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PhysiCell_POV_writer.cpp
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PhysiCell_POV_writer.cpp
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/*
###############################################################################
# If you use PhysiCell in your project, please cite PhysiCell and the version #
# number, such as below: #
# #
# We implemented and solved the model using PhysiCell (Version x.y.z) [1]. #
# #
# [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, #
# PhysiCell: an Open Source Physics-Based Cell Simulator for Multicellu- #
# lar Systems, PLoS Comput. Biol. 14(2): e1005991, 2018 #
# DOI: 10.1371/journal.pcbi.1005991 #
# #
# See VERSION.txt or call get_PhysiCell_version() to get the current version #
# x.y.z. Call display_citations() to get detailed information on all cite-#
# able software used in your PhysiCell application. #
# #
# Because PhysiCell extensively uses BioFVM, we suggest you also cite BioFVM #
# as below: #
# #
# We implemented and solved the model using PhysiCell (Version x.y.z) [1], #
# with BioFVM [2] to solve the transport equations. #
# #
# [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, #
# PhysiCell: an Open Source Physics-Based Cell Simulator for Multicellu- #
# lar Systems, PLoS Comput. Biol. 14(2): e1005991, 2018 #
# DOI: 10.1371/journal.pcbi.1005991 #
# #
# [2] A Ghaffarizadeh, SH Friedman, and P Macklin, BioFVM: an efficient para- #
# llelized diffusive transport solver for 3-D biological simulations, #
# Bioinformatics 32(8): 1256-8, 2016. DOI: 10.1093/bioinformatics/btv730 #
# #
###############################################################################
# #
# BSD 3-Clause License (see https://opensource.org/licenses/BSD-3-Clause) #
# #
# Copyright (c) 2015-2019, Paul Macklin and the PhysiCell Project #
# All rights reserved. #
# #
# Redistribution and use in source and binary forms, with or without #
# modification, are permitted provided that the following conditions are met: #
# #
# 1. Redistributions of source code must retain the above copyright notice, #
# this list of conditions and the following disclaimer. #
# #
# 2. Redistributions in binary form must reproduce the above copyright #
# notice, this list of conditions and the following disclaimer in the #
# documentation and/or other materials provided with the distribution. #
# #
# 3. Neither the name of the copyright holder nor the names of its #
# contributors may be used to endorse or promote products derived from this #
# software without specific prior written permission. #
# #
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" #
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE #
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE #
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE #
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR #
# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF #
# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS #
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN #
# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) #
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE #
# POSSIBILITY OF SUCH DAMAGE. #
# #
###############################################################################
*/
#include <cstdio>
#include <cstdlib>
#include <cmath>
#include <vector>
#include <iostream>
#include <string>
#include <omp.h>
#include "./modules/PhysiCell_POV.h"
#include "./modules/PhysiCell_pugixml.h"
#include "./BioFVM/BioFVM_matlab.h"
#include "./BioFVM/BioFVM_vector.h"
#include "./custom_modules/povwriter.h"
int main( int argc, char* argv[] )
{
display_splash( std::cout );
std::string config_file = "./config/povwriter-settings.xml";
std::vector<int> file_indices;
// process command-line arguments
bool XML_status = false;
if( argc > 1 )
{
if( is_xml(argv[1]) )
{
config_file = argv[1];
}
else
{
file_indices = create_index_list( argv[1] );
}
}
XML_status = load_config_file( config_file );
if( !XML_status )
{ exit(-1); }
if( file_indices.size() == 0 )
{
file_indices.push_back( options.time_index );
}
// set options
default_POV_options.set_camera_from_spherical_location( options.camera_distance , options.camera_theta, options.camera_phi ); // 1500, 5*pi/4.0 , pi/3.0 ); // do
default_POV_options.light_position[0] *= 0.5;
// process all the files
omp_set_num_threads(options.threads);
#pragma omp parallel for
for( int n =0 ; n < file_indices.size() ; n++ )
{
// read the matrix
// std::vector< std::vector<double> > MAT = read_matlab( options.filename.c_str() );
std::string filename = create_filename( file_indices[n] );
std::cout << "Processing file " << filename << "... " << std::endl;
std::vector< std::vector<double> > MAT = read_matlab( filename );
std::cout << "Matrix size: " << MAT.size() << " x " << MAT[0].size() << std::endl;
// start output
char temp [1024];
// sprintf( temp , "pov%08i.pov" , options.time_index );
sprintf( temp , "pov%08i.pov" , file_indices[n] );
filename = temp ;
std::ofstream os( filename.c_str() , std::ios::out );
std::cout << "Creating file " << filename << " for output ... " << std::endl;
Write_POV_start( os );
// now, place the cells
std::cout << "Writing " << MAT[0].size() << " cells ... " <<std::endl;
plot_all_cells(os,MAT);
os.close();
std::cout << "done!" << std::endl << std::endl ;
}
std::cout << "Done processing all " << file_indices.size() << " files!" << std::endl << std::endl;
return 0;
}