SAFIRCListmodeInputFileFormat.h

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/* SAFIRCListmodeInputFileFormat.h

 Class defining input file format for coincidence listmode data for SAFIR.

        Copyright 2015 ETH Zurich, Institute of Particle Physics
        Copyright 2020 Positrigo AG, Zurich

        Licensed under the Apache License, Version 2.0 (the "License");
        you may not use this file except in compliance with the License.
        You may obtain a copy of the License at

                http://www.apache.org/licenses/LICENSE-2.0

        Unless required by applicable law or agreed to in writing, software
        distributed under the License is distributed on an "AS IS" BASIS,
        WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
        See the License for the specific language governing permissions and
        limitations under the License.
 */

#ifndef __stir_IO_SAFIRCListmodeInputFileFormat_H__
#define __stir_IO_SAFIRCListmodeInputFileFormat_H__

#include <algorithm>
#include <cstring>
#include <string>
#include <iostream>

#include "boost/algorithm/string.hpp"

#include "stir/IO/InputFileFormat.h"
#include "stir/info.h"
#include "stir/error.h"
#include "stir/utilities.h"
#include "stir/ParsingObject.h"

#include "stir/listmode/CListRecordSAFIR.h"
#include "stir/listmode/CListModeDataSAFIR.h"

START_NAMESPACE_STIR

template <class EventDataType>
class SAFIRCListmodeInputFileFormat : public InputFileFormat<ListModeData>, public ParsingObject
{
public:
  SAFIRCListmodeInputFileFormat() {}
  const std::string get_name() const override { return "SAFIR Coincidence Listmode File Format"; }

  bool can_read(const FileSignature& signature, std::istream& input) const override
  {
    return false; // cannot read from istream
  }

  bool can_read(const FileSignature& signature, const std::string& filename) const override
  {
    // Looking for the right key in the parameter file
    std::ifstream par_file(filename.c_str());
    std::string key;
    std::getline(par_file, key, ':');
    key = standardise_interfile_keyword(key);
    if (key != std::string("clistmodedatasafir parameters"))
      {
        return false;
      }
    if (!actual_do_parsing(filename))
      return false;
    std::ifstream data_file(listmode_filename.c_str(), std::ios::binary);
    char* buffer = new char[32];
    data_file.read(buffer, 32);
    bool cr = false;
    // depending on used template, check header of listmode file for correct format
    if (std::is_same<EventDataType, CListEventDataSAFIR>::value)
      {
        cr = (!strncmp(buffer, "MUPET CListModeData\0", 20) || !strncmp(buffer, "SAFIR CListModeData\0", 20));
      }
    else if (std::is_same<EventDataType, CListEventDataNeuroLF>::value)
      {
        cr = !strncmp(buffer, "NeuroLF CListModeData\0", 20);
      }
    else
      {
        warning("SAFIRCListModeInputFileFormat was initialised with an unexpected template.");
      }

    if (!cr)
      {
        warning("SAFIRCListModeInputFileFormat tried to read file " + listmode_filename
                + " but it seems to have the wrong signature.");
      }

    delete[] buffer;
    return cr;
  }

  std::unique_ptr<data_type> read_from_file(std::istream& input) const override
  {
    error("read_from_file for SAFIRCListmodeData with istream not implemented %s:%d. Sorry", __FILE__, __LINE__);
    return unique_ptr<data_type>();
  }

  std::unique_ptr<data_type> read_from_file(const std::string& filename) const override
  {
    info("SAFIRCListmodeInputFileFormat: read_from_file(" + std::string(filename) + ")");
    actual_do_parsing(filename);
    return std::unique_ptr<data_type>(new CListModeDataSAFIR<CListRecordSAFIR<EventDataType>>(
        listmode_filename, crystal_map_filename, template_proj_data_filename, lor_randomization_sigma));
  }

protected:
  typedef ParsingObject base_type;
  mutable std::string listmode_filename;
  mutable std::string crystal_map_filename;
  mutable std::string template_proj_data_filename;
  mutable double lor_randomization_sigma;

  bool actual_can_read(const FileSignature& signature, std::istream& input) const override
  {
    return false; // cannot read from istream
  }

  void initialise_keymap() override
  {
    base_type::initialise_keymap();
    this->parser.add_start_key("CListModeDataSAFIR Parameters");
    this->parser.add_key("listmode data filename", &listmode_filename);
    this->parser.add_key("crystal map filename", &crystal_map_filename);
    this->parser.add_key("template projection data filename", &template_proj_data_filename);
    this->parser.add_key("LOR randomization (Gaussian) sigma", &lor_randomization_sigma);
    this->parser.add_stop_key("END CListModeDataSAFIR Parameters");
  }

  void set_defaults() override
  {
    base_type::set_defaults();
    crystal_map_filename = "";
    template_proj_data_filename = "";
    lor_randomization_sigma = 0.0;
  }

  bool actual_do_parsing(const std::string& filename) const
  {
    // Ugly const_casts here, but I don't see an other nice way to use the parser
    if (const_cast<SAFIRCListmodeInputFileFormat<EventDataType>*>(this)->parse(filename.c_str()))
      {
        info(const_cast<SAFIRCListmodeInputFileFormat<EventDataType>*>(this)->parameter_info());
        return true;
      }
    else
      return false;
  }

  bool post_processing() override
  {
    if (!file_exists(listmode_filename))
      return true;
    else if (!file_exists(template_proj_data_filename))
      return true;
    else
      {
        return false;
      }
    return true;
  }

private:
  bool file_exists(const std::string& filename)
  {
    std::ifstream infile(filename.c_str());
    return infile.good();
  }
};
END_NAMESPACE_STIR
#endif