rapidSTORM/ModuleLoader.cpp at master · Immuno-Oncology/rapidSTORM · GitHub

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#include "ModuleLoader.h"

#include "andor-sif/AndorSIF.h"
#include "base/Config.h"
#include "calibrate_3d/fwd.h"
#include "engine/ChainLink.h"
#include "engine/SpotFinder.h"
#include "engine/SpotFitterFactory.h"
#include "engine_stm/ChainLink.h"
#include "estimate_psf_form/decl.h"
#include "helpers/make_unique.hpp"
#include "input_simulation/NoiseSource.h"
#include "input/Choice.h"
#include "input/FilterFactoryLink.hpp"
#include "inputs/inputs.h"
#include "inputs/MedianFilter.h"
#include "inputs/WarnAboutLocalizationFile.h"
#include "kalman_filter/EmissionTracker.h"
#include "kalman_filter/NonlinearDriftEstimator.h"
#include "localization_file/writer.h"
#include "outputs/BasicTransmissions.h"
#include "ripley_k/fwd.h"
#include "test-plugin/DummyFileInput.h"
#include "test-plugin/plugin.h"
#include "tiff/RawImageFile.h"
#include "tiff/TIFF.h"
#include "viewer/plugin.h"

#include "debug.h"
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif

#if HAVE_PROTOBUF
#include "tsf/Output.h"
#endif

namespace dStorm {

void add_image_input_modules( dStorm::Config& car_config )
{
    auto file_methods = make_unique<inputs::FileMethod>();
#ifdef HAVE_TIFFIO_H
    file_methods->add_choice(tiff::make_input());
#endif
#ifdef HAVE_LIBREADSIF
    file_methods->add_choice(andor_sif::make_input());
#endif
    file_methods->add_choice(inputs::make_warn_about_localization_file());
    file_methods->add_choice(dummy_file_input::make());

    auto input_methods = make_unique<input::Choice>("InputMethod", false);
    input_methods->add_choice(std::move(file_methods));
    input_methods->add_choice(make_unique<input_simulation::NoiseConfig>());

    car_config.add_input( CreateLink(engine::make_rapidSTORM_engine_link()) );
    car_config.add_input( make_input_base() );

    car_config.add_input( CreateLink(input::resolution::create()) );
    car_config.add_input( CreateLink(input::sample_info::create()) );
    car_config.add_input( basename_input_field::makeLink() );
    car_config.add_input( CreateLink(input_buffer::create()) );
    car_config.add_input( CreateLink(median_filter::create()) );
    car_config.add_input( CreateLink(plane_filter::create()) );
    car_config.add_input( CreateLink(splitter::create()) );

    car_config.add_input( inputs::join::create_link() );
    car_config.add_input( CreateLink(YMirror::create()) );
    car_config.add_input( CreateLink(ROIFilter::create()) );
    car_config.add_input( std::move(input_methods) );
}

void add_stm_input_modules( dStorm::Config& car_config )
{
    auto file_methods = make_unique<inputs::FileMethod>();
    auto p = CreateLink(engine_stm::create());
    p->insert_new_node( inputs::LocalizationFile::create() );
    file_methods->add_choice(std::move(p));

    auto input_methods = make_unique<input::Choice>("InputMethod", false);
    input_methods->add_choice(std::move(file_methods));

    car_config.add_input( make_input_base() );
    car_config.add_input( basename_input_field::makeLink() );
    car_config.add_input( inputs::join::create_link() );
    car_config.add_input( std::move(input_methods) );
}

void add_output_modules( dStorm::Config& car_config )
{
    dStorm::viewer::augment_config( car_config );
    dStorm::output::basic_outputs( &car_config );

#ifdef HAVE_TIFFIO_H
    car_config.add_output( new output::FileOutputBuilder<output::RawImageFile::Config,output::RawImageFile>() );
#endif

    car_config.add_output( estimate_psf_form::make_output_source() );
    car_config.add_output( calibrate_3d::make_output_source() );
    car_config.add_output( calibrate_3d::sigma_curve::make_output_source() );
    car_config.add_output( kalman_filter::emission_tracker::create() );
    car_config.add_output( kalman_filter::drift_estimator::create() );
    car_config.add_output( localization_file::make_output_source() );
    car_config.add_output( ripley_k::make_output_source().release() );
    test::output_modules( &car_config );

#if HAVE_PROTOBUF
    car_config.add_output( tsf::CreateOutput() );
#endif
}

}