eerio.h

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/*
 * Author: tunay.durmaz@bcm.edu, 08/20/2020
 * Copyright (c) 2020- Baylor College of Medicine
 * 
 * This software is issued under a joint BSD/GNU license. You may use the
 * source code in this file under either license. However, note that the
 * complete EMAN2 and SPARX software packages have some GPL dependencies,
 * so you are responsible for compliance with the licenses of these packages
 * if you opt to use BSD licensing. The warranty disclaimer below holds
 * in either instance.
 * 
 * This complete copyright notice must be included in any revised version of the
 * source code. Additional authorship citations may be added, but existing
 * author citations must be preserved.
 * 
 * This program is free software; you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation; either version 2 of the License, or
 * (at your option) any later version.
 * 
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
 * GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 * 
 * */
 
#ifndef eman__eerio_h__
#define eman__eerio_h__ 1
 
#include "imageio.h"
 
#include <tiffio.h>
#include <bitset>
 
 
namespace EMAN
{
        template <class T>
        class BitStream {
        public:
                BitStream(T *buf)
                : buffer(buf), cur(*buffer)
                {}
 
                T get_bits(int N) {
                        auto result = cur & ((1 << N) - 1);
 
                        if(N < bit_counter) {
                                cur        >>= N;
                                bit_counter -= N;
                        }
                        else {
                                auto remaining_bits = N - bit_counter;
 
                                cur = *(++buffer);
                                result |= ((cur & ((1 << remaining_bits) - 1)) << bit_counter);
 
                                cur >>= remaining_bits;
                                bit_counter = max_num_bits - remaining_bits;
                        }
 
                        return result;
                }
 
        private:
                T *buffer;
                T cur;
                const size_t max_num_bits = 8*sizeof(T);
                size_t bit_counter        = max_num_bits;
 
                friend std::ostream &operator<<(std::ostream &out, const BitStream &obj) {
                        return out<<"cur: "<<std::bitset<8*sizeof(T)>(obj.cur)
                                                <<endl
                                                <<"bit_counter: "<<obj.bit_counter<<endl
                                                <<"max_num_bits: "<<obj.max_num_bits<<endl;
                }
        };
 
        template<unsigned int T, bool BIT_OVERFLOW, class U>
        class BitReader {
        private:
                const decltype(T) num_bits = T;
                const decltype(T) max_val = (1 << num_bits) - 1;
                uintmax_t val = 0;
 
        public:
                operator decltype(val) const () {
                        return val;
                }
 
                friend BitStream<U>& operator>>(BitStream<U> &in, BitReader<T, BIT_OVERFLOW, U> &obj) {
                        decltype(val) count;
                        obj.val = 0;
                        do {
                                count = in.get_bits(obj.num_bits);
                                obj.val += count;
                        } while(BIT_OVERFLOW && count == obj.max_val);
 
                        return in;
                }
        };
 
        template<unsigned int T, class U>
        using Rle = BitReader<T, true, U>;
 
        template<unsigned int T, class U>
        using SubPix = BitReader<T, false, U>;
 
        using EerWord = uint64_t;
        using EerStream = BitStream<EerWord>;
        using EerRle    = Rle   <7, EerWord>;
        using EerSubPix = SubPix<4, EerWord>;
 
        
        class Decoder {
        public:
                virtual unsigned int num_pix() const =0;
                auto operator()(unsigned int count, unsigned int sub_pix) const;
 
                const unsigned int camera_size_bits = 12;
                const unsigned int camera_size     = 1 << camera_size_bits; // 2^12 = 4096
 
        private:
                virtual unsigned int x(unsigned int count, unsigned int sub_pix) const =0;
                virtual unsigned int y(unsigned int count, unsigned int sub_pix) const =0;
        };
        
        
        template <unsigned int I>
        struct DecoderIx : public Decoder {
                unsigned int num_pix() const override;
                unsigned int x(unsigned int count, unsigned int sub_pix) const override;
                unsigned int y(unsigned int count, unsigned int sub_pix) const override;
        };
 
        template <unsigned int I>
        unsigned int DecoderIx<I>::num_pix() const {
//                    4096 *   1     //  4k 
//                    4096 *   2     //  8k
//                    4096 *   4     // 16k
                return camera_size * (1 << I);
        }
 
        template <unsigned int I>
        unsigned int DecoderIx<I>::x(unsigned int count, unsigned int sub_pix) const {
//                               (((count & 4095) << 2) |  ((sub_pix & 3) ^ 2))       // 16k
//                               (((count & 4095) << 1) |  ((sub_pix & 3) ^ 2) >> 1)  //  8k
                return  (DecoderIx<0>().x(count, sub_pix) << I) | (((sub_pix & 3) ^ 2) >> (2 - I));
        }
 
        template <unsigned int I>
        unsigned int DecoderIx<I>::y(unsigned int count, unsigned int sub_pix) const {
//                               (((count >> 12) << 2) |  ((sub_pix >> 2) ^ 2))       // 16k
//                               (((count >> 12) << 1) |  ((sub_pix >> 2) ^ 2) >> 1)  //  8k
                return (DecoderIx<0>().y(count, sub_pix) << I) | (((sub_pix >> 2) ^ 2) >> (2 - I));
        }
 
        template <>
        inline unsigned int DecoderIx<0>::x(unsigned int count, unsigned int sub_pix) const {
//                     count & ((1 << 12)   - 1)
                return count & (camera_size - 1);
        }
 
        template <>
        inline unsigned int DecoderIx<0>::y(unsigned int count, unsigned int sub_pix) const {
//                     count >> 12
                return count >> camera_size_bits;
        }
 
        static DecoderIx<0> decoder0x;
        static DecoderIx<1> decoder1x;
        static DecoderIx<2> decoder2x;
 
 
        class EerIO : public ImageIO
        {
        public:
                EerIO(const string & fname, IOMode rw_mode = READ_ONLY, Decoder &dec=decoder0x);
                ~EerIO();
 
                int get_nimg();
                bool is_single_image_format() const override;
 
 
                DEFINE_IMAGEIO_FUNC;
 
        private:
                bool is_big_endian;
                TIFF *tiff_file;
                size_t num_frames = 0;
                Dict acquisition_data_dict;
                
                Decoder &decoder;
        };
}
 
#endif  //eman__eerio_h__