saving work

src/common/defs.hpp

@@ -47,3 +47,4 @@ template <> DetectorType StringTo(std::string);
 template <> TimingMode StringTo(std::string);
 
 using DataTypeVariants = std::variant<uint16_t, uint32_t>;
+

src/core/Frame.cpp

@@ -2,7 +2,7 @@
 #include <iostream>
 
 
-IFrame::IFrame(std::byte* bytes, ssize_t rows, ssize_t cols, ssize_t bitdepth)
+FrameImpl::FrameImpl(std::byte* bytes, ssize_t rows, ssize_t cols, ssize_t bitdepth)
  {
   this->rows = rows;
   this->cols = cols;
@@ -10,7 +10,7 @@ IFrame::IFrame(std::byte* bytes, ssize_t rows, ssize_t cols, ssize_t bitdepth)
   std::memcpy(data, bytes, bitdepth/8 * rows * cols);
 }
 
-std::byte* IFrame::get(int row, int col) {
+std::byte* FrameImpl::get(int row, int col) {
   if (row < 0 || row >= rows || col < 0 || col >= cols) {
     std::cerr << "Invalid row or column index" << std::endl;
     return 0;

src/core/Frame.hpp

@@ -13,24 +13,29 @@
  * model class
  * should be able to work with streams coming from files or network
 */
-class IFrame {
+class FrameImpl {
-
+    protected:
     std::byte* data{nullptr};
     ssize_t rows{};
     ssize_t cols{};
     ssize_t bitdepth{};
     public:
-    IFrame(std::byte* fp, ssize_t rows, ssize_t cols, ssize_t bitdepth);
+    FrameImpl(std::byte* fp, ssize_t rows, ssize_t cols, ssize_t bitdepth);
     std::byte* get(int row, int col);
-    ~IFrame(){
+    ~FrameImpl(){
         delete[] data;
     }
 };
 
-template <class DataType> class Frame: public IFrame {
+template <class DataType> class Frame: public FrameImpl {
     public:
-    Frame(std::byte* fp, ssize_t rows, ssize_t cols):IFrame(fp, rows, cols, sizeof(DataType)){}
+    Frame(std::byte* fp, ssize_t rows, ssize_t cols):FrameImpl(fp, rows, cols, sizeof(DataType)){}
     DataType get(int row, int col){
-        return *((DataType*) IFrame::get(row, col));
+        return *((DataType*) FrameImpl::get(row, col));
     }
-};
+
+};
+
+typedef Frame<uint16_t> Frame16;
+typedef Frame<uint8_t> Frame8;
+typedef Frame<uint32_t> Frame32;

src/file_io/file/File.hpp

@@ -1,14 +1,11 @@
 #pragma once
 
+#include "Frame.hpp"
+#include "SubFile.hpp"
 #include "defs.hpp"
 #include <filesystem>
 #include <fmt/core.h>
-#include "SubFile.hpp"
 #include <iostream>
-#include "Frame.hpp"
-
-
-
 
 struct RawFileConfig {
     int module_gap_row{};
@@ -23,13 +20,16 @@ struct RawFileConfig {
     }
 };
 
-
-
 class File {
-    private:
+
-    using config = RawFileConfig;
   public:
-    std::vector<SubFileBase*> subfiles;
+    virtual FrameImpl* get_frame(int frame_number) = 0;
+
+  private:
+    using config = RawFileConfig;
+
+  public:
+    std::vector<SubFile*> subfiles;
     std::filesystem::path fname;
     std::filesystem::path base_path;
     std::string base_name, ext;
@@ -49,13 +49,13 @@ class File {
     using data_type = uint16_t;
     std::vector<xy> positions;
 
-    config cfg{0,0};
+    config cfg{0, 0};
     // File();
     ~File();
 
     inline size_t bytes_per_frame() const { return rows * cols * bitdepth / 8; }
     inline size_t pixels() const { return rows * cols; }
-    inline void set_config(int row,int col){
+    inline void set_config(int row, int col) {
         cfg.module_gap_row = row;
         cfg.module_gap_col = col;
     }
@@ -63,21 +63,17 @@ class File {
     // TODO! Deal with fast quad and missing files
     void find_number_of_subfiles() {
         int n_mod = 0;
-        while (std::filesystem::exists(data_fname(++n_mod, 0)));
+        while (std::filesystem::exists(data_fname(++n_mod, 0)))
+            ;
         n_subfiles = n_mod;
-        
     }
 
     inline std::filesystem::path master_fname() {
-        return base_path /
+        return base_path / fmt::format("{}_master_{}{}", base_name, findex, ext);
-               fmt::format("{}_master_{}{}", base_name, findex, ext);
     }
     inline std::filesystem::path data_fname(int mod_id, int file_id) {
-        return base_path / fmt::format("{}_d{}_f{}_{}.raw", base_name, file_id,
+        return base_path / fmt::format("{}_d{}_f{}_{}.raw", base_name, file_id, mod_id, findex);
-                                       mod_id, findex);
     }
 
-
-    virtual Frame<uint16_t> get_frame(int frame_number)=0;
     // size_t total_frames();
 };

src/file_io/file/FileHandler.hpp

@@ -0,0 +1,29 @@
+#include <filesystem>
+#include "FileFactory.hpp"
+#include "File.hpp"
+class FileHandler{
+    private:
+    std::filesystem::path fpath;
+    FileFactory* fileFactory;
+    File* f;
+
+    public:
+    FileHandler(std::filesystem::path fpath){
+        this->fpath = fpath;
+         this->fileFactory= FileFactory::get_factory(fpath);
+         this->f= fileFactory->load_file();
+         delete fileFactory;
+    }
+
+    template <typename DataType>
+    Frame<DataType>* get_frame(int index){
+         FrameImpl* frame =f->get_frame(index);
+         return  static_cast<Frame<DataType>*>(frame);
+    }
+
+    
+
+    ~FileHandler(){
+        delete f;
+    }
+};

src/file_io/file/JsonFile.cpp

@@ -1,8 +1,7 @@
 #include "JsonFile.hpp"
 #include <typeinfo>
 
-template <class T>
+FrameImpl* JsonFile::get_frame(int frame_number){
-Frame<T> JsonFile::get_frame(int frame_number){
     int subfile_id=frame_number/max_frames_per_file;
     std::byte* buffer;
     size_t frame_size = subfiles[subfile_id]->bytes_per_frame();
@@ -12,7 +11,7 @@ Frame<T> JsonFile::get_frame(int frame_number){
 
 
 
-    auto f =  Frame<T>(buffer, rows, cols);
+    auto f = new FrameImpl(buffer, rows, cols, bitdepth);
 
     delete[] buffer;
     return f;

src/file_io/file/JsonFile.hpp

@@ -5,9 +5,7 @@
 
 class JsonFile: public File
 {
-    template <class T>
-    Frame<T> get_frame(int frame_number);
 
-    IFrame get_frame(int frame_number);
+    FrameImpl* get_frame(int frame_number);
     
 };

src/file_io/file/SubFile.cpp

@@ -7,52 +7,42 @@
  *
  *
  */
-template <class Header, class DataType>
+
-SubFile<Header, DataType>::SubFile(std::filesystem::path fname, ssize_t rows, ssize_t cols)  {
+SubFile::SubFile(std::filesystem::path fname, DetectorType detector, ssize_t rows, ssize_t cols, uint16_t bitdepth) {
     this->rows = rows;
     this->cols = cols;
     this->fname = fname;
+    this->bitdepth = bitdepth;
     fp = fopen(fname.c_str(), "rb");
     if (fp == nullptr) {
         throw std::runtime_error("Could not open file " + fname.string());
     }
-    std::cout<<"File opened"<<std::endl;
+    std::cout << "File opened" << std::endl;
-    n_frames = std::filesystem::file_size(fname) / (sizeof(Header) + rows * cols * sizeof(DataType));
+    n_frames = std::filesystem::file_size(fname) / (sizeof(sls_detector_header) + rows * cols * bitdepth / 8);
-    std::cout<<"Number of frames: "<<n_frames<<std::endl;
+    std::cout << "Number of frames: " << n_frames << std::endl;
+    
+    if (detector == DetectorType::Moench) {
+        read_impl = &SubFile::read_impl_reorder<uint16_t>;
+    } else if (detector == DetectorType::Jungfrau) {
+        read_impl = &SubFile::read_impl_normal;
+    }
+    else {
+        throw std::runtime_error("Detector type not implemented");
+    }
 }
 
-
+size_t SubFile::get_frame(std::byte *buffer, int frame_number) {
-template <class Header, class DataType>
-size_t SubFile<Header, DataType>::get_frame(std::byte *buffer, int frame_number) {
     if (frame_number >= n_frames or frame_number < 0) {
         throw std::runtime_error("Frame number out of range");
     }
-    fseek(fp, sizeof(Header)+(sizeof(Header) + bytes_per_frame()) *frame_number, SEEK_SET);
+    fseek(fp, sizeof(sls_detector_header) + (sizeof(sls_detector_header) + bytes_per_frame()) * frame_number, SEEK_SET);
-    return read_impl(buffer);
+    return (this->*read_impl)(buffer);
 }
 
-/**
+size_t SubFile::read_impl_normal(std::byte *buffer) { return fread(buffer, this->bytes_per_frame(), 1, this->fp); }
- * NormalSubFile methods
-*/
-template <class Header, class DataType>
-NormalSubFile<Header, DataType>::NormalSubFile(std::filesystem::path fname, ssize_t rows, ssize_t cols)
-    : SubFile<Header, DataType>(fname, rows, cols){};
 
-template <class Header, class DataType> size_t NormalSubFile<Header, DataType>::read_impl(std::byte *buffer) {
+template <typename DataType> size_t SubFile::read_impl_reorder(std::byte *buffer) {
-    return fread(buffer, this->bytes_per_frame(), 1, this->fp);
-};
 
-
-
-/**
- * ReorderM03SubFile methods
-*/
-template <class Header, class DataType>
-ReorderM03SubFile<Header, DataType>::ReorderM03SubFile(std::filesystem::path fname, ssize_t rows, ssize_t cols)
-    : SubFile<Header, DataType>(fname, rows, cols){};
-
-template <class Header, class DataType> 
-size_t ReorderM03SubFile<Header, DataType>::read_impl(std::byte *buffer) {
     std::vector<DataType> tmp(this->pixels_per_frame());
     size_t rc = fread(reinterpret_cast<char *>(&tmp[0]), this->bytes_per_frame(), 1, this->fp);
 
@@ -79,13 +69,24 @@ size_t ReorderM03SubFile<Header, DataType>::read_impl(std::byte *buffer) {
     }
     return rc;
 };
+template <typename DataType> size_t SubFile::read_impl_flip(std::byte *buffer) {
 
-template class NormalSubFile<sls_detector_header, uint16_t>;
+    // read to temporary buffer
-template class NormalSubFile<sls_detector_header, uint32_t>;
+    // TODO! benchmark direct reads
-template class ReorderM03SubFile<sls_detector_header, uint16_t>;
+    std::vector<std::byte> tmp(this->bytes_per_frame());
+    size_t rc = fread(reinterpret_cast<char *>(&tmp[0]), this->bytes_per_frame(), 1, this->fp);
 
-// template size_t ReorderM03SubFile<sls_detector_header, uint16_t>::read_impl(std::byte *buffer); 
+    // copy to place
-// template size_t ReorderM03SubFile<sls_detector_header, uint32_t>::read_impl(std::byte *buffer); 
+    const size_t start = this->cols * (this->rows - 1) * sizeof(DataType);
+    const size_t row_size = this->cols * sizeof(DataType);
+    auto dst = buffer + start;
+    auto src = &tmp[0];
 
-// template size_t NormalSubFile<sls_detector_header, uint32_t>::read_impl(std::byte *buffer);
+    for (int i = 0; i != this->rows; ++i) {
-// template size_t NormalSubFile<sls_detector_header, uint16_t>::read_impl(std::byte *buffer);
+        memcpy(dst, src, row_size);
+        dst -= row_size;
+        src += row_size;
+    }
+
+    return rc;
+};

src/file_io/file/SubFile.hpp

@@ -4,50 +4,29 @@
 #include <filesystem>
 #include <variant>
 
-class SubFileBase {
+class SubFile {
   protected:
     FILE *fp = nullptr;
+    uint16_t bitdepth;
 
   public:
-    virtual inline size_t bytes_per_frame() =0;
+    // pointer to a read_impl function. pointer will be set to the appropriate read_impl function in the constructor
-    virtual inline size_t pixels_per_frame() =0;
+    size_t (SubFile::*read_impl)(std::byte *buffer) = nullptr;
-    std::filesystem::path fname;
+    size_t read_impl_normal(std::byte *buffer);
+    template <typename DataType> size_t  read_impl_flip(std::byte *buffer);
+    template <typename DataType> size_t  read_impl_reorder(std::byte *buffer);
 
+
+    SubFile(std::filesystem::path fname,DetectorType detector, ssize_t rows, ssize_t cols, uint16_t bitdepth);
+
+    size_t get_frame(std::byte *buffer, int frame_number);
+
+    // TODO: define the inlines as variables and assign them in constructor
+    inline size_t bytes_per_frame() { return (bitdepth / 8) * rows * cols; }
+    inline size_t pixels_per_frame() { return rows * cols; }
+    std::filesystem::path fname;
     ssize_t rows{};
     ssize_t cols{};
     ssize_t n_frames{};
     int sub_file_index_{};
-    virtual size_t read_impl(std::byte *buffer)=0;
-    virtual size_t get_frame(std::byte *buffer, int frame_number)=0;
-
 };
-
-template <class Header, class DataType> class SubFile : public SubFileBase{
-  public:
-    SubFile(std::filesystem::path fname, ssize_t rows, ssize_t cols);
-    inline size_t bytes_per_frame() override { return sizeof(DataType) * rows * cols; }
-    inline size_t pixels_per_frame() override { return rows * cols; }
-    virtual size_t read_impl(std::byte *buffer)=0;
-    size_t get_frame(std::byte *buffer, int frame_number);
-
-    
-};
-
-template <class Header, class DataType> class NormalSubFile : public SubFile<Header, DataType> {
-  public:
-    NormalSubFile(std::filesystem::path fname, ssize_t rows, ssize_t cols);
-    size_t read_impl(std::byte *buffer);
-};
-
-template <class Header, class DataType> class ReorderM03SubFile : public SubFile<Header, DataType> {
-  public:
-    ReorderM03SubFile(std::filesystem::path fname, ssize_t rows, ssize_t cols);
-    size_t read_impl(std::byte *buffer);
-};
-
-using JungfrauSubFile = NormalSubFile<sls_detector_header, uint16_t>;
-using Moench03SubFile = ReorderM03SubFile<sls_detector_header, uint16_t>;
-using Mythen3SubFile = NormalSubFile<sls_detector_header, uint32_t>;
-
-// using SubFileVariants = std::variant<JungfrauSubFile, Mythen3SubFile, Moench03SubFile>;
-

src/file_io/file_factory/FileFactory.cpp

@@ -6,7 +6,7 @@
 
 
 
- FileFactory* FileFactory::getFactory(std::filesystem::path fpath){
+ FileFactory* FileFactory::get_factory(std::filesystem::path fpath, uint16_t bitdepth){
     // check if file exists
     if(!std::filesystem::exists(fpath)){
         throw std::runtime_error("File does not exist");
@@ -18,7 +18,7 @@
     }
     else if(fpath.extension() == ".json"){
         std::cout<<"Loading json file"<<std::endl;
-        return new JsonFileFactory(fpath);
+        return new JsonFileFactory(fpath, bitdepth);
     }
     //check if extension is numpy
     else if(fpath.extension() == ".npy"){

src/file_io/file_factory/FileFactory.hpp

@@ -7,10 +7,11 @@ class FileFactory{
     // follows the factory pattern
     protected:
     std::filesystem::path fpath;
+    uint16_t bitdepth;
 public:
-    static FileFactory* getFactory(std::filesystem::path);
+    static FileFactory* get_factory(std::filesystem::path,uint16_t bitdepth=16);
     // virtual int deleteFile() = 0;
-    virtual File* loadFile()=0;//TODO: add option to load all file to memory or keep it on disk
+    virtual File* load_file()=0;//TODO: add option to load all file to memory or keep it on disk
     virtual void parse_metadata(File*)=0;
     
     

src/file_io/file_factory/JsonFileFactory.cpp

@@ -9,13 +9,14 @@
 
 using json = nlohmann::json;
 
-JsonFileFactory::JsonFileFactory(std::filesystem::path fpath) {
+JsonFileFactory::JsonFileFactory(std::filesystem::path fpath, uint16_t bitdepth=16) {
     if (not is_master_file(fpath))
         throw std::runtime_error("Json file is not a master file");
     this->fpath = fpath;
+    this->bitdepth = bitdepth;
 }
 
-void JsonFileFactory::parse_metadata(File* file) {
+void JsonFileFactory::parse_metadata(File *file) {
     std::cout << "Parsing metadata" << std::endl;
     std::ifstream ifs(file->master_fname());
     json j;
@@ -35,6 +36,9 @@ void JsonFileFactory::parse_metadata(File* file) {
         std::cerr << "master file does not have Dynamic Range. Defaulting to 16 bit" << '\n';
         file->bitdepth = 16;
     }
+    // if (file->bitdepth != this->bitdepth)
+    //     throw std::runtime_error("Bitdepth mismatch: file bitdepth (" + std::to_string(file->bitdepth) +
+    //                              ") != specified bitdepth (" + std::to_string(this->bitdepth) + ")");
 
     // only Eiger had quad
     if (file->type == DetectorType::Eiger) {
@@ -42,22 +46,17 @@ void JsonFileFactory::parse_metadata(File* file) {
     }
 }
 
-void JsonFileFactory::open_subfiles(File* file) {
+void JsonFileFactory::open_subfiles(File *file) {
     for (int i = 0; i != file->n_subfiles; ++i) {
-        if (file->type == DetectorType::Jungfrau) {
+
-            file->subfiles.push_back(new JungfrauSubFile(file->data_fname(i, 0), file->subfile_rows, file->subfile_cols));
+        file->subfiles.push_back(
-        } else if (file->type == DetectorType::Mythen3)
+            new SubFile(file->data_fname(i, 0), file->type, file->subfile_rows, file->subfile_cols, file->bitdepth));
-            file->subfiles.push_back(new Mythen3SubFile(file->data_fname(i, 0), file->subfile_rows, file->subfile_cols));
-        else if (file->type == DetectorType::Moench)
-            file->subfiles.push_back(new Moench03SubFile(file->data_fname(i, 0), file->subfile_rows, file->subfile_cols));
-        else
-            throw std::runtime_error("File not supported");
     }
 }
 
-File* JsonFileFactory::loadFile() {
+File *JsonFileFactory::load_file() {
     std::cout << "Loading json file" << std::endl;
-    JsonFile* file = new JsonFile();
+    JsonFile *file = new JsonFile();
     file->fname = fpath;
     this->parse_fname(file);
     this->parse_metadata(file);

src/file_io/file_factory/JsonFileFactory.hpp

@@ -5,9 +5,9 @@ class JsonFileFactory: public FileFactory
 private:
     /* data */
 public:
-    File* loadFile() override;
+    File* load_file() override;
     void parse_metadata(File*) override;
-    JsonFileFactory(std::filesystem::path fpath);
+    JsonFileFactory(std::filesystem::path fpath, uint16_t bitdepth);
     void open_subfiles(File*);
     
 

src/main.cpp

@@ -1,37 +1,22 @@
 // Your First C++ Program
 #include <iostream>
-#include "file_io/file_factory/FileFactory.hpp"
+#include <FileHandler.hpp>
-
+void test(FileHandler* f,int frame_number){
-void test(File* f,int frame_number){
     std::cout << "frame number: " << frame_number << std::endl;
-    auto frame = f->get_frame(frame_number);
+    Frame16* frame = f->get_frame<uint16_t>(frame_number);
-    std::cout << frame.get(0,0) << ' ';
+    std::cout << frame->get(0,0) << ' ';
-    std::cout << frame.get(0,1) << ' ';
+    std::cout << frame->get(0,1) << ' ';
-    std::cout << frame.get(1,0) << ' ';
+    std::cout << frame->get(1,0) << ' ';
-    std::cout << frame.get(511,1023) << std::endl;
+    std::cout << frame->get(511,1023) << std::endl;
-
 
+    delete frame;
 }
 
 int main() {
-    FileFactory* fileFactory=FileFactory::getFactory(std::filesystem::path("/home/l_bechir/github/aare")/"data"/"jungfrau_single_master_0.json");
+    std::filesystem::path fpath("/home/l_bechir/github/aare/data/jungfrau_single_master_0.json");
-    File* f = fileFactory->loadFile();
+    FileHandler* fileHandler = new FileHandler(fpath);
+    test(fileHandler,0);
 
-    test(f,0);
+    delete fileHandler;
-    test(f,1);
-    test(f,2);
-    test(f,3);
-    test(f,4);
-    test(f,5);
-    test(f,6);
-    test(f,7);
-    test(f,8);
-    test(f,9);
 
-
-
-
-
-    delete fileFactory;
-    delete f;
 }