');
157+
savePath = strcat(basepath, filesep, 'Barrage_Files', filesep, basename, '.');
158158
end
159159

160160
fprintf('\n');
@@ -336,7 +336,7 @@
336336
end
337337

338338
% SaveEvents([basename '_' name '.HSE.evt'],events1);
339-
createEVT(HSE.timestamps(:,1), HSE.peaks, HSE.timestamps(:,2), 'saveName', 'H', 'savePath', strcat(pwd,'\Barrage_Files'));
339+
createEVT(HSE.timestamps(:,1), HSE.peaks, HSE.timestamps(:,2), 'saveName', 'H', 'savePath', strcat(pwd, filesep, 'Barrage_Files'));
340340
end
341341

342342
if futEVT
@@ -444,10 +444,10 @@
444444

445445
%disp('Removing Ripples...');
446446
try
447-
load(strcat(basepath,'\',basename,'.ripples.events.mat'));
447+
load(strcat(basepath,filesep,basename,'.ripples.events.mat'));
448448
SWRt = ripples.timestamps;
449449
catch
450-
load(strcat(basepath, '\', basename, '.SWR.events.mat'));
450+
load(strcat(basepath, filesep, basename, '.SWR.events.mat'));
451451
SWRt = SWR.timestamps;
452452
end
453453
spiket = cat(1,spikes.times{:});

‎BARRs/pareBARRs.m‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -114,7 +114,7 @@
114114
end
115115

116116

117-
load(strcat(basepath,'\',basename,'.SleepState.states.mat'));
117+
load(strcat(basepath,filesep,basename,'.SleepState.states.mat'));
118118
if ~isempty(SleepState.ints.NREMstate)
119119
HSEnREM = eventIntervals(HSE,SleepState.ints.NREMstate,1);
120120
if ~isempty(HSEnREM)

‎BARRs/pullSpikes.m‎

Lines changed: 11 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@ function pullSpikes(varargin)
66
%%%%%%%%%%%%%%
77
% basepath: Full path where session is located. Default: pwd
88
% savePath: Location for spike structures to be saved. For example,
9-
% '[basepath '\Barrage_Files']'. Default: pwd
9+
% '[basepath '/Barrage_Files']'. Default: pwd
1010
% force: Logical option to force redetection of spikes. Default:
1111
% false
1212
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -34,7 +34,7 @@ function pullSpikes(varargin)
3434
toDelete = zeros(size(getFiles,1),1);
3535
for j = 1:size(getFiles,1)
3636
if fun_existsPyr(getFiles(j).name)||fun_existsInt(getFiles(j).name)
37-
disp(['Deleting ' getFiles(j).folder '\' getFiles(j).name]);
37+
disp(['Deleting ' getFiles(j).folder filesep getFiles(j).name]);
3838
toDelete(j) = 1;
3939
end
4040
end
@@ -43,8 +43,8 @@ function pullSpikes(varargin)
4343
keyboard
4444
for j = 1:size(getFiles,1)
4545
if toDelete(j)==1
46-
delete([getFiles(j).folder '\' getFiles(j).name]);
47-
disp(['Deleted ' getFiles(j).folder '\' getFiles(j).name]);
46+
delete([getFiles(j).folder filesep getFiles(j).name]);
47+
disp(['Deleted ' getFiles(j).folder filesep getFiles(j).name]);
4848
end
4949
end
5050
end
@@ -61,8 +61,8 @@ function pullSpikes(varargin)
6161

6262
cd(basepath);
6363
%% Load and prepare cell_metrics
64-
if exist([basepath '\' basename '.cell_metrics.cellinfo.mat'])
65-
load([basepath '\' basename '.cell_metrics.cellinfo.mat']);
64+
if exist([basepath filesep basename '.cell_metrics.cellinfo.mat'])
65+
load([basepath filesep basename '.cell_metrics.cellinfo.mat']);
6666
else
6767
warning('cell_metrics does not exist, computing');
6868
load([basename '.session.mat']);
@@ -76,7 +76,7 @@ function pullSpikes(varargin)
7676

7777
if ~isfield(cell_metrics,'tags')
7878
cell_metrics.tags.Bad = [];
79-
save([basepath '\' basename '.cell_metrics.cellinfo.mat'], 'cell_metrics');
79+
save([basepath filesep basename '.cell_metrics.cellinfo.mat'], 'cell_metrics');
8080
end
8181

8282
%% Pull regions
@@ -125,7 +125,7 @@ function pullSpikes(varargin)
125125
end
126126
end
127127
if sum(UIDcheck==spikes.UID)==length(spikes.times)
128-
save(strcat(savePath, '\', basename, '.', useReg{i}, 'pyr.cellinfo.mat'), 'spikes');
128+
save(strcat(savePath, filesep, basename, '.', useReg{i}, 'pyr.cellinfo.mat'), 'spikes');
129129
else
130130
error('Issue with importing');
131131
end
@@ -150,7 +150,7 @@ function pullSpikes(varargin)
150150
end
151151
end
152152
if sum(UIDcheck==spikes.UID)==length(spikes.times)
153-
save(strcat(savePath, '\', basename, '.', useReg{i}, 'int.cellinfo.mat'), 'spikes');
153+
save(strcat(savePath, filesep, basename, '.', useReg{i}, 'int.cellinfo.mat'), 'spikes');
154154
else
155155
error('Issue with importing');
156156
end
@@ -159,10 +159,10 @@ function pullSpikes(varargin)
159159
%% Pull all pyr or int cells
160160
spikes = [];
161161
spikes = importSpikes('cellType', "Pyramidal Cell");
162-
save([savePath '\' basename '.allpyr.cellinfo.mat'], 'spikes');
162+
save([savePath filesep basename '.allpyr.cellinfo.mat'], 'spikes');
163163
spikes = [];
164164
spikes = importSpikes('cellType', ["Narrow Interneuron"; "Wide Interneuron"]);
165-
save([savePath '\' basename '.allint.cellinfo.mat'], 'spikes');
165+
save([savePath filesep basename '.allint.cellinfo.mat'], 'spikes');
166166

167167
cd(original);
168168
end

‎BARRs/unitsForDetection.m‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -18,14 +18,14 @@
1818
basepath = pwd;
1919
basename = basenameFromBasepath(basepath);
2020

21-
if ~exist(strcat(basepath,'\','Barrage_Files'))
21+
if ~exist(strcat(basepath,filesep,'Barrage_Files'))
2222
mkdir('Barrage_Files');
2323
end
2424

2525
load([basename '.cell_metrics.cellinfo.mat']);
2626

2727
%% Produce spike structure
28-
load([basepath '\Barrage_Files\' basename '.CA2pyr.cellinfo.mat']);
28+
load([basepath filesep 'Barrage_Files' filesep basename '.CA2pyr.cellinfo.mat']);
2929

3030
%% Get cell by cell firing rate
3131
tSmooth = 0.05; binsz = 0.01;

‎SharpWaveRipples/getRipSpikes.m‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -180,9 +180,9 @@
180180
% 4. Save
181181
if saveMat
182182
if (saveNum ~= 0)
183-
save(strcat(savePath, '\', basename, '.', num2str(saveNum), '.spkEventTimes.mat'), 'spkEventTimes');
183+
save(strcat(savePath, filesep, basename, '.', num2str(saveNum), '.spkEventTimes.mat'), 'spkEventTimes');
184184
else
185-
save(strcat(savePath, '\', basename, '.spkEventTimes.mat'), 'spkEventTimes');
185+
save(strcat(savePath, filesep, basename, '.spkEventTimes.mat'), 'spkEventTimes');
186186
end
187187
end
188188

‎SpectralAnalyses/chronux/old/tutorial/significant-spike-field-coherenceMBL2005.m‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
[fname,pname]=uigetfile('*');
2-
eval(['load ' pname '\' fname]);
2+
eval(['load ' pname filesep fname]);
33
params.tapers=[5 9]; params.pad=2; params.Fs=1000; params.fpass=[0 100]; params.trialave=1;params.err=[1 0.05];
44
movingwin=[0.5 0.1]; % duration of moving window used to evaluate spectrograms
55
win=[2 2]; % window around events

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