Merge pull request #15 from slsdetectorgroup/numpy

read numpy file: works

.env.dev

@@ -0,0 +1 @@
+export PROJECT_ROOT_DIR=/home/l_bechir/github/aare

.vscode/c_cpp_properties.json

@@ -3,7 +3,10 @@
         {
             "name": "Linux",
             "includePath": [
-                "${workspaceFolder}/**",
+                "${workspaceFolder}/file_io/**",
+                "${workspaceFolder}/core/**",
+                "${workspaceFolder}/tests/**",
+                "${workspaceFolder}/tests/**",
                 "/usr/include"
             ],
             "defines": [],

CMakeLists.txt

@@ -86,4 +86,4 @@ target_link_libraries(example PUBLIC aare)
 
 if(AARE_PYTHON_BINDINGS)
     add_subdirectory(python)
-endif()
+endif()

core/include/aare/Frame.hpp

@@ -19,8 +19,10 @@ template <class DataType> class Frame {
     ssize_t m_bitdepth = sizeof(DataType) * 8;
 
   public:
+    Frame(ssize_t rows, ssize_t cols);
     Frame(std::byte *fp, ssize_t rows, ssize_t cols);
     DataType get(int row, int col);
+    std::vector<std::vector<DataType>> get_array();
     ssize_t rows() const{
         return m_rows;
     }
@@ -30,6 +32,9 @@ template <class DataType> class Frame {
     ssize_t bitdepth() const{
         return m_bitdepth;
     }
+    DataType* _get_data(){
+        return m_data;
+    }
 
     ~Frame() { delete[] m_data; }
 };

core/src/Frame.cpp

@@ -8,6 +8,13 @@ Frame<DataType>::Frame(std::byte* bytes, ssize_t rows, ssize_t cols):
     std::memcpy(m_data, bytes, m_rows*m_cols*sizeof(DataType));
   }
 
+template <typename DataType>
+Frame<DataType>::Frame(ssize_t rows, ssize_t cols):
+  m_rows(rows), m_cols(cols) {
+    m_data = new DataType[m_rows*m_cols];
+  }
+
+
 
 template <typename DataType>
 DataType Frame<DataType>::get(int row, int col) {
@@ -18,5 +25,17 @@ DataType Frame<DataType>::get(int row, int col) {
   return m_data[row*m_cols + col];
 }
 
+template <typename DataType>
+std::vector<std::vector<DataType>> Frame<DataType>::get_array() {
+  std::vector<std::vector<DataType>> array;
+  for (int i = 0; i < m_rows; i++) {
+    std::vector<DataType> row;
+    row.assign(m_data + i*m_cols, m_data + (i+1)*m_cols);
+    array.push_back(row);
+  }
+
+  return array;
+}
+
 
 template class Frame<uint16_t>;

examples/main.cpp

@@ -1,25 +1,35 @@
 // Your First C++ Program
-#include <iostream>
 #include "aare/FileHandler.hpp"
+#include <iostream>
 
-using JFileHandler = FileHandler<DetectorType::Jungfrau,uint16_t>;
-using JFile = File<DetectorType::Jungfrau,uint16_t>;
+#define AARE_ROOT_DIR_VAR "PROJECT_ROOT_DIR"
+
+using JFileHandler = FileHandler<DetectorType::Jungfrau, uint16_t>;
+using JFile = File<DetectorType::Jungfrau, uint16_t>;
 using JFrame = Frame<uint16_t>;
 
-
-void test(JFileHandler* f,int frame_number){
+void test(JFileHandler *f, int frame_number) {
     std::cout << "frame number: " << frame_number << std::endl;
-    JFrame* frame = f->get_frame(frame_number);
-    std::cout << frame->get(0,0) << ' ';
-    std::cout << frame->get(0,1) << ' ';
-    std::cout << frame->get(1,0) << ' ';
-    std::cout << frame->get(511,1023) << std::endl;
+    JFrame *frame = f->get_frame(frame_number);
+    std::cout << frame->get(0, 0) << std::endl;
+    std::cout << frame->get(0, 1) << std::endl;
+    std::cout << frame->get(1, 0) << std::endl;
+    std::cout << frame->get(49, 49) << std::endl;
 
     delete frame;
 }
 
 int main() {
-    std::filesystem::path fpath("/home/bb/github/aare/data/jungfrau_single_master_0.json");
-    auto fileHandler = new JFileHandler (fpath);
+    auto  PROJECT_ROOT_DIR = std::filesystem::path(getenv(AARE_ROOT_DIR_VAR));
+    // std::filesystem::path fpath("/home/bb/github/aare/data/jungfrau_single_master_0.json");
+    std::filesystem::path fpath(PROJECT_ROOT_DIR / "data" / "test_numpy_file.npy");
+        std::cout<<fpath<<std::endl;
+
+
+    auto fileHandler = new JFileHandler(fpath);
+    test(fileHandler, 0);
+    test(fileHandler, 24);
+
     delete fileHandler;
+
 }

file_io/include/aare/File.hpp

@@ -15,6 +15,8 @@ class File {
     virtual Frame<DataType>* get_frame(int frame_number) = 0;
 
   private:
+  //comment
+  
 
   public:
     virtual ~File() = default;

file_io/include/aare/JsonFileFactory.hpp

@@ -5,11 +5,10 @@ class JsonFileFactory: public FileFactory<detector,DataType>
 private:
     /* data */
 public:
+    JsonFileFactory(std::filesystem::path fpath);
     File<detector,DataType>* load_file() override;
     void parse_metadata(File<detector,DataType>*) override;
     void parse_fname(File<detector,DataType>*) override;
-
-    JsonFileFactory<detector,DataType>(std::filesystem::path fpath);
     void open_subfiles(File<detector,DataType>*);
     sls_detector_header read_header(const std::filesystem::path &fname);
     void find_geometry(File<detector,DataType>*);

file_io/include/aare/NumpyFile.hpp

@@ -1,9 +1,52 @@
+#pragma once
 #include "aare/File.hpp"
 #include "aare/defs.hpp"
+#include <iostream>
+#include <numeric>
 
-template <DetectorType detector, typename DataType>
-class NumpyFile : public File<detector, DataType>
-{
+using shape_t = std::vector<uint64_t>;
+
+struct dtype_t {
+    char byteorder;
+    char kind;
+    unsigned int itemsize;
+    std::string to_string() {
+        std::stringstream sstm;
+        sstm << byteorder << kind << itemsize;
+        return sstm.str();
+    }
+};
+struct header_t {
+    dtype_t dtype;
+    bool fortran_order;
+    shape_t shape;
+    std::string to_string() {
+        std::stringstream sstm;
+        sstm << "dtype: " << dtype.to_string() << ", fortran_order: " << fortran_order << ' ';
+
+        sstm << "shape: (";
+        for (auto item : shape)
+            sstm << item << ',';
+        sstm << ')';
+        return sstm.str();
+    }
+};
+template <DetectorType detector, typename DataType> class NumpyFile : public File<detector, DataType> {
+    FILE *fp = nullptr;
     
-
+  public:
+    NumpyFile(std::filesystem::path fname);
+    Frame<DataType> *get_frame(int frame_number) override;
+    header_t header{};
+    static constexpr std::array<char, 6> magic_str{'\x93', 'N', 'U', 'M', 'P', 'Y'};
+    uint8_t major_ver_{};
+    uint8_t minor_ver_{};
+    uint32_t header_len{};
+    uint8_t header_len_size{};
+    const uint8_t magic_string_length{6};
+    ssize_t header_size{};
+    inline ssize_t pixels_per_frame() {
+        return std::accumulate(header.shape.begin() + 1, header.shape.end(), 1, std::multiplies<uint64_t>());
+    };
+    inline ssize_t bytes_per_frame() { return header.dtype.itemsize * pixels_per_frame(); };
 };

file_io/include/aare/NumpyFileFactory.hpp

@@ -1,29 +1,20 @@
-#include "aare/defs.hpp"
+#pragma once
 #include "aare/FileFactory.hpp"
 #include "aare/NumpyFile.hpp"
-#include <algorithm>
-#include <array>
-#include <filesystem>
+#include "aare/defs.hpp"
 #include <fstream>
-#include <string>
-#include <unordered_map>
-#include <vector>
+
+
 
 template <DetectorType detector, typename DataType> class NumpyFileFactory : public FileFactory<detector, DataType> {
+  private:
+    std::ifstream f;
+    void read_data(File<detector, DataType> *_file);
+
   public:
     NumpyFileFactory(std::filesystem::path fpath);
     void parse_metadata(File<detector, DataType> *_file) override;
-    void open_subfiles(File<detector, DataType> *_file) override;
     File<detector, DataType> *load_file() override;
+    void parse_fname(File<detector, DataType> *){};
 
-    uint8_t major_ver() const noexcept { return major_ver_; }
-    uint8_t minor_ver() const noexcept { return minor_ver_; }
-
-  private:
-    static constexpr std::array<char, 6> magic_str{'\x93', 'N', 'U', 'M', 'P', 'Y'};
-    uint8_t major_ver_{};
-    uint8_t minor_ver_{};
-    uint32_t header_len{};
-    uint8_t header_len_size{};
-    const uint8_t magic_string_length{6};
 };

file_io/include/aare/NumpyHelpers.hpp

@@ -0,0 +1,146 @@
+
+#include <algorithm>
+#include <array>
+#include <filesystem>
+#include <fstream>
+#include <string>
+#include <unordered_map>
+#include <vector>
+#include <sstream>
+
+inline std::string parse_str(const std::string &in) {
+    if ((in.front() == '\'') && (in.back() == '\''))
+        return in.substr(1, in.length() - 2);
+
+    throw std::runtime_error("Invalid python string.");
+}
+/**
+  Removes leading and trailing whitespaces
+  */
+inline std::string trim(const std::string &str) {
+    const std::string whitespace = " \t\n";
+    auto begin = str.find_first_not_of(whitespace);
+
+    if (begin == std::string::npos)
+        return "";
+
+    auto end = str.find_last_not_of(whitespace);
+
+    return str.substr(begin, end - begin + 1);
+}
+inline std::vector<std::string> parse_tuple(std::string in) {
+    std::vector<std::string> v;
+    const char seperator = ',';
+
+    in = trim(in);
+
+    if ((in.front() == '(') && (in.back() == ')'))
+        in = in.substr(1, in.length() - 2);
+    else
+        throw std::runtime_error("Invalid Python tuple.");
+
+    std::istringstream iss(in);
+
+    for (std::string token; std::getline(iss, token, seperator);) {
+        v.push_back(token);
+    }
+
+    return v;
+}
+inline bool parse_bool(const std::string &in) {
+    if (in == "True")
+        return true;
+    if (in == "False")
+        return false;
+
+    throw std::runtime_error("Invalid python boolan.");
+}
+
+inline std::string get_value_from_map(const std::string &mapstr) {
+    size_t sep_pos = mapstr.find_first_of(":");
+    if (sep_pos == std::string::npos)
+        return "";
+
+    std::string tmp = mapstr.substr(sep_pos + 1);
+    return trim(tmp);
+}
+std::unordered_map<std::string, std::string> parse_dict(std::string in, const std::vector<std::string> &keys) {
+    std::unordered_map<std::string, std::string> map;
+    if (keys.size() == 0)
+        return map;
+
+    in = trim(in);
+
+    // unwrap dictionary
+    if ((in.front() == '{') && (in.back() == '}'))
+        in = in.substr(1, in.length() - 2);
+    else
+        throw std::runtime_error("Not a Python dictionary.");
+
+    std::vector<std::pair<size_t, std::string>> positions;
+
+    for (auto const &value : keys) {
+        size_t pos = in.find("'" + value + "'");
+
+        if (pos == std::string::npos)
+            throw std::runtime_error("Missing '" + value + "' key.");
+
+        std::pair<size_t, std::string> position_pair{pos, value};
+        positions.push_back(position_pair);
+    }
+
+    // sort by position in dict
+    std::sort(positions.begin(), positions.end());
+
+    for (size_t i = 0; i < positions.size(); ++i) {
+        std::string raw_value;
+        size_t begin{positions[i].first};
+        size_t end{std::string::npos};
+
+        std::string key = positions[i].second;
+
+        if (i + 1 < positions.size())
+            end = positions[i + 1].first;
+
+        raw_value = in.substr(begin, end - begin);
+
+        raw_value = trim(raw_value);
+
+        if (raw_value.back() == ',')
+            raw_value.pop_back();
+
+        map[key] = get_value_from_map(raw_value);
+    }
+
+    return map;
+}
+
+template <typename T, size_t N> inline bool in_array(T val, const std::array<T, N> &arr) {
+    return std::find(std::begin(arr), std::end(arr), val) != std::end(arr);
+}
+inline bool is_digits(const std::string &str) { return std::all_of(str.begin(), str.end(), ::isdigit); }
+
+inline dtype_t parse_descr(std::string typestring) {
+    if (typestring.length() < 3) {
+        throw std::runtime_error("invalid typestring (length)");
+    }
+
+    char byteorder_c = typestring.at(0);
+    char kind_c = typestring.at(1);
+    std::string itemsize_s = typestring.substr(2);
+
+    if (!in_array(byteorder_c, endian_chars)) {
+        throw std::runtime_error("invalid typestring (byteorder)");
+    }
+
+    if (!in_array(kind_c, numtype_chars)) {
+        throw std::runtime_error("invalid typestring (kind)");
+    }
+
+    if (!is_digits(itemsize_s)) {
+        throw std::runtime_error("invalid typestring (itemsize)");
+    }
+    unsigned int itemsize = std::stoul(itemsize_s);
+
+    return {byteorder_c, kind_c, itemsize};
+}

file_io/src/FileFactory.cpp

@@ -1,6 +1,7 @@
 #include "aare/FileFactory.hpp"
 #include "aare/File.hpp"
 #include "aare/JsonFileFactory.hpp"
+#include "aare/NumpyFileFactory.hpp"
 #include <iostream>
 
 template <DetectorType detector, typename DataType>
@@ -20,7 +21,7 @@ FileFactory<detector, DataType> *FileFactory<detector, DataType>::get_factory(st
     // check if extension is numpy
     else if (fpath.extension() == ".npy") {
         std::cout << "Loading numpy file" << std::endl;
-        throw std::runtime_error("Numpy file not implemented");
+        return new NumpyFileFactory<detector, DataType>(fpath);
     }
 
     throw std::runtime_error("Unsupported file type");

file_io/src/JsonFile.cpp

@@ -2,6 +2,9 @@
 
 template <DetectorType detector, typename DataType>
 Frame<DataType> *JsonFile<detector, DataType>::get_frame(int frame_number) {
+    if (frame_number > this->total_frames) {
+        throw std::runtime_error("Frame number out of range");
+    }
     int subfile_id = frame_number / this->max_frames_per_file;
     std::byte *buffer;
     size_t frame_size = this->subfiles[subfile_id]->bytes_per_frame();

file_io/src/NumpyFile.cpp

@@ -0,0 +1,24 @@
+
+#include "aare/NumpyFile.hpp"
+
+template <DetectorType detector, typename DataType>
+NumpyFile<detector, DataType>::NumpyFile(std::filesystem::path fname){
+    this->fname = fname;
+    fp = fopen(fname.c_str(), "rb");
+}
+
+template <DetectorType detector, typename DataType>
+Frame<DataType> *NumpyFile<detector, DataType>::get_frame(int frame_number) {
+    if (fp == nullptr) {
+        throw std::runtime_error("File not open");
+    }
+    if (frame_number > header.shape[0]) {
+        throw std::runtime_error("Frame number out of range");
+    }
+    Frame<DataType> *frame = new Frame<DataType>(header.shape[1], header.shape[2]);
+    fseek(fp, header_size + frame_number * bytes_per_frame(), SEEK_SET);
+    fread(frame->_get_data(), sizeof(DataType), pixels_per_frame(), fp);
+    return frame;
+}
+
+template class NumpyFile<DetectorType::Jungfrau, uint16_t>;

file_io/src/NumpyFileFactory.cpp

@@ -1,173 +1,22 @@
 #include "aare/NumpyFileFactory.hpp"
-
+#include "aare/NumpyHelpers.hpp"
 template <DetectorType detector, typename DataType>
 NumpyFileFactory<detector, DataType>::NumpyFileFactory(std::filesystem::path fpath) {
-    this->fpath = fpath;
+    this->m_fpath = fpath;
 }
-inline std::string parse_str(const std::string &in) {
-    if ((in.front() == '\'') && (in.back() == '\''))
-        return in.substr(1, in.length() - 2);
-
-    throw std::runtime_error("Invalid python string.");
-}
-/**
-  Removes leading and trailing whitespaces
-  */
-inline std::string trim(const std::string& str) {
-    const std::string whitespace = " \t";
-    auto begin = str.find_first_not_of(whitespace);
-
-    if (begin == std::string::npos)
-        return "";
-
-    auto end = str.find_last_not_of(whitespace);
-
-    return str.substr(begin, end - begin + 1);
-}
-inline std::vector<std::string> parse_tuple(std::string in) {
-    std::vector<std::string> v;
-    const char seperator = ',';
-
-    in = trim(in);
-
-    if ((in.front() == '(') && (in.back() == ')'))
-        in = in.substr(1, in.length() - 2);
-    else
-        throw std::runtime_error("Invalid Python tuple.");
-
-    std::istringstream iss(in);
-
-    for (std::string token; std::getline(iss, token, seperator);) {
-        v.push_back(token);
-    }
-
-    return v;
-}
-inline bool parse_bool(const std::string &in) {
-    if (in == "True")
-        return true;
-    if (in == "False")
-        return false;
-
-    throw std::runtime_error("Invalid python boolan.");
-}
-
-
-inline std::string get_value_from_map(const std::string &mapstr) {
-    size_t sep_pos = mapstr.find_first_of(":");
-    if (sep_pos == std::string::npos)
-        return "";
-
-    std::string tmp = mapstr.substr(sep_pos + 1);
-    return trim(tmp);
-}
-std::unordered_map<std::string, std::string> parse_dict(std::string in, const std::vector<std::string> &keys) {
-    std::unordered_map<std::string, std::string> map;
-
-    if (keys.size() == 0)
-        return map;
-
-    in = trim(in);
-
-    // unwrap dictionary
-    if ((in.front() == '{') && (in.back() == '}'))
-        in = in.substr(1, in.length() - 2);
-    else
-        throw std::runtime_error("Not a Python dictionary.");
-
-    std::vector<std::pair<size_t, std::string>> positions;
-
-    for (auto const &value : keys) {
-        size_t pos = in.find("'" + value + "'");
-
-        if (pos == std::string::npos)
-            throw std::runtime_error("Missing '" + value + "' key.");
-
-        std::pair<size_t, std::string> position_pair{pos, value};
-        positions.push_back(position_pair);
-    }
-
-    // sort by position in dict
-    std::sort(positions.begin(), positions.end());
-
-    for (size_t i = 0; i < positions.size(); ++i) {
-        std::string raw_value;
-        size_t begin{positions[i].first};
-        size_t end{std::string::npos};
-
-        std::string key = positions[i].second;
-
-        if (i + 1 < positions.size())
-            end = positions[i + 1].first;
-
-        raw_value = in.substr(begin, end - begin);
-
-        raw_value = trim(raw_value);
-
-        if (raw_value.back() == ',')
-            raw_value.pop_back();
-
-        map[key] = get_value_from_map(raw_value);
-    }
-
-    return map;
-}
-
-
-using shape_t = std::vector<uint64_t>;
-
-struct dtype_t {
-    char byteorder;
-    char kind;
-    unsigned int itemsize;
-};
-struct header_t {
-    dtype_t dtype;
-    bool fortran_order;
-    shape_t shape;
-};
-template <typename T, size_t N> inline bool in_array(T val, const std::array<T, N> &arr) {
-    return std::find(std::begin(arr), std::end(arr), val) != std::end(arr);
-}
-inline bool is_digits(const std::string &str) { return std::all_of(str.begin(), str.end(), ::isdigit); }
-
-inline dtype_t parse_descr(std::string typestring) {
-    if (typestring.length() < 3) {
-        throw std::runtime_error("invalid typestring (length)");
-    }
-
-    char byteorder_c = typestring.at(0);
-    char kind_c = typestring.at(1);
-    std::string itemsize_s = typestring.substr(2);
-
-    if (!in_array(byteorder_c, endian_chars)) {
-        throw std::runtime_error("invalid typestring (byteorder)");
-    }
-
-    if (!in_array(kind_c, numtype_chars)) {
-        throw std::runtime_error("invalid typestring (kind)");
-    }
-
-    if (!is_digits(itemsize_s)) {
-        throw std::runtime_error("invalid typestring (itemsize)");
-    }
-    unsigned int itemsize = std::stoul(itemsize_s);
-
-    return {byteorder_c, kind_c, itemsize};
-}
-
 template <DetectorType detector, typename DataType>
 void NumpyFileFactory<detector, DataType>::parse_metadata(File<detector, DataType> *_file) {
     auto file = dynamic_cast<NumpyFile<detector, DataType> *>(_file);
     // open ifsteam to file
-    std::ifstream f(file->fname, std::ios::binary);
+    f = std::ifstream(file->fname, std::ios::binary);
+    // check if file exists
     if (!f.is_open()) {
         throw std::runtime_error(fmt::format("Could not open: {} for reading", file->fname.c_str()));
     }
     // read magic number
     std::array<char, 6> tmp{};
     f.read(tmp.data(), tmp.size());
-    if (tmp != NumpyFileFactory<detector, DataType>::magic_str) {
+    if (tmp != NumpyFile<detector, DataType>::magic_str) {
         for (auto item : tmp)
             fmt::print("{}, ", int(item));
         fmt::print("\n");
@@ -175,29 +24,31 @@ void NumpyFileFactory<detector, DataType>::parse_metadata(File<detector, DataTyp
     }
 
     // read version
-    f.read(reinterpret_cast<char *>(&major_ver_), 1);
-    f.read(reinterpret_cast<char *>(&minor_ver_), 1);
+    f.read(reinterpret_cast<char *>(&file->major_ver_), 1);
+    f.read(reinterpret_cast<char *>(&file->minor_ver_), 1);
 
-    if (major_ver_ == 1) {
-        header_len_size = 2;
-    } else if (major_ver_ == 2) {
-        header_len_size = 4;
+    if (file->major_ver_ == 1) {
+        file->header_len_size = 2;
+    } else if (file->major_ver_ == 2) {
+        file->header_len_size = 4;
     } else {
         throw std::runtime_error("Unsupported numpy version");
     }
     // read header length
-    f.read(reinterpret_cast<char *>(&header_len), header_len_size);
-    if ((magic_string_length + 2 + header_len_size + header_len) % 16 != 0) {
+    f.read(reinterpret_cast<char *>(&file->header_len), file->header_len_size);
+    file->header_size = file->magic_string_length + 2 + file->header_len_size + file->header_len;
+    if (file->header_size % 16 != 0) {
         fmt::print("Warning: header length is not a multiple of 16\n");
     }
     // read header
-    auto buf_v = std::vector<char>(header_len);
-    f.read(buf_v.data(), header_len);
-    std::string header(buf_v.data(), header_len);
+    auto buf_v = std::vector<char>(file->header_len);
+    f.read(buf_v.data(), file->header_len);
+    std::string header(buf_v.data(), file->header_len);
 
     // parse header
 
     std::vector<std::string> keys{"descr", "fortran_order", "shape"};
+    std::cout << "original header: " << '"' << header << '"' << std::endl;
 
     auto dict_map = parse_dict(header, keys);
     if (dict_map.size() == 0)
@@ -220,6 +71,23 @@ void NumpyFileFactory<detector, DataType>::parse_metadata(File<detector, DataTyp
         auto dim = static_cast<unsigned long>(std::stoul(item));
         shape.push_back(dim);
     }
+    file->header = {dtype, fortran_order, shape};
+}
+
+template <DetectorType detector, typename DataType>
+ File<detector, DataType>* NumpyFileFactory<detector, DataType>::load_file() {
+    NumpyFile<detector, DataType> *file = new NumpyFile<detector, DataType>(this->m_fpath);
+    parse_metadata(file);
+    NumpyFile<detector, DataType> *f = dynamic_cast<NumpyFile<detector, DataType> *>(file);
+    std::cout << "parsed header: " << f->header.to_string() << std::endl;
+
+    if(sizeof(DataType) != f->header.dtype.itemsize){
+        std::stringstream  s;
+        s << "Data type size mismatch: " << sizeof(DataType) << " != " << f->header.dtype.itemsize;
+        throw std::runtime_error(s.str());
+    }       
+    return file;
+};
+template class NumpyFileFactory<DetectorType::Jungfrau, uint16_t>;
+
 
-    // {dtype, fortran_order, shape};
-};

python/aare/File.py

@@ -21,7 +21,7 @@ class File:
             raise FileNotFoundError(f"File not found: {path}")
         ext = os.path.splitext(path)[1]
 
-        if ext not in (".raw", ".json"):
+        if ext not in (".raw", ".json", ".npy"):
             raise ValueError(f"Invalid file extension: {ext}")
         
         if ext == ".json":
@@ -33,6 +33,17 @@ class File:
                 bitdepth = 16
             else:
                 bitdepth = master_data["Dynamic Range"]
+        elif ext == ".npy":
+            # TODO: find solution for this. maybe add a None detector type
+            detector = "Jungfrau"
+            with open(path, "rb") as fobj:
+                import numpy as np
+                version = np.lib.format.read_magic(fobj)
+                # find what function to call based on the version
+                func_name = 'read_array_header_' + '_'.join(str(v) for v in version)
+                func = getattr(np.lib.format, func_name)
+                header = func(fobj)
+                bitdepth = header[2].itemsize * 8
         else:
             NotImplementedError("Raw file not implemented yet")
 

python/example/read_frame.py

@@ -1,7 +1,32 @@
+import os
+from pathlib import Path
 from aare import File, Frame
+import numpy as np
 
 if __name__ == "__main__":
-    file = File("/home/bb/github/aare/data/jungfrau_single_master_0.json")
+
+
+    #get env variable
+    root_dir = Path(os.environ.get("PROJECT_ROOT_DIR"))
+
+    # read JSON master file
+    data_path = str(root_dir / "data"/"jungfrau_single_master_0.json")
+
+    file = File(data_path)
     frame = file.get_frame(0)
     print(frame.rows, frame.cols)
-    print(frame.get(0,0))
+    print(frame.get(0,0))
+
+    # read Numpy file
+
+    data_path = str(root_dir / "data"/"test_numpy_file.npy")
+    file = File(data_path)
+    frame = file.get_frame(0)
+    print(frame.rows, frame.cols)
+    print(frame.get(0,0))
+    
+    arr = np.array(frame.get_array())
+    print(arr)
+    print(arr.shape)
+    
+    print(np.array_equal(arr, np.load(data_path)[0]))

python/src/bindings.cpp

@@ -1,6 +1,7 @@
 #include <cstdint>
 #include <filesystem>
 #include <pybind11/pybind11.h>
+#include <pybind11/stl.h>
 #include <string>
 
 #include "aare/defs.hpp"
@@ -27,10 +28,13 @@ PYBIND11_MODULE(_aare, m) {
     py::class_<Frame<uint16_t>>(m, "_Frame16")
         .def(py::init<std::byte*, ssize_t, ssize_t>())
         .def("get", &Frame<uint16_t>::get)
+        .def("get_array", &Frame<uint16_t>::get_array)
         .def_property_readonly("rows", &Frame<uint16_t>::rows)
         .def_property_readonly("cols", &Frame<uint16_t>::cols)
         .def_property_readonly("bitdepth", &Frame<uint16_t>::bitdepth);
 
+    
+