extract.h

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/* Copyright (c) 2008-2022 the MRtrix3 contributors.
 *
 * This Source Code Form is subject to the terms of the Mozilla Public
 * License, v. 2.0. If a copy of the MPL was not distributed with this
 * file, You can obtain one at http://mozilla.org/MPL/2.0/.
 *
 * Covered Software is provided under this License on an "as is"
 * basis, without warranty of any kind, either expressed, implied, or
 * statutory, including, without limitation, warranties that the
 * Covered Software is free of defects, merchantable, fit for a
 * particular purpose or non-infringing.
 * See the Mozilla Public License v. 2.0 for more details.
 *
 * For more details, see http://www.mrtrix.org/.
 */
 
#ifndef __dwi_tractography_connectome_extract_h__
#define __dwi_tractography_connectome_extract_h__
 
 
#include "file/ofstream.h"
 
#include "dwi/tractography/file.h"
#include "dwi/tractography/properties.h"
#include "dwi/tractography/connectome/connectome.h"
#include "dwi/tractography/connectome/exemplar.h"
 
 
namespace MR {
namespace DWI {
namespace Tractography {
namespace Connectome {
 
 
 
 
 
 
class Selector
{ MEMALIGN(Selector)
  public:
    Selector (const node_t node, const bool keep_self = true) :
      list (1, node),
      exact_match (false),
      keep_self (keep_self) { }
    Selector (const node_t node_one, const node_t node_two) :
      exact_match (true),
      keep_self (true) { list.push_back (node_one); list.push_back (node_two); }
    Selector (const vector<node_t>& node_list, const bool both, const bool keep_self = false) :
      list (node_list),
      exact_match (both),
      keep_self (keep_self) { }
    Selector (const Selector& that) :
      list (that.list), exact_match (that.exact_match), keep_self (that.keep_self) { }
    Selector (Selector&& that) :
      list (std::move (that.list)), exact_match (that.exact_match), keep_self (that.keep_self) { }
 
    bool operator() (const node_t) const;
    bool operator() (const NodePair&) const;
    bool operator() (const node_t one, const node_t two) const { return (*this) (NodePair (one, two)); }
    bool operator() (const vector<node_t>&) const;
 
  private:
    vector<node_t> list;
    bool exact_match, keep_self;
 
};
 
 
 
 
 
 
class WriterExemplars
{ MEMALIGN(WriterExemplars)
  public:
    WriterExemplars (const Tractography::Properties&, const vector<node_t>&, const bool, const node_t, const vector<Eigen::Vector3f>&);
 
    bool operator() (const Tractography::Connectome::Streamline_nodepair&);
    bool operator() (const Tractography::Connectome::Streamline_nodelist&);
 
    void finalize();
 
    void write (const node_t, const node_t, const std::string&, const std::string&);
    void write (const node_t, const std::string&, const std::string&);
    void write (const std::string&, const std::string&);
 
 
  private:
    float step_size;
    vector<Selector> selectors;
    vector<Exemplar> exemplars;
};
 
 
 
 
 
 
 
 
 
class WriterExtraction
{ MEMALIGN(WriterExtraction)
 
  public:
    WriterExtraction (const Tractography::Properties&, const vector<node_t>&, const bool, const bool);
 
    void add (const node_t, const std::string&, const std::string);
    void add (const node_t, const node_t, const std::string&, const std::string);
    void add (const vector<node_t>&, const std::string&, const std::string);
 
    void clear();
 
    bool operator() (const Connectome::Streamline_nodepair&) const;
    bool operator() (const Connectome::Streamline_nodelist&) const;
 
    size_t file_count() const { return writers.size(); }
 
 
  private:
    const Tractography::Properties& properties;
    const vector<node_t>& node_list;
    const bool exclusive;
    const bool keep_self;
    vector< Selector > selectors;
    vector< std::unique_ptr< Tractography::WriterUnbuffered<float> > > writers;
    Tractography::Streamline<> empty_tck;
 
};
 
 
 
 
 
 
}
}
}
}
 
 
#endif