Contents
SET FILE NAMES ACCORDING TO FOLDER NAME
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% Get directory of folders in Group
% Index through folder list, copy name of folder
% Index inside folder through all file names and rename each file
% Use the '_' token as a marker
% Example
% Folder name: 'T-4-944-P30'
% File name: 'T-4-944-P35_0001.abf'
% 'T-4-944-P35_0001_autoEventStats.abf'
% 'T-4-944-P35_0001_Events.abf'
%
% Folder name: 'T-4-944-P30'
% File name: 'T-4-944-P30_0001.abf'
% 'T-4-944-P30_0001_autoEventStats.abf'
% 'T-4-944-P30_0001_Events.abf'
%
% Copy entire folder name = part1
% Copy file name after '_' token = part2
% Combine [part1, part2] and rename file
% MAKE LIST OF EXISTING DATA FOLDERS
% Folder names with all data
% '...\EPC\Group 1'
% '...\EPC\Group 2'
% '...\MEPPs\Group 1'
% '...\MEPPs\Group 2'
% loop through existing data folders
myGroups = {'\EPCs\Group 1';...
'\EPCs\Group 2';...
'\MEPPs\Group 1';...
'\MEPPs\Group 2'};
% loop through all groups
for n = 1:size(myGroups,1)
% make list from directory append above to pwd
currentFolder = pwd;
searchFolder = [pwd, myGroups{n}]; %change to change folder
% get list of searchfolder contents using dir command
searchDir = dir(searchFolder);
% get rid of hidden files and folders
searchDirtemp = struct('name',{}, 'date',{}, 'bytes',{}, 'isdir',{}, 'datenum',{});
Dircount = 1; %initialize Dircount
for k = 1:length(searchDir)
if strcmpi(searchDir(k).name,'.') || strcmpi(searchDir(k).name,'..') || ~searchDir(k).isdir
continue; %skip if hidden dir found
else
searchDirtemp(Dircount,1) = searchDir(k);
Dircount = Dircount +1;
end
end
searchDir = searchDirtemp;
clear searchDirtemp Dircount
% GO THROUGH CONTENTS OF EACH FOLDER, EX: '...\EPC\Group 1'
% Generate directory of fies and then index through all files
for j = 1:length(searchDir)
filePath = [searchFolder, '\', searchDir(j).name]; %get path to file location
fileDir = dir(filePath); %get list of all files in path
fileDirtemp = struct('name',{}, 'date',{}, 'bytes',{}, 'isdir',{}, 'datenum',{}); %preallocate structure for file directory list
filecount = 1; %initialize file counter
% loop through list, and remove hidden files/folders from list
for k = 1:length(fileDir)
if strcmpi(fileDir(k).name,'.') || strcmpi(fileDir(k).name,'..') %hidden files/folders are called '.' or '..'
continue; %skip if hidden dir found and do not increment file counter
else
fileDirtemp(filecount,1) = fileDir(k); %populate temp file directory list
filecount = filecount + 1; %increment conter
end
end
fileDir = fileDirtemp; % reassign variable
clear fileDirtemp filecount%remove unused variable
% Loop through each file in fileDir and use folder name from
% searchDir to rename each file
for k = 1:length(fileDir)
% rename file, combining folder name and part of old file name
oldfileName = fileDir(k).name; %old file name
newName1 = searchDir(j).name; %part1 of new file name
newName2temp = oldfileName; %make temp variable for part2 of new file name
newName2ind = strfind(newName2temp,'_'); %find all indices of '_' token
newName2 = newName2temp(newName2ind:end); %get part of file name after first '_' token
newfileName = [newName1, newName2]; %combine parts
% move file if newfileName is different form oldfileName
if ~strcmp(newfileName,oldfileName)
movefile([filePath, '\', oldfileName], [filePath, '\', newfileName]); %move new '.mat' file to original file location
end
end
end
end
REGENERATE AUTOEVENTSTATS FILE, SPECIFICALLY EVENTDATASTATS
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% NEW RESAMPLING AND NEW CRITERIA FOR CURVE FITTING & AUC & AMP
% 08-May-2014 07:16:41
% Scan all .mat files that only have a file name:
% 'T-19-P30_0001_autoEvents.mat'
% use the 'autoEvents.mat' string to identify files of interest
% MAKE LIST OF EXISTING DATA FOLDERS
% Folder names with all data
% '...\EPC\Group 1'
% '...\EPC\Group 2'
% '...\MEPPs\Group 1'
% '...\MEPPs\Group 2'
% loop through existing data folders
clear all
myGroups = {'\EPCs\Group 1';...
'\EPCs\Group 2';...
'\MEPPs\Group 1';...
'\MEPPs\Group 2'};
%
% make list from directory append folder names with all data to pwd
for n = 1:size(myGroups,1)
currentFolder = pwd;
searchFolder = [pwd myGroups{n}]; %change to change folder
% get list of searchfolder contents using dir command
searchDir = dir(searchFolder);
% get rid of hidden files and folders
searchDirtemp = struct('name',{}, 'date',{}, 'bytes',{}, 'isdir',{}, 'datenum',{});
Dircount = 1; %initialize Dircount
for k = 1:length(searchDir)
if strcmpi(searchDir(k).name,'.') || strcmpi(searchDir(k).name,'..') || ~searchDir(k).isdir
continue; %skip if hidden dir found
else
searchDirtemp(Dircount,1) = searchDir(k);
Dircount = Dircount +1;
end
end
searchDir = searchDirtemp;
clear searchDirtemp Dircount
% index through the directories and files, generate '...autoEventStats.mat'
% extract myEvents [#x3] and regenerate EventDataStats variable
% use getEventStats function and resave autoEventDataStats
for j = 1:length(searchDir) %index through folders
fileDirtemp = struct('name',{}, 'date',{}, 'bytes',{}, 'isdir',{}, 'datenum',{});
filecount = 1; %initialize folder count
fileDir = dir([searchFolder, '\', searchDir(j).name]);
for k = 1:length(fileDir)
if strcmpi(fileDir(k).name,'.') || strcmpi(fileDir(k).name,'..')
continue; %skip if hidden dir found
else
fileDirtemp(filecount,1) = fileDir(k);
filecount = filecount + 1;
end
end
fileDir = fileDirtemp;
% find all files with string 'autoEventStats.mat' and generate
for k = 1:length(fileDir) %index through files
if ~isempty(strfind(fileDir(k).name,'_autoEventStats.mat')) %if the current file in loop contains '_autoEventStats.mat'
Eventsfile = fileDir(k).name; % get name of the '_autoEventStats.mat' file
cellnameidx = strfind(Eventsfile,'_autoEventStats.mat'); % find index in file name where '_autoEventStats.mat' begins
cellname = Eventsfile(1:cellnameidx(end)-1); % cellname is all string data before last index of '_'
limitsCrop = []; % initialize variable because all 'autoEventStats.mat' contain a variable 'limitsCrop'
peakThreshold = []; % initialize variable because all 'autoEventStats.mat' contain a variable 'peakThreshold'
abfFile = [cellname,'.abf']; % generate the name of the associated .abf file
movefile([searchFolder, '\', searchDir(j).name, '\', Eventsfile], pwd) % move .mat file
copyfile([searchFolder, '\', searchDir(j).name, '\', abfFile], pwd) % copy .abf file
load(Eventsfile); % load data in '_autoEventStats.mat' file
% return file and go to next loop if file corrupt
if exist('fileCorrupt','var')
movefile(Eventsfile, [searchFolder, '\', searchDir(j).name]); % move the autoEventStats.mat file
clear fileCorrupt
delete(abfFile);
continue
end
% load .abf .mat files. regenerate autoEventStats.mat
[mycell si] = abfload(abfFile); % load abf file and sample interval, 'si'
si = si/1e6; % convert sample interval usec to sec
mycell = myFilter(mycell); % filter signal
% determine if limitsCrop was erroneous, carried over from
% previous analysis that used a cropped signal
if ~isempty(limitsCrop)
leftlimit = myEvents(1,1); %find leftmost point
rightlimit = myEvents(3,end); %find rightmost point
EventsRange = rightlimit - leftlimit; %get span of events
% compare span of events to span of crop limits
if limitsCrop(2)-limitsCrop(1) < EventsRange
limitsCrop = [];
end
end
% determine if signal needs to be cropped
if isempty(limitsCrop)
y1 = mycell;
else
y1 = mycell(limitsCrop(1):limitsCrop(2));
end
% recompute EventDataStats
[EventDataStats hfigStats] = getEventStats(myEvents,y1,myEventsFlag,si); %run getEventStats function
close(hfigStats)
save([cellname,'_','autoEventStats', '.mat'],...
'EventDataStats', 'limitsCrop', 'myEvents',...
'myEventsFlag', 'peakSet', 'si', 'peakThreshold'); % save the 'autoEventStats.mat' file
movefile(Eventsfile, [searchFolder, '\', searchDir(j).name]); % move the autoEventStats.mat file
delete(abfFile); %delete .abf file
clear EventDataStats limitsCrop myEvents myEventsFlag peakSet si peakThreshold y1 mycell
end
end
end
clear fileDirtemp filecount
end
SEPERATE ALL FILES INTO RESPECTIVE GROUPS
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% BY EPC OR MEPP & T OR W & P15 OR P30
% This is where all 8 groups are generated and files are assigned to groups
% based on title of folder where they are contained
% clear workspace and command window
evalin('base','clear all; clc');
% get cell string of partial paths to destination folders
Analysisfolders = {'\Analysis\EPC\T\P15'; %1
'\Analysis\EPC\T\P30'; %2
'\Analysis\EPC\W\P15'; %3
'\Analysis\EPC\W\P30'; %4
'\Analysis\MEP\T\P15'; %5
'\Analysis\MEP\T\P30'; %6
'\Analysis\MEP\W\P15'; %7
'\Analysis\MEP\W\P30';}; %8
% make new folders
for k = 1:size(Analysisfolders,1)
mkdir([pwd, Analysisfolders{k}]);
end
% MAKE LIST OF EXISTING DATA FOLDERS
% Folder names with all data
% '...\EPC\Group 1'
% '...\EPC\Group 2'
% '...\MEP\Group 1'
% '...\MEP\Group 2'
% loop through existing data folders
myGroups = {'\EPCs\Group 1';...
'\EPCs\Group 2';...
'\MEPPs\Group 1';...
'\MEPPs\Group 2'};
for n = 1:size(myGroups,1)
% make list from directory append above to pwd
currentFolder = pwd;
searchFolder = [pwd, myGroups{n}]; %change to change folder
% get list of searchfolder contents using dir command
searchDir = dir(searchFolder);
% get rid of hidden files and folders
searchDirtemp = struct('name',{}, 'date',{}, 'bytes',{}, 'isdir',{}, 'datenum',{});
Dircount = 1; %initialize Dircount
for k = 1:length(searchDir)
if strcmpi(searchDir(k).name,'.') || strcmpi(searchDir(k).name,'..') || ~searchDir(k).isdir
continue; %skip if hidden dir found
else
searchDirtemp(Dircount,1) = searchDir(k);
Dircount = Dircount +1;
end
end
searchDir = searchDirtemp;
clear searchDirtemp Dircount
% select the first folder in list to populate with files
% Follow order of myGroups determined by var 'n' or by 'EPCs' or
% 'MEPPs
if ~isempty(strfind(myGroups{n},'EPCs'))
recordType = 'EPCs';
else
recordType = 'MEPPs';
end
% GO THROUGH CONTENTS OF EACH FOLDER, EX: '...\EPCs\Group 1'
% Generate directory of fies and then scan all files that match description
% of a '...autoEventStats.mat' file
for j = 1:length(searchDir)
% use mysearchfoldername to help determine which analysis folder to
% populate extract gene and age information
searchfolderName = searchDir(j).name;
if strcmp(searchfolderName(1),'T')
recordGene = 'T';
elseif strcmp(searchfolderName(1),'W')
recordGene = 'W';
end
if ~isempty(strfind(searchfolderName,'P15')) || ~isempty(strfind(searchfolderName,'P1'))
recordAge = 'P15';
elseif ~isempty(strfind(searchfolderName,'P30')) || ~isempty(strfind(searchfolderName,'P3'))
recordAge = 'P30';
end
% Build a string used to determine analysis path
folderStringBuild = [recordType,recordGene,recordAge];
% create analysis folder path strings and store in cell array
analysisString = {['EPCs','T','P15']; %1
['EPCs','T','P30']; %2
['EPCs','W','P15']; %3
['EPCs','W','P30']; %4
['MEPPs','T','P15']; %5
['MEPPs','T','P30']; %6
['MEPPs','W','P15']; %7
['MEPPs','W','P30']}; %8
% construct string of search folder and compare to analysis string
for k = 1:size(analysisString,1) %index through all rows
if strcmp(folderStringBuild,analysisString{k}) %
analysisPath = Analysisfolders{k};
break;
end
end
%iterate through all files in folder and copy
%'...autoEventStats.mat' to analysis folders
fileDirtemp = struct('name',{}, 'date',{}, 'bytes',{}, 'isdir',{}, 'datenum',{});
filecount = 1; %initialize folder count
searchPath = [searchFolder, '\', searchDir(j).name]; %folder path
fileDir = dir(searchPath); %get dir of folder path
for k = 1:length(fileDir)
if strcmpi(fileDir(k).name,'.') || strcmpi(fileDir(k).name,'..')
continue; %skip if hidden dir found
else
fileDirtemp(filecount,1) = fileDir(k);
filecount = filecount + 1;
end
end
fileDir = fileDirtemp;
% go through each file in fileDir and copy 'autoEventStats.mat'
% files to analysis folders
% find all files with string 'autoEventStats.mat'
for k = 1:length(fileDir)
if ~isempty(strfind(fileDir(k).name,'autoEventStats.mat'))
Eventsfile = fileDir(k).name; % get name of file
%Copy file if not corrupt
load([searchPath, '\', Eventsfile]); %load file into workspace
% do not attempt to extract data from corrupt file or files missing
% variables
if exist('fileCorrupt','var');
clear fileCorrupt
continue;
else
copyfile([searchPath, '\', Eventsfile], [pwd, analysisPath]) % copy 'autoEventStats.mat' file
end
end
end
end
end
SEARCH THE ANALYSIS FOLDER DATA FOR ERRORS
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% EXECUTE IN RAW DATA DIRECTORY
% clear workspace and commmand prompt
evalin('base','clear all; clc');
% addpath to abf files, for search queries
% ADD SPECIFIC FOLDERS TO SEARCH PATH CONTAINING RAW DATA, ABF FILES
% ...\EPCs\Group 1;
% ...\EPCs\Group 2;
% ...\MEPPs\Group 1;
% ...\MEPPs\Group 2;
% along with all subfolders
rawDataPaths
% create partial path to folders with data
Analysisfolders = {'\Analysis\EPC\T\P15'; %1
'\Analysis\EPC\T\P30'; %2
'\Analysis\EPC\W\P15'; %3
'\Analysis\EPC\W\P30'; %4
'\Analysis\MEP\T\P15'; %5
'\Analysis\MEP\T\P30'; %6
'\Analysis\MEP\W\P15'; %7
'\Analysis\MEP\W\P30';}; %8
for n = 1:size(Analysisfolders,1)
% enter code here
% make list from directory append above to pwd
searchFolder = [pwd, Analysisfolders{n}];
% get list of searchfolder contents using dir command
fileDir = dir(searchFolder);
% get rid of hidden files and folders
fileDirtemp = struct('name',{}, 'date',{}, 'bytes',{}, 'isdir',{}, 'datenum',{});
filecount = 1; %initialize filecount
for k = 1:length(fileDir)
if strcmpi(fileDir(k).name,'.') || strcmpi(fileDir(k).name,'..')
continue; %skip if hidden file found
else
fileDirtemp(filecount,1) = fileDir(k);
filecount = filecount +1;
end
end
fileDir = fileDirtemp;
clear fileDirtemp filecount
%open new file
fid = fopen(['Check_Events_Group_', num2str(n),'.txt'],'w'); %open new file
%write header
myheader = 'File_Name \t Corrupt \t Events \t Flags \t Percent_Flags \t Re-analyze \r\n\n';
fprintf(fid, myheader);
hplot = figure('numbertitle','off'); %get handle to figure
for j = 1:length(fileDir)
%enter code here
if ~isempty(strfind(fileDir(j).name,'autoEventStats.mat'))
%enter code here
Eventsfile = fileDir(j).name; %get name of .mat file
cellnameidx = strfind(Eventsfile,'_autoEventStats.mat'); % find index in file name where '_autoEventStats.mat' begins
cellname = Eventsfile(1:cellnameidx(end)-1); % cellname is all string data before last index of '_'
abfFile = [cellname,'.abf']; % generate the name of the associated .abf file
load([searchFolder,'\',Eventsfile]); %load file
%skip if file is corrupt
if exist('fileCorrupt','var');
clear fileCorrupt
fprintf(fid,'%s \t', Eventsfile); %print file name
fprintf(fid,'%d \t %d \t %d \t %d \t %d \r\n', [1 NaN NaN NaN NaN]); %print corrupt, events, flags, fraction
disp(['File Corrupt ', Eventsfile]);
continue;
end
% load .abf .mat files. regenerate autoEventStats.mat
[mycell si] = abfload(abfFile); % load abf file and sample interval, 'si'
si = si/1e6; % convert sample interval usec to sec
mycell = myFilter(mycell); % filter signal
% determine if signal needs to be cropped
if isempty(limitsCrop)
y1 = mycell;
else
y1 = mycell(limitsCrop(1):limitsCrop(2));
end
% Get proper print of title
Eventsfile_print = regexprep(Eventsfile,'_','\\_');
%plot the signal and overlay the events
set(hplot, 'Name', Eventsfile); %set figure name
plot(y1,'k'); %plot the signal
title({['Events = ', num2str(size(myEvents,1))]; Eventsfile_print}); %create title
hold on;
% plot each event green for non flagged and red for flagged
for k = 1:size(myEvents,1)
if myEventsFlag(k) == 0
plot(myEvents(k,1):myEvents(k,3),y1(myEvents(k,1):myEvents(k,3)),'g')
else
plot(myEvents(k,1):myEvents(k,3),y1(myEvents(k,1):myEvents(k,3)),'r')
end
end
hold off;
%get user feedback from plot to determine if events file needs to be regenerated
choice = questdlg('Are the Events Properly Aligned?', ...
'Event Detection Feedback', ...
'No','Yes','Yes');
% Handle response
switch choice
case 'No'
reAnalyze = 1; %set to 1 to indicate flag
case 'Yes'
reAnalyze = 0; %set to zero to indicate no flag
case ''
fclose(fid); %close text file
return %stop if exit dialog box, return control to command window
end
%get event info of non corrupt files
A = size(myEventsFlag,1); %number of events
B = sum(myEventsFlag); %total flags
C = B/A; %fraction of flags
fprintf(fid,'%s \t', Eventsfile); %print file name
fprintf(fid,'%d \t %d \t %d \t %d \t %d \r\n', [0 A B C reAnalyze]); %print corrupt, events, flags, fraction, reAnalyze
end
end
fclose(fid); %close file
end
USE ANALYSIS FOLDER TO GENERATE GROUP STATISTICS FOR EXPORT
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% *MODIFIED*
% 29-Apr-2014 13:56:43
% ADDING FREQUENCY CALCULATION
% frequency will be calculated as the cell average value
% frequency = total number of peaks/ span of peaks in seconds
% the start of file length is the start point of the first event
% the end of the file length is the last point of the last event
% 30-Apr-2014 17:43:55
% NORMALIZING ALL DATA BASED ON GAIN SETTING
% extract gain information from binary file
% 01-May-2014 23:01:49
% FIXING MISSPELLING SAMPLES WAS SMAPLES
% will replace with Frequency(events/sec)
% Metrics:
% Animal
% Cell
% Amplitude
% Area Under Curve
% Tau Rise
% Tau Decay
% Rsquare Tau Rise
% Rsquare Tau Decay
% Time
% InterpeakInterval
% Frequency
% clear workspace and commmand prompt
evalin('base','clear all; clc');
% ADD SPECIFIC FOLDERS TO SEARCH PATH CONTAINING RAW DATA, ABF FILES
% ...\EPCs\Group 1;
% ...\EPCs\Group 2;
% ...\MEPPs\Group 1;
% ...\MEPPs\Group 2;
% along with all subfolders
rawDataPaths
Analysisfolders = {'\Analysis\EPC\T\P15'; %1
'\Analysis\EPC\T\P30'; %2
'\Analysis\EPC\W\P15'; %3
'\Analysis\EPC\W\P30'; %4
'\Analysis\MEP\T\P15'; %5
'\Analysis\MEP\T\P30'; %6
'\Analysis\MEP\W\P15'; %7
'\Analysis\MEP\W\P30';}; %8
nameAnalysisfolders = regexprep(Analysisfolders, '\', '_'); %search and replace '\' with '_'
% Generate summary statistics for each group
% Save data in foder titled Summary_Analysis
SummaryAnalysisPath = [pwd '\Summary_Analysis'];
mkdir(SummaryAnalysisPath);
%
animalcountAll = 1; %initialize all animal counter animals
cellcountAll = 1; %initialize cell counter cells
%
animalcountEPCAll = 1; %initialize counter for all EPC animals
cellcountEPCAll = 1; %initialize counter of all EPC cells
%
animalcountMEPAll = 1; %initialize counter for all MEP animals
cellcountMEPAll = 1; %initialize counter for all MEP cells
%
AllmyData = []; %initialize variable to store all data
AllmyEPCData = []; %initialize variable to store all data
AllmyMEPData = []; %initialize variable to store all data
% loop index through all group folders
for n = 1:size(Analysisfolders,1);
searchPath = [pwd, Analysisfolders{n}];
fileDir = dir(searchPath);
fileDirtemp = struct('name',{}, 'date',{}, 'bytes',{}, 'isdir',{}, 'datenum',{});
filecount = 1; %initialize folder count
for k = 1:length(fileDir)
if strcmpi(fileDir(k).name,'.') || strcmpi(fileDir(k).name,'..')
continue; %skip if hidden dir found
else
fileDirtemp(filecount,1) = fileDir(k);
filecount = filecount + 1;
end
end
fileDir = fileDirtemp;
clear fileDirtemp filecount
%load each .mat file and extract analysis metrics
cellcount = 1; %initialize cell count for each new group
animalcount = 1; %initialize cell count for each new group
fileName_string = {}; %initialize fileName cell string
events_string = {}; %initialize event cell string
myDataSummary = []; %initialize dataSummary for each new group
myDataSummaryAll = []; %initialize all dataSummary for each new group
myDataSummaryEPCAll = []; %initialize all EPC dataSummary for each new group
myDataSummaryMEPAll = []; %initialize all MEP dataSummary for each new group
for k = 1:length(fileDir) %index through all files in directory
if k > 1 %increment animal count by checking previous file name, do not check when k=1
fileName1 = fileDir(k-1).name; %previous file name
fileName2 = fileDir(k).name; %current file name
token1 = strfind(fileName1,'_'); %use '_' token to parse file
animalName1 = fileName(1:token1(1)-1); %parse file name preserving animal ID only
token2 =strfind(fileName2,'_');
animalName2 = fileName2(1:token2(1)-1);
if ~strcmp(animalName1,animalName2) %compare animal id name only
animalcount = animalcount+1; %incremet animal count
animalcountAll = animalcountAll +1; %incremnt all animal count when indexing inside group
end
if ~strcmp(animalName1,animalName2) && n <= 4
animalcountEPCAll = animalcountEPCAll +1; %increment EPC all animal count
end
if ~strcmp(animalName1,animalName2) && n >= 5
animalcountMEPAll = animalcountMEPAll +1; %increment MEP all animal count
end
end
fileName = fileDir(k).name; %get file name
load([searchPath, '\', fileName]); %load .mat file into workspace
%generate new data with following fields
% Amplitude - taken from EventDataStats
% Tau Rise - taken from EventDataStats
% Tau Decay - taken from EventDataStats
% Area Under Curve - taken from EventDataStats
% R square error of Tau Rise - taken from EventDataStats
% R square error of Tau Decay - taken from EventDataStats
% InterpeakInterval - computed from peakSet and si
% Frequency - computed as the # of peaks/time(start peak to end
% peak)
% do not attempt to extract data from corrupt file or files missing
% variables
if exist('fileCorrupt','var');
clear fileCorrupt
continue;
end
if ~exist('EventDataStats','var') || ~exist('si','var')...
|| ~exist('peakSet','var') || ~exist('myEventsFlag','var')
continue;
end
% Make variable storing time stamp of events
mytime = myEvents(:,2)*si; %time of event = index of event*sample interval
% if events were flagged, need to eliminate flagged events from mytime
if size(EventDataStats,1) ~= size(mytime,1) %if sizes do not agree
mytimetemp = ones(size(EventDataStats,1),1); %create temporary array
mytimecount = 1; %initialize time counter
for j = 1:length(mytime)
if myEventsFlag(j) == 1 % continue loop if event is flagged
continue
else
mytimetemp(mytimecount) = mytime(j);
mytimecount = mytimecount +1;
end
end
mytime = mytimetemp;
end
% Make variable storing computed cell average frequency
rateF = nan(size(mytime)); %make temporary variable for the frequency measurement
%find first real event
for countF = 1:length(myEventsFlag) %count from start to end
if myEventsFlag(countF) == 0 %break on first good event
startF = myEvents(countF,1); %start of event series, begins with first good event
break %stop search when first good event found
end
end
%find last real event
for countF = length(myEventsFlag):-1:1 %count *backward* from end to start
if myEventsFlag(countF) == 0 %break on first good event
endF = myEvents(countF,3); %start of event series, begins with first good event
break %stop search when first good event found
end
end
%compute
timeF = endF - startF; %number of data points spaning event series
timeF = timeF*si; %convert data points into time, using the sample interval
eventsF = sum(~myEventsFlag); %get the total number of good events
rateF(1) = eventsF / timeF; %frequency of events given in samples/second, entered in to the 1st entry of rateF array
%Make variable to store the computed interpeak interval
iPitemp = nan(size(mytime)); %make temporary variable for interpeak interval filled with NaN's
iPi = diff(mytime); %compute interpeak interval
iPitemp(1:length(iPi)) = iPi; %enter interpeak interval values into preinitialized array
iPi = iPitemp; %interpeak interval will have one entry with NaN
%Make cellstring of file name and event#
% Get proper print of title, remove .mat
fileName_print = regexprep(fileName,'.mat','');
fileName_string_temp = repmat(fileName_print, size(EventDataStats,1),1); %make row array of fileName
fileName_string_temp = cellstr(fileName_string_temp); %convert to cell string
fileName_string = [fileName_string; fileName_string_temp]; %concatenate string
% Make string of individual events
events_string_temp = 1:size(EventDataStats,1); %get count of all events
events_string_temp = events_string_temp(:); %make row array
events_string_temp = num2str(events_string_temp); %make charachter array
events_string_temp = cellstr(events_string_temp); %convert to cell string
events_string = [events_string;events_string_temp]; %concatenate string
%make [group animal cell amplitude(nA) Tau-Rise(sec) Tau-Decay(sec) AreaUnderCurve(nA*sec) R(rise) R(fall) InterPeakInterval(sec) time(sec)]
animalArray = ones(size(EventDataStats,1),1)*animalcount; %make array of animal ID
cellsArray = ones(size(EventDataStats,1),1)*cellcount; %make array of cell ID
animalArrayAll = ones(size(EventDataStats,1),1)*animalcountAll; %make array of animal ID for storing into composite data file
cellsArrayAll = ones(size(EventDataStats,1),1)*cellcountAll; %make array of cell ID for storing into composite data file
if n <= 4
animalArrayEPCAll = ones(size(EventDataStats,1),1)*animalcountEPCAll; %make array of animal ID
cellsArrayEPCAll = ones(size(EventDataStats,1),1)*cellcountEPCAll; %make array of cell ID
else
animalArrayMEPAll = ones(size(EventDataStats,1),1)*animalcountMEPAll; %make array of animal ID
cellsArrayMEPAll = ones(size(EventDataStats,1),1)*cellcountMEPAll; %make array of cell ID
end
groupArray = ones(size(EventDataStats,1),1)*n; %make array of group ID
%concatenate [group animal cell EventDataStats iPi mytime]
%EventDataStats
%EPC
%amplitude(nA) Tau-Rise(sec) Tau-Decay(sec) AreaUnderCurve(nA*sec) R(rise) R(decay)
%MEP
%amplitude(mV/100) Tau-Rise(sec) Tau-Decay(sec) AreaUnderCurve(mV/100*sec) R(rise) R(decay)
%filter EventDataStats error, <0sec, entries and replace with NaN
for p = 1:numel(EventDataStats)
if EventDataStats(p) < 0
EventDataStats(p) = NaN;
end
end
%filter Tau should be <0.1sec
for p = 1:size(EventDataStats,1)
if EventDataStats(p,2) > 0.1
EventDataStats(p,2) = NaN;
end
if EventDataStats(p,3) > 0.1
EventDataStats(p,3) = NaN;
end
end
%Find the cell Gain and correct for the gain
%fileName = the autoEventStats.mat file
cellnameidx = strfind(fileName,'_autoEventStats.mat'); % find index in file name where '_autoEventStats.mat' begins
cellname = fileName(1:cellnameidx(end)-1); % cellname is all string data before last index of '_'
abfFile = [cellname,'.abf']; % generate the name of the associated .abf file
%Search the file for the Gain information
myfileN = abfFile; %enter file name
fid = fopen(myfileN,'r','ieee-le'); %open the abf file
sz=1; %# of data entries to read
numType = 'float'; %precision format
myGainfileoffset = 268; %find the correct offset where data entry for gain begins
fseek(fid,myGainfileoffset,'bof'); %move field position
cellGain = fread(fid,sz,numType); %read formatted data
fclose(fid); %close file
%Correct for cell gain
EventDataStats(:,1) = EventDataStats(:,1)/cellGain; %convert amplitude
EventDataStats(:,4) = EventDataStats(:,4)/cellGain; %convert AreaUnderCurve
%Build Data Arrays
myDataSummarytemp = [groupArray animalArray cellsArray EventDataStats iPi rateF mytime];
myDataSummaryAlltemp = [groupArray animalArrayAll cellsArrayAll EventDataStats iPi rateF mytime];
myDataSummary = [myDataSummary; myDataSummarytemp]; %concatenate arrays
myDataSummaryAll = [myDataSummaryAll; myDataSummaryAlltemp]; %concatenate arrays
cellcount = cellcount +1; %increment cell count before next loop iteration
cellcountAll = cellcountAll +1; %increment all cell count
if n <= 4 %Buld EPC data array
myDataSummaryEPCAlltemp = [groupArray animalArrayEPCAll cellsArrayEPCAll EventDataStats iPi rateF mytime];
myDataSummaryEPCAll = [myDataSummaryEPCAll; myDataSummaryEPCAlltemp]; %concatenate arrays
cellcountEPCAll = cellcountEPCAll +1; %increment all EPC cell count
else %Build MEP data array
myDataSummaryMEPAlltemp = [groupArray animalArrayMEPAll cellsArrayMEPAll EventDataStats iPi rateF mytime];
myDataSummaryMEPAll = [myDataSummaryMEPAll; myDataSummaryMEPAlltemp]; %concatenate arrays
cellcountMEPAll = cellcountMEPAll +1; %increment all EPC cell count
end
clear EventDataStats limitsCrop myEvents myEventsFlag peakSet peakThreshold si %clear variables
end
%concatenate myDataSummary from same group
eval(['DataSummary', nameAnalysisfolders{n}, '= myDataSummary;']); %save DataSummary as variable to workspace
%make cell aray for Event; EPC, MEPP, Gene; T, W, Age; P15, P30
EventGeneAge = {['EPC','\t', 'TWI','\t', 'P15','\t']; %1
['EPC','\t', 'TWI','\t', 'P30','\t']; %2
['EPC','\t', 'WT ','\t', 'P15','\t']; %3
['EPC','\t', 'WT ','\t', 'P30','\t']; %4
['MEP','\t', 'TWI','\t', 'P15','\t']; %5
['MEP','\t', 'TWI','\t', 'P30','\t']; %6
['MEP','\t', 'WT ','\t', 'P15','\t']; %7
['MEP','\t', 'WT ','\t', 'P30','\t']}; %8
%header
% myheader = {'Event', 'Gene', 'Age', 'Group', 'Animal', 'Cell', 'Amplitude(nA)', '1/Tau-Rise(sec)', '1/Tau-Decay(sec)', 'AreaUnderCurve(nA*sec)', 'Rsquare(rise)', 'Rsquare(decay)', 'InterPeakInterval(sec)', 'time(sec)', 'Event', 'File name'};
%open a text file to enter data for individual groups
if n <= 4 %print header for EPC group
fid = fopen(['Data_Summary', nameAnalysisfolders{n}, '.txt'], 'w'); %open file and assign group name
fprintf(fid, 'Event \t Gene \t Age \t Group \t Animal \t Cell \t Amplitude(nA) \t 1/Tau-Rise(sec) \t 1/Tau-Decay(sec) \t AreaUnderCurve(nA*sec) \t Rsquare(rise) \t Rsquare(decay) \t InterPeakInterval(sec) \t Frequency(events/sec) \t time(sec) \t Event \t File Name \r\n\n'); % write header
for p = 1:size(myDataSummary,1) %loop through each row of myDataSummary
fprintf(fid, EventGeneAge{n}); %wite Event Gene Age info
fprintf(fid, '%10d \t %10d \t %10d \t %10.5f \t %10.5e \t %10.5e \t %10.5e \t %10.5e \t %10.5e \t %10.5e \t %10.5e \t %10.5e \t', myDataSummary(p,:)); %write Data to file
fprintf(fid, [events_string{p}, ' \t ', fileName_string{p}, ' \r']); %write last two columns in row and move to next row
end
else %print header for MEPP group
fid = fopen(['Data_Summary', nameAnalysisfolders{n}, '.txt'], 'w'); %open file and assign group name
fprintf(fid, 'Event \t Gene \t Age \t Group \t Animal \t Cell \t Amplitude(mV) \t 1/Tau-Rise(sec) \t 1/Tau-Decay(sec) \t AreaUnderCurve(mV*sec) \t Rsquare(rise) \t Rsquare(decay) \t InterPeakInterval(sec) \t Frequency(events/sec) \t time(sec) \t Event \t File Name \r\n\n'); % write header
for p = 1:size(myDataSummary,1) %loop through each row of myDataSummary
fprintf(fid, EventGeneAge{n}); %wite Event Gene Age info
fprintf(fid, '%10d \t %10d \t %10d \t %10.5f \t %10.5e \t %10.5e \t %10.5e \t %10.5e \t %10.5e \t %10.5e \t %10.5e \t %10.5e \t', myDataSummary(p,:)); %write Data to file
fprintf(fid, [events_string{p}, ' \t ', fileName_string{p}, ' \r']); %write last two columns in row and move to next row
end
end
fclose(fid); %close file
movefile(['*',nameAnalysisfolders{n}, '.txt'], SummaryAnalysisPath); % move file(s) to Summaryanalysis folder
clear myDataSummary %remove variable so that it does not concatenate with other groups DataSummary
%Write all data to a single text file
%open a text file to write and save ALL data
if n == 1 %open a new file and print header for EPC gropus
fidAll = fopen(['Data_Summary_ALL', '.txt'], 'w'); %open file and assign group name
fprintf(fidAll, 'Event \t Gene \t Age \t Group \t Animal \t Cell \t Amplitude(nA) \t 1/Tau-Rise(sec) \t 1/Tau-Decay(sec) \t AreaUnderCurve(nA*sec) \t Rsquare(rise) \t Rsquare(decay) \t InterPeakInterval(sec) \t Frequency(events/sec) \t time(sec) \r\n\n'); % write header
for p = 1:size(myDataSummaryAll,1) %loop through each row of myDataSummary
fprintf(fidAll, EventGeneAge{n}); %wite Event Gene Age info
fprintf(fidAll, '%10d \t %10d \t %10d \t %10.5f \t %10.5e \t %10.5e \t %10.5e \t %10.5e \t %10.5e \t %10.5e \t %10.5e \t %10.5e \r', myDataSummaryAll(p,:)); %write to file
end
elseif n == 5 %print a new header for start of MEPP gropus but dont reopen file that is already open
fprintf(fidAll, ' \r\n\n'); %line feed
fprintf(fidAll, 'Event \t Gene \t Age \t Group \t Animal \t Cell \t Amplitude(mV) \t 1/Tau-Rise(sec) \t 1/Tau-Decay(sec) \t AreaUnderCurve(mV*sec) \t Rsquare(rise) \t Rsquare(decay) \t InterPeakInterval(sec) \t Frequency(events/sec) \t time(sec) \r\n\n'); % write header
for p = 1:size(myDataSummaryAll,1) %loop through each row of myDataSummary
fprintf(fidAll, EventGeneAge{n}); %wite Event Gene Age info
fprintf(fidAll, '%10d \t %10d \t %10d \t %10.5f \t %10.5e \t %10.5e \t %10.5e \t %10.5e \t %10.5e \t %10.5e \t %10.5e \t %10.5e \r', myDataSummaryAll(p,:)); %write to file
end
else %print data only for groups
for p = 1:size(myDataSummaryAll,1) %loop through each row of myDataSummary
fprintf(fidAll, EventGeneAge{n}); %wite Event Gene Age info
fprintf(fidAll, '%10d \t %10d \t %10d \t %10.5f \t %10.5e \t %10.5e \t %10.5e \t %10.5e \t %10.5e \t %10.5e \t %10.5e \t %10.5e \r', myDataSummaryAll(p,:)); %write to file
end
end
AllmyData = [AllmyData; myDataSummaryAll]; %concatenate AllmyData
animalcountAll = animalcountAll +1; %incremnt all animal count when indexing between groups
clear myDataSummaryAll %remove variable so that it does not concatenate with other group's DataSummary
%Write all EPC data to a single text file
%open a text file to write and save ALL data
if n <= 4
if n == 1 %open a new file and print header for EPC gropus
fidEPCAll = fopen(['Data_Summary_EPC_ALL', '.txt'], 'w'); %open file and assign group name
fprintf(fidEPCAll, 'Event \t Gene \t Age \t Group \t Animal \t Cell \t Amplitude(nA) \t 1/Tau-Rise(sec) \t 1/Tau-Decay(sec) \t AreaUnderCurve(nA*sec) \t Rsquare(rise) \t Rsquare(decay) \t InterPeakInterval(sec) \t Frequency(events/sec) \t time(sec) \r\n\n'); % write header
for p = 1:size(myDataSummaryEPCAll,1) %loop through each row of myDataSummary
fprintf(fidEPCAll, EventGeneAge{n}); %wite Event Gene Age info
fprintf(fidEPCAll, '%10d \t %10d \t %10d \t %10.5f \t %10.5e \t %10.5e \t %10.5e \t %10.5e \t %10.5e \t %10.5e \t %10.5e \t %10.5e \r', myDataSummaryEPCAll(p,:)); %write to file
end
else %print data only for groups
for p = 1:size(myDataSummaryEPCAll,1) %loop through each row of myDataSummary
fprintf(fidEPCAll, EventGeneAge{n}); %wite Event Gene Age info
fprintf(fidEPCAll, '%10d \t %10d \t %10d \t %10.5f \t %10.5e \t %10.5e \t %10.5e \t %10.5e \t %10.5e \t %10.5e \t %10.5e \t %10.5e \r', myDataSummaryEPCAll(p,:)); %write to file
end
end
AllmyEPCData = [AllmyEPCData; myDataSummaryEPCAll]; %concatenate all EPC data
animalcountEPCAll = animalcountEPCAll +1;
clear myDataSummaryEPCAll %remove variable so that it does not concatenate with other EPC group's DataSummary
end
%Write all EPC data to a single text file
%open a text file to write and save ALL data
if n >= 5
if n == 5 %open a new file and print header for MEP gropus
fidMEPAll = fopen(['Data_Summary_MEP_ALL', '.txt'], 'w'); %open file and assign group name
fprintf(fidMEPAll, 'Event \t Gene \t Age \t Group \t Animal \t Cell \t Amplitude(mV) \t 1/Tau-Rise(sec) \t 1/Tau-Decay(sec) \t AreaUnderCurve(mV*sec) \t Rsquare(rise) \t Rsquare(decay) \t InterPeakInterval(sec) \t Frequency(events/sec) \t time(sec) \r\n\n'); % write header
for p = 1:size(myDataSummaryMEPAll,1) %loop through each row of myDataSummary
fprintf(fidMEPAll, EventGeneAge{n}); %wite Event Gene Age info
fprintf(fidMEPAll, '%10d \t %10d \t %10d \t %10.5f \t %10.5e \t %10.5e \t %10.5e \t %10.5e \t %10.5e \t %10.5e \t %10.5e \t %10.5e \r', myDataSummaryMEPAll(p,:)); %write to file
end
else %print data only for groups
for p = 1:size(myDataSummaryMEPAll,1) %loop through each row of myDataSummary
fprintf(fidMEPAll, EventGeneAge{n}); %wite Event Gene Age info
fprintf(fidMEPAll, '%10d \t %10d \t %10d \t %10.5f \t %10.5e \t %10.5e \t %10.5e \t %10.5e \t %10.5e \t %10.5e \t %10.5e \t %10.5e \r', myDataSummaryMEPAll(p,:)); %write to file
end
end
AllmyMEPData = [AllmyMEPData; myDataSummaryMEPAll]; %concatenate all MEP data
animalcountMEPAll = animalcountMEPAll +1;
clear myDataSummaryEPCAll %remove variable so that it does not concatenate with other MEP group's DataSummary
end
end
fclose(fidAll); %close SummaryAll Data file
fclose(fidEPCAll); %close SummaryEPCAll Data file
fclose(fidMEPAll); %close SummaryMEPAll Data file
movefile('Data_Summary_ALL.txt', SummaryAnalysisPath); %move file to summaryAnalysisPath
movefile('Data_Summary_EPC_ALL.txt', SummaryAnalysisPath); %move file to summaryAnalysisPath
movefile('Data_Summary_MEP_ALL.txt', SummaryAnalysisPath); %move file to summaryAnalysisPath
% combine each group's 'DataSummary_Analysis*' variables into one .mat file
% called 'DataSummary_Analysis.mat'
save('Data_Summary_Analysis','DataSummary_Analysis*'); %save each variable beginning with DataSummary_Analysis* as DataSummary_Analysis.mat
% move into Summaryanalysis folder
movefile('Data_Summary_Analysis.mat', SummaryAnalysisPath);
% save AllmyData variable as a mat file
save('All_Summary_Analysis','AllmyData'); %save to workspace
% move into SummaryAnalysis folder
movefile('All_Summary_Analysis.mat', SummaryAnalysisPath);
% save AllmyEPCData variable as mat file
save('All_EPC_Summary_Analysis','AllmyEPCData'); %save to workspace
% move into SummaryAnalysis folder
movefile('All_EPC_Summary_Analysis.mat', SummaryAnalysisPath);
% save AllmyEPCData variable as mat file
save('All_MEP_Summary_Analysis','AllmyMEPData'); %save to workspace
% move into SummaryAnalysis folder
movefile('All_MEP_Summary_Analysis.mat', SummaryAnalysisPath);
% make headers and store them as .mat files
EPCheader = {'Group'; 'Animal'; 'Cell'; 'Amplitude(nA)'; '1/Tau-Rise(sec)'; '1/Tau-Decay(sec)'; 'AreaUnderCurve(nA*sec)'; 'Rsquare(rise)'; 'Rsquare(decay)'; 'InterPeakInterval(sec)'; 'Frequency(events/sec)'; 'time(sec)'; 'Events'; 'File Name'};
MEPheader = {'Group'; 'Animal'; 'Cell'; 'Amplitude(mV)'; '1/Tau-Rise(sec)'; '1/Tau-Decay(sec)'; 'AreaUnderCurve(mV*sec)'; 'Rsquare(rise)'; 'Rsquare(decay)'; 'InterPeakInterval(sec)'; 'Frequency(events/sec)'; 'time(sec)'; 'Events'; 'File Name'};
save('Data_Summary_EPCHeader', 'EPCheader'); %save myheader to workspace as .mat file
save('Data_Summary_MEPHeader', 'MEPheader'); %save myheader to workspace as .mat file
% move into SummaryAnalysis folder
movefile('Data_Summary_EPCHeader.mat', SummaryAnalysisPath);
movefile('Data_Summary_MEPHeader.mat', SummaryAnalysisPath);