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renamed NumpyFile member variable header to m_header

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This commit is contained in:
Erik Frojdh 2024-04-02 14:36:55 +02:00
parent 9854500a6f
commit 390ceb02d8
3 changed files with 34 additions and 34 deletions
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20
file_io/include/aare/NumpyFile.hpp
View File

@ -11,7 +11,9 @@ namespace aare{
class NumpyFile : public FileInterface { class NumpyFile : public FileInterface {
FILE *fp = nullptr; FILE *fp = nullptr;
size_t initial_header_len = 0; size_t initial_header_len = 0;
size_t current_frame{};
void get_frame_into(size_t, std::byte *);
Frame get_frame(size_t frame_number);
public: public:
@ -30,12 +32,12 @@ class NumpyFile : public FileInterface {
size_t pixels() override; size_t pixels() override;
void seek(size_t frame_number) override { this->current_frame = frame_number; } void seek(size_t frame_number) override { this->current_frame = frame_number; }
size_t tell() override { return this->current_frame; } size_t tell() override { return this->current_frame; }
size_t total_frames() const override { return header.shape[0]; } size_t total_frames() const override { return m_header.shape[0]; }
ssize_t rows() const override { return header.shape[1]; } ssize_t rows() const override { return m_header.shape[1]; }
ssize_t cols() const override { return header.shape[2]; } ssize_t cols() const override { return m_header.shape[2]; }
ssize_t bitdepth() const override { return header.dtype.bitdepth(); } ssize_t bitdepth() const override { return m_header.dtype.bitdepth(); }
header_t header; header_t m_header;
uint8_t major_ver_{}; uint8_t major_ver_{};
uint8_t minor_ver_{}; uint8_t minor_ver_{};
uint32_t header_len{}; uint32_t header_len{};
@ -44,10 +46,8 @@ class NumpyFile : public FileInterface {
~NumpyFile(); ~NumpyFile();
private:
size_t current_frame{};
void get_frame_into(size_t, std::byte *);
Frame get_frame(size_t frame_number);
}; };
} // namespace aare } // namespace aare

46
file_io/src/NumpyFile.cpp
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@ -4,25 +4,25 @@
namespace aare{ namespace aare{
NumpyFile::NumpyFile(const std::filesystem::path& fname) { NumpyFile::NumpyFile(const std::filesystem::path& fname) {
this->m_fname = fname; m_fname = fname;
fp = fopen(this->m_fname.c_str(), "rb"); fp = fopen(m_fname.c_str(), "rb");
} }
NumpyFile::NumpyFile(FileConfig config, header_t header) { NumpyFile::NumpyFile(FileConfig config, header_t header) {
this->mode = "w"; mode = "w";
this->m_fname = config.fname; m_fname = config.fname;
this->m_bitdepth = config.dtype.bitdepth(); m_bitdepth = config.dtype.bitdepth();
this->m_rows = config.rows; m_rows = config.rows;
this->m_cols = config.cols; m_cols = config.cols;
this->header = header; m_header = header;
this->header.shape = {0, config.rows, config.cols}; m_header.shape = {0, config.rows, config.cols};
fp = fopen(this->m_fname.c_str(), "wb"); fp = fopen(m_fname.c_str(), "wb");
if (!fp) { if (!fp) {
throw std::runtime_error(fmt::format("Could not open: {} for reading", this->m_fname.c_str())); throw std::runtime_error(fmt::format("Could not open: {} for reading", m_fname.c_str()));
} }
this->initial_header_len = initial_header_len =
aare::NumpyHelpers::write_header(std::filesystem::path(this->m_fname.c_str()), this->header); aare::NumpyHelpers::write_header(std::filesystem::path(m_fname.c_str()), header);
} }
void NumpyFile::write(Frame &frame) { void NumpyFile::write(Frame &frame) {
@ -39,7 +39,7 @@ void NumpyFile::write(Frame &frame) {
Frame NumpyFile::get_frame(size_t frame_number) { Frame NumpyFile::get_frame(size_t frame_number) {
Frame frame(header.shape[1], header.shape[2], header.dtype.bitdepth()); Frame frame(m_header.shape[1], m_header.shape[2], m_header.dtype.bitdepth());
get_frame_into(frame_number, frame._get_data()); get_frame_into(frame_number, frame._get_data());
return frame; return frame;
} }
@ -47,7 +47,7 @@ void NumpyFile::get_frame_into(size_t frame_number, std::byte *image_buf) {
if (fp == nullptr) { if (fp == nullptr) {
throw std::runtime_error("File not open"); throw std::runtime_error("File not open");
} }
if (frame_number > header.shape[0]) { if (frame_number > m_header.shape[0]) {
throw std::runtime_error("Frame number out of range"); throw std::runtime_error("Frame number out of range");
} }
fseek(fp, header_size + frame_number * bytes_per_frame(), SEEK_SET); fseek(fp, header_size + frame_number * bytes_per_frame(), SEEK_SET);
@ -55,24 +55,24 @@ void NumpyFile::get_frame_into(size_t frame_number, std::byte *image_buf) {
} }
size_t NumpyFile::pixels() { size_t NumpyFile::pixels() {
return std::accumulate(header.shape.begin() + 1, header.shape.end(), 1, std::multiplies<uint64_t>()); return std::accumulate(m_header.shape.begin() + 1, m_header.shape.end(), 1, std::multiplies<uint64_t>());
}; };
size_t NumpyFile::bytes_per_frame() { return header.dtype.bitdepth() / 8 * pixels(); }; size_t NumpyFile::bytes_per_frame() { return m_header.dtype.bitdepth() / 8 * pixels(); };
std::vector<Frame> NumpyFile::read(size_t n_frames) { std::vector<Frame> NumpyFile::read(size_t n_frames) {
// TODO: implement this in a more efficient way // TODO: implement this in a more efficient way
std::vector<Frame> frames; std::vector<Frame> frames;
for (size_t i = 0; i < n_frames; i++) { for (size_t i = 0; i < n_frames; i++) {
frames.push_back(this->get_frame(this->current_frame)); frames.push_back(get_frame(current_frame));
this->current_frame++; current_frame++;
} }
return frames; return frames;
} }
void NumpyFile::read_into(std::byte *image_buf, size_t n_frames) { void NumpyFile::read_into(std::byte *image_buf, size_t n_frames) {
// TODO: implement this in a more efficient way // TODO: implement this in a more efficient way
for (size_t i = 0; i < n_frames; i++) { for (size_t i = 0; i < n_frames; i++) {
this->get_frame_into(this->current_frame++, image_buf); get_frame_into(current_frame++, image_buf);
image_buf += this->bytes_per_frame(); image_buf += bytes_per_frame();
} }
} }
@ -84,11 +84,11 @@ NumpyFile::~NumpyFile() {
size_t data_size = file_size - initial_header_len; size_t data_size = file_size - initial_header_len;
size_t n_frames = data_size / bytes_per_frame(); size_t n_frames = data_size / bytes_per_frame();
// update number of frames in header (first element of shape) // update number of frames in header (first element of shape)
this->header.shape[0] = n_frames; m_header.shape[0] = n_frames;
fseek(fp, 0, SEEK_SET); fseek(fp, 0, SEEK_SET);
// create string stream to contain header // create string stream to contain header
std::stringstream ss; std::stringstream ss;
aare::NumpyHelpers::write_header(ss, this->header); aare::NumpyHelpers::write_header(ss, m_header);
std::string header_str = ss.str(); std::string header_str = ss.str();
// write header // write header
fwrite(header_str.c_str(), header_str.size(), 1, fp); fwrite(header_str.c_str(), header_str.size(), 1, fp);

2
file_io/src/NumpyFileFactory.cpp
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@ -70,7 +70,7 @@ void NumpyFileFactory::parse_metadata(FileInterface *_file) {
auto dim = static_cast<unsigned long>(std::stoul(item)); auto dim = static_cast<unsigned long>(std::stoul(item));
shape.push_back(dim); shape.push_back(dim);
} }
file->header = {dtype, fortran_order, shape}; file->m_header = {dtype, fortran_order, shape};
} }
NumpyFile *NumpyFileFactory::load_file_read() { NumpyFile *NumpyFileFactory::load_file_read() {