libpressio version 0.6.0

Major Features
+ Implemented a set of helper functions for POSIX compatible IO and
  accompanying set of tests.

Minor Features
+ New pressio_data_num_elements to get the number of elements in a
  pressio_data buffer

Bug Fixes
+ previous pressio_data_has_data returned the opposite value of what it
  should have

CMakeLists.txt

@@ -1,5 +1,5 @@
 cmake_minimum_required(VERSION 3.14 FATAL_ERROR)
-project(libpressio VERSION "0.5.0" LANGUAGES CXX C)
+project(libpressio VERSION "0.6.0" LANGUAGES CXX C)
 
 enable_testing()
 set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
@@ -22,37 +22,46 @@ configure_file(
   )
 
 add_library(libpressio
-  #public headers
-  ./include/pressio_data.h
-  ./include/pressio_compressor.h
-  ./include/pressio.h
-  ./include/pressio_options.h
-  ./include/pressio_dtype.h
-  ./include/pressio_option.h
-  ./include/libpressio_ext/cpp/compressor.h
-
-  #implementations
+  #core implementation
+  ./src/pressio.cc
+  ./src/pressio_compressor.cc
+  ./src/pressio_data.cc
+  ./src/pressio_dtype.cc
   ./src/pressio_metrics.cc
-  ./src/pressio_options.cc
   ./src/pressio_option.cc
+  ./src/pressio_options.cc
+  ./src/pressio_options_iter.cc
+
+  #plugins
   ./src/plugins/compressors/compressor_base.cc
   ./src/plugins/compressors/sz_plugin.cc
   ./src/plugins/compressors/zfp_plugin.cc
+  ./src/plugins/metrics/composite.cc
   ./src/plugins/metrics/metrics_base.cc
-  ./src/plugins/metrics/time.cc
   ./src/plugins/metrics/size.cc
-  ./src/plugins/metrics/composite.cc
-  ./src/pressio_data.cc
-  ./src/pressio_dtype.cc
-  ./src/pressio.cc
-  ./src/pressio_compressor.cc
-  ./src/pressio_options_iter.cc
+  ./src/plugins/metrics/time.cc
+  ./src/plugins/io/posix.cc
 
+  #public headers
+  include/libpressio.h
+  include/libpressio_ext/compressors/sz.h
+  include/libpressio_ext/compressors/zfp.h
+  include/libpressio_ext/cpp/compressor.h
+  include/libpressio_ext/cpp/metrics.h
+  include/libpressio_ext/cpp/plugins.h
+  include/libpressio_ext/io/posix.h
+  include/pressio.h
+  include/pressio_compressor.h
+  include/pressio_data.h
+  include/pressio_dtype.h
+  include/pressio_metrics.h
+  include/pressio_option.h
+  include/pressio_options.h
+  include/pressio_options_iter.h
 
   #private headers
-  ./src/plugins.h
-  ./src/pressio_compressor_impl.h
-  ./src/pressio_options_impl.h
+  src/pressio_compressor_impl.h
+  src/pressio_options_impl.h
   )
 
 target_include_directories(libpressio

include/libpressio_ext/io/posix.h

@@ -0,0 +1,93 @@
+#include <stdio.h>
+
+#ifdef __cplusplus
+extern "C" {
+#endif 
+
+  struct pressio_data;
+
+  /** \file
+   *  \brief IO functions for POSIX compatible systems
+   *
+   *  NOTE attempting to read files written by different machines has undefined behavior!!
+   */
+
+#ifndef PRESSIO_POSIX_IO
+#define PRESSIO_POSIX_IO
+
+  /** read in a file from a POSIX FILE pointer
+   *
+   *  NOTE attempting to read files written by different machines has undefined behavior!!
+   *
+   * \param[in,out] dims description of the dimension of the data if it known or NULL.  
+   *            If dims is NULL, the remainder of the file will be read and the size of the resulting pointer will be a 1d pressio_byte_dtype of appropriate length
+   *            If dims is not null, The user SHOULD assume that the memory pointed to by this pointer has been "moved" in a C++11 sense and the user MUST not rely on its contents.
+   *            The implementation MAY return this pointer and reuse the underlying space if pressio_data_has_data(dims) returns true.
+   * \param[in,out] in_file an file open for reading seeked to the beginning of the data to read in.
+   * \returns a pointer to a (possibly new) pressio data structure.
+   *
+   */
+  struct pressio_data* pressio_io_data_fread(struct pressio_data* dims, FILE* in_file); 
+
+
+  /** read in a file from a POSIX file descriptor
+   *
+   *  NOTE attempting to read files written by different machines has undefined behavior!!
+   *
+   * \param[in,out] dims description of the dimension of the data if it known or NULL.  
+   *            If dims is NULL, the remainder of the file will be read and the size of the resulting pointer will be a 1d pressio_byte_dtype of appropriate length
+   *            If dims is not null, The user SHOULD assume that the memory pointed to by this pointer has been "moved" in a C++11 sense and the user MUST not rely on its contents.
+   *            The implementation MAY return this pointer and reuse the underlying space if pressio_data_has_data(ptr) returns true.
+   * \param[in,out] in_file an file open for reading seeked to the beginning of the data to read in.  If dims is not null, only pressio_data_get_bytes(dims) bytes are read.
+   * \returns a pointer to a (possibly new) pressio data structure.
+   *
+   */
+  struct pressio_data* pressio_io_data_read(struct pressio_data* dims, int in_filedes); 
+
+  /** read in a file at a specifed location on the file-system
+   *
+   *  NOTE attempting to read files written by different machines has undefined behavior!!
+   *
+   * \param[in,out] dims description of the dimension of the data if it known or NULL.  
+   *            If dims is NULL, the remainder of the file will be read and the size of the resulting pointer will be a 1d pressio_byte_dtype of appropriate length
+   *            If dims is not null, The user SHOULD assume that the memory pointed to by this pointer has been "moved" in a C++11 sense and the user MUST not rely on its contents.
+   *            The implementation MAY return this pointer and reuse the underlying space if pressio_data_has_data(dims) returns true.
+   * \param[in,out] in_file an file open for reading seeked to the beginning of the data to read in.
+   * \returns a pointer to a (possibly new) pressio data structure.
+   *
+   */
+  struct pressio_data* pressio_io_data_path_read(struct pressio_data* dims, const char* out_file); 
+
+  /** write in a file to the specified POSIX FILE pointer
+   *
+   * \param[in] data the data to be written.
+   * \param[in,out] out_file 
+   * \returns the number of bytes written
+   *
+   */
+  size_t pressio_io_data_fwrite(struct pressio_data* data, FILE* out_file); 
+
+  /** write in a file to the specified POSIX file descriptor
+   *
+   * \param[in] data the data to be written.
+   * \param[in,out] out_filedes the file descriptor to write to
+   * \returns the number of bytes written
+   *
+   */
+  size_t pressio_io_data_write(struct pressio_data* data, int out_filedes); 
+
+  /** write in a file to the specified path on the file-system
+   *
+   * \param[in] data the data to be written.
+   * \param[in,out] path the path to write to
+   * \returns the number of bytes written
+   *
+   */
+  size_t pressio_io_data_path_write(struct pressio_data* data, const char* path); 
+
+
+#endif /*PRESSIO_POSIX_IO*/
+
+#ifdef __cplusplus
+}
+#endif

include/pressio_data.h

@@ -137,6 +137,13 @@ size_t pressio_data_get_dimention(struct pressio_data const* data, size_t const
  */
 size_t pressio_data_get_bytes(struct pressio_data const* data);
 
+/**
+ * returns the total number of elements to represent the data
+ * \param[in] data the pressio data to query
+ * \returns the total number of elements to represent the data
+ */
+size_t pressio_data_num_elements(struct pressio_data const* data);
+
 #endif
 
 #ifdef __cplusplus

src/plugins/io/posix.cc

@@ -0,0 +1,90 @@
+#include <sys/stat.h>
+#include <unistd.h>
+#include <vector>
+#include "pressio_data.h"
+#include "libpressio_ext/io/posix.h"
+
+namespace {
+  std::vector<size_t> get_all_dimentions(struct pressio_data const* data) {
+    std::vector<size_t> dims;
+    if(data) {
+      for (size_t i = 0; i < pressio_data_num_dimentions(data); ++i) {
+        dims.emplace_back(pressio_data_get_dimention(data, i));
+      }
+    }
+    return dims;
+  }
+}
+
+extern "C" {
+
+  struct pressio_data* pressio_io_data_read(struct pressio_data* dims, int in_filedes) {
+    pressio_data* ret;
+    if(dims != nullptr) {
+      if(pressio_data_has_data(dims)) {
+        //re-use the buffer provided by dims
+        ret = dims;
+      } else {
+        //create a new buffer of the appropriate size
+        auto dtype = pressio_data_dtype(dims);
+        auto dims_v = get_all_dimentions(dims);
+        pressio_data_free(dims);
+        ret = pressio_data_new_owning(dtype, dims_v.size(), dims_v.data());
+      }
+    } else {
+      struct stat statbuf;
+      if(fstat(in_filedes, &statbuf)) {
+        return nullptr;
+      } 
+      size_t size = static_cast<size_t>(statbuf.st_size); 
+      ret = pressio_data_new_owning(pressio_byte_dtype, 1, &size);
+    }
+    read(in_filedes, pressio_data_ptr(ret, nullptr), pressio_data_get_bytes(ret));
+    return ret;
+  }
+
+  struct pressio_data* pressio_io_data_fread(struct pressio_data* dims, FILE* in_file) {
+    return pressio_io_data_read(dims, fileno(in_file));
+  }
+
+
+  struct pressio_data* pressio_io_data_path_read(struct pressio_data* dims, const char* path) {
+    FILE* in_file = fopen(path, "r");
+    if(in_file != nullptr) {
+      auto ret = pressio_io_data_fread(dims, in_file);
+      fclose(in_file);
+      return ret;
+    } else {
+      return nullptr;
+    }
+  }
+
+
+  size_t pressio_io_data_fwrite(struct pressio_data* data, FILE* out_file) {
+
+    return fwrite(pressio_data_ptr(data, nullptr),
+        pressio_dtype_size(pressio_data_dtype(data)),
+        pressio_data_num_elements(data),
+        out_file
+        );
+  }
+
+  size_t pressio_io_data_write(struct pressio_data* data, int out_filedes) {
+    return write(out_filedes,
+        pressio_data_ptr(data, nullptr),
+        pressio_data_get_bytes(data)
+        );
+  }
+
+  size_t pressio_io_path_path_write(struct pressio_data* data, const char* path) {
+    FILE* out_file = fopen(path, "w");
+    if(out_file != nullptr) {
+      auto ret = pressio_io_data_fwrite(data, out_file);
+      fclose(out_file);
+      return ret;
+    } else {
+      return 0;
+    }
+  }
+
+}

src/pressio_data.cc

@@ -11,12 +11,16 @@ void pressio_data_libc_free_fn(void* data, void*) {
 
 namespace {
   template <class T>
-  size_t data_size_in_bytes(pressio_dtype type, size_t dimentions, T const dims[]) {
+  size_t data_size_in_elements(size_t dimentions, T const dims[]) {
     size_t totalsize = 1;
     for (size_t i = 0; i < dimentions; ++i) {
       totalsize *= dims[i];
     }
-    return totalsize * pressio_dtype_size(type);
+    return totalsize;
+  }
+  template <class T>
+  size_t data_size_in_bytes(pressio_dtype type, size_t dimentions, T const dims[]) {
+    return data_size_in_elements(dimentions, dims) * pressio_dtype_size(type);
   }
 }
 
@@ -89,6 +93,10 @@ struct pressio_data {
     return data_size_in_bytes(data_dtype, dimentions(), dims.data());
   }
 
+  size_t num_elements() const {
+    return data_size_in_elements(dimentions(), dims.data());
+  }
+
   private:
   pressio_data(const pressio_dtype dtype,
       void* data,
@@ -158,7 +166,7 @@ pressio_dtype pressio_data_dtype(struct pressio_data const* data) {
 }
 
 bool pressio_data_has_data(struct pressio_data const* data) {
-  return data->data() == nullptr;
+  return data->data() != nullptr;
 }
 
 size_t pressio_data_num_dimentions(struct pressio_data const* data) {
@@ -173,4 +181,9 @@ size_t pressio_data_get_bytes(struct pressio_data const* data) {
   return data->size_in_bytes();
 }
 
+size_t pressio_data_num_elements(struct pressio_data const* data) {
+  return data->num_elements();
+}
+
+
 }

test/CMakeLists.txt

@@ -37,6 +37,7 @@ endfunction()
 add_gtest(test_pressio_data.cc)
 add_gtest(test_pressio_options.cc)
 add_gtest(test_sz_plugin.cc)
+add_gtest(test_io.cc)
 target_include_directories(test_sz_plugin PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/../include)
 
 add_executable(sz_basic sz_basic.c make_input_data.cc)