Merge pull request #39 from slsdetectorgroup/namespace

moving code into aare:: namespace

core/include/aare/Frame.hpp

@@ -14,6 +14,8 @@
  * should be able to work with streams coming from files or network
  */
 
+namespace aare {
+
 class Frame {
     ssize_t m_rows;
     ssize_t m_cols;
@@ -65,3 +67,4 @@ class Frame {
 };
 
 
+} // namespace aare

core/include/aare/NDArray.hpp

@@ -18,6 +18,7 @@ TODO! Add expression templates for operators
 #include <iostream>
 #include <numeric>
 
+namespace aare {
 
 template <typename T, ssize_t Ndim = 2> class NDArray {
   public:
@@ -427,3 +428,4 @@ NDArray<T, Ndim> load(const std::string &pathname,
 }
 
 
+} // namespace aare

core/include/aare/NDView.hpp

@@ -6,6 +6,8 @@
 #include <numeric>
 #include <vector>
 
+namespace aare {
+
 template <ssize_t Ndim> using Shape = std::array<ssize_t, Ndim>;
 
 template <ssize_t Dim = 0, typename Strides> ssize_t element_offset(const Strides &) { return 0; }
@@ -125,3 +127,4 @@ template <typename T, ssize_t Ndim=2> class NDView {
 
 template class NDView<uint16_t, 2>;
 
+} // namespace aare

core/include/aare/VariableSizeClusterFinder.hpp

@@ -9,7 +9,7 @@
 #include "aare/NDArray.hpp"
 
 const int MAX_CLUSTER_SIZE = 200;
-namespace pl {
+namespace aare {
 
 template <typename T> class ClusterFinder {
   public:
@@ -307,4 +307,4 @@ template <typename T> void ClusterFinder<T>::store_clusters() {
 
 }
 
-} // namespace pl
+} // namespace aare

core/include/aare/defs.hpp

@@ -9,6 +9,8 @@
 #include <fmt/format.h>
 #include <variant>
 
+namespace aare{
+
 typedef struct {
     uint64_t frameNumber;
     uint32_t expLength;
@@ -75,4 +77,6 @@ const char big_endian_char = '>';
 const char no_endian_char = '|';
 
 const std::array<char, 3> endian_chars = {little_endian_char, big_endian_char, no_endian_char};
-const std::array<char, 4> numtype_chars = {'f', 'i', 'u', 'c'};
+const std::array<char, 4> numtype_chars = {'f', 'i', 'u', 'c'};
+
+} // namespace aare

core/src/Frame.cpp

@@ -2,6 +2,9 @@
 #include "aare/utils/logger.hpp"
 #include <iostream>
 #include <cassert>
+
+namespace aare {
+
 Frame::Frame(std::byte* bytes, ssize_t rows, ssize_t cols, ssize_t bitdepth):
   m_rows(rows), m_cols(cols), m_bitdepth(bitdepth) {
     m_data = new std::byte[rows*cols*bitdepth/8];
@@ -48,4 +51,4 @@ template void Frame::set(int row, int col, uint32_t data);
 //   return array;
 // }
 
-
+} // namespace aare

core/src/defs.cpp

@@ -1,5 +1,7 @@
 #include "aare/defs.hpp"
 
+namespace aare {
+
 template <> std::string toString(DetectorType type) {
     switch (type) {
     case DetectorType::Jungfrau:
@@ -45,4 +47,6 @@ template <> TimingMode StringTo(std::string mode) {
     }
 }
 
-// template <> TimingMode StringTo<TimingMode>(std::string mode);
+// template <> TimingMode StringTo<TimingMode>(std::string mode);
+
+} // namespace aare

core/test/NDArray.test.cpp

@@ -3,8 +3,10 @@
 #include <array>
 
 
-// using reuss::DataSpan;
-// using reuss::Shape;
+using aare::NDArray;
+using aare::NDView;
+using aare::Shape;
+
 
 TEST_CASE("Initial size is zero if no size is specified")
 {

core/test/NDView.test.cpp

@@ -4,7 +4,8 @@
 #include <iostream>
 #include <vector>
 
-
+using aare::NDView;
+using aare::Shape;
 
 TEST_CASE("Element reference 1D") {
     std::vector<int> vec;

core/test/defs.test.cpp

@@ -4,5 +4,5 @@
 TEST_CASE("Enum to string conversion"){
     //By the way I don't think the enum string conversions should be in the defs.hpp file
     //but let's use this to show a test
-    REQUIRE(toString(DetectorType::Jungfrau) == "Jungfrau");
+    REQUIRE(toString(aare::DetectorType::Jungfrau) == "Jungfrau");
 }

core/test/wrappers.test.cpp

@@ -4,6 +4,10 @@
 #include <catch2/catch_test_macros.hpp>
 #include <cstdint>
 
+using aare::Frame;
+using aare::NDView;
+using aare::NDArray;
+
 TEST_CASE("Frame") {
     auto data = new uint16_t[100];
     for (int i = 0; i < 100; i++) {

examples/json_example.cpp

@@ -5,6 +5,9 @@
 
 #define AARE_ROOT_DIR_VAR "PROJECT_ROOT_DIR"
 
+using aare::File;
+using aare::Frame;
+
 void test(File& f, int frame_number) {
     std::cout << "frame number: " << frame_number << std::endl;
     Frame frame = f.iread(frame_number);

examples/multiport_example.cpp

@@ -6,6 +6,9 @@
 
 #define AARE_ROOT_DIR_VAR "PROJECT_ROOT_DIR"
 
+using aare::File;
+using aare::Frame;
+
 void test(File &f, int frame_number) {
     std::cout << "frame number: " << frame_number << std::endl;
     Frame frame = f.iread(frame_number);

examples/mythen_example.cpp

@@ -5,6 +5,9 @@
 
 #define AARE_ROOT_DIR_VAR "PROJECT_ROOT_DIR"
 
+using aare::File;
+using aare::Frame;
+
 void test1(File &f, int frame_number) {
     std::cout << "frame number: " << frame_number << std::endl;
     Frame frame = f.iread(frame_number);

examples/numpy_read_example.cpp

@@ -4,6 +4,9 @@
 
 #define AARE_ROOT_DIR_VAR "PROJECT_ROOT_DIR"
 
+using aare::File;
+using aare::Frame;
+
 void test(File& f, int frame_number) {
     std::cout << "frame number: " << frame_number << std::endl;
     Frame frame = f.iread(frame_number);

examples/numpy_write_example.cpp

@@ -5,6 +5,10 @@
 
 #define AARE_ROOT_DIR_VAR "PROJECT_ROOT_DIR"
 
+using aare::File;
+using aare::FileConfig;
+using aare::Frame;
+
 
 int main() {
     auto path = std::filesystem::path("/tmp/test.npy");

examples/raw_example.cpp

@@ -5,6 +5,9 @@
 
 #define AARE_ROOT_DIR_VAR "PROJECT_ROOT_DIR"
 
+using aare::File;
+using aare::Frame;
+
 void test(File& f, int frame_number) {
     std::cout << "frame number: " << frame_number << std::endl;
     Frame frame = f.iread(frame_number);

file_io/include/aare/File.hpp

@@ -1,6 +1,6 @@
 #include "aare/FileInterface.hpp"
 
-
+namespace aare{
 class File {
   private:
     FileInterface *file_impl;
@@ -32,3 +32,5 @@ class File {
 
     ~File();
 };
+
+} // namespace aare

file_io/include/aare/FileFactory.hpp

@@ -4,6 +4,8 @@
 #include "aare/utils/logger.hpp"
 #include <filesystem>
 
+namespace aare{
+
 class FileFactory {
     // Class that will be used to create FileInterface objects
     // follows the factory pattern
@@ -35,3 +37,5 @@ class FileFactory {
     virtual void parse_fname(FileInterface *) = 0;
     virtual ~FileFactory() = default;
 };
+
+} // namespace aare

file_io/include/aare/FileInterface.hpp

@@ -6,6 +6,8 @@
 #include <filesystem>
 #include <vector>
 
+namespace aare {
+
 struct FileConfig {
     std::filesystem::path fname;
     aare::DType dtype = aare::DType(typeid(uint16_t));
@@ -93,3 +95,5 @@ class FileInterface {
     ssize_t m_cols{};
     ssize_t m_bitdepth{};
 };
+
+}

file_io/include/aare/NumpyFile.hpp

@@ -5,6 +5,8 @@
 #include <iostream>
 #include <numeric>
 
+namespace aare{
+
 class NumpyFile : public FileInterface {
     FILE *fp = nullptr;
     size_t initial_header_len = 0;
@@ -42,4 +44,6 @@ class NumpyFile : public FileInterface {
     size_t current_frame{};
     void get_frame_into(size_t, std::byte *);
     Frame get_frame(size_t frame_number);
-};
+};
+
+} // namespace aare

file_io/include/aare/NumpyFileFactory.hpp

@@ -4,7 +4,7 @@
 #include "aare/defs.hpp"
 #include <fstream>
 
-
+namespace aare {
 
 class NumpyFileFactory : public FileFactory {
   private:
@@ -18,4 +18,6 @@ class NumpyFileFactory : public FileFactory {
     NumpyFile* load_file_write(FileConfig) override;
     void parse_fname(FileInterface*)override{};
 
-};
+};
+
+} // namespace aare

file_io/include/aare/RawFile.hpp

@@ -4,6 +4,8 @@
 #include "aare/SubFile.hpp"
 #include "aare/defs.hpp"
 
+namespace aare {
+
 class RawFile : public FileInterface {
 
     using config = RawFileConfig;
@@ -69,4 +71,6 @@ class RawFile : public FileInterface {
     size_t current_frame{};
     void get_frame_into(size_t frame_number, std::byte *image_buf);
     Frame get_frame(size_t frame_number);
-};
+};
+
+}

file_io/include/aare/RawFileFactory.hpp

@@ -1,5 +1,8 @@
 #include "aare/FileFactory.hpp"
 #include "aare/RawFile.hpp"
+
+namespace aare {
+
 class RawFileFactory : public FileFactory {
   private:
     void parse_json_metadata(RawFile *file);
@@ -16,3 +19,5 @@ class RawFileFactory : public FileFactory {
     sls_detector_header read_header(const std::filesystem::path &fname);
     void find_geometry(FileInterface *);
 };
+
+}

file_io/include/aare/SubFile.hpp

@@ -5,6 +5,8 @@
 #include <map>
 #include <variant>
 
+namespace aare {
+
 class SubFile {
   protected:
     FILE *fp = nullptr;
@@ -42,3 +44,5 @@ class SubFile {
     inline size_t bytes_per_part() { return (m_bitdepth / 8) * m_rows * m_cols; }
     inline size_t pixels_per_part() { return m_rows * m_cols; }
 };
+
+} // namespace aare

file_io/include/aare/helpers.hpp

@@ -4,5 +4,8 @@
 #include <filesystem>
 #include <fmt/core.h>
 
+namespace aare {
+
 bool is_master_file(std::filesystem::path fpath);
 
+}

file_io/src/File.cpp

@@ -2,6 +2,8 @@
 #include "aare/FileFactory.hpp"
 #include "aare/utils/logger.hpp"
 
+namespace aare {
+
 File::File(std::filesystem::path fname, std::string mode, FileConfig cfg) {
     file_impl = FileFactory::load_file(fname, mode, cfg);
 }
@@ -30,3 +32,5 @@ File::File(File &&other) {
 }
 
 // write move assignment operator
+
+}

file_io/src/FileFactory.cpp

@@ -6,6 +6,8 @@
 #include "aare/utils/logger.hpp"
 #include <iostream>
 
+namespace aare {
+
 FileFactory *FileFactory::get_factory(std::filesystem::path fpath) {
     if (fpath.extension() == ".raw" || fpath.extension() == ".json"){
         aare::logger::debug("Loading",fpath.extension(),"file");
@@ -18,11 +20,12 @@ FileFactory *FileFactory::get_factory(std::filesystem::path fpath) {
     // check if extension is numpy
     else if (fpath.extension() == ".npy") {
         aare::logger::debug("Loading numpy file");
-        return new NumpyFileFactory(fpath);
+        return new aare::NumpyFileFactory(fpath);
     }
 
     throw std::runtime_error("Unsupported file type");
 }
 
+} // namespace aare
 
 

file_io/src/NumpyFile.cpp

@@ -1,6 +1,8 @@
 
 #include "aare/NumpyFile.hpp"
 
+namespace aare{
+
 void NumpyFile::write(Frame &frame) {
     if (fp == nullptr) {
         throw std::runtime_error("File not open");
@@ -96,4 +98,6 @@ NumpyFile::~NumpyFile() {
         fclose(fp);
         
     }
-}
+}
+
+} // namespace aare

file_io/src/NumpyFileFactory.cpp

@@ -1,7 +1,7 @@
 #include "aare/NumpyFileFactory.hpp"
 #include "aare/NumpyHelpers.hpp"
 
-using namespace aare;
+namespace aare {
 
 NumpyFileFactory::NumpyFileFactory(std::filesystem::path fpath) { this->m_fpath = fpath; }
 void NumpyFileFactory::parse_metadata(FileInterface *_file) {
@@ -86,3 +86,5 @@ NumpyFile *NumpyFileFactory::load_file_write(FileConfig config) {
 
     return file;
 };
+
+} // namespace aare

file_io/src/RawFile.cpp

@@ -1,6 +1,8 @@
 #include "aare/RawFile.hpp"
 #include "aare/utils/logger.hpp"
 
+namespace aare{
+
 Frame RawFile::get_frame(size_t frame_number) {
     auto f = Frame(this->m_rows, this->m_cols, this->m_bitdepth);
     std::byte *frame_buffer = f._get_data();
@@ -77,3 +79,5 @@ RawFile::~RawFile() {
         }
     }
 }
+
+} // namespace aare

file_io/src/RawFileFactory.cpp

@@ -11,6 +11,8 @@
 
 using json = nlohmann::json;
 
+namespace aare {
+
 RawFileFactory::RawFileFactory(std::filesystem::path fpath) {
     if (not is_master_file(fpath))
         throw std::runtime_error("Json file is not a master file");
@@ -180,3 +182,5 @@ void RawFileFactory::parse_fname(FileInterface *file) {
     pos = file->m_base_name.find("_master_");
     file->m_base_name.erase(pos);
 }
+
+} // namespace aare

file_io/src/SubFile.cpp

@@ -3,6 +3,8 @@
 #include <iostream>
 // #include <filesystem>
 
+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;
@@ -97,3 +99,5 @@ size_t SubFile::frame_number(int frame_index) {
 
     return h.frameNumber;
 }
+
+} // namespace aare

file_io/src/helpers.cpp

@@ -1,5 +1,6 @@
 #include "aare/helpers.hpp"
 
+namespace aare {
 
 bool is_master_file(std::filesystem::path fpath) {
     std::string stem = fpath.stem();
@@ -9,3 +10,4 @@ bool is_master_file(std::filesystem::path fpath) {
         return false;
 }
 
+}// namespace aare

file_io/test/RawFile.test.cpp

@@ -5,6 +5,7 @@
 
 #include "test_config.hpp"
 
+using aare::File;
 
 TEST_CASE("Read number of frames from a jungfrau raw file") {