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read numpy file: works

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This commit is contained in:
Bechir
2024-03-08 18:26:02 +01:00
parent 146d2aed19
commit 765bbdc295
14 changed files with 154 additions and 67 deletions
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2
file_io/include/aare/File.hpp
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@ -15,6 +15,8 @@ class File {
virtual Frame<DataType>* get_frame(int frame_number) = 0;
private:
//comment
public:
std::filesystem::path fname;

3
file_io/include/aare/JsonFileFactory.hpp
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@ -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>*);

51
file_io/include/aare/NumpyFile.hpp
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@ -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(); };
};

20
file_io/include/aare/NumpyFileFactory.hpp
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@ -1,6 +1,7 @@
#include "aare/defs.hpp"
#pragma once
#include "aare/FileFactory.hpp"
#include "aare/NumpyFile.hpp"
#include "aare/defs.hpp"
#include <algorithm>
#include <array>
#include <filesystem>
@ -8,22 +9,17 @@
#include <string>
#include <unordered_map>
#include <vector>
#include <sstream>
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};
};