detectors/aare
25
0
Fork 0
mirror of https://github.com/slsdetectorgroup/aare.git synced 2025-06-23 11:57:58 +02:00
Code Issues Actions Packages Releases Activity

format headers

Browse Source
This commit is contained in:
Bechir Braham
2024-04-03 14:53:06 +02:00
parent 76c0f7a757
commit 9e96f8b150
19 changed files with 296 additions and 400 deletions
Download Patch File Download Diff File Expand all files Collapse all files

9
file_io/include/aare/File.hpp
View File

@ -1,7 +1,7 @@
#pragma once
#include "aare/FileInterface.hpp"
namespace aare{
namespace aare {
class File {
private:
FileInterface *file_impl;
@ -12,8 +12,8 @@ class File {
// - w writing (overwrites existing file)
// - a appending (appends to existing file)
// TODO! do we need to support w+, r+ and a+?
File(std::filesystem::path fname, std::string mode,FileConfig cfg = {});
void write(Frame& frame);
File(std::filesystem::path fname, std::string mode, FileConfig cfg = {});
void write(Frame &frame);
Frame read();
Frame iread(size_t frame_number);
std::vector<Frame> read(size_t n_frames);
@ -27,10 +27,9 @@ class File {
size_t total_frames() const;
ssize_t rows() const;
ssize_t cols() const;
ssize_t bitdepth() const;
ssize_t bitdepth() const;
File(File &&other);
~File();
};

4
file_io/include/aare/FileFactory.hpp
View File

@ -4,7 +4,7 @@
#include "aare/utils/logger.hpp"
#include <filesystem>
namespace aare{
namespace aare {
class FileFactory {
// Class that will be used to create FileInterface objects
@ -17,7 +17,7 @@ class FileFactory {
// virtual int deleteFile() = 0;
static FileInterface *load_file(std::filesystem::path p, std::string mode, FileConfig cfg = {}) {
if ((mode == "r" or mode == "a") and not std::filesystem::exists(p)) {
throw std::runtime_error(LOCATION+"File does not exist");
throw std::runtime_error(LOCATION + "File does not exist");
}
auto factory = get_factory(p);

4
file_io/include/aare/FileInterface.hpp
View File

@ -1,7 +1,7 @@
#pragma once
#include "aare/DType.hpp"
#include "aare/Frame.hpp"
#include "aare/defs.hpp"
#include "aare/DType.hpp"
#include "aare/utils/logger.hpp"
#include <filesystem>
#include <vector>
@ -96,4 +96,4 @@ class FileInterface {
ssize_t m_bitdepth{};
};
}
} // namespace aare

21
file_io/include/aare/NumpyFile.hpp
View File

@ -1,19 +1,19 @@
#pragma once
#include "aare/DType.hpp"
#include "aare/FileInterface.hpp"
#include "aare/NumpyHelpers.hpp"
#include "aare/DType.hpp"
#include "aare/defs.hpp"
#include <filesystem>
#include <iostream>
#include <numeric>
#include <filesystem>
namespace aare{
namespace aare {
class NumpyFile : public FileInterface {
FILE *fp = nullptr;
size_t initial_header_len = 0;
size_t current_frame{};
std::filesystem::path m_fname;
std::filesystem::path m_fname;
uint32_t header_len{};
uint8_t header_len_size{};
ssize_t header_size{};
@ -26,9 +26,7 @@ class NumpyFile : public FileInterface {
Frame get_frame(size_t frame_number);
public:
NumpyFile(const std::filesystem::path& fname);
NumpyFile(const std::filesystem::path &fname);
NumpyFile(FileConfig, NumpyHeader);
void write(Frame &frame) override;
Frame read() override { return get_frame(this->current_frame++); }
@ -48,11 +46,10 @@ class NumpyFile : public FileInterface {
DType dtype() const { return m_header.dtype; }
std::vector<size_t> shape() const { return m_header.shape; }
//load the full numpy file into a NDArray
template<typename T, size_t NDim>
NDArray<T,NDim> load(){
NDArray<T,NDim> arr(make_shape<NDim>(m_header.shape));
// load the full numpy file into a NDArray
template <typename T, size_t NDim> NDArray<T, NDim> load() {
NDArray<T, NDim> arr(make_shape<NDim>(m_header.shape));
fseek(fp, header_size, SEEK_SET);
fread(arr.data(), sizeof(T), arr.size(), fp);
return arr;

7
file_io/include/aare/NumpyFileFactory.hpp
View File

@ -14,10 +14,9 @@ class NumpyFileFactory : public FileFactory {
public:
NumpyFileFactory(std::filesystem::path fpath);
void parse_metadata(FileInterface *_file) override{/*TODO! remove after refactor*/};
NumpyFile* load_file_read() override;
NumpyFile* load_file_write(FileConfig) override;
void parse_fname(FileInterface*)override{};
NumpyFile *load_file_read() override;
NumpyFile *load_file_write(FileConfig) override;
void parse_fname(FileInterface *) override{};
};
} // namespace aare

7
file_io/include/aare/NumpyHelpers.hpp
View File

@ -21,7 +21,7 @@ using shape_t = std::vector<size_t>;
struct NumpyHeader {
DType dtype{aare::DType::ERROR};
bool fortran_order{false};
shape_t shape{};
shape_t shape{};
std::string to_string() const;
};
@ -51,9 +51,8 @@ template <typename T, size_t N> bool in_array(T val, const std::array<T, N> &arr
bool is_digits(const std::string &str);
aare::DType parse_descr(std::string typestring);
size_t write_header(std::filesystem::path fname, const NumpyHeader &header) ;
size_t write_header(std::ostream &out, const NumpyHeader &header) ;
size_t write_header(std::filesystem::path fname, const NumpyHeader &header);
size_t write_header(std::ostream &out, const NumpyHeader &header);
} // namespace NumpyHelpers
} // namespace aare

13
file_io/include/aare/RawFile.hpp
View File

@ -9,10 +9,9 @@ namespace aare {
class RawFile : public FileInterface {
using config = RawFileConfig;
public:
std::filesystem::path m_fname; //TO be made private!
std::filesystem::path m_fname; // TO be made private!
void write(Frame &frame) override{};
Frame read() override { return get_frame(this->current_frame++); };
std::vector<Frame> read(size_t n_frames) override;
@ -27,10 +26,10 @@ class RawFile : public FileInterface {
size_t pixels() override { return m_rows * m_cols; }
// goto frame number
void seek(size_t frame_number) override{ this->current_frame = frame_number; };
void seek(size_t frame_number) override { this->current_frame = frame_number; };
// return the position of the file pointer (in number of frames)
size_t tell() override{ return this->current_frame; };
size_t tell() override { return this->current_frame; };
size_t n_subfiles;
size_t n_subfile_parts;
@ -66,8 +65,8 @@ class RawFile : public FileInterface {
size_t total_frames() const override { return m_total_frames; }
ssize_t rows() const override { return m_rows; }
ssize_t cols() const override{ return m_cols; }
ssize_t bitdepth() const override{ return m_bitdepth; }
ssize_t cols() const override { return m_cols; }
ssize_t bitdepth() const override { return m_bitdepth; }
private:
size_t current_frame{};
@ -75,4 +74,4 @@ class RawFile : public FileInterface {
Frame get_frame(size_t frame_number);
};
}
} // namespace aare

5
file_io/include/aare/RawFileFactory.hpp
View File

@ -10,10 +10,9 @@ class RawFileFactory : public FileFactory {
void parse_raw_metadata(RawFile *file);
public:
RawFileFactory(std::filesystem::path fpath);
RawFile *load_file_read() override;
RawFile *load_file_write(FileConfig) override{return new RawFile();};
RawFile *load_file_write(FileConfig) override { return new RawFile(); };
void parse_metadata(FileInterface *) override;
void parse_fname(FileInterface *) override;
void open_subfiles(FileInterface *);
@ -21,4 +20,4 @@ class RawFileFactory : public FileFactory {
void find_geometry(FileInterface *);
};
}
} // namespace aare