runCreateTotalMask.m

%% add the neededs path for the analysis
clear all
addpath(genpath('\\phhydra\phhydraB\Analysis\users\Liora\Codes\'));
warning('off', 'MATLAB:MKDIR:DirectoryExists');% this supresses warning of existing directory

scriptDir = regexprep(mfilename('fullpath'), '\\\w*$', '');

%% Define mainDirList
topMainDir='W:\Analysis\users\Yonit\Movie_Analysis\Channels\2019_07_11_pos1\'; % main folder of original files for layer separation

mainDirList= { ... % enter in the following line all the  movie dirs for cost calculation.
    
'Stitching\Final\C0\',...


};
for i=1:length(mainDirList),mainInDirList{i}=[topMainDir,mainDirList{i}];end

topAnalysisDir='W:\Analysis\users\Yonit\Movie_Analysis\Channels\'; % main folder for layer separation results

mainAnalysisDirList= { ... % enter in the following line all the output dirs for cost calculation.

'\2019_07_11_pos1\', ...


};
for i=1:length(mainAnalysisDirList),AnalysisDirList{i}=[topAnalysisDir,mainAnalysisDirList{i}];end
%%
toSave=1; % If zero, doesn't save images and doesn't overwrite existing images.
Is2D = 1; % If the image is a 2d projected image
IsLS=0; %1 for Lightsheet, 0 otherwise
IsEndo = 0; %1 for Endo, 0 otherwise
IsLabel = 0; %1 for tissue label, 0 otherwise
IsCaEpi = 0 ; % 1 for Ca strain

calibration = 1.28; % In um/pixel. 1.28 um/pixel for 10x air.

% Comment out the following irrelevant choice for framelist:
 framesList = cell(1,length(mainAnalysisDirList));
% framesList = {1:6,1:9}; % Enter specific frame ranges in this format if you
% want to run on particular frames (in this example, 1:6 is for the first
% movie, 1:9 is for the second). If left empty, runs on all frames.

exePath = '%HOMEDRIVE%%HOMEPATH%\\Fiji.app\\ImageJ-win64.exe --headless -macro';
cd (scriptDir)

%% run over each movie folder to create total masks from the raw masks in the folder.
for i=1:length(AnalysisDirList)

    % Create analysis folder, and add .txt file indicating path to raw data
    mkdir(AnalysisDirList{i});
    cd(AnalysisDirList{i});

    writeExperimentParametersGUI(AnalysisDirList{i}, 'experiment_details.yml');

    fileID = fopen('experiment_path.txt','w');
    fprintf(fileID,'%s',topMainDir);
    fclose(fileID);

    mainAnalysisDir=[AnalysisDirList{i},'\Display'];
    mkdir(mainAnalysisDir);
    mainOrigDir=[mainInDirList{i}];

    % Create .txt file indicating path to raw data

    if (Is2D==0 && IsLS==0 && IsLabel==0 && IsEndo==0 && IsCaEpi==0)
        
        % NEW: RUN IMAGEJ MACRO TO CREATE RAW MASKS
        % Arguments for imageJ macro:
        % mainAnalysisDir - string
        % mainOrigDir - string

        system(sprintf('%s %s/cmd_make_raw_mask_from_stack.ijm "%s %s "', exePath, scriptDir, mainAnalysisDir, mainOrigDir));

        if length (framesList{i}) == 0 % run on all frames
            createMaskMovie (mainAnalysisDir, toSave, calibration);
        else % run on frames indicated
            createMaskMovie (mainAnalysisDir, toSave, calibration, framesList{i});
        end

    elseif Is2D==1

        % NEW: RUN IMAGEJ MACRO TO CREATE RAW MASKS
        % Arguments for imageJ macro:
        % mainAnalysisDir - string
        % mainOrigDir - string

        system(sprintf('%s %s/cmd_make_raw_mask_from_2d.ijm "%s %s "', exePath, scriptDir, mainAnalysisDir, mainOrigDir));

        if length (framesList{i}) == 0 % run on all frames
            createMaskMovie (mainAnalysisDir, toSave, calibration);
        else % run on frames indicated
            createMaskMovie (mainAnalysisDir, toSave, calibration, framesList{i});
        end


    elseif IsLS==1
        
        % NEW: RUN IMAGEJ MACRO TO CREATE RAW MASKS
        % Arguments for imageJ macro:
        % mainAnalysisDir - string
        % mainOrigDir - string

        system(sprintf('%s %s/cmd_make_raw_mask_from_stack_lightsheet.ijm "%s %s "', exePath, scriptDir, mainAnalysisDir, mainOrigDir));
        
        if length (framesList{i}) == 0 % run on all frames
            createMaskMovie_lightsheet (mainAnalysisDir, toSave, calibration);
        else % run on frames indicated
            createMaskMovie_lightsheet (mainAnalysisDir, toSave, calibration, framesList{i});
        end
        
        
    elseif IsEndo==1
        
        % NEW: RUN IMAGEJ MACRO TO CREATE RAW MASKS
        % Arguments for imageJ macro:
        % mainAnalysisDir - string
        % mainOrigDir - string


        system(sprintf('%s %s/cmd_make_raw_mask_from_stack_endo.ijm "%s %s "', exePath, scriptDir, mainAnalysisDir, mainOrigDir));
        
        if length (framesList{i}) == 0 % run on all frames
            createMaskMovie_lightsheet (mainAnalysisDir, toSave, calibration);
        else % run on frames indicated
            createMaskMovie_lightsheet (mainAnalysisDir, toSave, calibration, framesList{i});
        end
        
    elseif IsLabel==1
        
        % NEW: RUN IMAGEJ MACRO TO CREATE RAW MASKS
        % Arguments for imageJ macro:
        % mainAnalysisDir - string
        % mainOrigDir - string

        system(sprintf('%s %s/cmd_make_raw_mask_tissue_label.ijm "%s %s "', exePath, scriptDir, mainAnalysisDir, mainOrigDir));
        
        if length (framesList{i}) == 0 % run on all frames
            createMaskMovie_label (mainAnalysisDir, toSave, calibration);
        else % run on frames indicated
            createMaskMovie_label (mainAnalysisDir, toSave, calibration, framesList{i});
        end

        elseif IsCaEpi==1

        % NEW: RUN IMAGEJ MACRO TO CREATE RAW MASKS
        % Arguments for imageJ macro:
        % mainAnalysisDir - string
        % mainOrigDir - string

        if length (framesList{i}) == 0 % run on all frames
            createMaskMovie_caEpi (mainOrigDir, mainAnalysisDir, toSave, calibration,framesList{i});
        else % run on frames indicated
            createMaskMovie_caEpi (mainOrigDir, mainAnalysisDir, toSave, calibration, framesList{i});
        end
    end
end