tif_to_jpeg2000_master_OAR.m

% that function aims to convert tif stacks into jpeg2000 format to reduce
% considerably the size while keeping the 16 bits dynamical range. The
% argument for compression factor can be adapted depending on the final
% size of the data requested. Nevertheless, a too high value may imply
% substantial degradation of the data.

% origin Paul Tafforeau ESRF 07/2014

function tif_to_jpeg2000_master_OAR(compression_factor)

if nargin<1
    compression_factor=10;
    disp('no compression factor has been specified, I put 10 by default')
    
end


%% parameters for parallelization
start_now         = 1;

secure_process    = 1;
waiting_time      = 200 ; % how long (in minutes) the system will wait before restarting the job submission
number_of_trials  = 2 ; % in case of blocked jobs, how many times will be the system resubmitted before exiting of the loop


%% parallel calculation parameters

gpu_cpu        =  'cpu';
walltime       =  '02:00:00'
slices_per_job =  50 ; % number of slices processed by each job to calculate automatically the number of jobs

%% selection of all the files having the same radix
d=dir('*.tif');
fname={d.name};
number_of_files=size(d,1);

first=1;
last=number_of_files;

scan_dir=cleandirectoryname(pwd);
% n2: fileprefix, taken from directory name
pos=findstr(scan_dir,'/');
scan_dir=scan_dir(pos(end)+1:end);

directory=cleandirectoryname(pwd);

cd ..
voltif_dir=cleandirectoryname(pwd);
resultdir=[voltif_dir '/' scan_dir sprintf('jp2-%1.0i_',compression_factor)];
cd (directory)

%%%%%%%%%%%%%%%%%
% create result directory if not-existing
%%%%%%%%%%%%%%%%%
newdirectory=isempty(what(resultdir));
if newdirectory
    unix(sprintf('mkdir %s',resultdir))
    stat = 1;
    if stat
        disp(sprintf('New directory %s created successfully',resultdir))
        unix(sprintf('chmod 777 %s',resultdir));
    else
        disp('Problems creating new directory, permissions ???')
        return % EXITING PROGRAM !!!
    end
end


%% starting of the parallel calculation

param_string=sprintf('%1.0f',compression_factor);

number_of_jobs=ceil((last-first+1)/slices_per_job);


if number_of_jobs>100
   
    number_of_jobs=100;
    walltime='02:00:00'
    
end
       
    do_OAR_id19_2017('tif_to_jpeg2000_slave_OAR',first,last,number_of_jobs,directory,start_now,gpu_cpu,walltime,param_string)    
   

%% waiting system for checking of processing evolution

 
   % cd (resultdir)

   
    waiting=1;
    prec_treated=0;
    disp('the survey of the number of files will be updated every 10 seconds, do not take into account the first measurement')


    if secure_process
        non_running_time=0;
        job_restart=0;
    end



    while waiting==1

        d=dir([ resultdir '/*.jp2']);
        number_of_files=size(d,1);



        if number_of_files<round(last-first)
            waiting=1;
            pause(10)

            treated=number_of_files-prec_treated;
            remaining_time=((last-first-number_of_files)/treated)*10;


            if secure_process

                if treated==0
                    non_running_time=non_running_time+1;
                    disp('it seems that nothing new happened during the last minute, I am waiting before restarting the submission')
                else
                    non_running_time=0;
                end

                if non_running_time==waiting_time
                    if job_restart==number_of_trials
                        disp('it seems impossible to do the processing, I stop the waiting loop, please investigate the problem more in details')
                        return
                    end
                    
                    cd (directory)
                    disp('some of the jobs are not starting, I resubmit all of them');
                    %! oardel_myjobs
                    do_OAR_id19_2017('tif_to_jpeg2000_slave_OAR',first,last,number_of_jobs,directory,start_now,gpu_cpu,walltime,param_string)
                 %   cd (resultdir)
                    job_restart=job_restart+1;
                    non_running_time=0;
                    
                end

            end




            if remaining_time>3600
                remaining_time=remaining_time/3600;
                disp(sprintf('%1.0f files processed in 10 seconds, %1.0f files on %1.0f processed, it should finish in about %1.1f hours',treated,number_of_files, last-first,remaining_time));
            else
                if remaining_time<60
                    disp(sprintf('%1.0f files processed in 10 seconds, %1.0f files on %1.0f processed, it should finish in about %1.0f seconds',treated,number_of_files,last-first,remaining_time));
                else
                    remaining_time=remaining_time/60;
                    disp(sprintf('%1.0f files processed in 10 seconds, %1.0f files on %1.0f processed, it should finish in about %1.1f minutes',treated,number_of_files,last-first,remaining_time));
                end
            end


            prec_treated=number_of_files;


        else
            waiting=0;
            break
        end

    end

    disp('the conversion of the volume to jpeg2000 stack is finished, I hope that you will enjoy the results')
    
    cd (resultdir)

   close all

end