seaStarProcessingSegmentation/mainFeaturesExtractionBulk.m at main · ComplexOrganizationOfLivingMatter/seaStarProcessingSegmentation · GitHub

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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% mainfeaturesExtractionBulk
% Same as mainSegmentation but for processing
% several folders.
% Main code for extracting sea star cellular features
% from segmentations. Segmentations should be
% in .tif or .tiff format.
% Some paths must be changed by user --> inPath
% Both raw images and segmented images should be
% inside each one of the inPath folders
%
% EXAMPLE
%
% fullPathTo\SeaStarSegmentations
%         > segmentedImages
%               >SegmentedImg1.tif
%               >SegmentedImg2.tif
%         > originalImages
%               >OriginalImg1.tif
%               >OriginalImg2.tif
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

addpath(genpath('src'))
addpath(genpath('lib'))

clear all
close all

inPath = uigetdir('E:\Antonio\SeaStar Proyect\SeaStar_Segmentation\animalEmbryos\20200114_pos1');

embryosFiles=dir(inPath);
dirEmbryos = [embryosFiles.isdir];
subDirs = embryosFiles(dirEmbryos);
embryosFiles = subDirs(3:end);

for nEmbryos=1:length(embryosFiles)
    segmentedEmbryosFiles = dir(strcat(embryosFiles(nEmbryos).folder,'\',embryosFiles(nEmbryos).name,'\segmentedImages\*.tif*'));
    originalEmbryosFiles = dir(strcat(embryosFiles(nEmbryos).folder,'\',embryosFiles(nEmbryos).name,'\originalImages\*.tif*'));

    allGeneralInfo = cell(size(segmentedEmbryosFiles,1),1);
    allTissues = cell(size(segmentedEmbryosFiles,1),1);
    allMeanCellsFeatures = cell(size(segmentedEmbryosFiles,1),1);
    allStdCellsFeatures = cell(size(segmentedEmbryosFiles,1),1);
    load(fullfile(originalEmbryosFiles.folder,originalEmbryosFiles.name));
    for nFiles=1:length(segmentedEmbryosFiles)

        originalImagePath = originalEmbryosFiles(nFiles).folder;
        segmentPath = segmentedEmbryosFiles(nFiles).folder;
        imageName=originalEmbryosFiles(nFiles).name;
        segmentName=segmentedEmbryosFiles(nFiles).name;
        fileName=strsplit(segmentName,'_itkws');
        fileName=strsplit(fileName{1},'.tif');

        if exist(fullfile(segmentPath, fileName{1})) ~=7
            fileName=strsplit(segmentName,'_itkws');
            mkdir(segmentPath, fileName{1})

        end
        [generalInfo,tissue3dFeatures,meanCellsFeatures,stdCellsFeatures] = seaStarPostProcessing(originalImagePath,segmentPath,imageName,segmentName);

        allGeneralInfo{nFiles} = generalInfo;
        allTissues{nFiles} = tissue3dFeatures;
        allMeanCellsFeatures{nFiles} = meanCellsFeatures;
        allStdCellsFeatures{nFiles} = stdCellsFeatures;

    end

    summarizeAllTissuesProperties(allGeneralInfo,allTissues,allMeanCellsFeatures,allStdCellsFeatures,inPath,[],1);

end