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use clang-tidy (#59)

Browse Source 
* use clang-tidy for Frame.cpp

* fixes for defs.cpp

* clang-tidy 6/45

* clang-tidy for core

* clang-tidy fixes: for hpp File,FileInterface,SubFile.cpp

* ci fixes

* fix build errors

* fix clang-tidy command ci

* fix clang-tidy ci

* clang-tidy for rawfile.cpp

* clang-tidy numpy helpers

* fix ci

* clang-tidy file_io

* clang-tidy file_io and core working

* zmqheader

* clagn-tidy: network_io,file_io,core

* clang-tidy working

* format

---------

Co-authored-by: Bechir <bechir.brahem420@gmail.com>
This commit is contained in:
Bechir Braham
2024-04-12 17:35:36 +02:00
committed by GitHub
parent eb7108b837
commit 9dfd388927
44 changed files with 1055 additions and 470 deletions
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62
file_io/src/SubFile.cpp
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@@ -7,12 +7,10 @@
namespace aare {
SubFile::SubFile(std::filesystem::path fname, DetectorType detector, ssize_t rows, ssize_t cols, uint16_t bitdepth) {
this->m_rows = rows;
this->m_cols = cols;
this->m_fname = fname;
this->m_bitdepth = bitdepth;
this->n_frames = std::filesystem::file_size(fname) / (sizeof(sls_detector_header) + rows * cols * bitdepth / 8);
SubFile::SubFile(const std::filesystem::path &fname, DetectorType detector, size_t rows, size_t cols, size_t bitdepth)
: m_bitdepth(bitdepth), m_fname(fname), m_rows(rows), m_cols(cols),
n_frames(std::filesystem::file_size(fname) / (sizeof(sls_detector_header) + rows * cols * bitdepth / 8)) {
if (read_impl_map.find({detector, bitdepth}) == read_impl_map.end()) {
auto error_msg = LOCATION + "No read_impl function found for detector: " + toString(detector) +
" and bitdepth: " + std::to_string(bitdepth);
@@ -21,8 +19,8 @@ SubFile::SubFile(std::filesystem::path fname, DetectorType detector, ssize_t row
this->read_impl = read_impl_map.at({detector, bitdepth});
}
size_t SubFile::get_part(std::byte *buffer, int frame_number) {
if (frame_number >= n_frames or frame_number < 0) {
size_t SubFile::get_part(std::byte *buffer, size_t frame_number) {
if (frame_number >= n_frames) {
throw std::runtime_error("Frame number out of range");
}
// TODO: find a way to avoid opening and closing the file for each frame
@@ -31,9 +29,11 @@ size_t SubFile::get_part(std::byte *buffer, int frame_number) {
if (!fp) {
throw std::runtime_error(fmt::format("Could not open: {} for reading", m_fname.c_str()));
}
fseek(fp, sizeof(sls_detector_header) + (sizeof(sls_detector_header) + bytes_per_part()) * frame_number, SEEK_SET);
fseek(fp, sizeof(sls_detector_header) + (sizeof(sls_detector_header) + bytes_per_part()) * frame_number, // NOLINT
SEEK_SET);
auto ret = (this->*read_impl)(buffer);
fclose(fp);
if (fclose(fp))
throw std::runtime_error(LOCATION + "Could not close file");
return ret;
}
@@ -42,24 +42,24 @@ size_t SubFile::read_impl_normal(std::byte *buffer) { return fread(buffer, this-
template <typename DataType> size_t SubFile::read_impl_reorder(std::byte *buffer) {
std::vector<DataType> tmp(this->pixels_per_part());
size_t rc = fread(reinterpret_cast<char *>(&tmp[0]), this->bytes_per_part(), 1, this->fp);
size_t const rc = fread(reinterpret_cast<char *>(tmp.data()), this->bytes_per_part(), 1, this->fp);
int adc_nr[32] = {300, 325, 350, 375, 300, 325, 350, 375, 200, 225, 250, 275, 200, 225, 250, 275,
100, 125, 150, 175, 100, 125, 150, 175, 0, 25, 50, 75, 0, 25, 50, 75};
int sc_width = 25;
int nadc = 32;
int pixels_per_sc = 5000;
std::array<int, 32> const adc_nr = {300, 325, 350, 375, 300, 325, 350, 375, 200, 225, 250, 275, 200, 225, 250, 275,
100, 125, 150, 175, 100, 125, 150, 175, 0, 25, 50, 75, 0, 25, 50, 75};
int const sc_width = 25;
int const nadc = 32;
int const pixels_per_sc = 5000;
auto dst = reinterpret_cast<DataType *>(buffer);
int pixel = 0;
for (int i = 0; i != pixels_per_sc; ++i) {
for (int i_adc = 0; i_adc != nadc; ++i_adc) {
int col = adc_nr[i_adc] + (i % sc_width);
int row;
int const col = adc_nr[i_adc] + (i % sc_width);
int row = 0;
if ((i_adc / 4) % 2 == 0)
row = 199 - int(i / sc_width);
row = 199 - (i / sc_width);
else
row = 200 + int(i / sc_width);
row = 200 + (i / sc_width);
dst[col + row * 400] = tmp[pixel];
pixel++;
@@ -72,15 +72,15 @@ template <typename DataType> size_t SubFile::read_impl_flip(std::byte *buffer) {
// read to temporary buffer
// TODO! benchmark direct reads
std::vector<std::byte> tmp(this->bytes_per_part());
size_t rc = fread(reinterpret_cast<char *>(&tmp[0]), this->bytes_per_part(), 1, this->fp);
size_t const rc = fread(reinterpret_cast<char *>(tmp.data()), this->bytes_per_part(), 1, this->fp);
// copy to place
const size_t start = this->m_cols * (this->m_rows - 1) * sizeof(DataType);
const size_t row_size = this->m_cols * sizeof(DataType);
auto dst = buffer + start;
auto src = &tmp[0];
auto *dst = buffer + start;
auto *src = tmp.data();
for (int i = 0; i != this->m_rows; ++i) {
for (size_t i = 0; i != this->m_rows; ++i) {
std::memcpy(dst, src, row_size);
dst -= row_size;
src += row_size;
@@ -89,16 +89,18 @@ template <typename DataType> size_t SubFile::read_impl_flip(std::byte *buffer) {
return rc;
};
size_t SubFile::frame_number(int frame_index) {
size_t SubFile::frame_number(size_t frame_index) {
sls_detector_header h{};
fp = fopen(this->m_fname.c_str(), "r");
if (!fp)
throw std::runtime_error(fmt::format("Could not open: {} for reading", m_fname.c_str()));
fseek(fp, (sizeof(sls_detector_header) + bytes_per_part()) * frame_index, SEEK_SET);
size_t rc = fread(reinterpret_cast<char *>(&h), sizeof(h), 1, fp);
fclose(fp);
throw std::runtime_error(LOCATION + fmt::format("Could not open: {} for reading", m_fname.c_str()));
fseek(fp, (sizeof(sls_detector_header) + bytes_per_part()) * frame_index, SEEK_SET); // NOLINT
size_t const rc = fread(reinterpret_cast<char *>(&h), sizeof(h), 1, fp);
if (rc != 1)
throw std::runtime_error("Could not read header from file");
throw std::runtime_error(LOCATION + "Could not read header from file");
if (fclose(fp)) {
throw std::runtime_error(LOCATION + "Could not close file");
}
return h.frameNumber;
}