stir_data_containers.h

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/*
SyneRBI Synergistic Image Reconstruction Framework (SIRF)
Copyright 2015 - 2023 Rutherford Appleton Laboratory STFC
Copyright 2018 - 2024 University College London
 
This is software developed for the Collaborative Computational
Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR)
(http://www.ccpsynerbi.ac.uk/).
 
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_DATA_CONTAINER_TYPES
#define STIR_DATA_CONTAINER_TYPES
 
#include <stdlib.h>
 
#include <chrono>
#include <fstream>
#include <exception>
#include <iterator>
#include "sirf/STIR/stir_types.h"
#include "sirf/iUtilities/LocalisedException.h"
#include "sirf/iUtilities/DataHandle.h"
#include "sirf/common/iequals.h"
#include "sirf/common/JacobiCG.h"
#include "sirf/common/DataContainer.h"
#include "sirf/common/ANumRef.h"
#include "sirf/common/ImageData.h"
#include "sirf/common/GeometricalInfo.h"
#include "stir/ZoomOptions.h"
 
#if STIR_VERSION < 050000
#define SPTR_WRAP(X) X->create_shared_clone()
#else
#define SPTR_WRAP(X) X
#endif
 
namespace sirf {
 
    class SIRFUtilities {
    public:
        static long long milliseconds()
        {
            auto now = std::chrono::system_clock::now();
            auto ms = std::chrono::duration_cast<std::chrono::milliseconds>(now.time_since_epoch());
            return (long long)ms.count();
        }
        static std::string scratch_file_name()
        {
            static int calls = 0;
            char buff[32];
            long long int ms = milliseconds();
            calls++;
            sprintf(buff, "tmp_%d_%lld", calls, ms);
            return std::string(buff);
        }
    };
 
    class ProjDataFile : public stir::ProjDataInterfile {
 
    public:
        ProjDataFile(const stir::ProjData& pd, const std::string& filename, bool owns_file = true) :
            stir::ProjDataInterfile(pd.get_exam_info_sptr(),
            pd.get_proj_data_info_sptr()->create_shared_clone(),
            filename, std::ios::in | std::ios::out | std::ios::trunc),
            _filename(filename),
            _owns_file(owns_file)
        {}
        ProjDataFile(stir::shared_ptr<const stir::ExamInfo> sptr_exam_info,
            stir::shared_ptr<stir::ProjDataInfo> sptr_proj_data_info,
            const std::string& filename, bool owns_file = true) :
            stir::ProjDataInterfile(SPTR_WRAP(sptr_exam_info), SPTR_WRAP(sptr_proj_data_info),
            filename, std::ios::in | std::ios::out | std::ios::trunc),
            _filename(filename),
            _owns_file(owns_file)
        {}
        ~ProjDataFile()
        {
            close_stream();
            clear_stream();
            if (!_owns_file)
                return;
            int err;
            err = std::remove((_filename + ".hs").c_str());
            if (err)
                std::cout << "deleting " << _filename << ".hs "
                << "failed, please delete manually" << std::endl;
            err = std::remove((_filename + ".s").c_str());
            if (err)
                std::cout << "deleting " << _filename << ".s "
                << "failed, please delete manually" << std::endl;
        }
        stir::shared_ptr<std::iostream> sino_stream_sptr()
        {
            return sino_stream;
        }
        void close_stream()
        {
            ((std::fstream*)sino_stream.get())->close();
        }
        void clear_stream()
        {
            ((std::fstream*)sino_stream.get())->clear();
        }
    private:
        bool _owns_file;
        std::string _filename;
    };
 
#if 0
        // not used yet. See also https://github.com/SyneRBI/SIRF/pull/1103
    class STIRScanData: public virtual ContainerBase {
    public:
        virtual ~STIRScanData() {}
        virtual stir::shared_ptr<stir::ExamData> data_sptr() const = 0;
        //virtual void set_data_sptr(stir::shared_ptr<stir::ExamData> data) = 0;
    };
#endif
    class STIRAcquisitionData : /*public STIRScanData, */public DataContainer {
    public:
 
        // virtual constructors
        virtual STIRAcquisitionData* same_acquisition_data
            (stir::shared_ptr<const stir::ExamInfo> sptr_exam_info,
            stir::shared_ptr<stir::ProjDataInfo> sptr_proj_data_info) const = 0;
        virtual std::shared_ptr<STIRAcquisitionData> new_acquisition_data() const = 0;
 
                std::string get_info() const
                {
                        return this->data()->get_exam_info_sptr()->parameter_info() +
                          this->data()->get_proj_data_info_sptr()->parameter_info();
                 }
 
        virtual bool is_complex() const
        {
            return false;
        }
 
        virtual std::unique_ptr<STIRAcquisitionData> get_subset(const std::vector<int>& views) const = 0;
 
 
        std::shared_ptr<STIRAcquisitionData> single_slice_rebinned_data(
            const int num_segments_to_combine,
            const int num_views_to_combine = 1,
            const int num_tang_poss_to_trim = 0,
            const bool do_normalisation = true,
            const int max_in_segment_num_to_process = -1,
            const int num_tof_bins_to_combine = 1
        )
        {
            stir::shared_ptr<stir::ProjDataInfo> out_proj_data_info_sptr(
                stir::SSRB(*data()->get_proj_data_info_sptr(),
                num_segments_to_combine,
                num_views_to_combine,
                num_tang_poss_to_trim,
                max_in_segment_num_to_process,
                num_tof_bins_to_combine
            ));
            std::shared_ptr<STIRAcquisitionData> 
                sptr(same_acquisition_data
                                     (this->get_exam_info_sptr(), out_proj_data_info_sptr));
            stir::SSRB(*sptr, *data(), do_normalisation);
            return sptr;
        }
 
        static std::string storage_scheme()
        {
            static bool initialized = false;
            if (!initialized) {
                _storage_scheme = "file";
                initialized = true;
            }
            return _storage_scheme;
        }
        static std::shared_ptr<STIRAcquisitionData> storage_template()
        {
            if (!_template)
                          error("storage_template error. You probably need to call set_storage_scheme() first");
            return _template;
        }
 
        stir::shared_ptr<stir::ProjData> data()
        {
            return _data;
        }
/*      virtual stir::shared_ptr<stir::ExamData> data_sptr()
        {
            return _data;
            //return stir::shared_ptr<stir::ExamData>(_data);
        }*/
        const stir::shared_ptr<stir::ProjData> data() const
        //stir::shared_ptr<const stir::ProjData> data() const // causes lots of problems
        {
            return _data;
        }
                #if 1
        virtual stir::shared_ptr<stir::ExamData> data_sptr() const
        {
            return _data;
        }
                #endif
        void set_data(stir::shared_ptr<stir::ProjData> data)
        {
            _data = data;
        }
 
        // data import/export
        virtual void fill(const float v) { data()->fill(v); }
        virtual void fill(const STIRAcquisitionData& ad)
        {
            if (ad.is_empty())
                THROW("The source of STIRAcquisitionData::fill is empty");
            stir::shared_ptr<const stir::ProjData> sptr = ad.data();
            data()->fill(*sptr);
        }
        virtual void fill_from(const float* d) { data()->fill_from(d); }
        virtual void copy_to(float* d) const { data()->copy_to(d); }
        std::unique_ptr<STIRAcquisitionData> clone() const
        {
            return std::unique_ptr<STIRAcquisitionData>(clone_impl());
        }
 
        // data container methods
        unsigned int items() const {
            if (_is_empty != -1)
                return _is_empty ? 0 : 1;
            try {
#ifdef STIR_TOF
                          get_segment_by_sinogram(0,0);
#else
                          get_segment_by_sinogram(0);
#endif
            }
            catch (...) {
                _is_empty = 1;
                return 0; // no data found - this must be a template
            }
            _is_empty = 0;
            return 1; // data ok
        }
        virtual float norm() const;
        virtual void sum(void* ptr) const;
        virtual void max(void* ptr) const;
        virtual void min(void* ptr) const;
        virtual void dot(const DataContainer& a_x, void* ptr) const;
        float dot(const DataContainer& a_x) const
        {
            float s;
            dot(a_x, &s);
            return s;
        }
        virtual void axpby(
            const void* ptr_a, const DataContainer& a_x,
            const void* ptr_b, const DataContainer& a_y);
        virtual void xapyb(
            const DataContainer& a_x, const void* ptr_a,
            const DataContainer& a_y, const void* ptr_b);   
        virtual void xapyb(
            const DataContainer& a_x, const DataContainer& a_a,
            const DataContainer& a_y, const DataContainer& a_b);
        virtual void xapyb(
            const DataContainer& a_x, const void* ptr_a,
            const DataContainer& a_y, const DataContainer& a_b);
        virtual void abs(const DataContainer& x)
        {
            unary_op(x, std::abs);
        }
        virtual void exp(const DataContainer& x)
        {
            unary_op(x, std::exp);
        }
        virtual void log(const DataContainer& x)
        {
            unary_op(x, std::log);
        }
        virtual void sqrt(const DataContainer& x)
        {
            unary_op(x, std::sqrt);
        }
        virtual void sign(const DataContainer& x)
        {
            unary_op(x, DataContainer::sign);
        }
        virtual void multiply(const DataContainer& x, const void* ptr_y)
        {
            float y = *static_cast<const float*>(ptr_y);
            semibinary_op(x, y, DataContainer::product<float>);
        }
        virtual void add(const DataContainer& x, const void* ptr_y)
        {
            float y = *static_cast<const float*>(ptr_y);
            semibinary_op(x, y, DataContainer::sum<float>);
        }
        virtual void divide(const DataContainer& x, const void* ptr_y)
        {
            float y = *static_cast<const float*>(ptr_y);
            semibinary_op(x, y, DataContainer::ratio<float>);
        }
        virtual void maximum(const DataContainer& x, const void* ptr_y)
        {
            float y = *static_cast<const float*>(ptr_y);
            semibinary_op(x, y, DataContainer::maximum<float>);
        }
        virtual void minimum(const DataContainer& x, const void* ptr_y)
        {
            float y = *static_cast<const float*>(ptr_y);
            semibinary_op(x, y, DataContainer::minimum<float>);
        }
        virtual void power(const DataContainer& x, const void* ptr_y)
        {
            float y = *static_cast<const float*>(ptr_y);
            semibinary_op(x, y, std::pow);
        }
        virtual void multiply(const DataContainer& x, const DataContainer& y)
        {
            binary_op(x, y, DataContainer::product<float>);
        }
        virtual void divide(const DataContainer& x, const DataContainer& y)
        {
            binary_op(x, y, DataContainer::ratio<float>);
        }
        virtual void maximum(const DataContainer& x, const DataContainer& y)
        {
            binary_op(x, y, DataContainer::maximum<float>);
        }
        virtual void minimum(const DataContainer& x, const DataContainer& y)
        {
            binary_op(x, y, DataContainer::minimum<float>);
        }
        virtual void power(const DataContainer& x, const DataContainer& y)
        {
            binary_op(x, y, std::pow);
        }
        virtual void inv(float a, const DataContainer& x);
        virtual void write(const std::string &filename) const
        {
            ProjDataFile pd(*data(), filename.c_str(), false);
            pd.fill(*data());
        }
 
        // ProjData methods
        int get_num_tangential_poss()
        {
            return data()->get_num_tangential_poss();
        }
        int get_num_views()
        {
            return data()->get_num_views();
        }
 
        int get_num_sinograms() const
        {
            return data()->get_num_sinograms();
        }
 
        int get_num_non_TOF_sinograms() const
        {
            return data()->get_num_non_tof_sinograms();
        }
 
        int get_num_TOF_bins()
        {
            return data()->get_num_tof_poss();
        }
 
        int get_tof_mash_factor() const
        {
            return data()->get_proj_data_info_sptr()->get_tof_mash_factor();
        }
 
        size_t get_dimensions(int* dim)
        {
            dim[0] = get_num_tangential_poss();
            dim[1] = get_num_views();
            dim[2] = get_num_non_TOF_sinograms();
            dim[3] = get_num_TOF_bins();
            return static_cast<size_t>(dim[0] * dim[1] * dim[2] * dim[3]);
        }
        int get_max_segment_num() const
        {
            return data()->get_max_segment_num();
        }
#ifdef STIR_TOF
        stir::SegmentBySinogram<float>
                  get_segment_by_sinogram(const int segment_num, const int timing_pos_num) const
        {
                  return data()->get_segment_by_sinogram(segment_num, timing_pos_num);
                }
#else
        stir::SegmentBySinogram<float>
                  get_segment_by_sinogram(const int segment_num) const
        {
                  return data()->get_segment_by_sinogram(segment_num);
                }
#endif
#ifdef STIR_TOF
        stir::SegmentBySinogram<float>
                  get_empty_segment_by_sinogram(const int segment_num, const int timing_pos_num) const
        {
                  return data()->get_empty_segment_by_sinogram(segment_num, false, timing_pos_num);
                }
#else
        stir::SegmentBySinogram<float>
                  get_empty_segment_by_sinogram(const int segment_num) const
        {
                  return data()->get_empty_segment_by_sinogram(segment_num);
                }
#endif
        void set_segment(const stir::SegmentBySinogram<float>& s)
        {
            if (data()->set_segment(s) != stir::Succeeded::yes)
                THROW("stir::ProjData set segment failed");
        }
        stir::shared_ptr<const stir::ExamInfo> get_exam_info_sptr() const
        {
            return data()->get_exam_info_sptr();
        }
        stir::shared_ptr<const stir::ProjDataInfo> get_proj_data_info_sptr() const
        {
            return data()->get_proj_data_info_sptr();
        }
        std::string modality() const
        {
            const ExamInfo& ex_info = *get_exam_info_sptr();
            return ex_info.imaging_modality.get_name();
        }
 
        // ProjData casts
        operator stir::ProjData&() { return *data(); }
        operator const stir::ProjData&() const { return *data(); }
        operator stir::shared_ptr<stir::ProjData>() { return data(); }
 
        static stir::shared_ptr<stir::ProjDataInfo>
            proj_data_info_from_scanner(std::string scanner_name,
            int span = 1, int max_ring_diff = -1, int view_mash_factor = 1)
        {
            stir::shared_ptr<stir::Scanner> 
                sptr_s(stir::Scanner::get_scanner_from_name(scanner_name));
            //std::cout << "scanner: " << sptr_s->get_name().c_str() << '\n';
            if (sirf::iequals(sptr_s->get_name(), "unknown")) {
                throw LocalisedException("Unknown scanner", __FILE__, __LINE__);
            }
            int num_views = sptr_s->get_num_detectors_per_ring() / 2 / view_mash_factor;
            int num_tang_pos = sptr_s->get_max_num_non_arccorrected_bins();
            if (max_ring_diff < 0)
                max_ring_diff = sptr_s->get_num_rings() - 1;
            return std::move(stir::ProjDataInfo::construct_proj_data_info
                (sptr_s, span, max_ring_diff, num_views, num_tang_pos, false));
        }
 
        void unary_op(const DataContainer& a_x, float(*f)(float));
        void semibinary_op(const DataContainer& a_x, float y, float(*f)(float, float));
        void binary_op(const DataContainer& a_x, const DataContainer& a_y, float(*f)(float, float));
 
    protected:
        static std::string _storage_scheme;
        static std::shared_ptr<STIRAcquisitionData> _template;
        stir::shared_ptr<stir::ProjData> _data;
        virtual STIRAcquisitionData* clone_impl() const = 0;
        STIRAcquisitionData* clone_base() const
        {
            stir::shared_ptr<stir::ProjDataInfo> sptr_pdi = this->get_proj_data_info_sptr()->create_shared_clone();
            STIRAcquisitionData* ptr = 
                _template->same_acquisition_data(this->get_exam_info_sptr(), sptr_pdi);
            if (!this->is_empty())
                ptr->fill(*this);
            return ptr;
        }
 
    private:
        mutable int _is_empty = -1;
    };
 
    class STIRAcquisitionDataInFile : public STIRAcquisitionData {
    public:
        STIRAcquisitionDataInFile() : _owns_file(false) {}
        STIRAcquisitionDataInFile(const char* filename) : _owns_file(false)
        {
            _data = stir::ProjData::read_from_file(filename);
        }
        STIRAcquisitionDataInFile(stir::shared_ptr<const stir::ExamInfo> sptr_exam_info,
            stir::shared_ptr<stir::ProjDataInfo> sptr_proj_data_info)
        {
            _data.reset(new ProjDataFile
                                    (MAKE_SHARED<stir::ExamInfo>(*sptr_exam_info), sptr_proj_data_info,
                                     _filename = SIRFUtilities::scratch_file_name()));
        }
        STIRAcquisitionDataInFile(const stir::ProjData& pd) : _owns_file(true)
        {
            _data.reset(new ProjDataFile
                (pd, _filename = SIRFUtilities::scratch_file_name()));
        }
        STIRAcquisitionDataInFile
            (stir::shared_ptr<stir::ExamInfo> sptr_ei, std::string scanner_name,
            int span = 1, int max_ring_diff = -1, int view_mash_factor = 1)
        {
            stir::shared_ptr<stir::ProjDataInfo> sptr_pdi =
                STIRAcquisitionData::proj_data_info_from_scanner
                (scanner_name, span, max_ring_diff, view_mash_factor);
            ProjDataFile* ptr = new ProjDataFile(sptr_ei, sptr_pdi,
                _filename = SIRFUtilities::scratch_file_name());
            ptr->fill(0.0f);
            _data.reset(ptr);
        }
        STIRAcquisitionDataInFile(std::unique_ptr<stir::ProjData> uptr_pd) : _owns_file(true)
        {
//          auto *pd_ptr = dynamic_cast<stir::ProjDataInterfile*>(uptr_pd.get());
            auto pd_ptr = dynamic_cast<stir::ProjDataInterfile*>(uptr_pd.get());
            if (pd_ptr)
                _data = std::move(uptr_pd);
            else {
                stir::ProjData& pd = *uptr_pd;
                stir::shared_ptr<const stir::ExamInfo> sptr_exam_info =
                    pd.get_exam_info_sptr();
                stir::shared_ptr<stir::ProjDataInfo> sptr_proj_data_info =
                    pd.get_proj_data_info_sptr()->create_shared_clone();
                _data.reset(new ProjDataFile
                                    (MAKE_SHARED<stir::ExamInfo>(*sptr_exam_info), sptr_proj_data_info,
                    _filename = SIRFUtilities::scratch_file_name()));
                _data->fill(pd);
            }
        }
        std::shared_ptr<STIRAcquisitionData> new_acquisition_data(std::string filename)
        {
            std::shared_ptr<STIRAcquisitionDataInFile> sptr_ad(new STIRAcquisitionDataInFile);
            sptr_ad->_data.reset(new ProjDataFile(*data(), filename, false));
            return sptr_ad;
        }
 
        static void init() {
            static bool initialized = false;
            if (!initialized) {
                _storage_scheme = "file";
                _template.reset(new STIRAcquisitionDataInFile());
                initialized = true;
                STIRAcquisitionData::storage_scheme();
            }
        }
        static void set_as_template()
        {
            init();
            _storage_scheme = "file";
            _template.reset(new STIRAcquisitionDataInFile);
        }
 
        virtual STIRAcquisitionData* same_acquisition_data
            (stir::shared_ptr<const stir::ExamInfo> sptr_exam_info,
            stir::shared_ptr<stir::ProjDataInfo> sptr_proj_data_info) const
        {
            STIRAcquisitionData* ptr_ad =
                new STIRAcquisitionDataInFile(sptr_exam_info, sptr_proj_data_info);
            return ptr_ad;
        }
        virtual ObjectHandle<DataContainer>* new_data_container_handle() const
        {
            init();
            DataContainer* ptr = _template->same_acquisition_data(
                                this->get_exam_info_sptr(),
                this->get_proj_data_info_sptr()->create_shared_clone());
            return new ObjectHandle<DataContainer>
                (std::shared_ptr<DataContainer>(ptr));
        }
        virtual std::shared_ptr<STIRAcquisitionData> new_acquisition_data() const
        {
            init();
            return std::shared_ptr < STIRAcquisitionData >
                (_template->same_acquisition_data(this->get_exam_info_sptr(),
                this->get_proj_data_info_sptr()->create_shared_clone()));
        }
        virtual std::unique_ptr<STIRAcquisitionData> get_subset(const std::vector<int>& views) const;
 
    private:
        bool _owns_file;
        std::string _filename;
        virtual STIRAcquisitionDataInFile* clone_impl() const
        {
            init();
            return (STIRAcquisitionDataInFile*)clone_base();
        }
    };
 
    class STIRAcquisitionDataInMemory : public STIRAcquisitionData {
    public:
        STIRAcquisitionDataInMemory() {}
        STIRAcquisitionDataInMemory(stir::shared_ptr<const stir::ExamInfo> sptr_exam_info,
            stir::shared_ptr<const stir::ProjDataInfo> sptr_proj_data_info)
        {
            _data = stir::shared_ptr<stir::ProjData>
                (new stir::ProjDataInMemory(SPTR_WRAP(sptr_exam_info), SPTR_WRAP(sptr_proj_data_info)));
        }
        STIRAcquisitionDataInMemory(const stir::ProjData& templ)
        {
            _data = stir::shared_ptr<stir::ProjData>
                (new stir::ProjDataInMemory(templ.get_exam_info_sptr(),
                    templ.get_proj_data_info_sptr()->create_shared_clone()));
        }
        STIRAcquisitionDataInMemory
            (stir::shared_ptr<stir::ExamInfo> sptr_ei, std::string scanner_name,
            int span = 1, int max_ring_diff = -1, int view_mash_factor = 1)
        {
            stir::shared_ptr<stir::ProjDataInfo> sptr_pdi =
                STIRAcquisitionData::proj_data_info_from_scanner
                (scanner_name, span, max_ring_diff, view_mash_factor);
            stir::ProjDataInMemory* ptr = new stir::ProjDataInMemory(sptr_ei, sptr_pdi);
            ptr->fill(0.0f);
            _data.reset(ptr);
        }
        STIRAcquisitionDataInMemory(std::unique_ptr<stir::ProjData> uptr_pd)
        {
//          auto *pd_ptr = dynamic_cast<stir::ProjDataInMemory*>(uptr_pd.get());
            auto pd_ptr = dynamic_cast<stir::ProjDataInMemory*>(uptr_pd.get());
            if (pd_ptr)
                _data = std::move(uptr_pd);
            else {
                std::cout << "copying ProjData to ProjDataInMemory...\n";
                const stir::ProjData& pd = *uptr_pd;
                auto exam_info_sptr = SPTR_WRAP(pd.get_exam_info_sptr());
                auto proj_data_info_sptr =
                    SPTR_WRAP(pd.get_proj_data_info_sptr()->create_shared_clone());
                _data.reset(new stir::ProjDataInMemory(exam_info_sptr, proj_data_info_sptr));
                _data->fill(pd);
            }
        }
        STIRAcquisitionDataInMemory(const char* filename)
        {
            auto pd_sptr = stir::ProjData::read_from_file(filename);
            bool is_empty = false;
            try {
                pd_sptr->get_segment_by_sinogram(0);
            }
            catch (...) {
                is_empty = true;
            }
            if (is_empty)
                _data = stir::shared_ptr<stir::ProjData>
                    (new stir::ProjDataInMemory(pd_sptr->get_exam_info_sptr(),
                        pd_sptr->get_proj_data_info_sptr()->create_shared_clone()));
            else
                _data = stir::shared_ptr<stir::ProjData>
                (new stir::ProjDataInMemory(*pd_sptr));
        }
 
        static void init();
 
        static void set_as_template()
        {
            init();
            _storage_scheme = "memory";
            _template.reset(new STIRAcquisitionDataInMemory);
        }
 
        virtual STIRAcquisitionData* same_acquisition_data
            (stir::shared_ptr<const stir::ExamInfo> sptr_exam_info,
            stir::shared_ptr<stir::ProjDataInfo> sptr_proj_data_info) const
        {
            STIRAcquisitionData* ptr_ad =
                new STIRAcquisitionDataInMemory(sptr_exam_info, sptr_proj_data_info);
            return ptr_ad;
        }
        virtual ObjectHandle<DataContainer>* new_data_container_handle() const
        {
            init();
            DataContainer* ptr = _template->same_acquisition_data
                (this->get_exam_info_sptr(),
                                 this->get_proj_data_info_sptr()->create_shared_clone());
            return new ObjectHandle<DataContainer>
                (std::shared_ptr<DataContainer>(ptr));
        }
        virtual std::shared_ptr<STIRAcquisitionData> new_acquisition_data() const
        {
            init();
            return std::shared_ptr < STIRAcquisitionData >
                (_template->same_acquisition_data
                (this->get_exam_info_sptr(),
                                 this->get_proj_data_info_sptr()->create_shared_clone()));
        }
        virtual std::unique_ptr<STIRAcquisitionData> get_subset(const std::vector<int>& views) const;
 
        virtual void fill(const float v)
        {
            stir::ProjDataInMemory *pd_ptr = dynamic_cast<stir::ProjDataInMemory*>(data().get());
            // If cast failed, fall back to general method
            if (is_null_ptr(pd_ptr))
                return this->STIRAcquisitionData::fill(v);
 
            // do it
            auto iter = pd_ptr->begin();
            while (iter != pd_ptr->end())
                *iter++ = v;
        }
        virtual void fill(const STIRAcquisitionData& ad)
        {
            // Can only do this if both are STIRAcquisitionDataInMemory
            stir::ProjDataInMemory *pd_ptr = dynamic_cast<stir::ProjDataInMemory*>(data().get());
            const stir::ProjDataInMemory *pd2_ptr = dynamic_cast<const stir::ProjDataInMemory*>(ad.data().get());
            // If either cast failed, fall back to general method
            if (is_null_ptr(pd_ptr) || is_null_ptr(pd2_ptr))
                return this->STIRAcquisitionData::fill(ad);
 
            // do it
            auto iter = pd_ptr->begin();
            auto iter_other = pd2_ptr->begin();
            while (iter != pd_ptr->end())
                *iter++ = *iter_other++;
        }
        virtual void fill_from(const float* d)
        {
            stir::ProjDataInMemory *pd_ptr = dynamic_cast<stir::ProjDataInMemory*>(data().get());
            // If cast failed, fall back to general method
            if (is_null_ptr(pd_ptr))
                return this->STIRAcquisitionData::fill_from(d);
 
            // do it
            auto iter = pd_ptr->begin();
            while (iter != pd_ptr->end())
                *iter++ = *d++;
        }
        virtual void copy_to(float* d) const
        {
            const stir::ProjDataInMemory *pd_ptr = dynamic_cast<const stir::ProjDataInMemory*>(data().get());
            // If cast failed, fall back to general method
            if (is_null_ptr(pd_ptr))
                return this->STIRAcquisitionData::copy_to(d);
 
            // do it
            auto iter = pd_ptr->begin();
            while (iter != pd_ptr->end())
                *d++ = *iter++;
        }
        virtual float norm() const
        {
            const stir::ProjDataInMemory *pd_ptr = dynamic_cast<const stir::ProjDataInMemory*>(data().get());
            // If cast failed, fall back to general method
            if (is_null_ptr(pd_ptr))
                return this->STIRAcquisitionData::norm();
 
            // do it
#if STIR_VERSION <= 060100
            double t = 0.0;
            auto iter = pd_ptr->begin();
            for (; iter != pd_ptr->end(); ++iter)
                t += (*iter) * (*iter);
            return std::sqrt((float)t);
#else
                        return static_cast<float>(pd_ptr->norm());
#endif
        }
        virtual void dot(const DataContainer& a_x, void* ptr) const
        {
            auto x = dynamic_cast<const STIRAcquisitionData*>(&a_x);
            // Can only do this if both are STIRAcquisitionDataInMemory
            stir::ProjDataInMemory *pd_ptr = dynamic_cast<stir::ProjDataInMemory*>(data().get());
            const stir::ProjDataInMemory *pd2_ptr = dynamic_cast<const stir::ProjDataInMemory*>(x->data().get());
            // If either cast failed, fall back to general method
            if (is_null_ptr(pd_ptr) || is_null_ptr(pd2_ptr))
                return this->STIRAcquisitionData::dot(a_x,ptr);
 
            // do it
            double t = 0.0;
            auto iter = pd_ptr->begin();
            auto iter_other = pd2_ptr->begin();
            while (iter != pd_ptr->end())
                t += (*iter++) * double(*iter_other++);
 
            float* ptr_t = static_cast<float*>(ptr);
            *ptr_t = (float)t;
        }
        virtual void multiply(const DataContainer& x, const DataContainer& y)
        {
            auto a_x = dynamic_cast<const STIRAcquisitionData*>(&x);
            auto a_y = dynamic_cast<const STIRAcquisitionData*>(&y);
 
            // Can only do this if all are STIRAcquisitionDataInMemory
            auto *pd_ptr   = dynamic_cast<stir::ProjDataInMemory*>(data().get());
            auto *pd_x_ptr = dynamic_cast<const stir::ProjDataInMemory*>(a_x->data().get());
            auto *pd_y_ptr = dynamic_cast<const stir::ProjDataInMemory*>(a_y->data().get());
 
            // If either cast failed, fall back to general method
            if (is_null_ptr(pd_ptr) || is_null_ptr(pd_x_ptr) || is_null_ptr(pd_x_ptr))
                return this->STIRAcquisitionData::multiply(x,y);
 
            // do it
            auto iter = pd_ptr->begin();
            auto iter_x = pd_x_ptr->begin();
            auto iter_y = pd_y_ptr->begin();
            while (iter != pd_ptr->end())
                *iter++ = (*iter_x++) * (*iter_y++);
        }
        virtual void divide(const DataContainer& x, const DataContainer& y)
        {
            auto a_x = dynamic_cast<const STIRAcquisitionData*>(&x);
            auto a_y = dynamic_cast<const STIRAcquisitionData*>(&y);
 
            // Can only do this if all are STIRAcquisitionDataInMemory
            auto *pd_ptr   = dynamic_cast<stir::ProjDataInMemory*>(data().get());
            auto *pd_x_ptr = dynamic_cast<const stir::ProjDataInMemory*>(a_x->data().get());
            auto *pd_y_ptr = dynamic_cast<const stir::ProjDataInMemory*>(a_y->data().get());
 
            // If either cast failed, fall back to general method
            if (is_null_ptr(pd_ptr) || is_null_ptr(pd_x_ptr) || is_null_ptr(pd_x_ptr))
                return this->STIRAcquisitionData::divide(x,y);
 
            // do it
            auto iter = pd_ptr->begin();
            auto iter_x = pd_x_ptr->begin();
            auto iter_y = pd_y_ptr->begin();
            while (iter != pd_ptr->end())
                *iter++ = (*iter_x++) / (*iter_y++);
        }
 
    private:
        virtual STIRAcquisitionDataInMemory* clone_impl() const
        {
            init();
            return (STIRAcquisitionDataInMemory*)clone_base();
        }
    };
 
    class STIRListmodeData : public ContainerBase /*STIRScanData*/ {
    public:
        STIRListmodeData(std::string lmdata_filename)
        {
            _data = stir::read_from_file<stir::ListModeData>(lmdata_filename);
        }
                virtual ~STIRListmodeData() {}
 
                // TODO remove
        virtual stir::shared_ptr<stir::ExamData> data_sptr() const {
            return _data;
        }
        virtual stir::shared_ptr<stir::ListModeData> data() const {
            return _data;
        }
#if 0
        virtual ObjectHandle<DataContainer>* new_data_container_handle() const
        {
            THROW("ListmodeData::new_data_container_handle not implemented");
            return 0;
        }
#endif
 
                std::shared_ptr<STIRAcquisitionData> acquisition_data_template() const
                {
            return std::shared_ptr < STIRAcquisitionData >
                          (STIRAcquisitionData::storage_template()->same_acquisition_data(this->data()->get_exam_info_sptr(),
                                                                                          this->data()->get_proj_data_info_sptr()->create_shared_clone()));
                }
          std::string get_info() const
                {
                  return this->data()->get_exam_info_sptr()->parameter_info() +
                          this->data()->get_proj_data_info_sptr()->parameter_info();
                 }
    protected:
        stir::shared_ptr<stir::ListModeData> _data;
        virtual DataContainer* clone_impl() const
        {
            THROW("ListmodeData::clone not implemented");
        }
    };
 
#if SIRF_VERSION_MAJOR < 4
    typedef STIRAcquisitionData PETAcquisitionData;
    typedef STIRAcquisitionDataInFile PETAcquisitionDataInFile;
    typedef STIRAcquisitionDataInMemory PETAcquisitionDataInMemory;
#endif
 
    typedef Image3DF::full_iterator Image3DFIterator;
    typedef Image3DF::const_full_iterator Image3DFIterator_const;
 
    class STIRImageData : public ImageData {
    public:
        typedef ImageData::Iterator BaseIter;
        typedef ImageData::Iterator_const BaseIter_const;
        class Iterator : public BaseIter {
        public:
 
            typedef Image3DFIterator::difference_type difference_type;
            typedef Image3DFIterator::value_type value_type;
            typedef Image3DFIterator::reference reference;
            typedef Image3DFIterator::pointer pointer;
            typedef std::forward_iterator_tag iterator_category;
            Iterator(const Image3DFIterator& iter) : _iter(iter)
            {}
            Iterator& operator=(const Iterator& iter)
            {
                _iter = iter._iter;
                _ref.copy(iter._ref);
                _sptr_iter = iter._sptr_iter;
                return *this;
            }
            virtual Iterator& operator++()
            {
                ++_iter;
                return *this;
            }
            //virtual Iterator& operator++(int)
            //{
            //  _sptr_iter.reset(new Iterator(_iter));
            //  ++_iter;
            //  return *_sptr_iter;
            //}
            virtual bool operator==(const BaseIter& an_iter) const
            {
                const Iterator& iter = (const Iterator&)an_iter;
                return _iter == iter._iter;
            }
            virtual bool operator!=(const BaseIter& an_iter) const
            {
                const Iterator& iter = (const Iterator&)an_iter;
                return _iter != iter._iter;
            }
            virtual FloatRef& operator*()
            {
                float& v = *_iter;
                _ref.set_ptr(&v);
                return _ref;
            }
        private:
            Image3DFIterator _iter;
            FloatRef _ref;
            std::shared_ptr<Iterator> _sptr_iter;
        };
        class Iterator_const : public BaseIter_const {
        public:
            Iterator_const(const Image3DFIterator_const& iter) : _iter(iter)
            {}
            Iterator_const& operator=(const Iterator_const& iter)
            {
                _iter = iter._iter;
                _ref.copy(iter._ref);
                _sptr_iter = iter._sptr_iter;
                return *this;
            }
            virtual Iterator_const& operator++()
            {
                ++_iter;
                return *this;
            }
            //virtual Iterator_const& operator++(int)
            //{
            //  _sptr_iter.reset(new Iterator_const(_iter));
            //  ++_iter;
            //  return *_sptr_iter;
            //}
            virtual bool operator==(const BaseIter_const& an_iter) const
            {
                const Iterator_const& iter = (const Iterator_const&)an_iter;
                return _iter == iter._iter;
            }
            virtual bool operator!=(const BaseIter_const& an_iter) const
            {
                const Iterator_const& iter = (const Iterator_const&)an_iter;
                return _iter != iter._iter;
            }
            virtual const FloatRef& operator*() const
            {
                const float& v = *_iter;
                _ref.set_ptr((void*)&v);
                return _ref;
            }
        private:
            Image3DFIterator_const _iter;
            mutable FloatRef _ref;
            std::shared_ptr<Iterator_const> _sptr_iter;
        };
        STIRImageData() {}
        STIRImageData(const ImageData& id);
        STIRImageData(const STIRImageData& image)
        {
            _data.reset(image.data().clone());
            this->set_up_geom_info();
        }
        STIRImageData(const STIRAcquisitionData& ad)
        {
            _data.reset(new Voxels3DF(MAKE_SHARED<stir::ExamInfo>(*ad.get_exam_info_sptr()), *ad.get_proj_data_info_sptr()));
            this->set_up_geom_info();
        }
        STIRImageData(const Image3DF& image)
        {
            _data.reset(image.clone());
            this->set_up_geom_info();
        }
        STIRImageData(const Voxels3DF& v)
        {
            _data.reset(v.clone());
            this->set_up_geom_info();
        }
        STIRImageData(const stir::ProjDataInfo& pdi)
        {
            _data.reset(new Voxels3DF(pdi));
            this->set_up_geom_info();
        }
        STIRImageData(stir::shared_ptr<Image3DF> ptr)
        {
            _data = ptr;
            this->set_up_geom_info();
        }
        STIRImageData(std::string filename)
        {
            _data = stir::read_from_file<Image3DF>(filename);
            this->set_up_geom_info();
        }
        STIRImageData* same_image_data() const
        {
            STIRImageData* ptr_image = new STIRImageData;
            ptr_image->_data.reset(_data->get_empty_copy());
            ptr_image->set_up_geom_info();
            return ptr_image;
        }
        std::shared_ptr<STIRImageData> new_image_data()
        {
            return std::shared_ptr<STIRImageData>(same_image_data());
        }
        virtual ObjectHandle<DataContainer>* new_data_container_handle() const
        {
            return new ObjectHandle<DataContainer>
                (std::shared_ptr<DataContainer>(same_image_data()));
        }
                std::string get_info() const
                {
                        return this->data().get_exam_info_sptr()->parameter_info();
                        // TODO geometric info, although that's handled separately in SIRF
                 }
        virtual bool is_complex() const
        {
            return false;
        }
        unsigned int items() const
        {
            return 1;
        }
 
        std::string modality() const
        {
            ExamInfo ex_info = data().get_exam_info();
            return ex_info.imaging_modality.get_name();
        }
        void set_modality(const std::string& mod)
        {
            ExamInfo ex_info = data().get_exam_info();
            ex_info.imaging_modality = ImagingModality(mod);
            data().set_exam_info(ex_info);
        }
 
        virtual void write(const std::string& filename) const;
 
        virtual void write(const std::string& filename, const std::string& format_file) const;
 
        virtual float norm() const;
        virtual void sum(void* ptr) const;
        virtual void max(void* ptr) const;
        virtual void min(void* ptr) const;
        virtual void dot(const DataContainer& a_x, void* ptr) const;
        virtual void axpby(
            const void* ptr_a, const DataContainer& a_x,
            const void* ptr_b, const DataContainer& a_y);
        virtual void xapyb(
            const DataContainer& a_x, const void* ptr_a,
            const DataContainer& a_y, const void* ptr_b);
        virtual void xapyb(
            const DataContainer& a_x, const DataContainer& a_a,
            const DataContainer& a_y, const DataContainer& a_b);
        virtual void xapyb(
            const DataContainer& a_x, const void* ptr_a,
            const DataContainer& a_y, const DataContainer& a_b);
        virtual void abs(const DataContainer& x)
        {
            unary_op(x, std::abs);
        }
        virtual void exp(const DataContainer& x)
        {
            unary_op(x, std::exp);
        }
        virtual void log(const DataContainer& x)
        {
            unary_op(x, std::log);
        }
        virtual void sqrt(const DataContainer& x)
        {
            unary_op(x, std::sqrt);
        }
        virtual void sign(const DataContainer& x)
        {
            unary_op(x, DataContainer::sign);
        }
        virtual void multiply(const DataContainer& x, const void* ptr_y)
        {
            float y = *static_cast<const float*>(ptr_y);
            semibinary_op(x, y, DataContainer::product<float>);
        }
        virtual void add(const DataContainer& x, const void* ptr_y)
        {
            float y = *static_cast<const float*>(ptr_y);
            semibinary_op(x, y, DataContainer::sum<float>);
        }
        virtual void divide(const DataContainer& x, const void* ptr_y)
        {
            float y = *static_cast<const float*>(ptr_y);
            semibinary_op(x, y, DataContainer::ratio<float>);
        }
        virtual void maximum(const DataContainer& x, const void* ptr_y)
        {
            float y = *static_cast<const float*>(ptr_y);
            semibinary_op(x, y, DataContainer::maximum<float>);
        }
        virtual void minimum(const DataContainer& x, const void* ptr_y)
        {
            float y = *static_cast<const float*>(ptr_y);
            semibinary_op(x, y, DataContainer::minimum<float>);
        }
        virtual void power(const DataContainer& x, const void* ptr_y)
        {
            float y = *static_cast<const float*>(ptr_y);
            semibinary_op(x, y, std::pow);
        }
        virtual void multiply(const DataContainer& x, const DataContainer& y)
        {
            binary_op(x, y, DataContainer::product<float>);
        }
        virtual void divide(const DataContainer& x, const DataContainer& y)
        {
            binary_op(x, y, DataContainer::ratio<float>);
        }
        virtual void maximum(const DataContainer& x, const DataContainer& y)
        {
            binary_op(x, y, DataContainer::maximum<float>);
        }
        virtual void minimum(const DataContainer& x, const DataContainer& y)
        {
            binary_op(x, y, DataContainer::minimum<float>);
        }
        virtual void power(const DataContainer& x, const DataContainer& y)
        {
            binary_op(x, y, std::pow);
        }
 
        Image3DF& data()
        {
            return *_data;
        }
        const Image3DF& data() const
        {
            return *_data;
        }
        Image3DF* data_ptr()
        {
            return _data.get();
        }
        const Image3DF* data_ptr() const
        {
            return _data.get();
        }
        stir::shared_ptr<Image3DF> data_sptr()
        {
            return _data;
        }
        stir::shared_ptr<const Image3DF> data_sptr() const
        {
            return _data;
        }
        void set_data_sptr(stir::shared_ptr<Image3DF> sptr_data)
        {
            _data = sptr_data;
        }
 
        void fill(float v)
        {
            _data->fill(v);
        }
        void scale(float s);
        float dot(const DataContainer& a_x) const
        {
            float s;
            dot(a_x, &s);
            return s;
        }
        void axpby(
            float a, const DataContainer& a_x,
            float b, const DataContainer& a_y)
        {
            axpby(&a, a_x, &b, a_y);
        }
        void xapyb(
            const DataContainer& a_x, float a,
            const DataContainer& a_y, float b)
        {
            xapyb(a_x, &a, a_y, &b);
        }
        size_t size() const
        {
            return _data->size_all();
        }
        virtual Dimensions dimensions() const
        {
            Dimensions dim;
            int d[4];
            get_dimensions(d);
            dim["z"] = d[0];
            dim["y"] = d[1];
            dim["x"] = d[2];
            return dim;
        }
        int get_dimensions(int* dim) const;
        void get_voxel_sizes(float* vsizes) const;
        virtual void get_data(float* data) const;
        virtual void set_data(const float* data);
        virtual Iterator& begin()
        {
            _begin.reset(new Iterator(data().begin_all()));
            return *_begin;
        }
        virtual Iterator_const& begin() const
        {
            _begin_const.reset(new Iterator_const(data().begin_all()));
            return *_begin_const;
        }
        virtual Iterator& end()
        {
            _end.reset(new Iterator(data().end_all()));
            return *_end;
        }
        virtual Iterator_const& end() const
        {
            _end_const.reset(new Iterator_const(data().end_all()));
            return *_end_const;
        }
 
        std::unique_ptr<STIRImageData> clone() const
        {
            return std::unique_ptr<STIRImageData>(this->clone_impl());
        }
 
        void zoom_image(const Coord3DF& zooms = { 1.f,1.f,1.f }, const Coord3DF& offsets_in_mm = { 0.f,0.f,0.f },
            const Coord3DI& new_sizes = { -1,-1,-1 }, const char* const zoom_options_str = "preserve_sum");
 
        void zoom_image(const Coord3DF& zooms = { 1.f,1.f,1.f }, const Coord3DF& offsets_in_mm = { 0.f,0.f,0.f },
            const Coord3DI& new_sizes = { -1,-1,-1 },
            const stir::ZoomOptions zoom_options = stir::ZoomOptions::preserve_sum);
 
        void move_to_scanner_centre(const STIRAcquisitionData&);
 
        virtual void set_up_geom_info();
 
        void unary_op(const DataContainer& a_x, float(*f)(float));
        void semibinary_op(const DataContainer& a_x, float y, float(*f)(float, float));
        void binary_op(const DataContainer& a_x, const DataContainer& a_y, float(*f)(float, float));
 
    private:
        virtual STIRImageData* clone_impl() const
        {
            return new STIRImageData(*this);
        }
 
    protected:
        stir::shared_ptr<Image3DF> _data;
        mutable std::shared_ptr<Iterator> _begin;
        mutable std::shared_ptr<Iterator> _end;
        mutable std::shared_ptr<Iterator_const> _begin_const;
        mutable std::shared_ptr<Iterator_const> _end_const;
    };
 
}  // namespace sirf
 
#endif