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Code Issues 2 Actions Packages Projects Releases Wiki Activity

Merge topic 'io-library'

Browse Source 
05fcda6c7 Compile IO library with device compilers
dce576bd1 Add BOVDataSetReader implementation to vtkm_io
8657a9b3c Update VTKDataSetWriter to compile into vtkm_io
086439e71 Update variants of VTKDataSetReaders to compile into vtkm_io
0612be9c5 Move VTKDataSetReaderBase code to vtkm_io

Acked-by: Kitware Robot <kwrobot@kitware.com>
Acked-by: Sujin Philip <sujin.philip@kitware.com>
Merge-request: !2100
This commit is contained in:
Kenneth Moreland 2020-05-20 16:21:28 +00:00 committed by Kitware Robot
commit bc5ecf262c
32 changed files with 2221 additions and 1869 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
benchmarking/CMakeLists.txt
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@ -52,7 +52,7 @@ set(VTKm_BENCHS_RANGE_UPPER_BOUNDARY 134217728 CACHE STRING "Biggest sample for
mark_as_advanced(VTKm_BENCHS_RANGE_LOWER_BOUNDARY VTKm_BENCHS_RANGE_UPPER_BOUNDARY)
foreach (benchmark ${benchmarks})
add_benchmark(NAME ${benchmark} FILE ${benchmark}.cxx LIBS vtkm_source vtkm_filter)
add_benchmark(NAME ${benchmark} FILE ${benchmark}.cxx LIBS vtkm_source vtkm_filter vtkm_io)
endforeach ()
target_compile_definitions(BenchmarkDeviceAdapter PUBLIC VTKm_BENCHS_RANGE_LOWER_BOUNDARY=${VTKm_BENCHS_RANGE_LOWER_BOUNDARY})

13
docs/changelog/vtk-io-in-library.md Normal file
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@ -0,0 +1,13 @@
# Move VTK file readers and writers into vtkm_io
The legacy VTK file reader and writer were created back when VTK-m was a
header-only library. Things have changed and we now compile quite a bit of
code into libraries. At this point, there is no reason why the VTK file
reader/writer should be any different.
Thus, `VTKDataSetReader`, `VTKDataSetWriter`, and several supporting
classes are now compiled into the `vtkm_io` library. Also similarly updated
`BOVDataSetReader` for good measure.
As a side effect, code using VTK-m will need to link to `vtkm_io` if they
are using any readers or writers.

2
examples/clipping/CMakeLists.txt
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@ -14,7 +14,7 @@ project(Clipping CXX)
find_package(VTKm REQUIRED QUIET)
add_executable(Clipping Clipping.cxx)
target_link_libraries(Clipping PRIVATE vtkm_filter)
target_link_libraries(Clipping PRIVATE vtkm_filter vtkm_io)
vtkm_add_target_information(Clipping
DROP_UNUSED_SYMBOLS MODIFY_CUDA_FLAGS

2
examples/hello_worklet/CMakeLists.txt
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@ -14,7 +14,7 @@ project(HelloWorklet CXX)
find_package(VTKm REQUIRED QUIET)
add_executable(HelloWorklet HelloWorklet.cxx)
target_link_libraries(HelloWorklet PRIVATE vtkm_filter)
target_link_libraries(HelloWorklet PRIVATE vtkm_filter vtkm_io)
vtkm_add_target_information(HelloWorklet
DROP_UNUSED_SYMBOLS MODIFY_CUDA_FLAGS

2
examples/mesh_quality/CMakeLists.txt
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@ -26,7 +26,7 @@ project(MeshQuality CXX)
find_package(VTKm REQUIRED QUIET)
add_executable(MeshQuality MeshQuality.cxx)
target_link_libraries(MeshQuality PRIVATE vtkm_filter)
target_link_libraries(MeshQuality PRIVATE vtkm_filter vtkm_io)
if(TARGET vtkm::tbb)
target_compile_definitions(MeshQuality PRIVATE BUILDING_TBB_VERSION)

2
examples/particle_advection/CMakeLists.txt
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@ -14,7 +14,7 @@ project(ParticleAdvection CXX)
find_package(VTKm REQUIRED QUIET)
add_executable(Particle_Advection ParticleAdvection.cxx)
target_link_libraries(Particle_Advection PRIVATE vtkm_filter)
target_link_libraries(Particle_Advection PRIVATE vtkm_filter vtkm_io)
vtkm_add_target_information(Particle_Advection
DROP_UNUSED_SYMBOLS MODIFY_CUDA_FLAGS
DEVICE_SOURCES ParticleAdvection.cxx)

2
examples/redistribute_points/CMakeLists.txt
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@ -13,7 +13,7 @@ project(RedistributePoints CXX)
#Find the VTK-m package
find_package(VTKm REQUIRED QUIET)
add_executable(RedistributePoints RedistributePoints.cxx RedistributePoints.h)
target_link_libraries(RedistributePoints PRIVATE vtkm_filter)
target_link_libraries(RedistributePoints PRIVATE vtkm_filter vtkm_io)
vtkm_add_target_information(RedistributePoints
DROP_UNUSED_SYMBOLS MODIFY_CUDA_FLAGS
DEVICE_SOURCES RedistributePoints.cxx)

2
examples/temporal_advection/CMakeLists.txt
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@ -19,4 +19,4 @@ add_executable(Temporal_Advection TemporalAdvection.cxx)
vtkm_add_target_information(Temporal_Advection
DROP_UNUSED_SYMBOLS MODIFY_CUDA_FLAGS
DEVICE_SOURCES TemporalAdvection.cxx)
target_link_libraries(Temporal_Advection PRIVATE vtkm_filter)
target_link_libraries(Temporal_Advection PRIVATE vtkm_filter vtkm_io)

4
examples/tetrahedra/CMakeLists.txt
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@ -14,10 +14,10 @@ project(Tetrahedra CXX)
find_package(VTKm REQUIRED QUIET)
add_executable(Tetrahedralize Tetrahedralize.cxx)
target_link_libraries(Tetrahedralize PRIVATE vtkm_filter)
target_link_libraries(Tetrahedralize PRIVATE vtkm_filter vtkm_io)
add_executable(Triangulate Triangulate.cxx)
target_link_libraries(Triangulate PRIVATE vtkm_filter)
target_link_libraries(Triangulate PRIVATE vtkm_filter vtkm_io)
vtkm_add_target_information(Tetrahedralize Triangulate
DROP_UNUSED_SYMBOLS

2
vtkm/filter/testing/CMakeLists.txt
View File

@ -69,7 +69,7 @@ set(unit_tests
vtkm_unit_tests(
SOURCES ${unit_tests}
LIBRARIES vtkm_filter vtkm_source
LIBRARIES vtkm_filter vtkm_source vtkm_io
ALL_BACKENDS
USE_VTKM_JOB_POOL
)

254
vtkm/io/BOVDataSetReader.cxx Normal file
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@ -0,0 +1,254 @@
//============================================================================
// Copyright (c) Kitware, Inc.
// All rights reserved.
// See LICENSE.txt for details.
//
// This software is distributed WITHOUT ANY WARRANTY; without even
// the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
// PURPOSE. See the above copyright notice for more information.
//============================================================================
#include <vtkm/io/BOVDataSetReader.h>
#include <vtkm/cont/DataSetBuilderUniform.h>
#include <vtkm/cont/DataSetFieldAdd.h>
#include <vtkm/io/ErrorIO.h>
#include <fstream>
namespace
{
enum class DataFormat
{
ByteData,
ShortData,
IntegerData,
FloatData,
DoubleData
};
template <typename T>
void ReadBuffer(const std::string& fName, const vtkm::Id& sz, std::vector<T>& buff)
{
FILE* fp = fopen(fName.c_str(), "rb");
size_t readSize = static_cast<size_t>(sz);
if (fp == nullptr)
{
throw vtkm::io::ErrorIO("Unable to open data file: " + fName);
}
buff.resize(readSize);
size_t nread = fread(&buff[0], sizeof(T), readSize, fp);
if (nread != readSize)
{
throw vtkm::io::ErrorIO("Data file read failed: " + fName);
}
fclose(fp);
}
template <typename T>
void ReadScalar(const std::string& fName, const vtkm::Id& nTuples, vtkm::cont::ArrayHandle<T>& var)
{
std::vector<T> buff;
ReadBuffer(fName, nTuples, buff);
var.Allocate(nTuples);
auto writePortal = var.WritePortal();
for (vtkm::Id i = 0; i < nTuples; i++)
{
writePortal.Set(i, buff[static_cast<size_t>(i)]);
}
}
template <typename T>
void ReadVector(const std::string& fName,
const vtkm::Id& nTuples,
vtkm::cont::ArrayHandle<vtkm::Vec<T, 3>>& var)
{
std::vector<T> buff;
ReadBuffer(fName, nTuples * 3, buff);
var.Allocate(nTuples);
vtkm::Vec<T, 3> v;
auto writePortal = var.WritePortal();
for (vtkm::Id i = 0; i < nTuples; i++)
{
v[0] = buff[static_cast<size_t>(i * 3 + 0)];
v[1] = buff[static_cast<size_t>(i * 3 + 1)];
v[2] = buff[static_cast<size_t>(i * 3 + 2)];
writePortal.Set(i, v);
}
}
} // anonymous namespace
namespace vtkm
{
namespace io
{
BOVDataSetReader::BOVDataSetReader(const char* fileName)
: FileName(fileName)
, Loaded(false)
, DataSet()
{
}
BOVDataSetReader::BOVDataSetReader(const std::string& fileName)
: FileName(fileName)
, Loaded(false)
, DataSet()
{
}
const vtkm::cont::DataSet& BOVDataSetReader::ReadDataSet()
{
try
{
this->LoadFile();
}
catch (std::ifstream::failure& e)
{
std::string message("IO Error: ");
throw vtkm::io::ErrorIO(message + e.what());
}
return this->DataSet;
}
void BOVDataSetReader::LoadFile()
{
if (this->Loaded)
return;
std::ifstream stream(this->FileName);
if (stream.fail())
throw vtkm::io::ErrorIO("Failed to open file: " + this->FileName);
DataFormat dataFormat = DataFormat::ByteData;
std::string bovFile, line, token, options, variableName;
vtkm::Id numComponents = 1;
vtkm::Id3 dim;
vtkm::Vec3f origin(0, 0, 0);
vtkm::Vec3f spacing(1, 1, 1);
bool spacingSet = false;
while (stream.good())
{
std::getline(stream, line);
if (line.size() == 0 || line[0] == '#')
continue;
//std::cout<<"::"<<line<<"::"<<std::endl;
std::size_t pos = line.find(":");
if (pos == std::string::npos)
throw vtkm::io::ErrorIO("Unsupported option: " + line);
token = line.substr(0, pos);
options = line.substr(pos + 1, line.size() - 1);
//std::cout<<token<<"::"<<options<<std::endl;
std::stringstream strStream(options);
//Format supports both space and "_" separated tokens...
if (token.find("DATA") != std::string::npos && token.find("FILE") != std::string::npos)
{
strStream >> bovFile >> std::ws;
}
else if (token.find("DATA") != std::string::npos && token.find("SIZE") != std::string::npos)
{
strStream >> dim[0] >> dim[1] >> dim[2] >> std::ws;
}
else if (token.find("BRICK") != std::string::npos && token.find("ORIGIN") != std::string::npos)
{
strStream >> origin[0] >> origin[1] >> origin[2] >> std::ws;
}
//DRP
else if (token.find("BRICK") != std::string::npos && token.find("SIZE") != std::string::npos)
{
strStream >> spacing[0] >> spacing[1] >> spacing[2] >> std::ws;
spacingSet = true;
}
else if (token.find("DATA") != std::string::npos && token.find("FORMAT") != std::string::npos)
{
std::string opt;
strStream >> opt >> std::ws;
if (opt.find("FLOAT") != std::string::npos || opt.find("REAL") != std::string::npos)
dataFormat = DataFormat::FloatData;
else if (opt.find("DOUBLE") != std::string::npos)
dataFormat = DataFormat::DoubleData;
else
throw vtkm::io::ErrorIO("Unsupported data type: " + token);
}
else if (token.find("DATA") != std::string::npos &&
token.find("COMPONENTS") != std::string::npos)
{
strStream >> numComponents >> std::ws;
if (numComponents != 1 && numComponents != 3)
throw vtkm::io::ErrorIO("Unsupported number of components");
}
else if (token.find("VARIABLE") != std::string::npos &&
token.find("PALETTE") == std::string::npos)
{
strStream >> variableName >> std::ws;
if (variableName[0] == '"')
variableName = variableName.substr(1, variableName.size() - 2);
}
}
if (spacingSet)
{
spacing[0] = (spacing[0]) / static_cast<vtkm::FloatDefault>(dim[0] - 1);
spacing[1] = (spacing[1]) / static_cast<vtkm::FloatDefault>(dim[1] - 1);
spacing[2] = (spacing[2]) / static_cast<vtkm::FloatDefault>(dim[2] - 1);
}
std::string fullPathDataFile;
std::size_t pos = FileName.rfind("/");
if (pos != std::string::npos)
{
std::string baseDir;
baseDir = this->FileName.substr(0, pos);
fullPathDataFile = baseDir + "/" + bovFile;
}
else
fullPathDataFile = bovFile;
vtkm::cont::DataSetBuilderUniform dataSetBuilder;
vtkm::cont::DataSetFieldAdd dsf;
this->DataSet = dataSetBuilder.Create(dim, origin, spacing);
vtkm::Id numTuples = dim[0] * dim[1] * dim[2];
if (numComponents == 1)
{
if (dataFormat == DataFormat::FloatData)
{
vtkm::cont::ArrayHandle<vtkm::Float32> var;
ReadScalar(fullPathDataFile, numTuples, var);
dsf.AddPointField(this->DataSet, variableName, var);
}
else if (dataFormat == DataFormat::DoubleData)
{
vtkm::cont::ArrayHandle<vtkm::Float64> var;
ReadScalar(fullPathDataFile, numTuples, var);
dsf.AddPointField(this->DataSet, variableName, var);
}
}
else if (numComponents == 3)
{
if (dataFormat == DataFormat::FloatData)
{
vtkm::cont::ArrayHandle<vtkm::Vec3f_32> var;
ReadVector(fullPathDataFile, numTuples, var);
dsf.AddPointField(this->DataSet, variableName, var);
}
else if (dataFormat == DataFormat::DoubleData)
{
vtkm::cont::ArrayHandle<vtkm::Vec3f_64> var;
ReadVector(fullPathDataFile, numTuples, var);
dsf.AddPointField(this->DataSet, variableName, var);
}
}
this->Loaded = true;
}
}
} // namespace vtkm::io

223
vtkm/io/BOVDataSetReader.h
View File

@ -10,234 +10,25 @@
#ifndef vtk_m_io_BOVDataSetReader_h
#define vtk_m_io_BOVDataSetReader_h
#include <fstream>
#include <vtkm/cont/DataSet.h>
#include <vtkm/cont/DataSetBuilderUniform.h>
#include <vtkm/cont/DataSetFieldAdd.h>
#include <vtkm/io/ErrorIO.h>
#include <vtkm/io/vtkm_io_export.h>
namespace vtkm
{
namespace io
{
class BOVDataSetReader
class VTKM_IO_EXPORT BOVDataSetReader
{
public:
BOVDataSetReader(const char* fileName)
: FileName(fileName)
, Loaded(false)
, DataSet()
{
}
BOVDataSetReader(const std::string& fileName)
: FileName(fileName)
, Loaded(false)
, DataSet()
{
}
VTKM_CONT BOVDataSetReader(const char* fileName);
VTKM_CONT BOVDataSetReader(const std::string& fileName);
const vtkm::cont::DataSet& ReadDataSet()
{
try
{
LoadFile();
}
catch (std::ifstream::failure& e)
{
std::string message("IO Error: ");
throw vtkm::io::ErrorIO(message + e.what());
}
return this->DataSet;
}
VTKM_CONT const vtkm::cont::DataSet& ReadDataSet();
private:
using DataFormat = enum { ByteData, ShortData, IntegerData, FloatData, DoubleData };
void LoadFile()
{
if (this->Loaded)
return;
std::ifstream stream(this->FileName);
if (stream.fail())
throw vtkm::io::ErrorIO("Failed to open file: " + this->FileName);
DataFormat dataFormat = ByteData;
std::string bovFile, line, token, options, variableName;
vtkm::Id numComponents = 1;
vtkm::Id3 dim;
vtkm::Vec3f origin(0, 0, 0);
vtkm::Vec3f spacing(1, 1, 1);
bool spacingSet = false;
while (stream.good())
{
std::getline(stream, line);
if (line.size() == 0 || line[0] == '#')
continue;
//std::cout<<"::"<<line<<"::"<<std::endl;
std::size_t pos = line.find(":");
if (pos == std::string::npos)
throw vtkm::io::ErrorIO("Unsupported option: " + line);
token = line.substr(0, pos);
options = line.substr(pos + 1, line.size() - 1);
//std::cout<<token<<"::"<<options<<std::endl;
std::stringstream strStream(options);
//Format supports both space and "_" separated tokens...
if (token.find("DATA") != std::string::npos && token.find("FILE") != std::string::npos)
{
strStream >> bovFile >> std::ws;
}
else if (token.find("DATA") != std::string::npos && token.find("SIZE") != std::string::npos)
{
strStream >> dim[0] >> dim[1] >> dim[2] >> std::ws;
}
else if (token.find("BRICK") != std::string::npos &&
token.find("ORIGIN") != std::string::npos)
{
strStream >> origin[0] >> origin[1] >> origin[2] >> std::ws;
}
//DRP
else if (token.find("BRICK") != std::string::npos && token.find("SIZE") != std::string::npos)
{
strStream >> spacing[0] >> spacing[1] >> spacing[2] >> std::ws;
spacingSet = true;
}
else if (token.find("DATA") != std::string::npos && token.find("FORMAT") != std::string::npos)
{
std::string opt;
strStream >> opt >> std::ws;
if (opt.find("FLOAT") != std::string::npos || opt.find("REAL") != std::string::npos)
dataFormat = FloatData;
else if (opt.find("DOUBLE") != std::string::npos)
dataFormat = DoubleData;
else
throw vtkm::io::ErrorIO("Unsupported data type: " + token);
}
else if (token.find("DATA") != std::string::npos &&
token.find("COMPONENTS") != std::string::npos)
{
strStream >> numComponents >> std::ws;
if (numComponents != 1 && numComponents != 3)
throw vtkm::io::ErrorIO("Unsupported number of components");
}
else if (token.find("VARIABLE") != std::string::npos &&
token.find("PALETTE") == std::string::npos)
{
strStream >> variableName >> std::ws;
if (variableName[0] == '"')
variableName = variableName.substr(1, variableName.size() - 2);
}
}
if (spacingSet)
{
spacing[0] = (spacing[0]) / static_cast<vtkm::FloatDefault>(dim[0] - 1);
spacing[1] = (spacing[1]) / static_cast<vtkm::FloatDefault>(dim[1] - 1);
spacing[2] = (spacing[2]) / static_cast<vtkm::FloatDefault>(dim[2] - 1);
}
std::string fullPathDataFile;
std::size_t pos = FileName.rfind("/");
if (pos != std::string::npos)
{
std::string baseDir;
baseDir = this->FileName.substr(0, pos);
fullPathDataFile = baseDir + "/" + bovFile;
}
else
fullPathDataFile = bovFile;
vtkm::cont::DataSetBuilderUniform dataSetBuilder;
vtkm::cont::DataSetFieldAdd dsf;
this->DataSet = dataSetBuilder.Create(dim, origin, spacing);
vtkm::Id numTuples = dim[0] * dim[1] * dim[2];
if (numComponents == 1)
{
if (dataFormat == FloatData)
{
vtkm::cont::ArrayHandle<vtkm::Float32> var;
ReadScalar(fullPathDataFile, numTuples, var);
dsf.AddPointField(this->DataSet, variableName, var);
}
else if (dataFormat == DoubleData)
{
vtkm::cont::ArrayHandle<vtkm::Float64> var;
ReadScalar(fullPathDataFile, numTuples, var);
dsf.AddPointField(this->DataSet, variableName, var);
}
}
else if (numComponents == 3)
{
if (dataFormat == FloatData)
{
vtkm::cont::ArrayHandle<vtkm::Vec3f_32> var;
ReadVector(fullPathDataFile, numTuples, var);
dsf.AddPointField(this->DataSet, variableName, var);
}
else if (dataFormat == DoubleData)
{
vtkm::cont::ArrayHandle<vtkm::Vec3f_64> var;
ReadVector(fullPathDataFile, numTuples, var);
dsf.AddPointField(this->DataSet, variableName, var);
}
}
this->Loaded = true;
}
template <typename T>
void ReadBuffer(const std::string& fName, const vtkm::Id& sz, std::vector<T>& buff)
{
FILE* fp = fopen(fName.c_str(), "rb");
size_t readSize = static_cast<size_t>(sz);
if (fp == nullptr)
throw vtkm::io::ErrorIO("Unable to open data file: " + fName);
buff.resize(readSize);
size_t nread = fread(&buff[0], sizeof(T), readSize, fp);
if (nread != readSize)
throw vtkm::io::ErrorIO("Data file read failed: " + fName);
fclose(fp);
}
template <typename T>
void ReadScalar(const std::string& fName,
const vtkm::Id& nTuples,
vtkm::cont::ArrayHandle<T>& var)
{
std::vector<T> buff;
ReadBuffer(fName, nTuples, buff);
var.Allocate(nTuples);
auto writePortal = var.WritePortal();
for (vtkm::Id i = 0; i < nTuples; i++)
writePortal.Set(i, buff[(size_t)i]);
}
template <typename T>
void ReadVector(const std::string& fName,
const vtkm::Id& nTuples,
vtkm::cont::ArrayHandle<vtkm::Vec<T, 3>>& var)
{
std::vector<T> buff;
ReadBuffer(fName, nTuples * 3, buff);
var.Allocate(nTuples);
vtkm::Vec<T, 3> v;
auto writePortal = var.WritePortal();
for (vtkm::Id i = 0; i < nTuples; i++)
{
v[0] = buff[static_cast<size_t>(i * 3 + 0)];
v[1] = buff[static_cast<size_t>(i * 3 + 1)];
v[2] = buff[static_cast<size_t>(i * 3 + 2)];
writePortal.Set(i, v);
}
}
VTKM_CONT void LoadFile();
std::string FileName;
bool Loaded;

19
vtkm/io/CMakeLists.txt
View File

@ -18,12 +18,12 @@ set(headers
PixelTypes.h
VTKDataSetReader.h
VTKDataSetReaderBase.h
VTKDataSetWriter.h
VTKPolyDataReader.h
VTKRectilinearGridReader.h
VTKStructuredGridReader.h
VTKStructuredPointsReader.h
VTKUnstructuredGridReader.h
VTKDataSetWriter.h
)
set(template_sources
@ -37,6 +37,22 @@ set(sources
EncodePNG.cxx
)
# TODO: None of these codes actually use a device. Rather, they access ArrayHandle, and we
# currently need to ensure that ArrayHandle is correctly compiled for all devices. This is
# kind of silly, so hopefully sometime in the future you will no longer need to compile for
# devices for ArrayHandle, and this requirement will go away.
set(device_sources
BOVDataSetReader.cxx
VTKDataSetReader.cxx
VTKDataSetReaderBase.cxx
VTKDataSetWriter.cxx
VTKPolyDataReader.cxx
VTKRectilinearGridReader.cxx
VTKStructuredGridReader.cxx
VTKStructuredPointsReader.cxx
VTKUnstructuredGridReader.cxx
)
vtkm_declare_headers(
${headers}
${template_sources}
@ -45,6 +61,7 @@ vtkm_declare_headers(
vtkm_library(
NAME vtkm_io
SOURCES ${sources}
DEVICE_SOURCES ${device_sources}
HEADERS ${headers}
TEMPLATE_SOURCES ${template_sources}
)

92
vtkm/io/VTKDataSetReader.cxx Normal file
View File

@ -0,0 +1,92 @@
//============================================================================
// Copyright (c) Kitware, Inc.
// All rights reserved.
// See LICENSE.txt for details.
//
// This software is distributed WITHOUT ANY WARRANTY; without even
// the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
// PURPOSE. See the above copyright notice for more information.
//============================================================================
#include <vtkm/io/VTKDataSetReader.h>
#include <vtkm/io/VTKPolyDataReader.h>
#include <vtkm/io/VTKRectilinearGridReader.h>
#include <vtkm/io/VTKStructuredGridReader.h>
#include <vtkm/io/VTKStructuredPointsReader.h>
#include <vtkm/io/VTKUnstructuredGridReader.h>
#include <memory>
namespace vtkm
{
namespace io
{
VTKDataSetReader::VTKDataSetReader(const char* fileName)
: VTKDataSetReaderBase(fileName)
{
}
VTKDataSetReader::VTKDataSetReader(const std::string& fileName)
: VTKDataSetReaderBase(fileName)
{
}
VTKDataSetReader::~VTKDataSetReader()
{
}
void VTKDataSetReader::PrintSummary(std::ostream& out) const
{
if (this->Reader)
{
this->Reader->PrintSummary(out);
}
else
{
VTKDataSetReaderBase::PrintSummary(out);
}
}
void VTKDataSetReader::CloseFile()
{
if (this->Reader)
{
this->Reader->CloseFile();
}
else
{
VTKDataSetReaderBase::CloseFile();
}
}
void VTKDataSetReader::Read()
{
switch (this->DataFile->Structure)
{
case vtkm::io::internal::DATASET_STRUCTURED_POINTS:
this->Reader.reset(new VTKStructuredPointsReader(""));
break;
case vtkm::io::internal::DATASET_STRUCTURED_GRID:
this->Reader.reset(new VTKStructuredGridReader(""));
break;
case vtkm::io::internal::DATASET_RECTILINEAR_GRID:
this->Reader.reset(new VTKRectilinearGridReader(""));
break;
case vtkm::io::internal::DATASET_POLYDATA:
this->Reader.reset(new VTKPolyDataReader(""));
break;
case vtkm::io::internal::DATASET_UNSTRUCTURED_GRID:
this->Reader.reset(new VTKUnstructuredGridReader(""));
break;
default:
throw vtkm::io::ErrorIO("Unsupported DataSet type.");
}
this->TransferDataFile(*this->Reader.get());
this->Reader->Read();
this->DataSet = this->Reader->GetDataSet();
}
}
} // namespace vtkm::io

77
vtkm/io/VTKDataSetReader.h
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@ -11,86 +11,27 @@
#define vtk_m_io_VTKDataSetReader_h
#include <vtkm/io/VTKDataSetReaderBase.h>
#include <vtkm/io/VTKPolyDataReader.h>
#include <vtkm/io/VTKRectilinearGridReader.h>
#include <vtkm/io/VTKStructuredGridReader.h>
#include <vtkm/io/VTKStructuredPointsReader.h>
#include <vtkm/io/VTKUnstructuredGridReader.h>
#include <memory>
namespace vtkm
{
namespace io
{
VTKM_SILENCE_WEAK_VTABLE_WARNING_START
class VTKDataSetReader : public VTKDataSetReaderBase
class VTKM_IO_EXPORT VTKDataSetReader : public VTKDataSetReaderBase
{
public:
explicit VTKDataSetReader(const char* fileName)
: VTKDataSetReaderBase(fileName)
{
}
VTKM_CONT VTKDataSetReader(const char* fileName);
VTKM_CONT VTKDataSetReader(const std::string& fileName);
VTKM_CONT ~VTKDataSetReader() override;
explicit VTKDataSetReader(const std::string& fileName)
: VTKDataSetReaderBase(fileName)
{
}
VTKDataSetReader(const VTKDataSetReader&) = delete;
void operator=(const VTKDataSetReader&) = delete;
virtual void PrintSummary(std::ostream& out) const
{
if (this->Reader)
{
this->Reader->PrintSummary(out);
}
else
{
VTKDataSetReaderBase::PrintSummary(out);
}
}
VTKM_CONT void PrintSummary(std::ostream& out) const override;
private:
virtual void CloseFile()
{
if (this->Reader)
{
this->Reader->CloseFile();
}
else
{
VTKDataSetReaderBase::CloseFile();
}
}
virtual void Read()
{
switch (this->DataFile->Structure)
{
case vtkm::io::internal::DATASET_STRUCTURED_POINTS:
this->Reader.reset(new VTKStructuredPointsReader(""));
break;
case vtkm::io::internal::DATASET_STRUCTURED_GRID:
this->Reader.reset(new VTKStructuredGridReader(""));
break;
case vtkm::io::internal::DATASET_RECTILINEAR_GRID:
this->Reader.reset(new VTKRectilinearGridReader(""));
break;
case vtkm::io::internal::DATASET_POLYDATA:
this->Reader.reset(new VTKPolyDataReader(""));
break;
case vtkm::io::internal::DATASET_UNSTRUCTURED_GRID:
this->Reader.reset(new VTKUnstructuredGridReader(""));
break;
default:
throw vtkm::io::ErrorIO("Unsupported DataSet type.");
}
this->TransferDataFile(*this->Reader.get());
this->Reader->Read();
this->DataSet = this->Reader->GetDataSet();
}
VTKM_CONT void CloseFile() override;
VTKM_CONT void Read() override;
std::unique_ptr<VTKDataSetReaderBase> Reader;
};

826
vtkm/io/VTKDataSetReaderBase.cxx Normal file
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@ -0,0 +1,826 @@
//============================================================================
// Copyright (c) Kitware, Inc.
// All rights reserved.
// See LICENSE.txt for details.
//
// This software is distributed WITHOUT ANY WARRANTY; without even
// the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
// PURPOSE. See the above copyright notice for more information.
//============================================================================
#include <vtkm/io/VTKDataSetReaderBase.h>
#include <vtkm/VecTraits.h>
#include <vtkm/cont/ArrayHandle.h>
#include <vtkm/cont/ArrayPortalToIterators.h>
#include <vtkm/cont/Logging.h>
#include <vtkm/cont/VariantArrayHandle.h>
#include <algorithm>
#include <string>
#include <vector>
namespace
{
inline void PrintVTKDataFileSummary(const vtkm::io::internal::VTKDataSetFile& df, std::ostream& out)
{
out << "\tFile: " << df.FileName << std::endl;
out << "\tVersion: " << df.Version[0] << "." << df.Version[0] << std::endl;
out << "\tTitle: " << df.Title << std::endl;
out << "\tFormat: " << (df.IsBinary ? "BINARY" : "ASCII") << std::endl;
out << "\tDataSet type: " << vtkm::io::internal::DataSetStructureString(df.Structure)
<< std::endl;
}
// Since Fields and DataSets store data in the default VariantArrayHandle, convert
// the data to the closest type supported by default. The following will
// need to be updated if VariantArrayHandle or TypeListCommon changes.
template <typename T>
struct ClosestCommonType
{
using Type = T;
};
template <>
struct ClosestCommonType<vtkm::Int8>
{
using Type = vtkm::Int32;
};
template <>
struct ClosestCommonType<vtkm::UInt8>
{
using Type = vtkm::Int32;
};
template <>
struct ClosestCommonType<vtkm::Int16>
{
using Type = vtkm::Int32;
};
template <>
struct ClosestCommonType<vtkm::UInt16>
{
using Type = vtkm::Int32;
};
template <>
struct ClosestCommonType<vtkm::UInt32>
{
using Type = vtkm::Int64;
};
template <>
struct ClosestCommonType<vtkm::UInt64>
{
using Type = vtkm::Int64;
};
template <typename T>
struct ClosestFloat
{
using Type = T;
};
template <>
struct ClosestFloat<vtkm::Int8>
{
using Type = vtkm::Float32;
};
template <>
struct ClosestFloat<vtkm::UInt8>
{
using Type = vtkm::Float32;
};
template <>
struct ClosestFloat<vtkm::Int16>
{
using Type = vtkm::Float32;
};
template <>
struct ClosestFloat<vtkm::UInt16>
{
using Type = vtkm::Float32;
};
template <>
struct ClosestFloat<vtkm::Int32>
{
using Type = vtkm::Float64;
};
template <>
struct ClosestFloat<vtkm::UInt32>
{
using Type = vtkm::Float64;
};
template <>
struct ClosestFloat<vtkm::Int64>
{
using Type = vtkm::Float64;
};
template <>
struct ClosestFloat<vtkm::UInt64>
{
using Type = vtkm::Float64;
};
template <typename T>
vtkm::cont::VariantArrayHandle CreateVariantArrayHandle(const std::vector<T>& vec)
{
switch (vtkm::VecTraits<T>::NUM_COMPONENTS)
{
case 1:
{
using CommonType = typename ClosestCommonType<T>::Type;
constexpr bool not_same = !std::is_same<T, CommonType>::value;
if (not_same)
{
VTKM_LOG_S(vtkm::cont::LogLevel::Info,
"Type " << vtkm::io::internal::DataTypeName<T>::Name()
<< " is currently unsupported. Converting to "
<< vtkm::io::internal::DataTypeName<CommonType>::Name()
<< ".");
}
vtkm::cont::ArrayHandle<CommonType> output;
output.Allocate(static_cast<vtkm::Id>(vec.size()));
auto portal = output.WritePortal();
for (vtkm::Id i = 0; i < output.GetNumberOfValues(); ++i)
{
portal.Set(i, static_cast<CommonType>(vec[static_cast<std::size_t>(i)]));
}
return vtkm::cont::VariantArrayHandle(output);
}
case 2:
case 3:
case 9:
{
constexpr auto numComps = vtkm::VecTraits<T>::NUM_COMPONENTS;
using InComponentType = typename vtkm::VecTraits<T>::ComponentType;
using OutComponentType = typename ClosestFloat<InComponentType>::Type;
using CommonType = vtkm::Vec<OutComponentType, numComps>;
constexpr bool not_same = !std::is_same<T, CommonType>::value;
if (not_same)
{
VTKM_LOG_S(vtkm::cont::LogLevel::Info,
"Type " << vtkm::io::internal::DataTypeName<InComponentType>::Name() << "["
<< vtkm::VecTraits<T>::GetNumberOfComponents(T())
<< "] "
<< "is currently unsupported. Converting to "
<< vtkm::io::internal::DataTypeName<OutComponentType>::Name()
<< "["
<< numComps
<< "].");
}
vtkm::cont::ArrayHandle<CommonType> output;
output.Allocate(static_cast<vtkm::Id>(vec.size()));
auto portal = output.WritePortal();
for (vtkm::Id i = 0; i < output.GetNumberOfValues(); ++i)
{
CommonType outval = CommonType();
for (vtkm::IdComponent j = 0; j < numComps; ++j)
{
outval[j] = static_cast<OutComponentType>(
vtkm::VecTraits<T>::GetComponent(vec[static_cast<std::size_t>(i)], j));
}
portal.Set(i, outval);
}
return vtkm::cont::VariantArrayHandle(output);
}
default:
{
VTKM_LOG_S(vtkm::cont::LogLevel::Warn, "Only 1, 2, 3, or 9 components supported. Skipping.");
return vtkm::cont::VariantArrayHandle(vtkm::cont::ArrayHandle<vtkm::Float32>());
}
}
}
} // anonymous namespace
namespace vtkm
{
namespace io
{
VTKDataSetReaderBase::VTKDataSetReaderBase(const char* fileName)
: DataFile(new internal::VTKDataSetFile)
, DataSet()
, Loaded(false)
{
this->DataFile->FileName = fileName;
}
VTKDataSetReaderBase::VTKDataSetReaderBase(const std::string& fileName)
: DataFile(new internal::VTKDataSetFile)
, DataSet()
, Loaded(false)
{
this->DataFile->FileName = fileName;
}
VTKDataSetReaderBase::~VTKDataSetReaderBase()
{
}
const vtkm::cont::DataSet& VTKDataSetReaderBase::ReadDataSet()
{
if (!this->Loaded)
{
try
{
this->OpenFile();
this->ReadHeader();
this->Read();
this->CloseFile();
this->Loaded = true;
}
catch (std::ifstream::failure& e)
{
std::string message("IO Error: ");
throw vtkm::io::ErrorIO(message + e.what());
}
}
return this->DataSet;
}
void VTKDataSetReaderBase::PrintSummary(std::ostream& out) const
{
out << "VTKDataSetReader" << std::endl;
PrintVTKDataFileSummary(*this->DataFile.get(), out);
this->DataSet.PrintSummary(out);
}
void VTKDataSetReaderBase::ReadPoints()
{
std::string dataType;
std::size_t numPoints;
this->DataFile->Stream >> numPoints >> dataType >> std::ws;
vtkm::cont::VariantArrayHandle points =
this->DoReadArrayVariant(vtkm::cont::Field::Association::POINTS, dataType, numPoints, 3);
this->DataSet.AddCoordinateSystem(vtkm::cont::CoordinateSystem("coordinates", points));
}
void VTKDataSetReaderBase::ReadCells(vtkm::cont::ArrayHandle<vtkm::Id>& connectivity,
vtkm::cont::ArrayHandle<vtkm::IdComponent>& numIndices)
{
vtkm::Id numCells, numInts;
this->DataFile->Stream >> numCells >> numInts >> std::ws;
connectivity.Allocate(numInts - numCells);
numIndices.Allocate(numCells);
std::vector<vtkm::Int32> buffer(static_cast<std::size_t>(numInts));
this->ReadArray(buffer);
vtkm::Int32* buffp = &buffer[0];
auto connectivityPortal = connectivity.WritePortal();
auto numIndicesPortal = numIndices.WritePortal();
for (vtkm::Id i = 0, connInd = 0; i < numCells; ++i)
{
vtkm::IdComponent numInds = static_cast<vtkm::IdComponent>(*buffp++);
numIndicesPortal.Set(i, numInds);
for (vtkm::IdComponent j = 0; j < numInds; ++j, ++connInd)
{
connectivityPortal.Set(connInd, static_cast<vtkm::Id>(*buffp++));
}
}
}
void VTKDataSetReaderBase::ReadShapes(vtkm::cont::ArrayHandle<vtkm::UInt8>& shapes)
{
std::string tag;
vtkm::Id numCells;
this->DataFile->Stream >> tag >> numCells >> std::ws;
internal::parseAssert(tag == "CELL_TYPES");
shapes.Allocate(numCells);
std::vector<vtkm::Int32> buffer(static_cast<std::size_t>(numCells));
this->ReadArray(buffer);
vtkm::Int32* buffp = &buffer[0];
auto shapesPortal = shapes.WritePortal();
for (vtkm::Id i = 0; i < numCells; ++i)
{
shapesPortal.Set(i, static_cast<vtkm::UInt8>(*buffp++));
}
}
void VTKDataSetReaderBase::ReadAttributes()
{
if (this->DataFile->Stream.eof())
{
return;
}
vtkm::cont::Field::Association association = vtkm::cont::Field::Association::ANY;
std::size_t size;
std::string tag;
this->DataFile->Stream >> tag;
while (!this->DataFile->Stream.eof())
{
if (tag == "POINT_DATA")
{
association = vtkm::cont::Field::Association::POINTS;
}
else if (tag == "CELL_DATA")
{
association = vtkm::cont::Field::Association::CELL_SET;
}
else
{
internal::parseAssert(false);
}
this->DataFile->Stream >> size;
while (!this->DataFile->Stream.eof())
{
this->DataFile->Stream >> tag;
if (tag == "SCALARS")
{
this->ReadScalars(association, size);
}
else if (tag == "COLOR_SCALARS")
{
this->ReadColorScalars(association, size);
}
else if (tag == "LOOKUP_TABLE")
{
this->ReadLookupTable();
}
else if (tag == "VECTORS" || tag == "NORMALS")
{
this->ReadVectors(association, size);
}
else if (tag == "TEXTURE_COORDINATES")
{
this->ReadTextureCoordinates(association, size);
}
else if (tag == "TENSORS")
{
this->ReadTensors(association, size);
}
else if (tag == "FIELD")
{
this->ReadFields(association, size);
}
else
{
break;
}
}
}
}
void VTKDataSetReaderBase::CloseFile()
{
this->DataFile->Stream.close();
}
void VTKDataSetReaderBase::OpenFile()
{
this->DataFile->Stream.exceptions(std::ifstream::failbit | std::ifstream::badbit);
try
{
this->DataFile->Stream.open(this->DataFile->FileName.c_str(),
std::ios_base::in | std::ios_base::binary);
}
catch (std::ifstream::failure&)
{
std::string message("could not open file \"" + this->DataFile->FileName + "\"");
throw vtkm::io::ErrorIO(message);
}
}
void VTKDataSetReaderBase::ReadHeader()
{
char vstring[] = "# vtk DataFile Version";
const std::size_t vlen = sizeof(vstring);
// Read version line
char vbuf[vlen];
this->DataFile->Stream.read(vbuf, vlen - 1);
vbuf[vlen - 1] = '\0';
if (std::string(vbuf) != std::string(vstring))
{
throw vtkm::io::ErrorIO("Incorrect file format.");
}
char dot;
this->DataFile->Stream >> this->DataFile->Version[0] >> dot >> this->DataFile->Version[1];
// skip rest of the line
std::string skip;
std::getline(this->DataFile->Stream, skip);
if ((this->DataFile->Version[0] > 4) ||
(this->DataFile->Version[0] == 4 && this->DataFile->Version[1] > 2))
{
VTKM_LOG_S(vtkm::cont::LogLevel::Warn,
"Reader may not correctly read >v4.2 files. Reading version "
<< this->DataFile->Version[0]
<< "."
<< this->DataFile->Version[1]
<< ".\n");
}
// Read title line
std::getline(this->DataFile->Stream, this->DataFile->Title);
// Read format line
this->DataFile->IsBinary = false;
std::string format;
this->DataFile->Stream >> format >> std::ws;
if (format == "BINARY")
{
this->DataFile->IsBinary = true;
}
else if (format != "ASCII")
{
throw vtkm::io::ErrorIO("Unsupported Format.");
}
// Read structure line
std::string tag, structStr;
this->DataFile->Stream >> tag >> structStr >> std::ws;
internal::parseAssert(tag == "DATASET");
this->DataFile->Structure = vtkm::io::internal::DataSetStructureId(structStr);
if (this->DataFile->Structure == vtkm::io::internal::DATASET_UNKNOWN)
{
throw vtkm::io::ErrorIO("Unsupported DataSet type.");
}
}
void VTKDataSetReaderBase::AddField(const std::string& name,
vtkm::cont::Field::Association association,
vtkm::cont::VariantArrayHandle& data)
{
if (data.GetNumberOfValues() > 0)
{
switch (association)
{
case vtkm::cont::Field::Association::POINTS:
case vtkm::cont::Field::Association::WHOLE_MESH:
this->DataSet.AddField(vtkm::cont::Field(name, association, data));
break;
case vtkm::cont::Field::Association::CELL_SET:
this->DataSet.AddField(vtkm::cont::Field(name, association, data));
break;
default:
VTKM_LOG_S(vtkm::cont::LogLevel::Warn,
"Not recording field '" << name << "' because it has an unknown association");
break;
}
}
}
void VTKDataSetReaderBase::ReadScalars(vtkm::cont::Field::Association association,
std::size_t numElements)
{
std::string dataName, dataType, lookupTableName;
vtkm::IdComponent numComponents = 1;
this->DataFile->Stream >> dataName >> dataType;
std::string tag;
this->DataFile->Stream >> tag;
if (tag != "LOOKUP_TABLE")
{
try
{
numComponents = std::stoi(tag);
}
catch (std::invalid_argument&)
{
internal::parseAssert(false);
}
this->DataFile->Stream >> tag;
}
internal::parseAssert(tag == "LOOKUP_TABLE");
this->DataFile->Stream >> lookupTableName >> std::ws;
vtkm::cont::VariantArrayHandle data =
this->DoReadArrayVariant(association, dataType, numElements, numComponents);
this->AddField(dataName, association, data);
}
void VTKDataSetReaderBase::ReadColorScalars(vtkm::cont::Field::Association association,
std::size_t numElements)
{
VTKM_LOG_S(vtkm::cont::LogLevel::Warn, "Support for COLOR_SCALARS is not implemented. Skipping.");
std::string dataName;
vtkm::IdComponent numComponents;
this->DataFile->Stream >> dataName >> numComponents >> std::ws;
std::string dataType = this->DataFile->IsBinary ? "unsigned_char" : "float";
vtkm::cont::VariantArrayHandle data =
this->DoReadArrayVariant(association, dataType, numElements, numComponents);
this->AddField(dataName, association, data);
}
void VTKDataSetReaderBase::ReadLookupTable()
{
VTKM_LOG_S(vtkm::cont::LogLevel::Warn, "Support for LOOKUP_TABLE is not implemented. Skipping.");
std::string dataName;
std::size_t numEntries;
this->DataFile->Stream >> dataName >> numEntries >> std::ws;
this->SkipArray(numEntries, vtkm::Vec<vtkm::io::internal::ColorChannel8, 4>());
}
void VTKDataSetReaderBase::ReadTextureCoordinates(vtkm::cont::Field::Association association,
std::size_t numElements)
{
std::string dataName;
vtkm::IdComponent numComponents;
std::string dataType;
this->DataFile->Stream >> dataName >> numComponents >> dataType >> std::ws;
vtkm::cont::VariantArrayHandle data =
this->DoReadArrayVariant(association, dataType, numElements, numComponents);
this->AddField(dataName, association, data);
}
void VTKDataSetReaderBase::ReadVectors(vtkm::cont::Field::Association association,
std::size_t numElements)
{
std::string dataName;
std::string dataType;
this->DataFile->Stream >> dataName >> dataType >> std::ws;
vtkm::cont::VariantArrayHandle data =
this->DoReadArrayVariant(association, dataType, numElements, 3);
this->AddField(dataName, association, data);
}
void VTKDataSetReaderBase::ReadTensors(vtkm::cont::Field::Association association,
std::size_t numElements)
{
std::string dataName;
std::string dataType;
this->DataFile->Stream >> dataName >> dataType >> std::ws;
vtkm::cont::VariantArrayHandle data =
this->DoReadArrayVariant(association, dataType, numElements, 9);
this->AddField(dataName, association, data);
}
void VTKDataSetReaderBase::ReadFields(vtkm::cont::Field::Association association,
std::size_t expectedNumElements)
{
std::string dataName;
vtkm::Id numArrays;
this->DataFile->Stream >> dataName >> numArrays >> std::ws;
for (vtkm::Id i = 0; i < numArrays; ++i)
{
std::size_t numTuples;
vtkm::IdComponent numComponents;
std::string arrayName, dataType;
this->DataFile->Stream >> arrayName >> numComponents >> numTuples >> dataType >> std::ws;
if (numTuples == expectedNumElements)
{
vtkm::cont::VariantArrayHandle data =
this->DoReadArrayVariant(association, dataType, numTuples, numComponents);
this->AddField(arrayName, association, data);
}
else
{
VTKM_LOG_S(vtkm::cont::LogLevel::Warn,
"Field " << arrayName
<< "'s size does not match expected number of elements. Skipping");
}
}
}
void VTKDataSetReaderBase::ReadGlobalFields(std::vector<vtkm::Float32>* visitBounds)
{
std::string dataName;
vtkm::Id numArrays;
this->DataFile->Stream >> dataName >> numArrays >> std::ws;
for (vtkm::Id i = 0; i < numArrays; ++i)
{
std::size_t numTuples;
vtkm::IdComponent numComponents;
std::string arrayName, dataType;
this->DataFile->Stream >> arrayName >> numComponents >> numTuples >> dataType >> std::ws;
if (arrayName == "avtOriginalBounds" && visitBounds)
{
visitBounds->resize(6);
internal::parseAssert(numComponents == 1 && numTuples == 6);
// parse the bounds and fill the bounds vector
this->ReadArray(*visitBounds);
}
else
{
VTKM_LOG_S(vtkm::cont::LogLevel::Info,
"Support for global field " << arrayName << " not implemented. Skipping.");
this->DoSkipArrayVariant(dataType, numTuples, numComponents);
}
}
}
class VTKDataSetReaderBase::SkipArrayVariant
{
public:
SkipArrayVariant(VTKDataSetReaderBase* reader, std::size_t numElements)
: Reader(reader)
, NumElements(numElements)
{
}
template <typename T>
void operator()(T) const
{
this->Reader->SkipArray(this->NumElements, T());
}
template <typename T>
void operator()(vtkm::IdComponent numComponents, T) const
{
this->Reader->SkipArray(this->NumElements * static_cast<std::size_t>(numComponents), T());
}
protected:
VTKDataSetReaderBase* Reader;
std::size_t NumElements;
};
class VTKDataSetReaderBase::ReadArrayVariant : public SkipArrayVariant
{
public:
ReadArrayVariant(VTKDataSetReaderBase* reader,
vtkm::cont::Field::Association association,
std::size_t numElements,
vtkm::cont::VariantArrayHandle& data)
: SkipArrayVariant(reader, numElements)
, Association(association)
, Data(&data)
{
}
template <typename T>
void operator()(T) const
{
std::vector<T> buffer(this->NumElements);
this->Reader->ReadArray(buffer);
if ((this->Association != vtkm::cont::Field::Association::CELL_SET) ||
(this->Reader->GetCellsPermutation().GetNumberOfValues() < 1))
{
*this->Data = CreateVariantArrayHandle(buffer);
}
else
{
// If we are reading data associated with a cell set, we need to (sometimes) permute the
// data due to differences between VTK and VTK-m cell shapes.
auto permutation = this->Reader->GetCellsPermutation().ReadPortal();
vtkm::Id outSize = permutation.GetNumberOfValues();
std::vector<T> permutedBuffer(static_cast<std::size_t>(outSize));
for (vtkm::Id outIndex = 0; outIndex < outSize; outIndex++)
{
std::size_t inIndex = static_cast<std::size_t>(permutation.Get(outIndex));
permutedBuffer[static_cast<std::size_t>(outIndex)] = buffer[inIndex];
}
*this->Data = CreateVariantArrayHandle(permutedBuffer);
}
}
template <typename T>
void operator()(vtkm::IdComponent numComponents, T) const
{
VTKM_LOG_S(vtkm::cont::LogLevel::Warn,
"Support for " << numComponents << " components not implemented. Skipping.");
SkipArrayVariant::operator()(numComponents, T());
}
private:
vtkm::cont::Field::Association Association;
vtkm::cont::VariantArrayHandle* Data;
};
void VTKDataSetReaderBase::DoSkipArrayVariant(std::string dataType,
std::size_t numElements,
vtkm::IdComponent numComponents)
{
// string is unsupported for SkipArrayVariant, so it requires some
// special handling
if (dataType == "string")
{
const vtkm::Id stringCount = numComponents * static_cast<vtkm::Id>(numElements);
for (vtkm::Id i = 0; i < stringCount; ++i)
{
std::string trash;
this->DataFile->Stream >> trash;
}
}
else
{
vtkm::io::internal::DataType typeId = vtkm::io::internal::DataTypeId(dataType);
vtkm::io::internal::SelectTypeAndCall(
typeId, numComponents, SkipArrayVariant(this, numElements));
}
}
vtkm::cont::VariantArrayHandle VTKDataSetReaderBase::DoReadArrayVariant(
vtkm::cont::Field::Association association,
std::string dataType,
std::size_t numElements,
vtkm::IdComponent numComponents)
{
// Create empty data to start so that the return can check if data were actually read
vtkm::cont::ArrayHandle<vtkm::Float32> empty;
vtkm::cont::VariantArrayHandle data(empty);
vtkm::io::internal::DataType typeId = vtkm::io::internal::DataTypeId(dataType);
vtkm::io::internal::SelectTypeAndCall(
typeId, numComponents, ReadArrayVariant(this, association, numElements, data));
return data;
}
void VTKDataSetReaderBase::ReadArray(std::vector<vtkm::io::internal::DummyBitType>& buffer)
{
VTKM_LOG_S(vtkm::cont::LogLevel::Warn,
"Support for data type 'bit' is not implemented. Skipping.");
this->SkipArray(buffer.size(), vtkm::io::internal::DummyBitType());
buffer.clear();
}
void VTKDataSetReaderBase::SkipArray(std::size_t numElements,
vtkm::io::internal::DummyBitType,
vtkm::IdComponent numComponents)
{
if (this->DataFile->IsBinary)
{
numElements = (numElements + 7) / 8;
this->DataFile->Stream.seekg(static_cast<std::streamoff>(numElements), std::ios_base::cur);
}
else
{
for (std::size_t i = 0; i < numElements; ++i)
{
vtkm::UInt16 val;
this->DataFile->Stream >> val;
}
}
this->DataFile->Stream >> std::ws;
this->SkipArrayMetaData(numComponents);
}
void VTKDataSetReaderBase::SkipArrayMetaData(vtkm::IdComponent numComponents)
{
if (!this->DataFile->Stream.good())
{
return;
}
auto begining = this->DataFile->Stream.tellg();
std::string tag;
this->DataFile->Stream >> tag;
if (tag != "METADATA")
{
this->DataFile->Stream.seekg(begining);
return;
}
VTKM_LOG_S(vtkm::cont::LogLevel::Warn, "METADATA is not supported. Attempting to Skip.");
this->DataFile->Stream >> tag >> std::ws;
if (tag == "COMPONENT_NAMES")
{
std::string name;
for (vtkm::IdComponent i = 0; i < numComponents; ++i)
{
this->DataFile->Stream >> name >> std::ws;
}
}
else if (tag == "INFORMATION")
{
int numKeys = 0;
this->DataFile->Stream >> numKeys >> std::ws;
// Skipping INFORMATION is tricky. The reader needs to be aware of the types of the
// information, which is not provided in the file.
// Here we will just skip until an empty line is found.
// However, if there are no keys, then there is nothing to read (and the stream tends
// to skip over empty lines.
if (numKeys > 0)
{
std::string line;
do
{
std::getline(this->DataFile->Stream, line);
} while (this->DataFile->Stream.good() && !line.empty());
// Eat any remaining whitespace after the INFORMATION to be ready to read the next token
this->DataFile->Stream >> std::ws;
}
}
else
{
internal::parseAssert(false);
}
}
}
} // namespace vtkm::io

872
vtkm/io/VTKDataSetReaderBase.h
View File

@ -10,25 +10,16 @@
#ifndef vtk_m_io_VTKDataSetReaderBase_h
#define vtk_m_io_VTKDataSetReaderBase_h
#include <vtkm/Types.h>
#include <vtkm/cont/DataSet.h>
#include <vtkm/io/ErrorIO.h>
#include <vtkm/io/vtkm_io_export.h>
#include <vtkm/io/internal/Endian.h>
#include <vtkm/io/internal/VTKDataSetCells.h>
#include <vtkm/io/internal/VTKDataSetStructures.h>
#include <vtkm/io/internal/VTKDataSetTypes.h>
#include <vtkm/Types.h>
#include <vtkm/VecTraits.h>
#include <vtkm/cont/ArrayHandle.h>
#include <vtkm/cont/ArrayPortalToIterators.h>
#include <vtkm/cont/DataSet.h>
#include <vtkm/cont/Logging.h>
#include <vtkm/cont/VariantArrayHandle.h>
#include <vtkm/internal/ExportMacros.h>
#include <vtkm/io/ErrorIO.h>
#include <algorithm>
#include <fstream>
#include <string>
#include <vector>
namespace vtkm
{
@ -48,16 +39,6 @@ struct VTKDataSetFile
std::ifstream Stream;
};
inline void PrintVTKDataFileSummary(const VTKDataSetFile& df, std::ostream& out)
{
out << "\tFile: " << df.FileName << std::endl;
out << "\tVersion: " << df.Version[0] << "." << df.Version[0] << std::endl;
out << "\tTitle: " << df.Title << std::endl;
out << "\tFormat: " << (df.IsBinary ? "BINARY" : "ASCII") << std::endl;
out << "\tDataSet type: " << vtkm::io::internal::DataSetStructureString(df.Structure)
<< std::endl;
}
inline void parseAssert(bool condition)
{
if (!condition)
@ -82,166 +63,6 @@ struct StreamIOType<vtkm::UInt8>
using Type = vtkm::UInt16;
};
// Since Fields and DataSets store data in the default VariantArrayHandle, convert
// the data to the closest type supported by default. The following will
// need to be updated if VariantArrayHandle or TypeListCommon changes.
template <typename T>
struct ClosestCommonType
{
using Type = T;
};
template <>
struct ClosestCommonType<vtkm::Int8>
{
using Type = vtkm::Int32;
};
template <>
struct ClosestCommonType<vtkm::UInt8>
{
using Type = vtkm::Int32;
};
template <>
struct ClosestCommonType<vtkm::Int16>
{
using Type = vtkm::Int32;
};
template <>
struct ClosestCommonType<vtkm::UInt16>
{
using Type = vtkm::Int32;
};
template <>
struct ClosestCommonType<vtkm::UInt32>
{
using Type = vtkm::Int64;
};
template <>
struct ClosestCommonType<vtkm::UInt64>
{
using Type = vtkm::Int64;
};
template <typename T>
struct ClosestFloat
{
using Type = T;
};
template <>
struct ClosestFloat<vtkm::Int8>
{
using Type = vtkm::Float32;
};
template <>
struct ClosestFloat<vtkm::UInt8>
{
using Type = vtkm::Float32;
};
template <>
struct ClosestFloat<vtkm::Int16>
{
using Type = vtkm::Float32;
};
template <>
struct ClosestFloat<vtkm::UInt16>
{
using Type = vtkm::Float32;
};
template <>
struct ClosestFloat<vtkm::Int32>
{
using Type = vtkm::Float64;
};
template <>
struct ClosestFloat<vtkm::UInt32>
{
using Type = vtkm::Float64;
};
template <>
struct ClosestFloat<vtkm::Int64>
{
using Type = vtkm::Float64;
};
template <>
struct ClosestFloat<vtkm::UInt64>
{
using Type = vtkm::Float64;
};
template <typename T>
vtkm::cont::VariantArrayHandle CreateVariantArrayHandle(const std::vector<T>& vec)
{
switch (vtkm::VecTraits<T>::NUM_COMPONENTS)
{
case 1:
{
using CommonType = typename ClosestCommonType<T>::Type;
constexpr bool not_same = !std::is_same<T, CommonType>::value;
if (not_same)
{
VTKM_LOG_S(vtkm::cont::LogLevel::Info,
"Type " << vtkm::io::internal::DataTypeName<T>::Name()
<< " is currently unsupported. Converting to "
<< vtkm::io::internal::DataTypeName<CommonType>::Name()
<< ".");
}
vtkm::cont::ArrayHandle<CommonType> output;
output.Allocate(static_cast<vtkm::Id>(vec.size()));
auto portal = output.WritePortal();
for (vtkm::Id i = 0; i < output.GetNumberOfValues(); ++i)
{
portal.Set(i, static_cast<CommonType>(vec[static_cast<std::size_t>(i)]));
}
return vtkm::cont::VariantArrayHandle(output);
}
case 2:
case 3:
case 9:
{
constexpr auto numComps = vtkm::VecTraits<T>::NUM_COMPONENTS;
using InComponentType = typename vtkm::VecTraits<T>::ComponentType;
using OutComponentType = typename ClosestFloat<InComponentType>::Type;
using CommonType = vtkm::Vec<OutComponentType, numComps>;
constexpr bool not_same = !std::is_same<T, CommonType>::value;
if (not_same)
{
VTKM_LOG_S(vtkm::cont::LogLevel::Info,
"Type " << vtkm::io::internal::DataTypeName<InComponentType>::Name() << "["
<< vtkm::VecTraits<T>::GetNumberOfComponents(T())
<< "] "
<< "is currently unsupported. Converting to "
<< vtkm::io::internal::DataTypeName<OutComponentType>::Name()
<< "["
<< numComps
<< "].");
}
vtkm::cont::ArrayHandle<CommonType> output;
output.Allocate(static_cast<vtkm::Id>(vec.size()));
auto portal = output.WritePortal();
for (vtkm::Id i = 0; i < output.GetNumberOfValues(); ++i)
{
CommonType outval = CommonType();
for (vtkm::IdComponent j = 0; j < numComps; ++j)
{
outval[j] = static_cast<OutComponentType>(
vtkm::VecTraits<T>::GetComponent(vec[static_cast<std::size_t>(i)], j));
}
portal.Set(i, outval);
}
return vtkm::cont::VariantArrayHandle(output);
}
default:
{
VTKM_LOG_S(vtkm::cont::LogLevel::Warn, "Only 1, 2, 3, or 9 components supported. Skipping.");
return vtkm::cont::VariantArrayHandle(vtkm::cont::ArrayHandle<vtkm::Float32>());
}
}
}
inline vtkm::cont::DynamicCellSet CreateCellSetStructured(const vtkm::Id3& dim)
{
if (dim[0] > 1 && dim[1] > 1 && dim[2] > 1)
@ -272,564 +93,102 @@ inline vtkm::cont::DynamicCellSet CreateCellSetStructured(const vtkm::Id3& dim)
} // namespace internal
VTKM_SILENCE_WEAK_VTABLE_WARNING_START
class VTKDataSetReaderBase
class VTKM_IO_EXPORT VTKDataSetReaderBase
{
protected:
std::unique_ptr<internal::VTKDataSetFile> DataFile;
vtkm::cont::DataSet DataSet;
private:
bool Loaded;
vtkm::cont::ArrayHandle<vtkm::Id> CellsPermutation;
friend class VTKDataSetReader;
public:
explicit VTKDataSetReaderBase(const char* fileName)
: DataFile(new internal::VTKDataSetFile)
, DataSet()
, Loaded(false)
{
this->DataFile->FileName = fileName;
}
explicit VTKM_CONT VTKDataSetReaderBase(const char* fileName);
explicit VTKDataSetReaderBase(const std::string& fileName)
: DataFile(new internal::VTKDataSetFile)
, DataSet()
, Loaded(false)
{
this->DataFile->FileName = fileName;
}
explicit VTKM_CONT VTKDataSetReaderBase(const std::string& fileName);
virtual ~VTKDataSetReaderBase() {}
virtual VTKM_CONT ~VTKDataSetReaderBase();
const vtkm::cont::DataSet& ReadDataSet()
{
if (!this->Loaded)
{
try
{
this->OpenFile();
this->ReadHeader();
this->Read();
this->CloseFile();
this->Loaded = true;
}
catch (std::ifstream::failure& e)
{
std::string message("IO Error: ");
throw vtkm::io::ErrorIO(message + e.what());
}
}
VTKDataSetReaderBase(const VTKDataSetReaderBase&) = delete;
void operator=(const VTKDataSetReaderBase&) = delete;
return this->DataSet;
}
const VTKM_CONT vtkm::cont::DataSet& ReadDataSet();
const vtkm::cont::DataSet& GetDataSet() const { return this->DataSet; }
virtual void PrintSummary(std::ostream& out) const
{
out << "VTKDataSetReader" << std::endl;
PrintVTKDataFileSummary(*this->DataFile.get(), out);
this->DataSet.PrintSummary(out);
}
virtual VTKM_CONT void PrintSummary(std::ostream& out) const;
protected:
void ReadPoints()
{
std::string dataType;
std::size_t numPoints;
this->DataFile->Stream >> numPoints >> dataType >> std::ws;
VTKM_CONT void ReadPoints();
vtkm::cont::VariantArrayHandle points =
this->DoReadArrayVariant(vtkm::cont::Field::Association::POINTS, dataType, numPoints, 3);
VTKM_CONT void ReadCells(vtkm::cont::ArrayHandle<vtkm::Id>& connectivity,
vtkm::cont::ArrayHandle<vtkm::IdComponent>& numIndices);
this->DataSet.AddCoordinateSystem(vtkm::cont::CoordinateSystem("coordinates", points));
}
VTKM_CONT void ReadShapes(vtkm::cont::ArrayHandle<vtkm::UInt8>& shapes);
void ReadCells(vtkm::cont::ArrayHandle<vtkm::Id>& connectivity,
vtkm::cont::ArrayHandle<vtkm::IdComponent>& numIndices)
{
vtkm::Id numCells, numInts;
this->DataFile->Stream >> numCells >> numInts >> std::ws;
connectivity.Allocate(numInts - numCells);
numIndices.Allocate(numCells);
std::vector<vtkm::Int32> buffer(static_cast<std::size_t>(numInts));
this->ReadArray(buffer);
vtkm::Int32* buffp = &buffer[0];
auto connectivityPortal = connectivity.WritePortal();
auto numIndicesPortal = numIndices.WritePortal();
for (vtkm::Id i = 0, connInd = 0; i < numCells; ++i)
{
vtkm::IdComponent numInds = static_cast<vtkm::IdComponent>(*buffp++);
numIndicesPortal.Set(i, numInds);
for (vtkm::IdComponent j = 0; j < numInds; ++j, ++connInd)
{
connectivityPortal.Set(connInd, static_cast<vtkm::Id>(*buffp++));
}
}
}
void ReadShapes(vtkm::cont::ArrayHandle<vtkm::UInt8>& shapes)
{
std::string tag;
vtkm::Id numCells;
this->DataFile->Stream >> tag >> numCells >> std::ws;
internal::parseAssert(tag == "CELL_TYPES");
shapes.Allocate(numCells);
std::vector<vtkm::Int32> buffer(static_cast<std::size_t>(numCells));
this->ReadArray(buffer);
vtkm::Int32* buffp = &buffer[0];
auto shapesPortal = shapes.WritePortal();
for (vtkm::Id i = 0; i < numCells; ++i)
{
shapesPortal.Set(i, static_cast<vtkm::UInt8>(*buffp++));
}
}
void ReadAttributes()
{
if (this->DataFile->Stream.eof())
{
return;
}
vtkm::cont::Field::Association association = vtkm::cont::Field::Association::ANY;
std::size_t size;
std::string tag;
this->DataFile->Stream >> tag;
while (!this->DataFile->Stream.eof())
{
if (tag == "POINT_DATA")
{
association = vtkm::cont::Field::Association::POINTS;
}
else if (tag == "CELL_DATA")
{
association = vtkm::cont::Field::Association::CELL_SET;
}
else
{
internal::parseAssert(false);
}
this->DataFile->Stream >> size;
while (!this->DataFile->Stream.eof())
{
this->DataFile->Stream >> tag;
if (tag == "SCALARS")
{
this->ReadScalars(association, size);
}
else if (tag == "COLOR_SCALARS")
{
this->ReadColorScalars(association, size);
}
else if (tag == "LOOKUP_TABLE")
{
this->ReadLookupTable();
}
else if (tag == "VECTORS" || tag == "NORMALS")
{
this->ReadVectors(association, size);
}
else if (tag == "TEXTURE_COORDINATES")
{
this->ReadTextureCoordinates(association, size);
}
else if (tag == "TENSORS")
{
this->ReadTensors(association, size);
}
else if (tag == "FIELD")
{
this->ReadFields(association, size);
}
else
{
break;
}
}
}
}
VTKM_CONT void ReadAttributes();
void SetCellsPermutation(const vtkm::cont::ArrayHandle<vtkm::Id>& permutation)
{
this->CellsPermutation = permutation;
}
vtkm::cont::ArrayHandle<vtkm::Id> GetCellsPermutation() const { return this->CellsPermutation; }
VTKM_CONT vtkm::cont::ArrayHandle<vtkm::Id> GetCellsPermutation() const
{
return this->CellsPermutation;
}
void TransferDataFile(VTKDataSetReaderBase& reader)
VTKM_CONT void TransferDataFile(VTKDataSetReaderBase& reader)
{
reader.DataFile.swap(this->DataFile);
this->DataFile.reset(nullptr);
}
virtual void CloseFile() { this->DataFile->Stream.close(); }
VTKM_CONT virtual void CloseFile();
VTKM_CONT virtual void Read() = 0;
private:
void OpenFile()
{
this->DataFile->Stream.exceptions(std::ifstream::failbit | std::ifstream::badbit);
try
{
this->DataFile->Stream.open(this->DataFile->FileName.c_str(),
std::ios_base::in | std::ios_base::binary);
}
catch (std::ifstream::failure&)
{
std::string message("could not open file \"" + this->DataFile->FileName + "\"");
throw vtkm::io::ErrorIO(message);
}
}
void ReadHeader()
{
char vstring[] = "# vtk DataFile Version";
const std::size_t vlen = sizeof(vstring);
// Read version line
char vbuf[vlen];
this->DataFile->Stream.read(vbuf, vlen - 1);
vbuf[vlen - 1] = '\0';
if (std::string(vbuf) != std::string(vstring))
{
throw vtkm::io::ErrorIO("Incorrect file format.");
}
char dot;
this->DataFile->Stream >> this->DataFile->Version[0] >> dot >> this->DataFile->Version[1];
// skip rest of the line
std::string skip;
std::getline(this->DataFile->Stream, skip);
if ((this->DataFile->Version[0] > 4) ||
(this->DataFile->Version[0] == 4 && this->DataFile->Version[1] > 2))
{
VTKM_LOG_S(vtkm::cont::LogLevel::Warn,
"Reader may not correctly read >v4.2 files. Reading version "
<< this->DataFile->Version[0]
<< "."
<< this->DataFile->Version[1]
<< ".\n");
}
// Read title line
std::getline(this->DataFile->Stream, this->DataFile->Title);
// Read format line
this->DataFile->IsBinary = false;
std::string format;
this->DataFile->Stream >> format >> std::ws;
if (format == "BINARY")
{
this->DataFile->IsBinary = true;
}
else if (format != "ASCII")
{
throw vtkm::io::ErrorIO("Unsupported Format.");
}
// Read structure line
std::string tag, structStr;
this->DataFile->Stream >> tag >> structStr >> std::ws;
internal::parseAssert(tag == "DATASET");
this->DataFile->Structure = vtkm::io::internal::DataSetStructureId(structStr);
if (this->DataFile->Structure == vtkm::io::internal::DATASET_UNKNOWN)
{
throw vtkm::io::ErrorIO("Unsupported DataSet type.");
}
}
virtual void Read() = 0;
void AddField(const std::string& name,
vtkm::cont::Field::Association association,
vtkm::cont::VariantArrayHandle& data)
{
if (data.GetNumberOfValues() > 0)
{
switch (association)
{
case vtkm::cont::Field::Association::POINTS:
case vtkm::cont::Field::Association::WHOLE_MESH:
this->DataSet.AddField(vtkm::cont::Field(name, association, data));
break;
case vtkm::cont::Field::Association::CELL_SET:
this->DataSet.AddField(vtkm::cont::Field(name, association, data));
break;
default:
VTKM_LOG_S(vtkm::cont::LogLevel::Warn,
"Not recording field '" << name << "' because it has an unknown association");
break;
}
}
}
void ReadScalars(vtkm::cont::Field::Association association, std::size_t numElements)
{
std::string dataName, dataType, lookupTableName;
vtkm::IdComponent numComponents = 1;
this->DataFile->Stream >> dataName >> dataType;
std::string tag;
this->DataFile->Stream >> tag;
if (tag != "LOOKUP_TABLE")
{
try
{
numComponents = std::stoi(tag);
}
catch (std::invalid_argument&)
{
internal::parseAssert(false);
}
this->DataFile->Stream >> tag;
}
internal::parseAssert(tag == "LOOKUP_TABLE");
this->DataFile->Stream >> lookupTableName >> std::ws;
vtkm::cont::VariantArrayHandle data =
this->DoReadArrayVariant(association, dataType, numElements, numComponents);
this->AddField(dataName, association, data);
}
void ReadColorScalars(vtkm::cont::Field::Association association, std::size_t numElements)
{
VTKM_LOG_S(vtkm::cont::LogLevel::Warn,
"Support for COLOR_SCALARS is not implemented. Skipping.");
std::string dataName;
vtkm::IdComponent numComponents;
this->DataFile->Stream >> dataName >> numComponents >> std::ws;
std::string dataType = this->DataFile->IsBinary ? "unsigned_char" : "float";
vtkm::cont::VariantArrayHandle data =
this->DoReadArrayVariant(association, dataType, numElements, numComponents);
this->AddField(dataName, association, data);
}
void ReadLookupTable()
{
VTKM_LOG_S(vtkm::cont::LogLevel::Warn,
"Support for LOOKUP_TABLE is not implemented. Skipping.");
std::string dataName;
std::size_t numEntries;
this->DataFile->Stream >> dataName >> numEntries >> std::ws;
this->SkipArray(numEntries, vtkm::Vec<vtkm::io::internal::ColorChannel8, 4>());
}
void ReadTextureCoordinates(vtkm::cont::Field::Association association, std::size_t numElements)
{
std::string dataName;
vtkm::IdComponent numComponents;
std::string dataType;
this->DataFile->Stream >> dataName >> numComponents >> dataType >> std::ws;
vtkm::cont::VariantArrayHandle data =
this->DoReadArrayVariant(association, dataType, numElements, numComponents);
this->AddField(dataName, association, data);
}
void ReadVectors(vtkm::cont::Field::Association association, std::size_t numElements)
{
std::string dataName;
std::string dataType;
this->DataFile->Stream >> dataName >> dataType >> std::ws;
vtkm::cont::VariantArrayHandle data =
this->DoReadArrayVariant(association, dataType, numElements, 3);
this->AddField(dataName, association, data);
}
void ReadTensors(vtkm::cont::Field::Association association, std::size_t numElements)
{
std::string dataName;
std::string dataType;
this->DataFile->Stream >> dataName >> dataType >> std::ws;
vtkm::cont::VariantArrayHandle data =
this->DoReadArrayVariant(association, dataType, numElements, 9);
this->AddField(dataName, association, data);
}
void ReadFields(vtkm::cont::Field::Association association, std::size_t expectedNumElements)
{
std::string dataName;
vtkm::Id numArrays;
this->DataFile->Stream >> dataName >> numArrays >> std::ws;
for (vtkm::Id i = 0; i < numArrays; ++i)
{
std::size_t numTuples;
vtkm::IdComponent numComponents;
std::string arrayName, dataType;
this->DataFile->Stream >> arrayName >> numComponents >> numTuples >> dataType >> std::ws;
if (numTuples == expectedNumElements)
{
vtkm::cont::VariantArrayHandle data =
this->DoReadArrayVariant(association, dataType, numTuples, numComponents);
this->AddField(arrayName, association, data);
}
else
{
VTKM_LOG_S(vtkm::cont::LogLevel::Warn,
"Field " << arrayName
<< "'s size does not match expected number of elements. Skipping");
}
}
}
VTKM_CONT void OpenFile();
VTKM_CONT void ReadHeader();
VTKM_CONT void AddField(const std::string& name,
vtkm::cont::Field::Association association,
vtkm::cont::VariantArrayHandle& data);
VTKM_CONT void ReadScalars(vtkm::cont::Field::Association association, std::size_t numElements);
VTKM_CONT void ReadColorScalars(vtkm::cont::Field::Association association,
std::size_t numElements);
VTKM_CONT void ReadLookupTable();
VTKM_CONT void ReadTextureCoordinates(vtkm::cont::Field::Association association,
std::size_t numElements);
VTKM_CONT void ReadVectors(vtkm::cont::Field::Association association, std::size_t numElements);
VTKM_CONT void ReadTensors(vtkm::cont::Field::Association association, std::size_t numElements);
VTKM_CONT void ReadFields(vtkm::cont::Field::Association association,
std::size_t expectedNumElements);
protected:
void ReadGlobalFields(std::vector<vtkm::Float32>* visitBounds = nullptr)
{
std::string dataName;
vtkm::Id numArrays;
this->DataFile->Stream >> dataName >> numArrays >> std::ws;
for (vtkm::Id i = 0; i < numArrays; ++i)
{
std::size_t numTuples;
vtkm::IdComponent numComponents;
std::string arrayName, dataType;
this->DataFile->Stream >> arrayName >> numComponents >> numTuples >> dataType >> std::ws;
if (arrayName == "avtOriginalBounds" && visitBounds)
{
visitBounds->resize(6);
internal::parseAssert(numComponents == 1 && numTuples == 6);
// parse the bounds and fill the bounds vector
this->ReadArray(*visitBounds);
}
else
{
VTKM_LOG_S(vtkm::cont::LogLevel::Info,
"Support for global field " << arrayName << " not implemented. Skipping.");
this->DoSkipArrayVariant(dataType, numTuples, numComponents);
}
}
}
VTKM_CONT void ReadGlobalFields(std::vector<vtkm::Float32>* visitBounds = nullptr);
private:
class SkipArrayVariant
{
public:
SkipArrayVariant(VTKDataSetReaderBase* reader, std::size_t numElements)
: Reader(reader)
, NumElements(numElements)
{
}
template <typename T>
void operator()(T) const
{
this->Reader->SkipArray(this->NumElements, T());
}
template <typename T>
void operator()(vtkm::IdComponent numComponents, T) const
{
this->Reader->SkipArray(this->NumElements * static_cast<std::size_t>(numComponents), T());
}
protected:
VTKDataSetReaderBase* Reader;
std::size_t NumElements;
};
class ReadArrayVariant : public SkipArrayVariant
{
public:
ReadArrayVariant(VTKDataSetReaderBase* reader,
vtkm::cont::Field::Association association,
std::size_t numElements,
vtkm::cont::VariantArrayHandle& data)
: SkipArrayVariant(reader, numElements)
, Association(association)
, Data(&data)
{
}
template <typename T>
void operator()(T) const
{
std::vector<T> buffer(this->NumElements);
this->Reader->ReadArray(buffer);
if ((this->Association != vtkm::cont::Field::Association::CELL_SET) ||
(this->Reader->GetCellsPermutation().GetNumberOfValues() < 1))
{
*this->Data = internal::CreateVariantArrayHandle(buffer);
}
else
{
// If we are reading data associated with a cell set, we need to (sometimes) permute the
// data due to differences between VTK and VTK-m cell shapes.
auto permutation = this->Reader->GetCellsPermutation().ReadPortal();
vtkm::Id outSize = permutation.GetNumberOfValues();
std::vector<T> permutedBuffer(static_cast<std::size_t>(outSize));
for (vtkm::Id outIndex = 0; outIndex < outSize; outIndex++)
{
std::size_t inIndex = static_cast<std::size_t>(permutation.Get(outIndex));
permutedBuffer[static_cast<std::size_t>(outIndex)] = buffer[inIndex];
}
*this->Data = internal::CreateVariantArrayHandle(permutedBuffer);
}
}
template <typename T>
void operator()(vtkm::IdComponent numComponents, T) const
{
VTKM_LOG_S(vtkm::cont::LogLevel::Warn,
"Support for " << numComponents << " components not implemented. Skipping.");
SkipArrayVariant::operator()(numComponents, T());
}
private:
vtkm::cont::Field::Association Association;
vtkm::cont::VariantArrayHandle* Data;
};
class SkipArrayVariant;
class ReadArrayVariant;
//Make the Array parsing methods protected so that derived classes
//can call the methods.
protected:
void DoSkipArrayVariant(std::string dataType,
std::size_t numElements,
vtkm::IdComponent numComponents)
{
// string is unsupported for SkipArrayVariant, so it requires some
// special handling
if (dataType == "string")
{
const vtkm::Id stringCount = numComponents * static_cast<vtkm::Id>(numElements);
for (vtkm::Id i = 0; i < stringCount; ++i)
{
std::string trash;
this->DataFile->Stream >> trash;
}
}
else
{
vtkm::io::internal::DataType typeId = vtkm::io::internal::DataTypeId(dataType);
vtkm::io::internal::SelectTypeAndCall(
typeId, numComponents, SkipArrayVariant(this, numElements));
}
}
vtkm::cont::VariantArrayHandle DoReadArrayVariant(vtkm::cont::Field::Association association,
std::string dataType,
std::size_t numElements,
vtkm::IdComponent numComponents)
{
// Create empty data to start so that the return can check if data were actually read
vtkm::cont::ArrayHandle<vtkm::Float32> empty;
vtkm::cont::VariantArrayHandle data(empty);
vtkm::io::internal::DataType typeId = vtkm::io::internal::DataTypeId(dataType);
vtkm::io::internal::SelectTypeAndCall(
typeId, numComponents, ReadArrayVariant(this, association, numElements, data));
return data;
}
VTKM_CONT void DoSkipArrayVariant(std::string dataType,
std::size_t numElements,
vtkm::IdComponent numComponents);
VTKM_CONT vtkm::cont::VariantArrayHandle DoReadArrayVariant(
vtkm::cont::Field::Association association,
std::string dataType,
std::size_t numElements,
vtkm::IdComponent numComponents);
template <typename T>
void ReadArray(std::vector<T>& buffer)
VTKM_CONT void ReadArray(std::vector<T>& buffer)
{
using ComponentType = typename vtkm::VecTraits<T>::ComponentType;
constexpr vtkm::IdComponent numComponents = vtkm::VecTraits<T>::NUM_COMPONENTS;
@ -861,7 +220,8 @@ protected:
}
template <vtkm::IdComponent NumComponents>
void ReadArray(std::vector<vtkm::Vec<vtkm::io::internal::DummyBitType, NumComponents>>& buffer)
VTKM_CONT void ReadArray(
std::vector<vtkm::Vec<vtkm::io::internal::DummyBitType, NumComponents>>& buffer)
{
VTKM_LOG_S(vtkm::cont::LogLevel::Warn,
"Support for data type 'bit' is not implemented. Skipping.");
@ -869,13 +229,7 @@ protected:
buffer.clear();
}
void ReadArray(std::vector<vtkm::io::internal::DummyBitType>& buffer)
{
VTKM_LOG_S(vtkm::cont::LogLevel::Warn,
"Support for data type 'bit' is not implemented. Skipping.");
this->SkipArray(buffer.size(), vtkm::io::internal::DummyBitType());
buffer.clear();
}
VTKM_CONT void ReadArray(std::vector<vtkm::io::internal::DummyBitType>& buffer);
template <typename T>
void SkipArray(std::size_t numElements, T)
@ -912,99 +266,13 @@ protected:
NumComponents);
}
void SkipArray(std::size_t numElements,
vtkm::io::internal::DummyBitType,
vtkm::IdComponent numComponents = 1)
{
if (this->DataFile->IsBinary)
{
numElements = (numElements + 7) / 8;
this->DataFile->Stream.seekg(static_cast<std::streamoff>(numElements), std::ios_base::cur);
}
else
{
for (std::size_t i = 0; i < numElements; ++i)
{
vtkm::UInt16 val;
this->DataFile->Stream >> val;
}
}
this->DataFile->Stream >> std::ws;
this->SkipArrayMetaData(numComponents);
}
VTKM_CONT void SkipArray(std::size_t numElements,
vtkm::io::internal::DummyBitType,
vtkm::IdComponent numComponents = 1);
void SkipArrayMetaData(vtkm::IdComponent numComponents)
{
if (!this->DataFile->Stream.good())
{
return;
}
auto begining = this->DataFile->Stream.tellg();
std::string tag;
this->DataFile->Stream >> tag;
if (tag != "METADATA")
{
this->DataFile->Stream.seekg(begining);
return;
}
VTKM_LOG_S(vtkm::cont::LogLevel::Warn, "METADATA is not supported. Attempting to Skip.");
this->DataFile->Stream >> tag >> std::ws;
if (tag == "COMPONENT_NAMES")
{
std::string name;
for (vtkm::IdComponent i = 0; i < numComponents; ++i)
{
this->DataFile->Stream >> name >> std::ws;
}
}
else if (tag == "INFORMATION")
{
int numKeys = 0;
this->DataFile->Stream >> numKeys >> std::ws;
// Skipping INFORMATION is tricky. The reader needs to be aware of the types of the
// information, which is not provided in the file.
// Here we will just skip until an empty line is found.
// However, if there are no keys, then there is nothing to read (and the stream tends
// to skip over empty lines.
if (numKeys > 0)
{
std::string line;
do
{
std::getline(this->DataFile->Stream, line);
} while (this->DataFile->Stream.good() && !line.empty());
// Eat any remaining whitespace after the INFORMATION to be ready to read the next token
this->DataFile->Stream >> std::ws;
}
}
else
{
internal::parseAssert(false);
}
}
protected:
std::unique_ptr<internal::VTKDataSetFile> DataFile;
vtkm::cont::DataSet DataSet;
private:
bool Loaded;
vtkm::cont::ArrayHandle<vtkm::Id> CellsPermutation;
friend class VTKDataSetReader;
VTKM_CONT void SkipArrayMetaData(vtkm::IdComponent numComponents);
};
VTKM_SILENCE_WEAK_VTABLE_WARNING_END
}
} // vtkm::io
VTKM_BASIC_TYPE_VECTOR(vtkm::io::internal::ColorChannel8)
VTKM_BASIC_TYPE_VECTOR(vtkm::io::internal::DummyBitType)
#endif // vtk_m_io_VTKDataSetReaderBase_h

407
vtkm/io/VTKDataSetWriter.cxx Normal file
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@ -0,0 +1,407 @@
//============================================================================
// Copyright (c) Kitware, Inc.
// All rights reserved.
// See LICENSE.txt for details.
//
// This software is distributed WITHOUT ANY WARRANTY; without even
// the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
// PURPOSE. See the above copyright notice for more information.
//============================================================================
#include <vtkm/io/VTKDataSetWriter.h>
#include <vtkm/CellShape.h>
#include <vtkm/cont/CellSetExplicit.h>
#include <vtkm/cont/CellSetSingleType.h>
#include <vtkm/cont/CellSetStructured.h>
#include <vtkm/cont/ErrorBadType.h>
#include <vtkm/cont/ErrorBadValue.h>
#include <vtkm/cont/Field.h>
#include <vtkm/io/ErrorIO.h>
#include <vtkm/io/internal/VTKDataSetTypes.h>
#include <algorithm>
#include <cctype>
#include <cstring>
#include <fstream>
#include <iostream>
#include <string>
#include <vector>
namespace
{
struct OutputPointsFunctor
{
private:
std::ostream& out;
template <typename PortalType>
VTKM_CONT void Output(const PortalType& portal) const
{
for (vtkm::Id index = 0; index < portal.GetNumberOfValues(); index++)
{
const int VTKDims = 3; // VTK files always require 3 dims for points
using ValueType = typename PortalType::ValueType;
using VecType = typename vtkm::VecTraits<ValueType>;
const ValueType& value = portal.Get(index);
vtkm::IdComponent numComponents = VecType::GetNumberOfComponents(value);
for (vtkm::IdComponent c = 0; c < numComponents && c < VTKDims; c++)
{
out << (c == 0 ? "" : " ") << VecType::GetComponent(value, c);
}
for (vtkm::IdComponent c = numComponents; c < VTKDims; c++)
{
out << " 0";
}
out << '\n';
}
}
public:
VTKM_CONT
OutputPointsFunctor(std::ostream& o)
: out(o)
{
}
template <typename T, typename Storage>
VTKM_CONT void operator()(const vtkm::cont::ArrayHandle<T, Storage>& array) const
{
this->Output(array.ReadPortal());
}
};
struct OutputFieldFunctor
{
private:
std::ostream& out;
template <typename PortalType>
VTKM_CONT void Output(const PortalType& portal) const
{
for (vtkm::Id index = 0; index < portal.GetNumberOfValues(); index++)
{
using ValueType = typename PortalType::ValueType;
using VecType = typename vtkm::VecTraits<ValueType>;
const ValueType& value = portal.Get(index);
vtkm::IdComponent numComponents = VecType::GetNumberOfComponents(value);
for (vtkm::IdComponent c = 0; c < numComponents; c++)
{
out << (c == 0 ? "" : " ") << VecType::GetComponent(value, c);
}
out << '\n';
}
}
public:
VTKM_CONT
OutputFieldFunctor(std::ostream& o)
: out(o)
{
}
template <typename T, typename Storage>
VTKM_CONT void operator()(const vtkm::cont::ArrayHandle<T, Storage>& array) const
{
this->Output(array.ReadPortal());
}
};
class GetDataTypeName
{
public:
GetDataTypeName(std::string& name)
: Name(&name)
{
}
template <typename ArrayHandleType>
void operator()(const ArrayHandleType&) const
{
using DataType = typename vtkm::VecTraits<typename ArrayHandleType::ValueType>::ComponentType;
*this->Name = vtkm::io::internal::DataTypeName<DataType>::Name();
}
private:
std::string* Name;
};
void WritePoints(std::ostream& out, const vtkm::cont::DataSet& dataSet)
{
///\todo: support other coordinate systems
int cindex = 0;
auto cdata = dataSet.GetCoordinateSystem(cindex).GetData();
vtkm::Id npoints = cdata.GetNumberOfValues();
out << "POINTS " << npoints << " " << vtkm::io::internal::DataTypeName<vtkm::FloatDefault>::Name()
<< " " << '\n';
OutputPointsFunctor{ out }(cdata);
}
template <class CellSetType>
void WriteExplicitCells(std::ostream& out, const CellSetType& cellSet)
{
vtkm::Id nCells = cellSet.GetNumberOfCells();
vtkm::Id conn_length = 0;
for (vtkm::Id i = 0; i < nCells; ++i)
{
conn_length += 1 + cellSet.GetNumberOfPointsInCell(i);
}
out << "CELLS " << nCells << " " << conn_length << '\n';
for (vtkm::Id i = 0; i < nCells; ++i)
{
vtkm::cont::ArrayHandle<vtkm::Id> ids;
vtkm::Id nids = cellSet.GetNumberOfPointsInCell(i);
cellSet.GetIndices(i, ids);
out << nids;
auto IdPortal = ids.ReadPortal();
for (int j = 0; j < nids; ++j)
out << " " << IdPortal.Get(j);
out << '\n';
}
out << "CELL_TYPES " << nCells << '\n';
for (vtkm::Id i = 0; i < nCells; ++i)
{
vtkm::Id shape = cellSet.GetCellShape(i);
out << shape << '\n';
}
}
void WriteVertexCells(std::ostream& out, const vtkm::cont::DataSet& dataSet)
{
vtkm::Id nCells = dataSet.GetCoordinateSystem(0).GetNumberOfPoints();
out << "CELLS " << nCells << " " << nCells * 2 << '\n';
for (int i = 0; i < nCells; i++)
{
out << "1 " << i << '\n';
}
out << "CELL_TYPES " << nCells << '\n';
for (int i = 0; i < nCells; i++)
{
out << vtkm::CELL_SHAPE_VERTEX << '\n';
}
}
void WritePointFields(std::ostream& out, const vtkm::cont::DataSet& dataSet)
{
bool wrote_header = false;
for (vtkm::Id f = 0; f < dataSet.GetNumberOfFields(); f++)
{
const vtkm::cont::Field field = dataSet.GetField(f);
if (field.GetAssociation() != vtkm::cont::Field::Association::POINTS)
{
continue;
}
vtkm::Id npoints = field.GetNumberOfValues();
int ncomps = field.GetData().GetNumberOfComponents();
if (ncomps > 4)
{
continue;
}
if (!wrote_header)
{
out << "POINT_DATA " << npoints << '\n';
wrote_header = true;
}
std::string typeName;
vtkm::cont::CastAndCall(field.GetData().ResetTypes(vtkm::TypeListAll{}),
GetDataTypeName(typeName));
std::string name = field.GetName();
for (auto& c : name)
{
if (std::isspace(c))
{
c = '_';
}
}
out << "SCALARS " << name << " " << typeName << " " << ncomps << '\n';
out << "LOOKUP_TABLE default" << '\n';
vtkm::cont::CastAndCall(field.GetData().ResetTypes(vtkm::TypeListAll{}),
OutputFieldFunctor(out));
}
}
void WriteCellFields(std::ostream& out, const vtkm::cont::DataSet& dataSet)
{
bool wrote_header = false;
for (vtkm::Id f = 0; f < dataSet.GetNumberOfFields(); f++)
{
const vtkm::cont::Field field = dataSet.GetField(f);
if (!field.IsFieldCell())
{
continue;
}
vtkm::Id ncells = field.GetNumberOfValues();
int ncomps = field.GetData().GetNumberOfComponents();
if (ncomps > 4)
continue;
if (!wrote_header)
{
out << "CELL_DATA " << ncells << '\n';
wrote_header = true;
}
std::string typeName;
vtkm::cont::CastAndCall(field.GetData().ResetTypes(vtkm::TypeListAll{}),
GetDataTypeName(typeName));
std::string name = field.GetName();
for (auto& c : name)
{
if (std::isspace(c))
{
c = '_';
}
}
out << "SCALARS " << name << " " << typeName << " " << ncomps << '\n';
out << "LOOKUP_TABLE default" << '\n';
vtkm::cont::CastAndCall(field.GetData().ResetTypes(vtkm::TypeListAll{}),
OutputFieldFunctor(out));
}
}
void WriteDataSetAsPoints(std::ostream& out, const vtkm::cont::DataSet& dataSet)
{
out << "DATASET UNSTRUCTURED_GRID" << '\n';
WritePoints(out, dataSet);
WriteVertexCells(out, dataSet);
}
template <class CellSetType>
void WriteDataSetAsUnstructured(std::ostream& out,
const vtkm::cont::DataSet& dataSet,
const CellSetType& cellSet)
{
out << "DATASET UNSTRUCTURED_GRID" << '\n';
WritePoints(out, dataSet);
WriteExplicitCells(out, cellSet);
}
template <vtkm::IdComponent DIM>
void WriteDataSetAsStructured(std::ostream& out,
const vtkm::cont::DataSet& dataSet,
const vtkm::cont::CellSetStructured<DIM>& cellSet)
{
///\todo: support uniform/rectilinear
out << "DATASET STRUCTURED_GRID" << '\n';
auto pointDimensions = cellSet.GetPointDimensions();
using VTraits = vtkm::VecTraits<decltype(pointDimensions)>;
out << "DIMENSIONS ";
out << VTraits::GetComponent(pointDimensions, 0) << " ";
out << (DIM > 1 ? VTraits::GetComponent(pointDimensions, 1) : 1) << " ";
out << (DIM > 2 ? VTraits::GetComponent(pointDimensions, 2) : 1) << " ";
WritePoints(out, dataSet);
}
void Write(std::ostream& out, const vtkm::cont::DataSet& dataSet, bool just_points = false)
{
// The Paraview parser cannot handle scientific notation:
out << std::fixed;
out << "# vtk DataFile Version 3.0" << '\n';
out << "vtk output" << '\n';
out << "ASCII" << '\n';
if (just_points)
{
WriteDataSetAsPoints(out, dataSet);
WritePointFields(out, dataSet);
}
else
{
vtkm::cont::DynamicCellSet cellSet = dataSet.GetCellSet();
if (cellSet.IsType<vtkm::cont::CellSetExplicit<>>())
{
WriteDataSetAsUnstructured(out, dataSet, cellSet.Cast<vtkm::cont::CellSetExplicit<>>());
}
else if (cellSet.IsType<vtkm::cont::CellSetStructured<1>>())
{
WriteDataSetAsStructured(out, dataSet, cellSet.Cast<vtkm::cont::CellSetStructured<1>>());
}
else if (cellSet.IsType<vtkm::cont::CellSetStructured<2>>())
{
WriteDataSetAsStructured(out, dataSet, cellSet.Cast<vtkm::cont::CellSetStructured<2>>());
}
else if (cellSet.IsType<vtkm::cont::CellSetStructured<3>>())
{
WriteDataSetAsStructured(out, dataSet, cellSet.Cast<vtkm::cont::CellSetStructured<3>>());
}
else if (cellSet.IsType<vtkm::cont::CellSetSingleType<>>())
{
// these function just like explicit cell sets
WriteDataSetAsUnstructured(out, dataSet, cellSet.Cast<vtkm::cont::CellSetSingleType<>>());
}
else
{
throw vtkm::cont::ErrorBadType("Could not determine type to write out.");
}
WritePointFields(out, dataSet);
WriteCellFields(out, dataSet);
}
}
} // anonymous namespace
namespace vtkm
{
namespace io
{
VTKDataSetWriter::VTKDataSetWriter(const char* fileName)
: FileName(fileName)
{
}
VTKDataSetWriter::VTKDataSetWriter(const std::string& fileName)
: FileName(fileName)
{
}
void VTKDataSetWriter::WriteDataSet(const vtkm::cont::DataSet& dataSet, bool just_points) const
{
if (dataSet.GetNumberOfCoordinateSystems() < 1)
{
throw vtkm::cont::ErrorBadValue(
"DataSet has no coordinate system, which is not supported by VTK file format.");
}
try
{
std::ofstream fileStream(this->FileName.c_str(), std::fstream::trunc);
Write(fileStream, dataSet, just_points);
fileStream.close();
}
catch (std::ofstream::failure& error)
{
throw vtkm::io::ErrorIO(error.what());
}
}
}
} // namespace vtkm::io

388
vtkm/io/VTKDataSetWriter.h
View File

@ -10,400 +10,22 @@
#ifndef vtk_m_io_DataSetWriter_h
#define vtk_m_io_DataSetWriter_h
#include <cctype>
#include <vtkm/CellShape.h>
#include <vtkm/cont/CellSetExplicit.h>
#include <vtkm/cont/CellSetSingleType.h>
#include <vtkm/cont/CellSetStructured.h>
#include <vtkm/cont/DataSet.h>
#include <vtkm/cont/ErrorBadType.h>
#include <vtkm/cont/ErrorBadValue.h>
#include <vtkm/cont/Field.h>
#include <vtkm/io/ErrorIO.h>
#include <vtkm/io/internal/VTKDataSetTypes.h>
#include <algorithm>
#include <cstring>
#include <fstream>
#include <iostream>
#include <string>
#include <vector>
#include <vtkm/io/vtkm_io_export.h>
namespace vtkm
{
namespace io
{
namespace detail
{
struct OutputPointsFunctor
{
private:
std::ostream& out;
template <typename PortalType>
VTKM_CONT void Output(const PortalType& portal) const
{
for (vtkm::Id index = 0; index < portal.GetNumberOfValues(); index++)
{
const int VTKDims = 3; // VTK files always require 3 dims for points
using ValueType = typename PortalType::ValueType;
using VecType = typename vtkm::VecTraits<ValueType>;
const ValueType& value = portal.Get(index);
vtkm::IdComponent numComponents = VecType::GetNumberOfComponents(value);
for (vtkm::IdComponent c = 0; c < numComponents && c < VTKDims; c++)
{
out << (c == 0 ? "" : " ") << VecType::GetComponent(value, c);
}
for (vtkm::IdComponent c = numComponents; c < VTKDims; c++)
{
out << " 0";
}
out << '\n';
}
}
public:
VTKM_CONT
OutputPointsFunctor(std::ostream& o)
: out(o)
{
}
template <typename T, typename Storage>
VTKM_CONT void operator()(const vtkm::cont::ArrayHandle<T, Storage>& array) const
{
this->Output(array.ReadPortal());
}
};
struct OutputFieldFunctor
{
private:
std::ostream& out;
template <typename PortalType>
VTKM_CONT void Output(const PortalType& portal) const
{
for (vtkm::Id index = 0; index < portal.GetNumberOfValues(); index++)
{
using ValueType = typename PortalType::ValueType;
using VecType = typename vtkm::VecTraits<ValueType>;
const ValueType& value = portal.Get(index);
vtkm::IdComponent numComponents = VecType::GetNumberOfComponents(value);
for (vtkm::IdComponent c = 0; c < numComponents; c++)
{
out << (c == 0 ? "" : " ") << VecType::GetComponent(value, c);
}
out << '\n';
}
}
public:
VTKM_CONT
OutputFieldFunctor(std::ostream& o)
: out(o)
{
}
template <typename T, typename Storage>
VTKM_CONT void operator()(const vtkm::cont::ArrayHandle<T, Storage>& array) const
{
this->Output(array.ReadPortal());
}
};
class GetDataTypeName
struct VTKM_IO_EXPORT VTKDataSetWriter
{
public:
GetDataTypeName(std::string& name)
: Name(&name)
{
}
VTKM_CONT VTKDataSetWriter(const char* fileName);
VTKM_CONT VTKDataSetWriter(const std::string& fileName);
template <typename ArrayHandleType>
void operator()(const ArrayHandleType&) const
{
using DataType = typename vtkm::VecTraits<typename ArrayHandleType::ValueType>::ComponentType;
*this->Name = vtkm::io::internal::DataTypeName<DataType>::Name();
}
private:
std::string* Name;
};
} // namespace detail
struct VTKDataSetWriter
{
private:
static void WritePoints(std::ostream& out, const vtkm::cont::DataSet& dataSet)
{
///\todo: support other coordinate systems
int cindex = 0;
auto cdata = dataSet.GetCoordinateSystem(cindex).GetData();
vtkm::Id npoints = cdata.GetNumberOfValues();
out << "POINTS " << npoints << " "
<< vtkm::io::internal::DataTypeName<vtkm::FloatDefault>::Name() << " " << '\n';
detail::OutputPointsFunctor{ out }(cdata);
}
template <class CellSetType>
static void WriteExplicitCells(std::ostream& out, const CellSetType& cellSet)
{
vtkm::Id nCells = cellSet.GetNumberOfCells();
vtkm::Id conn_length = 0;
for (vtkm::Id i = 0; i < nCells; ++i)
{
conn_length += 1 + cellSet.GetNumberOfPointsInCell(i);
}
out << "CELLS " << nCells << " " << conn_length << '\n';
for (vtkm::Id i = 0; i < nCells; ++i)
{
vtkm::cont::ArrayHandle<vtkm::Id> ids;
vtkm::Id nids = cellSet.GetNumberOfPointsInCell(i);
cellSet.GetIndices(i, ids);
out << nids;
auto IdPortal = ids.ReadPortal();
for (int j = 0; j < nids; ++j)
out << " " << IdPortal.Get(j);
out << '\n';
}
out << "CELL_TYPES " << nCells << '\n';
for (vtkm::Id i = 0; i < nCells; ++i)
{
vtkm::Id shape = cellSet.GetCellShape(i);
out << shape << '\n';
}
}
static void WriteVertexCells(std::ostream& out, const vtkm::cont::DataSet& dataSet)
{
vtkm::Id nCells = dataSet.GetCoordinateSystem(0).GetNumberOfPoints();
out << "CELLS " << nCells << " " << nCells * 2 << '\n';
for (int i = 0; i < nCells; i++)
{
out << "1 " << i << '\n';
}
out << "CELL_TYPES " << nCells << '\n';
for (int i = 0; i < nCells; i++)
{
out << vtkm::CELL_SHAPE_VERTEX << '\n';
}
}
static void WritePointFields(std::ostream& out, const vtkm::cont::DataSet& dataSet)
{
bool wrote_header = false;
for (vtkm::Id f = 0; f < dataSet.GetNumberOfFields(); f++)
{
const vtkm::cont::Field field = dataSet.GetField(f);
if (field.GetAssociation() != vtkm::cont::Field::Association::POINTS)
{
continue;
}
vtkm::Id npoints = field.GetNumberOfValues();
int ncomps = field.GetData().GetNumberOfComponents();
if (ncomps > 4)
{
continue;
}
if (!wrote_header)
{
out << "POINT_DATA " << npoints << '\n';
wrote_header = true;
}
std::string typeName;
vtkm::cont::CastAndCall(field.GetData().ResetTypes(TypeListAll{}),
detail::GetDataTypeName(typeName));
std::string name = field.GetName();
for (auto& c : name)
{
if (std::isspace(c))
{
c = '_';
}
}
out << "SCALARS " << name << " " << typeName << " " << ncomps << '\n';
out << "LOOKUP_TABLE default" << '\n';
vtkm::cont::CastAndCall(field.GetData().ResetTypes(TypeListAll{}),
detail::OutputFieldFunctor(out));
}
}
static void WriteCellFields(std::ostream& out, const vtkm::cont::DataSet& dataSet)
{
bool wrote_header = false;
for (vtkm::Id f = 0; f < dataSet.GetNumberOfFields(); f++)
{
const vtkm::cont::Field field = dataSet.GetField(f);
if (!field.IsFieldCell())
{
continue;
}
vtkm::Id ncells = field.GetNumberOfValues();
int ncomps = field.GetData().GetNumberOfComponents();
if (ncomps > 4)
continue;
if (!wrote_header)
{
out << "CELL_DATA " << ncells << '\n';
wrote_header = true;
}
std::string typeName;
vtkm::cont::CastAndCall(field.GetData().ResetTypes(TypeListAll{}),
detail::GetDataTypeName(typeName));
std::string name = field.GetName();
for (auto& c : name)
{
if (std::isspace(c))
{
c = '_';
}
}
out << "SCALARS " << name << " " << typeName << " " << ncomps << '\n';
out << "LOOKUP_TABLE default" << '\n';
vtkm::cont::CastAndCall(field.GetData().ResetTypes(TypeListAll{}),
detail::OutputFieldFunctor(out));
}
}
static void WriteDataSetAsPoints(std::ostream& out, const vtkm::cont::DataSet& dataSet)
{
out << "DATASET UNSTRUCTURED_GRID" << '\n';
WritePoints(out, dataSet);
WriteVertexCells(out, dataSet);
}
template <class CellSetType>
static void WriteDataSetAsUnstructured(std::ostream& out,
const vtkm::cont::DataSet& dataSet,
const CellSetType& cellSet)
{
out << "DATASET UNSTRUCTURED_GRID" << '\n';
WritePoints(out, dataSet);
WriteExplicitCells(out, cellSet);
}
template <vtkm::IdComponent DIM>
static void WriteDataSetAsStructured(std::ostream& out,
const vtkm::cont::DataSet& dataSet,
const vtkm::cont::CellSetStructured<DIM>& cellSet)
{
///\todo: support uniform/rectilinear
out << "DATASET STRUCTURED_GRID" << '\n';
auto pointDimensions = cellSet.GetPointDimensions();
using VTraits = vtkm::VecTraits<decltype(pointDimensions)>;
out << "DIMENSIONS ";
out << VTraits::GetComponent(pointDimensions, 0) << " ";
out << (DIM > 1 ? VTraits::GetComponent(pointDimensions, 1) : 1) << " ";
out << (DIM > 2 ? VTraits::GetComponent(pointDimensions, 2) : 1) << " ";
WritePoints(out, dataSet);
}
static void Write(std::ostream& out, const vtkm::cont::DataSet& dataSet, bool just_points = false)
{
// The Paraview parser cannot handle scientific notation:
out << std::fixed;
out << "# vtk DataFile Version 3.0" << '\n';
out << "vtk output" << '\n';
out << "ASCII" << '\n';
if (just_points)
{
WriteDataSetAsPoints(out, dataSet);
WritePointFields(out, dataSet);
}
else
{
vtkm::cont::DynamicCellSet cellSet = dataSet.GetCellSet();
if (cellSet.IsType<vtkm::cont::CellSetExplicit<>>())
{
WriteDataSetAsUnstructured(out, dataSet, cellSet.Cast<vtkm::cont::CellSetExplicit<>>());
}
else if (cellSet.IsType<vtkm::cont::CellSetStructured<1>>())
{
WriteDataSetAsStructured(out, dataSet, cellSet.Cast<vtkm::cont::CellSetStructured<1>>());
}
else if (cellSet.IsType<vtkm::cont::CellSetStructured<2>>())
{
WriteDataSetAsStructured(out, dataSet, cellSet.Cast<vtkm::cont::CellSetStructured<2>>());
}
else if (cellSet.IsType<vtkm::cont::CellSetStructured<3>>())
{
WriteDataSetAsStructured(out, dataSet, cellSet.Cast<vtkm::cont::CellSetStructured<3>>());
}
else if (cellSet.IsType<vtkm::cont::CellSetSingleType<>>())
{
// these function just like explicit cell sets
WriteDataSetAsUnstructured(out, dataSet, cellSet.Cast<vtkm::cont::CellSetSingleType<>>());
}
else
{
throw vtkm::cont::ErrorBadType("Could not determine type to write out.");
}
WritePointFields(out, dataSet);
WriteCellFields(out, dataSet);
}
}
public:
VTKM_CONT
explicit VTKDataSetWriter(const std::string& filename)
: FileName(filename)
{
}
VTKM_CONT
void WriteDataSet(const vtkm::cont::DataSet& dataSet, bool just_points = false) const
{
if (dataSet.GetNumberOfCoordinateSystems() < 1)
{
throw vtkm::cont::ErrorBadValue(
"DataSet has no coordinate system, which is not supported by VTK file format.");
}
try
{
std::ofstream fileStream(this->FileName.c_str(), std::fstream::trunc);
this->Write(fileStream, dataSet, just_points);
fileStream.close();
}
catch (std::ofstream::failure& error)
{
throw vtkm::io::ErrorIO(error.what());
}
}
VTKM_CONT void WriteDataSet(const vtkm::cont::DataSet& dataSet, bool just_points = false) const;
private:
std::string FileName;

152
vtkm/io/VTKPolyDataReader.cxx Normal file
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@ -0,0 +1,152 @@
//============================================================================
// Copyright (c) Kitware, Inc.
// All rights reserved.
// See LICENSE.txt for details.
//
// This software is distributed WITHOUT ANY WARRANTY; without even
// the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
// PURPOSE. See the above copyright notice for more information.
//============================================================================
#include <vtkm/io/VTKPolyDataReader.h>
namespace
{
template <typename T>
inline vtkm::cont::ArrayHandle<T> ConcatinateArrayHandles(
const std::vector<vtkm::cont::ArrayHandle<T>>& arrays)
{
vtkm::Id size = 0;
for (std::size_t i = 0; i < arrays.size(); ++i)
{
size += arrays[i].GetNumberOfValues();
}
vtkm::cont::ArrayHandle<T> out;
out.Allocate(size);
auto outp = vtkm::cont::ArrayPortalToIteratorBegin(out.WritePortal());
for (std::size_t i = 0; i < arrays.size(); ++i)
{
std::copy(vtkm::cont::ArrayPortalToIteratorBegin(arrays[i].ReadPortal()),
vtkm::cont::ArrayPortalToIteratorEnd(arrays[i].ReadPortal()),
outp);
using DifferenceType = typename std::iterator_traits<decltype(outp)>::difference_type;
std::advance(outp, static_cast<DifferenceType>(arrays[i].GetNumberOfValues()));
}
return out;
}
}
namespace vtkm
{
namespace io
{
VTKPolyDataReader::VTKPolyDataReader(const char* fileName)
: VTKDataSetReaderBase(fileName)
{
}
VTKPolyDataReader::VTKPolyDataReader(const std::string& fileName)
: VTKDataSetReaderBase(fileName)
{
}
void VTKPolyDataReader::Read()
{
if (this->DataFile->Structure != vtkm::io::internal::DATASET_POLYDATA)
{
throw vtkm::io::ErrorIO("Incorrect DataSet type");
}
//We need to be able to handle VisIt files which dump Field data
//at the top of a VTK file
std::string tag;
this->DataFile->Stream >> tag;
if (tag == "FIELD")
{
this->ReadGlobalFields();
this->DataFile->Stream >> tag;
}
// Read the points
internal::parseAssert(tag == "POINTS");
this->ReadPoints();
vtkm::Id numPoints = this->DataSet.GetNumberOfPoints();
// Read the cellset
std::vector<vtkm::cont::ArrayHandle<vtkm::Id>> connectivityArrays;
std::vector<vtkm::cont::ArrayHandle<vtkm::IdComponent>> numIndicesArrays;
std::vector<vtkm::UInt8> shapesBuffer;
while (!this->DataFile->Stream.eof())
{
vtkm::UInt8 shape = vtkm::CELL_SHAPE_EMPTY;
this->DataFile->Stream >> tag;
if (tag == "VERTICES")
{
shape = vtkm::io::internal::CELL_SHAPE_POLY_VERTEX;
}
else if (tag == "LINES")
{
shape = vtkm::io::internal::CELL_SHAPE_POLY_LINE;
}
else if (tag == "POLYGONS")
{
shape = vtkm::CELL_SHAPE_POLYGON;
}
else if (tag == "TRIANGLE_STRIPS")
{
shape = vtkm::io::internal::CELL_SHAPE_TRIANGLE_STRIP;
}
else
{
this->DataFile->Stream.seekg(-static_cast<std::streamoff>(tag.length()), std::ios_base::cur);
break;
}
vtkm::cont::ArrayHandle<vtkm::Id> cellConnectivity;
vtkm::cont::ArrayHandle<vtkm::IdComponent> cellNumIndices;
this->ReadCells(cellConnectivity, cellNumIndices);
connectivityArrays.push_back(cellConnectivity);
numIndicesArrays.push_back(cellNumIndices);
shapesBuffer.insert(
shapesBuffer.end(), static_cast<std::size_t>(cellNumIndices.GetNumberOfValues()), shape);
}
vtkm::cont::ArrayHandle<vtkm::Id> connectivity = ConcatinateArrayHandles(connectivityArrays);
vtkm::cont::ArrayHandle<vtkm::IdComponent> numIndices = ConcatinateArrayHandles(numIndicesArrays);
vtkm::cont::ArrayHandle<vtkm::UInt8> shapes;
shapes.Allocate(static_cast<vtkm::Id>(shapesBuffer.size()));
std::copy(shapesBuffer.begin(),
shapesBuffer.end(),
vtkm::cont::ArrayPortalToIteratorBegin(shapes.WritePortal()));
vtkm::cont::ArrayHandle<vtkm::Id> permutation;
vtkm::io::internal::FixupCellSet(connectivity, numIndices, shapes, permutation);
this->SetCellsPermutation(permutation);
if (vtkm::io::internal::IsSingleShape(shapes))
{
vtkm::cont::CellSetSingleType<> cellSet;
cellSet.Fill(
numPoints, shapes.ReadPortal().Get(0), numIndices.ReadPortal().Get(0), connectivity);
this->DataSet.SetCellSet(cellSet);
}
else
{
auto offsets = vtkm::cont::ConvertNumIndicesToOffsets(numIndices);
vtkm::cont::CellSetExplicit<> cellSet;
cellSet.Fill(numPoints, shapes, connectivity, offsets);
this->DataSet.SetCellSet(cellSet);
}
// Read points and cell attributes
this->ReadAttributes();
}
}
} // namespace vtkm::io

141
vtkm/io/VTKPolyDataReader.h
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@ -11,6 +11,7 @@
#define vtk_m_io_VTKPolyDataReader_h
#include <vtkm/io/VTKDataSetReaderBase.h>
#include <vtkm/io/internal/VTKDataSetCells.h>
#include <vtkm/cont/ArrayPortalToIterators.h>
@ -21,147 +22,15 @@ namespace vtkm
namespace io
{
namespace internal
{
template <typename T>
inline vtkm::cont::ArrayHandle<T> ConcatinateArrayHandles(
const std::vector<vtkm::cont::ArrayHandle<T>>& arrays)
{
vtkm::Id size = 0;
for (std::size_t i = 0; i < arrays.size(); ++i)
{
size += arrays[i].GetNumberOfValues();
}
vtkm::cont::ArrayHandle<T> out;
out.Allocate(size);
auto outp = vtkm::cont::ArrayPortalToIteratorBegin(out.WritePortal());
for (std::size_t i = 0; i < arrays.size(); ++i)
{
std::copy(vtkm::cont::ArrayPortalToIteratorBegin(arrays[i].ReadPortal()),
vtkm::cont::ArrayPortalToIteratorEnd(arrays[i].ReadPortal()),
outp);
using DifferenceType = typename std::iterator_traits<decltype(outp)>::difference_type;
std::advance(outp, static_cast<DifferenceType>(arrays[i].GetNumberOfValues()));
}
return out;
}
} // namespace internal
VTKM_SILENCE_WEAK_VTABLE_WARNING_START
class VTKPolyDataReader : public VTKDataSetReaderBase
class VTKM_IO_EXPORT VTKPolyDataReader : public VTKDataSetReaderBase
{
public:
explicit VTKPolyDataReader(const char* fileName)
: VTKDataSetReaderBase(fileName)
{
}
explicit VTKM_CONT VTKPolyDataReader(const char* fileName);
explicit VTKM_CONT VTKPolyDataReader(const std::string& fileName);
private:
virtual void Read()
{
if (this->DataFile->Structure != vtkm::io::internal::DATASET_POLYDATA)
{
throw vtkm::io::ErrorIO("Incorrect DataSet type");
}
//We need to be able to handle VisIt files which dump Field data
//at the top of a VTK file
std::string tag;
this->DataFile->Stream >> tag;
if (tag == "FIELD")
{
this->ReadGlobalFields();
this->DataFile->Stream >> tag;
}
// Read the points
internal::parseAssert(tag == "POINTS");
this->ReadPoints();
vtkm::Id numPoints = this->DataSet.GetNumberOfPoints();
// Read the cellset
std::vector<vtkm::cont::ArrayHandle<vtkm::Id>> connectivityArrays;
std::vector<vtkm::cont::ArrayHandle<vtkm::IdComponent>> numIndicesArrays;
std::vector<vtkm::UInt8> shapesBuffer;
while (!this->DataFile->Stream.eof())
{
vtkm::UInt8 shape = vtkm::CELL_SHAPE_EMPTY;
this->DataFile->Stream >> tag;
if (tag == "VERTICES")
{
shape = vtkm::io::internal::CELL_SHAPE_POLY_VERTEX;
}
else if (tag == "LINES")
{
shape = vtkm::io::internal::CELL_SHAPE_POLY_LINE;
}
else if (tag == "POLYGONS")
{
shape = vtkm::CELL_SHAPE_POLYGON;
}
else if (tag == "TRIANGLE_STRIPS")
{
shape = vtkm::io::internal::CELL_SHAPE_TRIANGLE_STRIP;
}
else
{
this->DataFile->Stream.seekg(-static_cast<std::streamoff>(tag.length()),
std::ios_base::cur);
break;
}
vtkm::cont::ArrayHandle<vtkm::Id> cellConnectivity;
vtkm::cont::ArrayHandle<vtkm::IdComponent> cellNumIndices;
this->ReadCells(cellConnectivity, cellNumIndices);
connectivityArrays.push_back(cellConnectivity);
numIndicesArrays.push_back(cellNumIndices);
shapesBuffer.insert(
shapesBuffer.end(), static_cast<std::size_t>(cellNumIndices.GetNumberOfValues()), shape);
}
vtkm::cont::ArrayHandle<vtkm::Id> connectivity =
internal::ConcatinateArrayHandles(connectivityArrays);
vtkm::cont::ArrayHandle<vtkm::IdComponent> numIndices =
internal::ConcatinateArrayHandles(numIndicesArrays);
vtkm::cont::ArrayHandle<vtkm::UInt8> shapes;
shapes.Allocate(static_cast<vtkm::Id>(shapesBuffer.size()));
std::copy(shapesBuffer.begin(),
shapesBuffer.end(),
vtkm::cont::ArrayPortalToIteratorBegin(shapes.WritePortal()));
vtkm::cont::ArrayHandle<vtkm::Id> permutation;
vtkm::io::internal::FixupCellSet(connectivity, numIndices, shapes, permutation);
this->SetCellsPermutation(permutation);
if (vtkm::io::internal::IsSingleShape(shapes))
{
vtkm::cont::CellSetSingleType<> cellSet;
cellSet.Fill(
numPoints, shapes.ReadPortal().Get(0), numIndices.ReadPortal().Get(0), connectivity);
this->DataSet.SetCellSet(cellSet);
}
else
{
auto offsets = vtkm::cont::ConvertNumIndicesToOffsets(numIndices);
vtkm::cont::CellSetExplicit<> cellSet;
cellSet.Fill(numPoints, shapes, connectivity, offsets);
this->DataSet.SetCellSet(cellSet);
}
// Read points and cell attributes
this->ReadAttributes();
}
void Read() override;
};
VTKM_SILENCE_WEAK_VTABLE_WARNING_END
}
} // namespace vtkm::io

95
vtkm/io/VTKRectilinearGridReader.cxx Normal file
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@ -0,0 +1,95 @@
//============================================================================
// Copyright (c) Kitware, Inc.
// All rights reserved.
// See LICENSE.txt for details.
//
// This software is distributed WITHOUT ANY WARRANTY; without even
// the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
// PURPOSE. See the above copyright notice for more information.
//============================================================================
#include <vtkm/io/VTKRectilinearGridReader.h>
namespace vtkm
{
namespace io
{
VTKRectilinearGridReader::VTKRectilinearGridReader(const char* fileName)
: VTKDataSetReaderBase(fileName)
{
}
VTKRectilinearGridReader::VTKRectilinearGridReader(const std::string& fileName)
: VTKDataSetReaderBase(fileName)
{
}
void VTKRectilinearGridReader::Read()
{
if (this->DataFile->Structure != vtkm::io::internal::DATASET_RECTILINEAR_GRID)
throw vtkm::io::ErrorIO("Incorrect DataSet type");
//We need to be able to handle VisIt files which dump Field data
//at the top of a VTK file
std::string tag;
this->DataFile->Stream >> tag;
if (tag == "FIELD")
{
this->ReadGlobalFields();
this->DataFile->Stream >> tag;
}
// Read structured grid specific meta-data
internal::parseAssert(tag == "DIMENSIONS");
vtkm::Id3 dim;
this->DataFile->Stream >> dim[0] >> dim[1] >> dim[2] >> std::ws;
//Read the points.
std::string dataType;
std::size_t numPoints[3];
vtkm::cont::VariantArrayHandle X, Y, Z;
// Always read coordinates as vtkm::FloatDefault
std::string readDataType = vtkm::io::internal::DataTypeName<vtkm::FloatDefault>::Name();
this->DataFile->Stream >> tag >> numPoints[0] >> dataType >> std::ws;
if (tag != "X_COORDINATES")
throw vtkm::io::ErrorIO("X_COORDINATES tag not found");
X = this->DoReadArrayVariant(vtkm::cont::Field::Association::ANY, readDataType, numPoints[0], 1);
this->DataFile->Stream >> tag >> numPoints[1] >> dataType >> std::ws;
if (tag != "Y_COORDINATES")
throw vtkm::io::ErrorIO("Y_COORDINATES tag not found");
Y = this->DoReadArrayVariant(vtkm::cont::Field::Association::ANY, readDataType, numPoints[1], 1);
this->DataFile->Stream >> tag >> numPoints[2] >> dataType >> std::ws;
if (tag != "Z_COORDINATES")
throw vtkm::io::ErrorIO("Z_COORDINATES tag not found");
Z = this->DoReadArrayVariant(vtkm::cont::Field::Association::ANY, readDataType, numPoints[2], 1);
if (dim != vtkm::Id3(static_cast<vtkm::Id>(numPoints[0]),
static_cast<vtkm::Id>(numPoints[1]),
static_cast<vtkm::Id>(numPoints[2])))
throw vtkm::io::ErrorIO("DIMENSIONS not equal to number of points");
vtkm::cont::ArrayHandleCartesianProduct<vtkm::cont::ArrayHandle<vtkm::FloatDefault>,
vtkm::cont::ArrayHandle<vtkm::FloatDefault>,
vtkm::cont::ArrayHandle<vtkm::FloatDefault>>
coords;
vtkm::cont::ArrayHandle<vtkm::FloatDefault> Xc, Yc, Zc;
X.CopyTo(Xc);
Y.CopyTo(Yc);
Z.CopyTo(Zc);
coords = vtkm::cont::make_ArrayHandleCartesianProduct(Xc, Yc, Zc);
vtkm::cont::CoordinateSystem coordSys("coordinates", coords);
this->DataSet.AddCoordinateSystem(coordSys);
this->DataSet.SetCellSet(internal::CreateCellSetStructured(dim));
// Read points and cell attributes
this->ReadAttributes();
}
}
} // namespace vtkm::io

82
vtkm/io/VTKRectilinearGridReader.h
View File

@ -17,89 +17,15 @@ namespace vtkm
namespace io
{
VTKM_SILENCE_WEAK_VTABLE_WARNING_START
class VTKRectilinearGridReader : public VTKDataSetReaderBase
class VTKM_IO_EXPORT VTKRectilinearGridReader : public VTKDataSetReaderBase
{
public:
explicit VTKRectilinearGridReader(const char* fileName)
: VTKDataSetReaderBase(fileName)
{
}
explicit VTKM_CONT VTKRectilinearGridReader(const char* fileName);
explicit VTKM_CONT VTKRectilinearGridReader(const std::string& fileName);
private:
virtual void Read()
{
if (this->DataFile->Structure != vtkm::io::internal::DATASET_RECTILINEAR_GRID)
throw vtkm::io::ErrorIO("Incorrect DataSet type");
//We need to be able to handle VisIt files which dump Field data
//at the top of a VTK file
std::string tag;
this->DataFile->Stream >> tag;
if (tag == "FIELD")
{
this->ReadGlobalFields();
this->DataFile->Stream >> tag;
}
// Read structured grid specific meta-data
internal::parseAssert(tag == "DIMENSIONS");
vtkm::Id3 dim;
this->DataFile->Stream >> dim[0] >> dim[1] >> dim[2] >> std::ws;
//Read the points.
std::string dataType;
std::size_t numPoints[3];
vtkm::cont::VariantArrayHandle X, Y, Z;
// Always read coordinates as vtkm::FloatDefault
std::string readDataType = vtkm::io::internal::DataTypeName<vtkm::FloatDefault>::Name();
this->DataFile->Stream >> tag >> numPoints[0] >> dataType >> std::ws;
if (tag != "X_COORDINATES")
throw vtkm::io::ErrorIO("X_COORDINATES tag not found");
X =
this->DoReadArrayVariant(vtkm::cont::Field::Association::ANY, readDataType, numPoints[0], 1);
this->DataFile->Stream >> tag >> numPoints[1] >> dataType >> std::ws;
if (tag != "Y_COORDINATES")
throw vtkm::io::ErrorIO("Y_COORDINATES tag not found");
Y =
this->DoReadArrayVariant(vtkm::cont::Field::Association::ANY, readDataType, numPoints[1], 1);
this->DataFile->Stream >> tag >> numPoints[2] >> dataType >> std::ws;
if (tag != "Z_COORDINATES")
throw vtkm::io::ErrorIO("Z_COORDINATES tag not found");
Z =
this->DoReadArrayVariant(vtkm::cont::Field::Association::ANY, readDataType, numPoints[2], 1);
if (dim != vtkm::Id3(static_cast<vtkm::Id>(numPoints[0]),
static_cast<vtkm::Id>(numPoints[1]),
static_cast<vtkm::Id>(numPoints[2])))
throw vtkm::io::ErrorIO("DIMENSIONS not equal to number of points");
vtkm::cont::ArrayHandleCartesianProduct<vtkm::cont::ArrayHandle<vtkm::FloatDefault>,
vtkm::cont::ArrayHandle<vtkm::FloatDefault>,
vtkm::cont::ArrayHandle<vtkm::FloatDefault>>
coords;
vtkm::cont::ArrayHandle<vtkm::FloatDefault> Xc, Yc, Zc;
X.CopyTo(Xc);
Y.CopyTo(Yc);
Z.CopyTo(Zc);
coords = vtkm::cont::make_ArrayHandleCartesianProduct(Xc, Yc, Zc);
vtkm::cont::CoordinateSystem coordSys("coordinates", coords);
this->DataSet.AddCoordinateSystem(coordSys);
this->DataSet.SetCellSet(internal::CreateCellSetStructured(dim));
// Read points and cell attributes
this->ReadAttributes();
}
VTKM_CONT void Read() override;
};
VTKM_SILENCE_WEAK_VTABLE_WARNING_END
}
} // namespace vtkm::io

62
vtkm/io/VTKStructuredGridReader.cxx Normal file
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@ -0,0 +1,62 @@
//============================================================================
// Copyright (c) Kitware, Inc.
// All rights reserved.
// See LICENSE.txt for details.
//
// This software is distributed WITHOUT ANY WARRANTY; without even
// the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
// PURPOSE. See the above copyright notice for more information.
//============================================================================
#include <vtkm/io/VTKStructuredGridReader.h>
namespace vtkm
{
namespace io
{
VTKStructuredGridReader::VTKStructuredGridReader(const char* fileName)
: VTKDataSetReaderBase(fileName)
{
}
VTKStructuredGridReader::VTKStructuredGridReader(const std::string& fileName)
: VTKDataSetReaderBase(fileName)
{
}
void VTKStructuredGridReader::Read()
{
if (this->DataFile->Structure != vtkm::io::internal::DATASET_STRUCTURED_GRID)
{
throw vtkm::io::ErrorIO("Incorrect DataSet type");
}
std::string tag;
//We need to be able to handle VisIt files which dump Field data
//at the top of a VTK file
this->DataFile->Stream >> tag;
if (tag == "FIELD")
{
this->ReadGlobalFields();
this->DataFile->Stream >> tag;
}
// Read structured grid specific meta-data
internal::parseAssert(tag == "DIMENSIONS");
vtkm::Id3 dim;
this->DataFile->Stream >> dim[0] >> dim[1] >> dim[2] >> std::ws;
this->DataSet.SetCellSet(internal::CreateCellSetStructured(dim));
// Read the points
this->DataFile->Stream >> tag;
internal::parseAssert(tag == "POINTS");
this->ReadPoints();
// Read points and cell attributes
this->ReadAttributes();
}
}
} // namespace vtkm::io

46
vtkm/io/VTKStructuredGridReader.h
View File

@ -17,53 +17,15 @@ namespace vtkm
namespace io
{
VTKM_SILENCE_WEAK_VTABLE_WARNING_START
class VTKStructuredGridReader : public VTKDataSetReaderBase
class VTKM_IO_EXPORT VTKStructuredGridReader : public VTKDataSetReaderBase
{
public:
explicit VTKStructuredGridReader(const char* fileName)
: VTKDataSetReaderBase(fileName)
{
}
explicit VTKM_CONT VTKStructuredGridReader(const char* fileName);
explicit VTKM_CONT VTKStructuredGridReader(const std::string& fileName);
private:
virtual void Read()
{
if (this->DataFile->Structure != vtkm::io::internal::DATASET_STRUCTURED_GRID)
{
throw vtkm::io::ErrorIO("Incorrect DataSet type");
}
std::string tag;
//We need to be able to handle VisIt files which dump Field data
//at the top of a VTK file
this->DataFile->Stream >> tag;
if (tag == "FIELD")
{
this->ReadGlobalFields();
this->DataFile->Stream >> tag;
}
// Read structured grid specific meta-data
internal::parseAssert(tag == "DIMENSIONS");
vtkm::Id3 dim;
this->DataFile->Stream >> dim[0] >> dim[1] >> dim[2] >> std::ws;
this->DataSet.SetCellSet(internal::CreateCellSetStructured(dim));
// Read the points
this->DataFile->Stream >> tag;
internal::parseAssert(tag == "POINTS");
this->ReadPoints();
// Read points and cell attributes
this->ReadAttributes();
}
VTKM_CONT void Read() override;
};
VTKM_SILENCE_WEAK_VTABLE_WARNING_END
}
} // namespace vtkm::io

79
vtkm/io/VTKStructuredPointsReader.cxx Normal file
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@ -0,0 +1,79 @@
//============================================================================
// Copyright (c) Kitware, Inc.
// All rights reserved.
// See LICENSE.txt for details.
//
// This software is distributed WITHOUT ANY WARRANTY; without even
// the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
// PURPOSE. See the above copyright notice for more information.
//============================================================================
#include <vtkm/io/VTKStructuredPointsReader.h>
namespace vtkm
{
namespace io
{
VTKStructuredPointsReader::VTKStructuredPointsReader(const char* fileName)
: VTKDataSetReaderBase(fileName)
{
}
VTKStructuredPointsReader::VTKStructuredPointsReader(const std::string& fileName)
: VTKDataSetReaderBase(fileName)
{
}
void VTKStructuredPointsReader::Read()
{
if (this->DataFile->Structure != vtkm::io::internal::DATASET_STRUCTURED_POINTS)
{
throw vtkm::io::ErrorIO("Incorrect DataSet type");
}
std::string tag;
// Read structured points specific meta-data
vtkm::Id3 dim;
vtkm::Vec3f_32 origin, spacing;
//Two ways the file can describe the dimensions. The proper way is by
//using the DIMENSIONS keyword, but VisIt written VTK files spicify data
//bounds instead, as a FIELD
std::vector<vtkm::Float32> visitBounds;
this->DataFile->Stream >> tag;
if (tag == "FIELD")
{
this->ReadGlobalFields(&visitBounds);
this->DataFile->Stream >> tag;
}
if (visitBounds.empty())
{
internal::parseAssert(tag == "DIMENSIONS");
this->DataFile->Stream >> dim[0] >> dim[1] >> dim[2] >> std::ws;
this->DataFile->Stream >> tag;
}
internal::parseAssert(tag == "SPACING");
this->DataFile->Stream >> spacing[0] >> spacing[1] >> spacing[2] >> std::ws;
if (!visitBounds.empty())
{
//now with spacing and physical bounds we can back compute the dimensions
dim[0] = static_cast<vtkm::Id>((visitBounds[1] - visitBounds[0]) / spacing[0]);
dim[1] = static_cast<vtkm::Id>((visitBounds[3] - visitBounds[2]) / spacing[1]);
dim[2] = static_cast<vtkm::Id>((visitBounds[5] - visitBounds[4]) / spacing[2]);
}
this->DataFile->Stream >> tag >> origin[0] >> origin[1] >> origin[2] >> std::ws;
internal::parseAssert(tag == "ORIGIN");
this->DataSet.SetCellSet(internal::CreateCellSetStructured(dim));
this->DataSet.AddCoordinateSystem(
vtkm::cont::CoordinateSystem("coordinates", dim, origin, spacing));
// Read points and cell attributes
this->ReadAttributes();
}
}
} // namespace vtkm::io

63
vtkm/io/VTKStructuredPointsReader.h
View File

@ -17,70 +17,15 @@ namespace vtkm
namespace io
{
VTKM_SILENCE_WEAK_VTABLE_WARNING_START
class VTKStructuredPointsReader : public VTKDataSetReaderBase
class VTKM_IO_EXPORT VTKStructuredPointsReader : public VTKDataSetReaderBase
{
public:
explicit VTKStructuredPointsReader(const char* fileName)
: VTKDataSetReaderBase(fileName)
{
}
explicit VTKM_CONT VTKStructuredPointsReader(const char* fileName);
explicit VTKM_CONT VTKStructuredPointsReader(const std::string& fileName);
private:
virtual void Read()
{
if (this->DataFile->Structure != vtkm::io::internal::DATASET_STRUCTURED_POINTS)
{
throw vtkm::io::ErrorIO("Incorrect DataSet type");
}
std::string tag;
// Read structured points specific meta-data
vtkm::Id3 dim;
vtkm::Vec3f_32 origin, spacing;
//Two ways the file can describe the dimensions. The proper way is by
//using the DIMENSIONS keyword, but VisIt written VTK files spicify data
//bounds instead, as a FIELD
std::vector<vtkm::Float32> visitBounds;
this->DataFile->Stream >> tag;
if (tag == "FIELD")
{
this->ReadGlobalFields(&visitBounds);
this->DataFile->Stream >> tag;
}
if (visitBounds.empty())
{
internal::parseAssert(tag == "DIMENSIONS");
this->DataFile->Stream >> dim[0] >> dim[1] >> dim[2] >> std::ws;
this->DataFile->Stream >> tag;
}
internal::parseAssert(tag == "SPACING");
this->DataFile->Stream >> spacing[0] >> spacing[1] >> spacing[2] >> std::ws;
if (!visitBounds.empty())
{
//now with spacing and physical bounds we can back compute the dimensions
dim[0] = static_cast<vtkm::Id>((visitBounds[1] - visitBounds[0]) / spacing[0]);
dim[1] = static_cast<vtkm::Id>((visitBounds[3] - visitBounds[2]) / spacing[1]);
dim[2] = static_cast<vtkm::Id>((visitBounds[5] - visitBounds[4]) / spacing[2]);
}
this->DataFile->Stream >> tag >> origin[0] >> origin[1] >> origin[2] >> std::ws;
internal::parseAssert(tag == "ORIGIN");
this->DataSet.SetCellSet(internal::CreateCellSetStructured(dim));
this->DataSet.AddCoordinateSystem(
vtkm::cont::CoordinateSystem("coordinates", dim, origin, spacing));
// Read points and cell attributes
this->ReadAttributes();
}
VTKM_CONT void Read() override;
};
VTKM_SILENCE_WEAK_VTABLE_WARNING_END
}
} // namespace vtkm::io

88
vtkm/io/VTKUnstructuredGridReader.cxx Normal file
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@ -0,0 +1,88 @@
//============================================================================
// Copyright (c) Kitware, Inc.
// All rights reserved.
// See LICENSE.txt for details.
//
// This software is distributed WITHOUT ANY WARRANTY; without even
// the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
// PURPOSE. See the above copyright notice for more information.
//============================================================================
#include <vtkm/io/VTKUnstructuredGridReader.h>
#include <vtkm/io/internal/VTKDataSetCells.h>
namespace vtkm
{
namespace io
{
VTKUnstructuredGridReader::VTKUnstructuredGridReader(const char* fileName)
: VTKDataSetReaderBase(fileName)
{
}
VTKUnstructuredGridReader::VTKUnstructuredGridReader(const std::string& fileName)
: VTKDataSetReaderBase(fileName)
{
}
void VTKUnstructuredGridReader::Read()
{
if (this->DataFile->Structure != vtkm::io::internal::DATASET_UNSTRUCTURED_GRID)
{
throw vtkm::io::ErrorIO("Incorrect DataSet type");
}
//We need to be able to handle VisIt files which dump Field data
//at the top of a VTK file
std::string tag;
this->DataFile->Stream >> tag;
if (tag == "FIELD")
{
this->ReadGlobalFields();
this->DataFile->Stream >> tag;
}
// Read the points
internal::parseAssert(tag == "POINTS");
this->ReadPoints();
vtkm::Id numPoints = this->DataSet.GetNumberOfPoints();
// Read the cellset
vtkm::cont::ArrayHandle<vtkm::Id> connectivity;
vtkm::cont::ArrayHandle<vtkm::IdComponent> numIndices;
vtkm::cont::ArrayHandle<vtkm::UInt8> shapes;
this->DataFile->Stream >> tag;
internal::parseAssert(tag == "CELLS");
this->ReadCells(connectivity, numIndices);
this->ReadShapes(shapes);
vtkm::cont::ArrayHandle<vtkm::Id> permutation;
vtkm::io::internal::FixupCellSet(connectivity, numIndices, shapes, permutation);
this->SetCellsPermutation(permutation);
//DRP
if (false) //vtkm::io::internal::IsSingleShape(shapes))
{
vtkm::cont::CellSetSingleType<> cellSet;
cellSet.Fill(
numPoints, shapes.ReadPortal().Get(0), numIndices.ReadPortal().Get(0), connectivity);
this->DataSet.SetCellSet(cellSet);
}
else
{
auto offsets = vtkm::cont::ConvertNumIndicesToOffsets(numIndices);
vtkm::cont::CellSetExplicit<> cellSet;
cellSet.Fill(numPoints, shapes, connectivity, offsets);
this->DataSet.SetCellSet(cellSet);
}
// Read points and cell attributes
this->ReadAttributes();
}
}
}

70
vtkm/io/VTKUnstructuredGridReader.h
View File

@ -17,77 +17,15 @@ namespace vtkm
namespace io
{
VTKM_SILENCE_WEAK_VTABLE_WARNING_START
class VTKUnstructuredGridReader : public VTKDataSetReaderBase
class VTKM_IO_EXPORT VTKUnstructuredGridReader : public VTKDataSetReaderBase
{
public:
explicit VTKUnstructuredGridReader(const char* fileName)
: VTKDataSetReaderBase(fileName)
{
}
explicit VTKM_CONT VTKUnstructuredGridReader(const char* fileName);
explicit VTKM_CONT VTKUnstructuredGridReader(const std::string& fileName);
private:
virtual void Read()
{
if (this->DataFile->Structure != vtkm::io::internal::DATASET_UNSTRUCTURED_GRID)
{
throw vtkm::io::ErrorIO("Incorrect DataSet type");
}
//We need to be able to handle VisIt files which dump Field data
//at the top of a VTK file
std::string tag;
this->DataFile->Stream >> tag;
if (tag == "FIELD")
{
this->ReadGlobalFields();
this->DataFile->Stream >> tag;
}
// Read the points
internal::parseAssert(tag == "POINTS");
this->ReadPoints();
vtkm::Id numPoints = this->DataSet.GetNumberOfPoints();
// Read the cellset
vtkm::cont::ArrayHandle<vtkm::Id> connectivity;
vtkm::cont::ArrayHandle<vtkm::IdComponent> numIndices;
vtkm::cont::ArrayHandle<vtkm::UInt8> shapes;
this->DataFile->Stream >> tag;
internal::parseAssert(tag == "CELLS");
this->ReadCells(connectivity, numIndices);
this->ReadShapes(shapes);
vtkm::cont::ArrayHandle<vtkm::Id> permutation;
vtkm::io::internal::FixupCellSet(connectivity, numIndices, shapes, permutation);
this->SetCellsPermutation(permutation);
//DRP
if (false) //vtkm::io::internal::IsSingleShape(shapes))
{
vtkm::cont::CellSetSingleType<> cellSet;
cellSet.Fill(
numPoints, shapes.ReadPortal().Get(0), numIndices.ReadPortal().Get(0), connectivity);
this->DataSet.SetCellSet(cellSet);
}
else
{
auto offsets = vtkm::cont::ConvertNumIndicesToOffsets(numIndices);
vtkm::cont::CellSetExplicit<> cellSet;
cellSet.Fill(numPoints, shapes, connectivity, offsets);
this->DataSet.SetCellSet(cellSet);
}
// Read points and cell attributes
this->ReadAttributes();
}
VTKM_CONT void Read() override;
};
VTKM_SILENCE_WEAK_VTABLE_WARNING_END
}
} // namespace vtkm::io

4
vtkm/io/internal/VTKDataSetTypes.h
View File

@ -11,6 +11,7 @@
#define vtk_m_io_internal_VTKDataSetTypes_h
#include <vtkm/Types.h>
#include <vtkm/VecTraits.h>
#include <algorithm>
#include <cassert>
@ -238,4 +239,7 @@ inline void SelectTypeAndCall(DataType dtype,
}
} // namespace vtkm::io::internal
VTKM_BASIC_TYPE_VECTOR(vtkm::io::internal::ColorChannel8)
VTKM_BASIC_TYPE_VECTOR(vtkm::io::internal::DummyBitType)
#endif // vtk_m_io_internal_VTKDataSetTypes_h

16
vtkm/io/testing/CMakeLists.txt
View File

@ -15,14 +15,14 @@ set(unit_tests
UnitTestVTKDataSetWriter.cxx
)
vtkm_unit_tests(SOURCES ${unit_tests} ALL_BACKENDS LIBRARIES vtkm_lodepng)
set(unit_test_libraries vtkm_lodepng vtkm_io)
if(NOT VTKm_ENABLE_RENDERING)
return()
if(VTKm_ENABLE_RENDERING)
set(unit_tests ${unit_tests}
UnitTestImageWriter.cxx
)
set(unit_test_libraries ${unit_test_libraries} vtkm_rendering)
endif()
set(image_unit_tests
UnitTestImageWriter.cxx
)
vtkm_unit_tests(NAME UnitTests_vtkm_io_image_testing SOURCES ${image_unit_tests} ALL_BACKENDS LIBRARIES vtkm_rendering vtkm_lodepng)
vtkm_unit_tests(SOURCES ${unit_tests} ALL_BACKENDS LIBRARIES ${unit_test_libraries})

1
vtkm/io/testing/UnitTestBOVDataSetReader.cxx
View File

@ -11,6 +11,7 @@
#include <string>
#include <vtkm/cont/testing/Testing.h>
#include <vtkm/io/BOVDataSetReader.h>
#include <vtkm/io/ErrorIO.h>
namespace
{