/*
 * Software License Agreement (BSD License)
 *
 * Point Cloud Library (PCL) - www.pointclouds.org
 * Copyright (c) 2009-2011, Willow Garage, Inc.
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 * All rights reserved.
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 * $Id:$
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#include <iostream>

#include <pcl/filters/filter.h>
#include <pcl/features/normal_3d.h>
#include <pcl/io/pcd_io.h>
#include <pcl/segmentation/region_growing.h>
#include <pcl/common/time.h>
#include <pcl/console/parse.h>

int
main (int argc, char** av)
{
  if (argc < 2)
  {
    pcl::console::print_info ("Syntax is: %s <source-pcd-file> [-dump]\n\n", av[0]);
    pcl::console::print_info ("If -dump is provided write the extracted clusters to cluster.dat\n\n");
    return (1);
  }

  pcl::PointCloud<pcl::PointXYZ>::Ptr cloud_ptr (new pcl::PointCloud<pcl::PointXYZ>());
  pcl::PointCloud<pcl::PointXYZ>::Ptr cloud_no_nans (new pcl::PointCloud<pcl::PointXYZ>());
  pcl::PointCloud<pcl::Normal>::Ptr cloud_normals (new pcl::PointCloud<pcl::Normal>());
  pcl::PointCloud<pcl::PointXYZRGB>::Ptr cloud_segmented (new pcl::PointCloud<pcl::PointXYZRGB>());

  pcl::PCDWriter writer;
  if (pcl::io::loadPCDFile(av[1], *cloud_ptr)==-1)
  {
    return -1;
  }

  pcl::console::print_highlight ("Loaded cloud %s of size %lu\n", av[1], cloud_ptr->points.size ());

  // Remove the nans
  cloud_ptr->is_dense = false;
  cloud_no_nans->is_dense = false;
  std::vector<int> indices;
  pcl::removeNaNFromPointCloud (*cloud_ptr, *cloud_no_nans, indices);
  pcl::console::print_highlight ("Removed nans from %lu to %lu\n", cloud_ptr->points.size (), cloud_no_nans->points.size ());

  // Estimate the normals
  pcl::NormalEstimation<pcl::PointXYZ, pcl::Normal> ne;
  ne.setInputCloud (cloud_no_nans);
  pcl::search::KdTree<pcl::PointXYZ>::Ptr tree_n (new pcl::search::KdTree<pcl::PointXYZ>());
  ne.setSearchMethod (tree_n);
  ne.setRadiusSearch (0.03);
  ne.compute (*cloud_normals);
  pcl::console::print_highlight ("Normals are computed and size is %lu\n", cloud_normals->points.size ());

  // Region growing
  pcl::RegionGrowing<pcl::PointXYZ, pcl::Normal> rg;
  rg.setSmoothModeFlag (false); // Depends on the cloud being processed
  rg.setInputCloud (cloud_no_nans);
  rg.setInputNormals (cloud_normals);

  std::vector <pcl::PointIndices> clusters;
  pcl::StopWatch watch;
  rg.extract (clusters);
  pcl::console::print_highlight ("Extraction time: %f\n", watch.getTimeSeconds());
  cloud_segmented = rg.getColoredCloud ();

  // Writing the resulting cloud into a pcd file
  pcl::console::print_highlight ("Number of segments done is %lu\n", clusters.size ());
  writer.write<pcl::PointXYZRGB> ("segment_result.pcd", *cloud_segmented, false);

  if (pcl::console::find_switch (argc, av, "-dump"))
  {
    pcl::console::print_highlight ("Writing clusters to clusters.dat\n");
    std::ofstream clusters_file;
    clusters_file.open ("clusters.dat");
    for (std::size_t i = 0; i < clusters.size (); ++i)
    {
      clusters_file << i << "#" << clusters[i].indices.size () << ": ";
      std::vector<int>::const_iterator pit = clusters[i].indices.begin ();
      clusters_file << *pit;
      for (; pit != clusters[i].indices.end (); ++pit)
        clusters_file << " " << *pit;
      clusters_file << std::endl;
    }
    clusters_file.close ();
  }

  return (0);
}
