neurons/processListOfPlates.m at master · fethallah/neurons · GitHub

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function processListOfPlates(datasets_paths_filename, resolution)

% processListOfPlates from a txt file under the format provided by
% OpenBis
%
% This code is specific to the Sinergia project
%
% resolution could be '10x' or '20x', it's used to select parameters
%
% (c) Fethallah Benmansour, fethallah@gmail.com
%
%   Written 4/07/2012

% ------------------- set the paths -----------------------

if isempty( strfind(path, [pwd '/Common']) )
    addpath([pwd '/Common']);
end

if isempty( strfind(path, [pwd '/IO']) )
    addpath([pwd '/IO']);
end

if isempty( strfind(path, [pwd '/Geodesics']) )
    addpath([pwd '/Geodesics']);
end

run([pwd '/vlfeat-0.9.16/toolbox/vl_setup']);

if isempty( strfind(path, [pwd '/CellsDetection']) )
    addpath([pwd '/CellsDetection']);
end

if isempty( strfind(path, [pwd '/GreedyTracking']) )
    addpath([pwd '/GreedyTracking']);
end

if isempty( strfind(path, [pwd '/NeuritesDetection']) )
    addpath([pwd '/NeuritesDetection']);
end

if isempty( strfind(path, [pwd '/NeuritesTracking']) )
    addpath([pwd '/NeuritesTracking']);
end

if isempty( strfind(path, [pwd '/FeaturesExtraction']) )
    addpath([pwd '/FeaturesExtraction']);
end

if isempty( strfind(path, [pwd '/frangi_filter_version2a']) )
    addpath([pwd '/frangi_filter_version2a']);
end

if isempty( strfind(path, [pwd '/gaimc']) )
    addpath([pwd '/gaimc']);
end


% some environement variables:
setenv('DYLD_LIBRARY_PATH', '/usr/local/bin/;/opt/local/lib/');
setenv('PATH', '/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/local/bin:/usr/local/git/bin:/usr/X11/bin');

% -------- get the list of plates and process -----------
fid = fopen(datasets_paths_filename);
C = textscan(fid, '%s %s %s %s %s');
fclose(fid);

inputDataRoot      = '/raid/data/store/';
outputAnalisysRoot = '/raid/data/analysis/ProcessingRiwal/';

matlabpool local

for i= 1:length(C{1})
    Sample	 = C{3}(i);
    Identifier = C{4}(i);
    Location = C{5}(i);
    inputFolder = [inputDataRoot Location{1} '/original/'];
    a = dir(inputFolder);
    for j = 1:length(a)
        if( a(j).isdir && length(a(j).name) > 4  )%&& ~isempty(regexpi(Sample{1},a(j).name))
            directoryName = a(j).name;
            break;
        end
    end
    inputFolder = [inputFolder   directoryName '/' ];%#ok<*AGROW>
    disp(inputFolder);
    resultsFolder = [outputAnalisysRoot  Sample{1} '/'];
    if( exist(resultsFolder, 'dir') )
        rmdir(resultsFolder, 's');
    end
    if( ~exist(resultsFolder, 'dir') )
        mkdir(resultsFolder);
    end
    processPlate(inputFolder , resultsFolder, Sample{1}, Identifier{1}, resolution);
end

matlabpool close;