/
conduit_data_array.cpp
1827 lines (1595 loc) · 52.2 KB
/
conduit_data_array.cpp
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// Copyright (c) Lawrence Livermore National Security, LLC and other Conduit
// Project developers. See top-level LICENSE AND COPYRIGHT files for dates and
// other details. No copyright assignment is required to contribute to Conduit.
//-----------------------------------------------------------------------------
///
/// file: conduit_data_array.cpp
///
//-----------------------------------------------------------------------------
#include "conduit_data_array.hpp"
//-----------------------------------------------------------------------------
// -- standard includes --
//-----------------------------------------------------------------------------
#include <algorithm>
#include <cstring>
#include <limits>
//-----------------------------------------------------------------------------
// -- conduit includes --
//-----------------------------------------------------------------------------
#include "conduit_node.hpp"
#include "conduit_utils.hpp"
#include "conduit_log.hpp"
// Easier access to the Conduit logging functions
using namespace conduit::utils;
//-----------------------------------------------------------------------------
// -- begin conduit:: --
//-----------------------------------------------------------------------------
namespace conduit
{
//-----------------------------------------------------------------------------
//
// -- conduit::DataArray public methods --
//
//-----------------------------------------------------------------------------
//---------------------------------------------------------------------------//
template <typename T>
DataArray<T>::DataArray()
: m_data(NULL),
m_dtype(DataType::empty())
{}
//---------------------------------------------------------------------------//
template <typename T>
DataArray<T>::DataArray(void *data,const DataType &dtype)
: m_data(data),
m_dtype(dtype)
{}
//---------------------------------------------------------------------------//
template <typename T>
DataArray<T>::DataArray(const void *data,const DataType &dtype)
: m_data(const_cast<void*>(data)),
m_dtype(dtype)
{}
//---------------------------------------------------------------------------//
template <typename T>
DataArray<T>::DataArray(const DataArray<T> &array)
: m_data(array.m_data),
m_dtype(array.m_dtype)
{}
//---------------------------------------------------------------------------//
template <typename T>
DataArray<T>::~DataArray()
{} // all data is external
//---------------------------------------------------------------------------//
template <typename T>
DataArray<T> &
DataArray<T>::operator=(const DataArray<T> &array)
{
if(this != &array)
{
m_data = array.m_data;
m_dtype = array.m_dtype;
}
return *this;
}
//---------------------------------------------------------------------------//
template <typename T>
T &
DataArray<T>::element(index_t idx)
{
return (*(T*)(element_ptr(idx)));
}
//---------------------------------------------------------------------------//
template <typename T>
T &
DataArray<T>::element(index_t idx) const
{
return (*(T*)(element_ptr(idx)));
}
//---------------------------------------------------------------------------//
template <typename T>
bool
DataArray<T>::compatible(const DataArray<T> &array) const
{
return dtype().compatible(array.dtype());
}
//---------------------------------------------------------------------------//
template <typename T>
bool
DataArray<T>::diff(const DataArray<T> &array, Node &info, const float64 epsilon) const
{
const std::string protocol = "data_array::diff";
bool res = false;
info.reset();
index_t t_nelems = number_of_elements();
index_t o_nelems = array.number_of_elements();
if(t_nelems != o_nelems)
{
std::ostringstream oss;
oss << "data length mismatch ("
<< t_nelems
<< " vs "
<< o_nelems
<< ")";
log::error(info, protocol, oss.str());
res = true;
}
else
{
if(dtype().is_char8_str())
{
uint8 *t_compact_data = new uint8[(size_t)dtype().bytes_compact()];
compact_elements_to(t_compact_data);
std::string t_string((const char*)t_compact_data, (size_t)t_nelems);
uint8 *o_compact_data = new uint8[(size_t)array.dtype().bytes_compact()];
array.compact_elements_to(o_compact_data);
std::string o_string((const char*)o_compact_data, (size_t)o_nelems);
if(t_string != o_string)
{
std::ostringstream oss;
oss << "data string mismatch ("
<< "\"" << t_string << "\""
<< " vs "
<< "\"" << o_string << "\""
<< ")";
log::error(info, protocol, oss.str());
res = true;
}
delete [] t_compact_data;
delete [] o_compact_data;
}
else
{
Node &info_value = info["value"];
info_value.set(DataType(array.dtype().id(), t_nelems));
T* info_ptr = (T*)info_value.data_ptr();
for(index_t i = 0; i < t_nelems; i++)
{
info_ptr[i] = (*this)[i] - array[i];
if(dtype().is_floating_point())
{
res |= info_ptr[i] > epsilon || info_ptr[i] < -epsilon;
}
else
{
res |= (*this)[i] != array[i];
}
}
if(res)
{
log::error(info, protocol, "data item(s) mismatch; see 'value' section");
}
}
}
log::validation(info, !res);
return res;
}
//---------------------------------------------------------------------------//
template <typename T>
bool
DataArray<T>::diff_compatible(const DataArray<T> &array, Node &info, const float64 epsilon) const
{
const std::string protocol = "data_array::diff_compatible";
bool res = false;
info.reset();
index_t t_nelems = number_of_elements();
index_t o_nelems = array.number_of_elements();
if(t_nelems > o_nelems)
{
std::ostringstream oss;
oss << "arg data length incompatible ("
<< t_nelems
<< " vs "
<< o_nelems
<< ")";
log::error(info, protocol, oss.str());
res = true;
}
else
{
if(dtype().is_char8_str())
{
// TODO(JRC): Currently, due to the way that strings are represented
// in C/C++ (i.e. null-terminated), a 'compatible'-type comparison
// isn't very useful/intuitive (e.g. "a" isn't compatible with "aa"
// because of the null terminator). Until a better compatible compare
// strategy is found, 'diff_compatible' just uses the 'diff' comparison
// operation for strings.
uint8 *t_compact_data = new uint8[(size_t)dtype().bytes_compact()];
compact_elements_to(t_compact_data);
std::string t_string((const char*)t_compact_data, (size_t)t_nelems);
uint8 *o_compact_data = new uint8[(size_t)array.dtype().bytes_compact()];
array.compact_elements_to(o_compact_data);
std::string o_string((const char*)o_compact_data, (size_t)o_nelems);
if(t_string != o_string)
{
std::ostringstream oss;
oss << "data string mismatch ("
<< "\"" << t_string << "\""
<< " vs "
<< "\"" << o_string << "\""
<< ")";
log::error(info, protocol, oss.str());
res = true;
}
delete [] t_compact_data;
delete [] o_compact_data;
}
else
{
Node &info_value = info["value"];
info_value.set(DataType(array.dtype().id(), t_nelems));
T* info_ptr = (T*)info_value.data_ptr();
for(index_t i = 0; i < t_nelems; i++)
{
info_ptr[i] = (*this)[i] - array[i];
if(dtype().is_floating_point())
{
res |= info_ptr[i] > epsilon || info_ptr[i] < -epsilon;
}
else
{
res |= (*this)[i] != array[i];
}
}
if(res)
{
log::error(info, protocol, "data item(s) mismatch; see diff below");
}
}
}
log::validation(info, !res);
return res;
}
//---------------------------------------------------------------------------//
///
/// Summary Stats Helpers
///
//---------------------------------------------------------------------------//
//---------------------------------------------------------------------------//
template <typename T>
T
DataArray<T>::min() const
{
T res = std::numeric_limits<T>::max();
for(index_t i = 0; i < number_of_elements(); i++)
{
const T &val = element(i);
if(val < res)
{
res = val;
}
}
return res;
}
//---------------------------------------------------------------------------//
template <typename T>
T
DataArray<T>::max() const
{
T res = std::numeric_limits<T>::min();
for(index_t i = 0; i < number_of_elements(); i++)
{
const T &val = element(i);
if(val > res)
{
res = val;
}
}
return res;
}
//---------------------------------------------------------------------------//
template <typename T>
T
DataArray<T>::sum() const
{
T res =0;
for(index_t i = 0; i < number_of_elements(); i++)
{
const T &val = element(i);
res += val;
}
return res;
}
//---------------------------------------------------------------------------//
template <typename T>
float64
DataArray<T>::mean() const
{
float64 res =0;
for(index_t i = 0; i < number_of_elements(); i++)
{
const T &val = element(i);
res += val;
}
res = res / float64(number_of_elements());
return res;
}
//---------------------------------------------------------------------------//
template <typename T>
std::string
DataArray<T>::to_string(const std::string &protocol) const
{
std::ostringstream oss;
to_string_stream(oss,protocol);
return oss.str();
}
//---------------------------------------------------------------------------//
template <typename T>
void
DataArray<T>::to_string_stream(std::ostream &os,
const std::string &protocol) const
{
if(protocol == "yaml")
{
to_yaml_stream(os);
}
else if(protocol == "json")
{
to_json_stream(os);
}
else
{
// unsupported
CONDUIT_ERROR("Unknown DataType::to_string protocol:" << protocol
<<"\nSupported protocols:\n"
<<" json, yaml");
}
}
//---------------------------------------------------------------------------//
template <typename T>
std::string
DataArray<T>::to_string_default() const
{
return to_string();
}
//---------------------------------------------------------------------------//
template <typename T>
std::string
DataArray<T>::to_json() const
{
std::ostringstream oss;
to_json_stream(oss);
return oss.str();
}
//---------------------------------------------------------------------------//
template <typename T>
void
DataArray<T>::to_json(std::ostream &os) const
{
to_json_stream(os);
}
//---------------------------------------------------------------------------//
template <typename T>
void
DataArray<T>::to_json_stream(std::ostream &os) const
{
index_t nele = number_of_elements();
if(nele > 1)
os << "[";
bool first=true;
for(index_t idx = 0; idx < nele; idx++)
{
if(!first)
os << ", ";
switch(m_dtype.id())
{
// ints
case DataType::INT8_ID:
case DataType::INT16_ID:
case DataType::INT32_ID:
case DataType::INT64_ID:
{
os << (int64) element(idx);
break;
}
// uints
case DataType::UINT8_ID:
case DataType::UINT16_ID:
case DataType::UINT32_ID:
case DataType::UINT64_ID:
{
os << (uint64) element(idx);
break;
}
// floats
case DataType::FLOAT32_ID:
case DataType::FLOAT64_ID:
{
std::string fs = utils::float64_to_string((float64)element(idx));
//check for inf and nan
// looking for 'n' covers inf and nan
bool inf_or_nan = fs.find('n') != std::string::npos;
if(inf_or_nan)
os << "\"";
os << fs;
if(inf_or_nan)
os << "\"";
break;
}
default:
{
CONDUIT_ERROR("Leaf type \""
<< m_dtype.name()
<< "\""
<< "is not supported in conduit::DataArray.")
}
}
first=false;
}
if(nele > 1)
os << "]";
}
//---------------------------------------------------------------------------//
template <typename T>
std::string
DataArray<T>::to_yaml() const
{
std::ostringstream oss;
to_yaml_stream(oss);
return oss.str();
}
//---------------------------------------------------------------------------//
template <typename T>
void
DataArray<T>::to_yaml_stream(std::ostream &os) const
{
// yep, its the same as to_json_stream ...
to_json_stream(os);;
}
//---------------------------------------------------------------------------//
template <typename T>
void
DataArray<T>::set(const int8 *values, index_t num_elements)
{
for(index_t i=0;i<num_elements;i++)
{
this->element(i) = (T)values[i];
}
}
//---------------------------------------------------------------------------//
template <typename T>
void
DataArray<T>::set(const int16 *values, index_t num_elements)
{
for(index_t i=0;i<num_elements;i++)
{
this->element(i) = (T)values[i];
}
}
//---------------------------------------------------------------------------//
template <typename T>
void
DataArray<T>::set(const int32 *values, index_t num_elements)
{
for(index_t i=0;i<num_elements;i++)
{
this->element(i) = (T)values[i];
}
}
//---------------------------------------------------------------------------//
template <typename T>
void
DataArray<T>::set(const int64 *values, index_t num_elements)
{
for(index_t i=0;i<num_elements;i++)
{
this->element(i) = (T)values[i];
}
}
//---------------------------------------------------------------------------//
template <typename T>
void
DataArray<T>::set(const uint8 *values, index_t num_elements)
{
for(index_t i=0;i<num_elements;i++)
{
this->element(i) = (T)values[i];
}
}
//---------------------------------------------------------------------------//
template <typename T>
void
DataArray<T>::set(const uint16 *values, index_t num_elements)
{
for(index_t i=0;i<num_elements;i++)
{
this->element(i) = (T)values[i];
}
}
//---------------------------------------------------------------------------//
template <typename T>
void
DataArray<T>::set(const uint32 *values, index_t num_elements)
{
for(index_t i=0;i<num_elements;i++)
{
this->element(i) = (T)values[i];
}
}
//---------------------------------------------------------------------------//
template <typename T>
void
DataArray<T>::set(const uint64 *values, index_t num_elements)
{
for(index_t i=0;i<num_elements;i++)
{
this->element(i) = (T)values[i];
}
}
//---------------------------------------------------------------------------//
template <typename T>
void
DataArray<T>::set(const float32 *values, index_t num_elements)
{
for(index_t i=0;i<num_elements;i++)
{
this->element(i) = (T)values[i];
}
}
//---------------------------------------------------------------------------//
template <typename T>
void
DataArray<T>::set(const float64 *values, index_t num_elements)
{
for(index_t i=0;i<num_elements;i++)
{
this->element(i) = (T)values[i];
}
}
//---------------------------------------------------------------------------//
// Set from std::initializer_list
//---------------------------------------------------------------------------//
//-----------------------------------------------------------------------------
#ifdef CONDUIT_USE_CXX11
//-----------------------------------------------------------------------------
//---------------------------------------------------------------------------//
template <typename T>
void
DataArray<T>::set(const std::initializer_list<int8> &values)
{
index_t idx = 0;
index_t num_elems = m_dtype.number_of_elements();
// iterate and set up to the number of elements of this array
std::initializer_list<int8>::const_iterator itr;
for( itr = values.begin();
idx < num_elems && itr != values.end();
++itr, idx++)
{
this->element(idx) = (T)*itr;
}
}
//---------------------------------------------------------------------------//
template <typename T>
void
DataArray<T>::set(const std::initializer_list<int16> &values)
{
index_t idx = 0;
index_t num_elems = m_dtype.number_of_elements();
// iterate and set up to the number of elements of this array
std::initializer_list<int16>::const_iterator itr;
for( itr = values.begin();
idx < num_elems && itr != values.end();
++itr, idx++)
{
this->element(idx) = (T)*itr;
}
}
//---------------------------------------------------------------------------//
template <typename T>
void
DataArray<T>::set(const std::initializer_list<int32> &values)
{
index_t idx = 0;
index_t num_elems = m_dtype.number_of_elements();
// iterate and set up to the number of elements of this array
std::initializer_list<int32>::const_iterator itr;
for( itr = values.begin();
idx < num_elems && itr != values.end();
++itr, idx++)
{
this->element(idx) = (T)*itr;
}
}
//---------------------------------------------------------------------------//
template <typename T>
void
DataArray<T>::set(const std::initializer_list<int64> &values)
{
index_t idx = 0;
index_t num_elems = m_dtype.number_of_elements();
// iterate and set up to the number of elements of this array
std::initializer_list<int64>::const_iterator itr;
for( itr = values.begin();
idx < num_elems && itr != values.end();
++itr, idx++)
{
this->element(idx) = (T)*itr;
}
}
//---------------------------------------------------------------------------//
template <typename T>
void
DataArray<T>::set(const std::initializer_list<uint8> &values)
{
index_t idx = 0;
index_t num_elems = m_dtype.number_of_elements();
// iterate and set up to the number of elements of this array
std::initializer_list<uint8>::const_iterator itr;
for( itr = values.begin();
idx < num_elems && itr != values.end();
++itr, idx++)
{
this->element(idx) = (T)*itr;
}
}
//---------------------------------------------------------------------------//
template <typename T>
void
DataArray<T>::set(const std::initializer_list<uint16> &values)
{
index_t idx = 0;
index_t num_elems = m_dtype.number_of_elements();
// iterate and set up to the number of elements of this array
std::initializer_list<uint16>::const_iterator itr;
for( itr = values.begin();
idx < num_elems && itr != values.end();
++itr, idx++)
{
this->element(idx) = (T)*itr;
}
}
//---------------------------------------------------------------------------//
template <typename T>
void
DataArray<T>::set(const std::initializer_list<uint32> &values)
{
index_t idx = 0;
index_t num_elems = m_dtype.number_of_elements();
// iterate and set up to the number of elements of this array
std::initializer_list<uint32>::const_iterator itr;
for( itr = values.begin();
idx < num_elems && itr != values.end();
++itr, idx++)
{
this->element(idx) = (T)*itr;
}
}
//---------------------------------------------------------------------------//
template <typename T>
void
DataArray<T>::set(const std::initializer_list<uint64> &values)
{
index_t idx = 0;
index_t num_elems = m_dtype.number_of_elements();
// iterate and set up to the number of elements of this array
std::initializer_list<uint64>::const_iterator itr;
for( itr = values.begin();
idx < num_elems && itr != values.end();
++itr, idx++)
{
this->element(idx) = (T)*itr;
}
}
//---------------------------------------------------------------------------//
template <typename T>
void
DataArray<T>::set(const std::initializer_list<float32> &values)
{
index_t idx = 0;
index_t num_elems = m_dtype.number_of_elements();
// iterate and set up to the number of elements of this array
std::initializer_list<float32>::const_iterator itr;
for( itr = values.begin();
idx < num_elems && itr != values.end();
++itr, idx++)
{
this->element(idx) = (T)*itr;
}
}
//---------------------------------------------------------------------------//
template <typename T>
void
DataArray<T>::set(const std::initializer_list<float64> &values)
{
index_t idx = 0;
index_t num_elems = m_dtype.number_of_elements();
// iterate and set up to the number of elements of this array
std::initializer_list<float64>::const_iterator itr;
for( itr = values.begin();
idx < num_elems && itr != values.end();
++itr, idx++)
{
this->element(idx) = (T)*itr;
}
}
//---------------------------------------------------------------------------//
// Set from std::initializer_list c native gap methods
//---------------------------------------------------------------------------//
//---------------------------------------------------------------------------//
template <typename T>
void
DataArray<T>::set(const std::initializer_list<char> &values)
{
index_t idx = 0;
index_t num_elems = m_dtype.number_of_elements();
// iterate and set up to the number of elements of this array
std::initializer_list<char>::const_iterator itr;
for( itr = values.begin();
idx < num_elems && itr != values.end();
++itr, idx++)
{
this->element(idx) = (T)*itr;
}
}
//---------------------------------------------------------------------------//
#ifndef CONDUIT_USE_CHAR
//---------------------------------------------------------------------------//
//---------------------------------------------------------------------------//
template <typename T>
void
DataArray<T>::set(const std::initializer_list<signed char> &values)
{
index_t idx = 0;
index_t num_elems = m_dtype.number_of_elements();
// iterate and set up to the number of elements of this array
std::initializer_list<signed char>::const_iterator itr;
for( itr = values.begin();
idx < num_elems && itr != values.end();
++itr, idx++)
{
this->element(idx) = (T)*itr;
}
}
//---------------------------------------------------------------------------//
template <typename T>
void
DataArray<T>::set(const std::initializer_list<unsigned char> &values)
{
index_t idx = 0;
index_t num_elems = m_dtype.number_of_elements();
// iterate and set up to the number of elements of this array
std::initializer_list<unsigned char>::const_iterator itr;
for( itr = values.begin();
idx < num_elems && itr != values.end();
++itr, idx++)
{
this->element(idx) = (T)*itr;
}
}
//---------------------------------------------------------------------------//
#endif // CONDUIT_USE_CHAR
//---------------------------------------------------------------------------//
//---------------------------------------------------------------------------//
#ifndef CONDUIT_USE_SHORT
//---------------------------------------------------------------------------//
//---------------------------------------------------------------------------//
template <typename T>
void
DataArray<T>::set(const std::initializer_list<short> &values)
{
index_t idx = 0;
index_t num_elems = m_dtype.number_of_elements();
// iterate and set up to the number of elements of this array
std::initializer_list<short>::const_iterator itr;
for( itr = values.begin();
idx < num_elems && itr != values.end();
++itr, idx++)
{
this->element(idx) = (T)*itr;
}
}
//---------------------------------------------------------------------------//
template <typename T>
void
DataArray<T>::set(const std::initializer_list<unsigned short> &values)
{
index_t idx = 0;
index_t num_elems = m_dtype.number_of_elements();
// iterate and set up to the number of elements of this array
std::initializer_list<unsigned short>::const_iterator itr;
for( itr = values.begin();
idx < num_elems && itr != values.end();
++itr, idx++)
{
this->element(idx) = (T)*itr;
}
}
//---------------------------------------------------------------------------//
#endif // CONDUIT_USE_SHORT
//---------------------------------------------------------------------------//
//---------------------------------------------------------------------------//
#ifndef CONDUIT_USE_INT
//---------------------------------------------------------------------------//
//---------------------------------------------------------------------------//
template <typename T>
void
DataArray<T>::set(const std::initializer_list<int> &values)
{
index_t idx = 0;
index_t num_elems = m_dtype.number_of_elements();
// iterate and set up to the number of elements of this array
std::initializer_list<int>::const_iterator itr;
for( itr = values.begin();
idx < num_elems && itr != values.end();
++itr, idx++)
{
this->element(idx) = (T)*itr;
}
}
//---------------------------------------------------------------------------//
template <typename T>
void
DataArray<T>::set(const std::initializer_list<unsigned int> &values)
{
index_t idx = 0;
index_t num_elems = m_dtype.number_of_elements();
// iterate and set up to the number of elements of this array
std::initializer_list<unsigned int>::const_iterator itr;
for( itr = values.begin();
idx < num_elems && itr != values.end();
++itr, idx++)
{
this->element(idx) = (T)*itr;
}
}
//---------------------------------------------------------------------------//
#endif // CONDUIT_USE_INT
//---------------------------------------------------------------------------//
//---------------------------------------------------------------------------//
#ifndef CONDUIT_USE_LONG
//---------------------------------------------------------------------------//
//---------------------------------------------------------------------------//
template <typename T>
void
DataArray<T>::set(const std::initializer_list<long> &values)
{
index_t idx = 0;
index_t num_elems = m_dtype.number_of_elements();
// iterate and set up to the number of elements of this array
std::initializer_list<long>::const_iterator itr;
for( itr = values.begin();
idx < num_elems && itr != values.end();
++itr, idx++)
{
this->element(idx) = (T)*itr;
}
}
//---------------------------------------------------------------------------//
template <typename T>
void
DataArray<T>::set(const std::initializer_list<unsigned long> &values)
{
index_t idx = 0;
index_t num_elems = m_dtype.number_of_elements();
// iterate and set up to the number of elements of this array
std::initializer_list<unsigned long>::const_iterator itr;
for( itr = values.begin();
idx < num_elems && itr != values.end();
++itr, idx++)
{
this->element(idx) = (T)*itr;
}
}
//---------------------------------------------------------------------------//
#endif // CONDUIT_USE_LONG
//---------------------------------------------------------------------------//
//---------------------------------------------------------------------------//
#if defined(CONDUIT_HAS_LONG_LONG) && !defined(CONDUIT_USE_LONG_LONG)
//---------------------------------------------------------------------------//
//---------------------------------------------------------------------------//
template <typename T>
void
DataArray<T>::set(const std::initializer_list<long long> &values)
{
index_t idx = 0;
index_t num_elems = m_dtype.number_of_elements();
// iterate and set up to the number of elements of this array
std::initializer_list<long long>::const_iterator itr;
for( itr = values.begin();
idx < num_elems && itr != values.end();
++itr, idx++)
{
this->element(idx) = (T)*itr;
}
}