minor changes, preparing for v0.8.2 release (#244)

Co-authored-by: Samuel Li <sam@cisl-m121a>

.github/workflows/clang-format.yml

@@ -22,9 +22,9 @@ jobs:
  steps:
  - uses: actions/checkout@v2
  - name: Run clang-format style check for C/C++ programs.
- uses: jidicula/clang-format-action@v4.8.0
+ uses: jidicula/clang-format-action@v4.13.0
  with:
- clang-format-version: '14'
+ clang-format-version: '18'
  check-path: ${{ matrix.path['check'] }}
  exclude-regex: ${{ matrix.path['exclude'] }}
  fallback-style: 'Chromium' # optional

CMakeLists.txt

@@ -2,7 +2,7 @@
 
 cmake_minimum_required(VERSION 3.14)
 
-project(SPERR VERSION 0.8.1 LANGUAGES CXX DESCRIPTION "Lossy Scientific Compression with SPERR")
+project(SPERR VERSION 0.8.2 LANGUAGES CXX DESCRIPTION "Lossy Scientific Compression with SPERR")
 
 if(NOT CMAKE_CXX_STANDARD)
  set(CMAKE_CXX_STANDARD "20" CACHE STRING "Choose the C++ Standard to use." FORCE)

include/SPECK3D_INT.h

@@ -62,7 +62,7 @@ class SPECK3D_INT : public SPECK_INT<T> {
  virtual void m_process_S(size_t idx1, size_t idx2, size_t& counter, bool) = 0;
  virtual void m_process_P(size_t i, size_t m, size_t& c, bool) = 0; // Called by `m_code_S()`.
  virtual void m_process_P_lite(size_t idx) = 0; // Called by `m_sorting_pass()` directly.
- virtual void m_additional_initialization(){};  // empty by default
+ virtual void m_additional_initialization() {}; // empty by default
 
  void m_code_S(size_t idx1, size_t idx2);
  auto m_partition_S_XYZ(Set3D, uint16_t) const -> std::tuple<std::array<Set3D, 8>, uint16_t>;

include/SPERR3D_Stream_Tools.h

@@ -56,8 +56,9 @@ class SPERR3D_Stream_Tools {
  // Given the header of a bitstream and a desired percentage to truncate, return an
  // updated header and a list of {offset, len} to access.
  // Note: this function assumes that the header is complete.
- auto m_progressive_helper(const void* header_buf, size_t buf_len, unsigned pct) const
- -> std::tuple<vec8_type, std::vector<size_t>>;
+ auto m_progressive_helper(const void* header_buf,
+ size_t buf_len,
+ unsigned pct) const -> std::tuple<vec8_type, std::vector<size_t>>;
 };
 
 } // End of namespace sperr

include/sperr_helper.h

@@ -136,8 +136,9 @@ auto read_whole_file(std::string filename) -> vec_type<T>;
 // Read sections of a file (extract sections from a memory buffer), and append those sections
 // to the end of `dst`. The read from file version avoids reading not-requested sections.
 // The sections are defined by pairs of offsets and lengths, both in number of bytes.
-auto read_sections(std::string filename, const std::vector<size_t>& sections, vec8_type& dst)
- -> RTNType;
+auto read_sections(std::string filename,
+ const std::vector<size_t>& sections,
+ vec8_type& dst) -> RTNType;
 auto extract_sections(const void* buf,
  size_t buf_len,
  const std::vector<size_t>& sections,

src/Conditioner.cpp

@@ -63,8 +63,9 @@ auto sperr::Conditioner::condition(vecd_type& buf, dims_type dims) -> condi_type
  return header;
 }
 
-auto sperr::Conditioner::inverse_condition(vecd_type& buf, dims_type dims, condi_type header)
- -> RTNType
+auto sperr::Conditioner::inverse_condition(vecd_type& buf,
+ dims_type dims,
+ condi_type header) -> RTNType
 {
  // unpack meta bit fields
  auto meta = sperr::unpack_8_booleans(header[0]);

src/SPECK_INT.cpp

@@ -410,7 +410,7 @@ void sperr::SPECK_INT<T>::m_refinement_pass_decode()
  goto INITIALIZE_NEWLY_FOUND_POINTS_LABEL; // <-- Point 4
  }
  }
- }  // Finish the case where `m_threshold >= 2`.
+ } // Finish the case where `m_threshold >= 2`.
  else { // Start the case where `m_threshold == 1`.
  for (size_t i = 0; i < bits_x64; i += 64) {
  auto value = m_LSP_mask.rlong(i);

src/SPERR3D_OMP_C.cpp

@@ -259,7 +259,9 @@ auto sperr::SPERR3D_OMP_C::m_gather_chunk(const T* vol,
  // Will be subject to Named Return Value Optimization.
  return chunk_buf;
 }
-template auto sperr::SPERR3D_OMP_C::m_gather_chunk(const float*, dims_type, std::array<size_t, 6>)
- -> vecd_type;
-template auto sperr::SPERR3D_OMP_C::m_gather_chunk(const double*, dims_type, std::array<size_t, 6>)
- -> vecd_type;
+template auto sperr::SPERR3D_OMP_C::m_gather_chunk(const float*,
+ dims_type,
+ std::array<size_t, 6>) -> vecd_type;
+template auto sperr::SPERR3D_OMP_C::m_gather_chunk(const double*,
+ dims_type,
+ std::array<size_t, 6>) -> vecd_type;

src/SPERR3D_Stream_Tools.cpp

@@ -104,8 +104,8 @@ auto sperr::SPERR3D_Stream_Tools::get_stream_header(const void* p) const -> SPER
  return header;
 }
 
-auto sperr::SPERR3D_Stream_Tools::progressive_read(const std::string& filename, unsigned pct) const
- -> vec8_type
+auto sperr::SPERR3D_Stream_Tools::progressive_read(const std::string& filename,
+  unsigned pct) const -> vec8_type
 {
  // Read the header of this bitstream.
  auto vec20 = sperr::read_n_bytes(filename, 20);

src/sperr_helper.cpp

@@ -333,8 +333,9 @@ auto sperr::write_n_bytes(std::string filename, size_t n_bytes, const void* buff
  return RTNType::Good;
 }
 
-auto sperr::read_sections(std::string filename, const std::vector<size_t>& sections, vec8_type& dst)
- -> RTNType
+auto sperr::read_sections(std::string filename,
+ const std::vector<size_t>& sections,
+ vec8_type& dst) -> RTNType
 {
  // Calculate the farthest file location to be read.
  size_t far = 0;
@@ -494,8 +495,10 @@ auto sperr::calc_stats(const T* arr1, const T* arr2, size_t arr_len, size_t omp_
  return {rmse, linfty, psnr, arr1min, arr1max};
 }
 template auto sperr::calc_stats(const float*, const float*, size_t, size_t) -> std::array<float, 5>;
-template auto sperr::calc_stats(const double*, const double*, size_t, size_t)
- -> std::array<double, 5>;
+template auto sperr::calc_stats(const double*,
+ const double*,
+ size_t,
+ size_t) -> std::array<double, 5>;
 
 template <typename T>
 auto sperr::kahan_summation(const T* arr, size_t len) -> T
@@ -514,8 +517,8 @@ auto sperr::kahan_summation(const T* arr, size_t len) -> T
 template auto sperr::kahan_summation(const float*, size_t) -> float;
 template auto sperr::kahan_summation(const double*, size_t) -> double;
 
-auto sperr::chunk_volume(dims_type vol_dim, dims_type chunk_dim)
- -> std::vector<std::array<size_t, 6>>
+auto sperr::chunk_volume(dims_type vol_dim,
+  dims_type chunk_dim) -> std::vector<std::array<size_t, 6>>
 {
  // Step 1: figure out how many segments are there along each axis.
  auto n_segs = std::array<size_t, 3>();

utilities/sperr2d.cpp

@@ -220,6 +220,13 @@ int main(int argc, char* argv[])
  std::cout << "SPERR needs an output destination when decoding!" << std::endl;
  return __LINE__;
  }
+ // Print a warning message if there's no output specified
+ if (cflag && bitstream.empty())
+ std::cout << "Warning: no output file provided. Consider using --bitstream option."
+ << std::endl;
+ if (dflag && decomp_f64.empty() && decomp_f32.empty() && decomp_lowres_f64.empty() &&
+ decomp_lowres_f32.empty())
+ std::cout << "Warning: no output file provided." << std::endl;
 
  //
  // Really starting the real work!

utilities/sperr3d.cpp

@@ -12,8 +12,9 @@
 
 // This functions takes in a filename, and a full resolution. It then creates a list of
 // filenames, each has the coarsened resolution appended.
-auto create_filenames(std::string name, sperr::dims_type vdims, sperr::dims_type cdims)
- -> std::vector<std::string>
+auto create_filenames(std::string name,
+ sperr::dims_type vdims,
+ sperr::dims_type cdims) -> std::vector<std::string>
 {
  auto filenames = std::vector<std::string>();
  auto resolutions = sperr::coarsened_resolutions(vdims, cdims);
@@ -254,6 +255,13 @@ int main(int argc, char* argv[])
  return __LINE__ % 256;
  }
  }
+ // Print a warning message if there's no output specified
+ if (cflag && bitstream.empty())
+ std::cout << "Warning: no output file provided. Consider using --bitstream option."
+ << std::endl;
+ if (dflag && decomp_f64.empty() && decomp_f32.empty() && decomp_lowres_f64.empty() &&
+ decomp_lowres_f32.empty())
+ std::cout << "Warning: no output file provided." << std::endl;
 
  //
  // Really starting the real work!