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// SPDX-FileCopyrightText: Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
// SPDX-License-Identifier: BSD-3-Clause
#include <array>
#include <limits>
#include <map>
#include <sstream>
#include <stdexcept>
#include <unordered_map>
#include "Core/vtkADIOS2CoreTypeTraits.h"
#include "vtkADIOS2CoreImageReader.h"
#include "vtkCellData.h"
#include "vtkCharArray.h"
#include "vtkDataArray.h"
#include "vtkDataArrayRange.h"
#include "vtkDataArraySelection.h"
#include "vtkDataObjectTreeRange.h"
#include "vtkDataObjectTypes.h"
#include "vtkDemandDrivenPipeline.h"
#include "vtkDoubleArray.h"
#include "vtkFieldData.h"
#include "vtkFloatArray.h"
#include "vtkImageData.h"
#include "vtkInformation.h"
#include "vtkInformationVector.h"
#include "vtkLongArray.h"
#include "vtkLongLongArray.h"
#include "vtkMultiBlockDataSet.h"
#include "vtkMultiPieceDataSet.h"
#include "vtkMultiProcessController.h" // For the MPI controller member
#include "vtkNew.h"
#include "vtkObjectFactory.h"
#include "vtkPointData.h"
#include "vtkPoints.h"
#include "vtkPolyData.h"
#include "vtkShortArray.h"
#include "vtkSignedCharArray.h"
#include "vtkStreamingDemandDrivenPipeline.h"
#include "vtkStringArray.h"
#include "vtkType.h"
#include "vtkUnsignedIntArray.h"
#include "vtkUnsignedLongArray.h"
#include "vtkUnsignedLongLongArray.h"
#include "vtkUnsignedShortArray.h"
#include "vtkUnstructuredGrid.h"
#include "vtksys/SystemTools.hxx"
#if VTK_MODULE_ENABLE_VTK_ParallelMPI
#include "vtkMPI.h"
#include "vtkMPIController.h"
#endif
#include <adios2.h> // adios2
#include <istream> // istringStream
#include <string>
//------------------------------------------------------------------------------
// Helper functions
//------------------------------------------------------------------------------
VTK_ABI_NAMESPACE_BEGIN
//------------------------------------------------------------------------------
vtkStandardNewMacro(vtkADIOS2CoreImageReader);
VTK_ABI_NAMESPACE_END
namespace
{
inline std::vector<int> parseDimensions(const std::string& dimsStr)
{
std::vector<int> dims;
std::istringstream f(dimsStr);
std::string token;
while (std::getline(f, token, ','))
{
dims.push_back(std::atoi(token.c_str()));
}
return dims;
}
}
VTK_ABI_NAMESPACE_BEGIN
//------------------------------------------------------------------------------
struct vtkADIOS2CoreImageReader::vtkADIOS2CoreImageReaderImpl
{
vtkNew<vtkMultiPieceDataSet> Flatten(vtkMultiBlockDataSet* ibds);
// ADIOS variables
std::unique_ptr<adios2::ADIOS> Adios;
adios2::IO AdiosIO;
adios2::Engine BpReader;
InquireVariablesType InquiredVars;
std::pair<std::string, VarType> ActiveScalar;
std::map<std::string, adios2::Params> AvailVars;
std::map<std::string, adios2::Params> AvailAtts;
size_t BlockStart{ 0 };
size_t BlockCount{ 0 };
std::vector<std::array<int, 6>> BlockExtents;
// VTK variables
bool HasReadMetaData{ false };
std::vector<double> TimeSteps;
// From time to time step(aka reference)
std::unordered_map<double, size_t> TimeStepsReverseMap;
// Index of the request time step. If it's a single time step data then it's default to be 0
size_t RequestStep{ 0 };
// Select the arrays that should be read in.
vtkNew<vtkDataArraySelection> ArraySelection;
// For ParaView GUI display usage.
vtkNew<vtkStringArray> AvailableArray;
};
vtkNew<vtkMultiPieceDataSet> vtkADIOS2CoreImageReader::vtkADIOS2CoreImageReaderImpl::Flatten(
vtkMultiBlockDataSet* ibds)
{
// found out how many pieces we have in current process
using Opts = vtk::DataObjectTreeOptions;
// Communicate to find out where the images of current process should go
int myLen = static_cast<int>(ibds->GetNumberOfBlocks());
int* allLens{ nullptr };
int procId{ 0 }, numProcess{ 0 };
#if VTK_MODULE_ENABLE_VTK_ParallelMPI
auto ctrl = vtkMultiProcessController::GetGlobalController();
if (ctrl)
{
procId = ctrl->GetLocalProcessId();
numProcess = ctrl->GetNumberOfProcesses();
allLens = new int[numProcess];
ctrl->AllGather(&myLen, allLens, 1);
}
else
{
procId = 0;
numProcess = 1;
allLens = new int[1];
allLens[0] = myLen;
}
#else
procId = 0;
numProcess = 1;
allLens = new int[1];
allLens[0] = myLen;
#endif
unsigned int start{ 0 }, total{ 0 };
for (int i = 0; i < numProcess; i++)
{
if (i < procId)
{
start += static_cast<unsigned int>(allLens[i]);
}
total += static_cast<unsigned int>(allLens[i]);
}
delete[] allLens;
vtkNew<vtkMultiPieceDataSet> mpds;
mpds->SetNumberOfPieces(total);
for (vtkDataObject* obj : vtk::Range(ibds, Opts::VisitOnlyLeaves))
{
mpds->SetPiece(start++, obj);
}
return mpds;
}
//------------------------------------------------------------------------------
void vtkADIOS2CoreImageReader::PrintSelf(ostream& os, vtkIndent indent)
{
this->Superclass::PrintSelf(os, indent);
}
//------------------------------------------------------------------------------
int vtkADIOS2CoreImageReader::CanReadFile(const std::string& name)
{
if (!vtksys::SystemTools::FileExists(name))
{
return 0;
}
if (vtksys::SystemTools::StringEndsWith(name, ".bp") ||
vtksys::SystemTools::StringEndsWith(name, ".bp4") ||
vtksys::SystemTools::StringEndsWith(name, ".bp5") ||
vtksys::SystemTools::StringEndsWith(name, "md.idx"))
{
return 1;
}
return 0;
}
//------------------------------------------------------------------------------
int vtkADIOS2CoreImageReader::CanReadFile(const char* fileName)
{
return this->CanReadFile(std::string(fileName));
}
//------------------------------------------------------------------------------
void vtkADIOS2CoreImageReader::SetFileName(const char* fileName)
{
this->FileName = std::string(fileName);
}
//------------------------------------------------------------------------------
int vtkADIOS2CoreImageReader::GetNumberOfArrays()
{
return this->Impl->ArraySelection->GetNumberOfArrays();
}
//------------------------------------------------------------------------------
const char* vtkADIOS2CoreImageReader::GetArrayName(int index)
{
return this->Impl->ArraySelection->GetArrayName(index);
}
//------------------------------------------------------------------------------
void vtkADIOS2CoreImageReader::SetArrayStatus(const char* name, int status)
{
this->Impl->ArraySelection->SetArraySetting(name, status);
}
//------------------------------------------------------------------------------
int vtkADIOS2CoreImageReader::GetArrayStatus(const char* name)
{
return this->Impl->ArraySelection->ArrayIsEnabled(name);
}
//------------------------------------------------------------------------------
vtkMTimeType vtkADIOS2CoreImageReader::GetMTime()
{
return std::max(this->Superclass::GetMTime(), this->Impl->ArraySelection->GetMTime());
}
//------------------------------------------------------------------------------
vtkStringArray* vtkADIOS2CoreImageReader::GetAllDimensionArrays()
{
return this->Impl->AvailableArray;
}
//------------------------------------------------------------------------------
vtkStringArray* vtkADIOS2CoreImageReader::GetAllTimeStepArrays()
{
return this->Impl->AvailableArray;
}
//------------------------------------------------------------------------------
void vtkADIOS2CoreImageReader::SetActiveScalar(const std::pair<std::string, VarType>& as)
{
this->Impl->ActiveScalar = as;
}
//------------------------------------------------------------------------------
std::pair<std::string, vtkADIOS2CoreImageReader::VarType>&
vtkADIOS2CoreImageReader::GetActiveScalar()
{
return this->Impl->ActiveScalar;
}
//------------------------------------------------------------------------------
const std::pair<std::string, vtkADIOS2CoreImageReader::VarType>&
vtkADIOS2CoreImageReader::GetActiveScalar() const
{
return this->Impl->ActiveScalar;
}
//------------------------------------------------------------------------------
vtkADIOS2CoreImageReader::StringToParams& vtkADIOS2CoreImageReader::GetAvilableVariables()
{
return this->Impl->AvailVars;
}
//------------------------------------------------------------------------------
const vtkADIOS2CoreImageReader::StringToParams& vtkADIOS2CoreImageReader::GetAvilableVariables()
const
{
return this->Impl->AvailVars;
}
//------------------------------------------------------------------------------
vtkADIOS2CoreImageReader::StringToParams& vtkADIOS2CoreImageReader::GetAvailableAttributes()
{
return this->Impl->AvailAtts;
}
//------------------------------------------------------------------------------
const vtkADIOS2CoreImageReader::StringToParams& vtkADIOS2CoreImageReader::GetAvailableAttributes()
const
{
return this->Impl->AvailAtts;
}
//------------------------------------------------------------------------------
void vtkADIOS2CoreImageReader::SetController(vtkMultiProcessController* controller)
{
#if VTK_MODULE_ENABLE_VTK_ParallelMPI
vtkMPIController* mpiController = vtkMPIController::SafeDownCast(controller);
if (controller && !mpiController)
{
vtkErrorMacro(
"vtkADIOS2CoreImageReader is built with MPI but an invalid MPI controller is provided");
return;
}
#endif
vtkSetSmartPointerBodyMacro(Controller, vtkMultiProcessController, controller);
}
//------------------------------------------------------------------------------
int vtkADIOS2CoreImageReader::ProcessRequest(
vtkInformation* request, vtkInformationVector** inputVector, vtkInformationVector* outputVector)
{
if (request->Has(vtkDemandDrivenPipeline::REQUEST_DATA_OBJECT()))
{
return this->RequestDataObjectInternal(outputVector);
}
return this->Superclass::ProcessRequest(request, inputVector, outputVector);
}
//------------------------------------------------------------------------------
int vtkADIOS2CoreImageReader::RequestDataObjectInternal(vtkInformationVector* outputVector)
{
vtkSmartPointer<vtkDataObject> output = vtkDataObject::GetData(outputVector, 0);
if (!output)
{
output = vtk::TakeSmartPointer(vtkDataObjectTypes::NewDataObject(VTK_MULTIBLOCK_DATA_SET));
outputVector->GetInformationObject(0)->Set(vtkDataObject::DATA_OBJECT(), output);
this->GetOutputInformation(0)->Set(vtkDataObject::DATA_EXTENT_TYPE(), output->GetExtentType());
}
return 1;
}
//------------------------------------------------------------------------------
bool vtkADIOS2CoreImageReader::OpenAndReadMetaData()
{
// Is name valid
if (!this->CanReadFile(this->FileName))
{
vtkErrorMacro("cannot read file" << this->FileName);
return false;
}
// Initialize the ADIOS2 data structures
if (!this->Impl->Adios)
{
#if VTK_MODULE_ENABLE_VTK_ParallelMPI
// Make sure the ADIOS subsystem is initialized before processing any
// sort of request.
if (!this->Controller)
{
vtkErrorMacro("The reader is built with MPI support but the application is not launched in "
"parallel mode. Abort reading.");
return false;
}
vtkMPICommunicator* comm =
static_cast<vtkMPICommunicator*>(this->Controller->GetCommunicator());
this->Impl->Adios.reset(new adios2::ADIOS(*comm->GetMPIComm()->GetHandle()));
#else
// Make sure the ADIOS subsystem is initialized before processing any
// sort of request.
this->Impl->Adios.reset(new adios2::ADIOS());
// Before processing any request, read the meta data first
#endif
}
// Before processing any request, read the meta data first
try
{
#if IOADIOS2_BP5_RANDOM_ACCESS
auto mode = adios2::Mode::ReadRandomAccess;
#else
auto mode = adios2::Mode::Read;
#endif
this->Impl->AdiosIO = this->Impl->Adios->DeclareIO("vtkADIOS2ImageRead");
if (vtksys::SystemTools::StringEndsWith(this->FileName, ".bp") ||
vtksys::SystemTools::StringEndsWith(this->FileName, ".bp4") ||
vtksys::SystemTools::StringEndsWith(this->FileName, ".bp5"))
{
this->Impl->AdiosIO.SetEngine("BPFile");
this->Impl->BpReader = this->Impl->AdiosIO.Open(this->FileName, mode);
}
else if (vtksys::SystemTools::StringEndsWith(this->FileName, "md.idx"))
{
this->Impl->AdiosIO.SetEngine("BP4");
this->Impl->BpReader =
this->Impl->AdiosIO.Open(this->FileName.substr(0, this->FileName.size() - 6), mode);
}
else
{
throw std::runtime_error("Unsupported file extension");
}
this->Impl->AvailVars = this->Impl->AdiosIO.AvailableVariables();
this->Impl->AvailAtts = this->Impl->AdiosIO.AvailableAttributes();
// Populate the array selection
this->Impl->AvailableArray->Allocate(static_cast<vtkIdType>(this->Impl->AvailVars.size()));
for (auto& iter : this->Impl->AvailVars)
{
this->Impl->ArraySelection->EnableArray(iter.first.c_str());
this->Impl->AvailableArray->InsertNextValue(iter.first);
}
}
catch (const std::exception& ex)
{
vtkErrorMacro("failed to open and read meta data: " << ex.what());
return false;
}
this->Impl->HasReadMetaData = true;
return true;
}
//------------------------------------------------------------------------------
vtkADIOS2CoreImageReader::vtkADIOS2CoreImageReader()
: DimensionArrayAsCell(true)
, IsColumnMajor(false)
, Impl(new vtkADIOS2CoreImageReaderImpl)
{
this->SetController(vtkMultiProcessController::GetGlobalController());
this->SetNumberOfInputPorts(0);
this->SetNumberOfOutputPorts(1);
this->Origin[0] = this->Origin[1] = this->Origin[2] = 0.0;
this->Spacing[0] = this->Spacing[1] = this->Spacing[2] = 1.0;
}
//------------------------------------------------------------------------------
vtkADIOS2CoreImageReader::~vtkADIOS2CoreImageReader() = default;
//------------------------------------------------------------------------------
int vtkADIOS2CoreImageReader::RequestInformation(
vtkInformation* request, vtkInformationVector** inputVector, vtkInformationVector* outputVector)
{
vtkInformation* outInfo = outputVector->GetInformationObject(0);
outputVector->GetInformationObject(0)->Set(CAN_HANDLE_PIECE_REQUEST(), 1);
// Initialize adios2 variables and read meta data
if (!this->Impl->HasReadMetaData && !this->OpenAndReadMetaData())
{
this->Impl->Adios.reset(nullptr);
vtkErrorMacro("unable to open file and data");
return 0;
}
if (this->Impl->AvailVars.empty())
{
vtkErrorMacro("No variables can be inquired in the provided file. Abort reading");
return 0;
}
// Set extent info
outInfo->Set(vtkDataObject::ORIGIN(), this->Origin, 3);
outInfo->Set(vtkDataObject::SPACING(), this->Spacing, 3);
this->UpdateDimensionFromDimensionArray();
int extent[6];
if (this->IsColumnMajor)
{
extent[0] = extent[2] = extent[4] = 0;
extent[1] = this->Dimension[0];
extent[3] = this->Dimension[1];
extent[5] = this->Dimension[2];
}
else
{
extent[0] = extent[2] = extent[4] = 0;
extent[1] = this->Dimension[2];
extent[3] = this->Dimension[1];
extent[5] = this->Dimension[0];
}
outInfo->Set(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT(), extent, 6);
if (!this->TimeStepArray.empty() && this->GatherTimeSteps())
{
// Publish time information
outInfo->Set(vtkStreamingDemandDrivenPipeline::TIME_STEPS(), this->Impl->TimeSteps.data(),
static_cast<int>(this->Impl->TimeSteps.size()));
double tRange[2];
tRange[0] = this->Impl->TimeSteps[0];
tRange[1] = this->Impl->TimeSteps[this->Impl->TimeSteps.size() - 1];
outInfo->Set(vtkStreamingDemandDrivenPipeline::TIME_RANGE(), tRange, 2);
}
return this->Superclass::RequestInformation(request, inputVector, outputVector);
}
//------------------------------------------------------------------------------
int vtkADIOS2CoreImageReader::RequestData(vtkInformation* vtkNotUsed(request),
vtkInformationVector** vtkNotUsed(inputVector), vtkInformationVector* outputVector)
{
// Convert user selected array names into inquire variables
this->ConvertArraySelectionToInqVar();
if (this->Impl->InquiredVars.empty())
{
this->Impl->Adios.reset(nullptr);
vtkErrorMacro("No inquire variable is specified. Abort reading now");
return 0;
}
if (!this->TimeStepArray.empty() &&
!this->Impl->ArraySelection->ArrayExists(this->TimeStepArray.c_str()))
{
this->Impl->Adios.reset(nullptr);
vtkErrorMacro("An invalid time step array name is specified. Abort reading now");
return 0;
}
vtkInformation* outInfo = outputVector->GetInformationObject(0);
if (!this->TimeStepArray.empty())
{
this->RequestTimeStep = outInfo->Get(vtkStreamingDemandDrivenPipeline::UPDATE_TIME_STEP());
if (!this->Impl->TimeStepsReverseMap.count(this->RequestTimeStep))
{
vtkErrorMacro("The requested time step " << this->RequestTimeStep << " is not available!");
return 0;
}
this->Impl->RequestStep = this->Impl->TimeStepsReverseMap[this->RequestTimeStep];
}
// Initialize work distribution for each rank
if (!this->InitWorkDistribution())
{
vtkErrorMacro("unable to initialize work distribution");
vtkNew<vtkMultiBlockDataSet> mbds;
mbds->SetNumberOfBlocks(0);
vtkSmartPointer<vtkMultiBlockDataSet> rootMB = vtkMultiBlockDataSet::GetData(outInfo);
rootMB->SetBlock(0, mbds);
if (!this->TimeStepArray.empty())
{
rootMB->GetInformation()->Set(vtkDataObject::DATA_TIME_STEP(), this->RequestTimeStep);
}
return 0;
}
vtkNew<vtkMultiBlockDataSet> mbds;
mbds->SetNumberOfBlocks(static_cast<unsigned int>(this->Impl->BlockCount));
this->ReadImageBlocks(mbds);
vtkSmartPointer<vtkMultiBlockDataSet> rootMB = vtkMultiBlockDataSet::GetData(outInfo);
vtkNew<vtkMultiPieceDataSet> mpds = this->Impl->Flatten(mbds);
rootMB->SetBlock(0, mpds);
if (!this->TimeStepArray.empty())
{
rootMB->GetInformation()->Set(vtkDataObject::DATA_TIME_STEP(), this->RequestTimeStep);
}
return 1;
}
//------------------------------------------------------------------------------
bool vtkADIOS2CoreImageReader::InitWorkDistribution()
{
try
{
// Determine the blocks that need to be read for the current rank
auto iter = this->Impl->InquiredVars.find(this->DimensionArray);
if (iter == this->Impl->InquiredVars.end())
{
vtkErrorMacro(
"Dimension Array (" << this->DimensionArray << ") must be one of the loaded arrays.");
return false;
}
std::string varName = iter->first;
std::string typeStr = this->FetchTypeStringFromVarName(varName);
if (typeStr.empty())
{
vtkErrorMacro("Cannot find a type for " << varName << " invalid name is provided");
return false;
}
// FIXME: adios2 IO object returns an template dependent class instance instead of
// a pointer or template independent object. Without using std::variant,
// if statements are used to overcome the limitation
// Use the adios_types_map in adios2 code base to generate types
if (typeStr == "string")
{
this->CalculateWorkDistribution<std::string>(varName);
}
else if (typeStr == "int8_t")
{
this->CalculateWorkDistribution<int8_t>(varName);
}
else if (typeStr == "uint8_t")
{
this->CalculateWorkDistribution<uint8_t>(varName);
}
else if (typeStr == "int16_t")
{
this->CalculateWorkDistribution<int16_t>(varName);
}
else if (typeStr == "uint16_t")
{
this->CalculateWorkDistribution<uint16_t>(varName);
}
else if (typeStr == "int32_t")
{
this->CalculateWorkDistribution<int32_t>(varName);
}
else if (typeStr == "uint32_t")
{
this->CalculateWorkDistribution<uint32_t>(varName);
}
else if (typeStr == "int64_t")
{
this->CalculateWorkDistribution<int64_t>(varName);
}
else if (typeStr == "uint64_t")
{
this->CalculateWorkDistribution<uint64_t>(varName);
}
else if (typeStr == "float")
{
this->CalculateWorkDistribution<float>(varName);
}
else if (typeStr == "double")
{
this->CalculateWorkDistribution<double>(varName);
}
else if (typeStr == "float complex")
{
this->CalculateWorkDistribution<std::complex<float>>(varName);
}
else if (typeStr == "double complex")
{
this->CalculateWorkDistribution<std::complex<double>>(varName);
}
}
catch (std::exception& e)
{
vtkErrorMacro("failed to initialize work distribution: " << e.what());
return false;
}
return true;
}
//------------------------------------------------------------------------------
std::string vtkADIOS2CoreImageReader::FetchTypeStringFromVarName(const std::string& name)
{
return (this->Impl->AvailVars.find(name) == this->Impl->AvailVars.end())
? std::string{}
: this->Impl->AvailVars[name]["Type"];
}
//------------------------------------------------------------------------------
void vtkADIOS2CoreImageReader::UpdateDimensionFromDimensionArray()
{
if (this->Impl->AvailVars.find(this->DimensionArray) == this->Impl->AvailVars.end())
{
return;
}
std::vector<int> dims = parseDimensions(this->Impl->AvailVars[this->DimensionArray]["Shape"]);
int offset = this->DimensionArrayAsCell ? 1 : 0;
if (dims.size() == 3)
{
this->Dimension[0] = dims[0] + offset;
this->Dimension[1] = dims[1] + offset;
this->Dimension[2] = dims[2] + offset;
}
else if (dims.size() == 2)
{
this->Dimension[0] = dims[0] + offset;
this->Dimension[1] = dims[1] + offset;
this->Dimension[2] = 1;
}
else
{
vtkErrorMacro("Can not use the dimension of array "
<< this->DimensionArray
<< " to set the dimension of image data. Its size is neither 2 nor 3");
}
}
//------------------------------------------------------------------------------
void vtkADIOS2CoreImageReader::ConvertArraySelectionToInqVar()
{
InquireVariablesType inqVars;
for (int ii = 0; ii < this->Impl->ArraySelection->GetNumberOfArrays(); ++ii)
{
std::string arrayName = this->Impl->ArraySelection->GetArrayName(ii);
if (this->Impl->ArraySelection->ArrayIsEnabled(arrayName.c_str())) // Enabled by the user
{
std::vector<int> dims = parseDimensions(this->Impl->AvailVars[arrayName]["Shape"]);
if (dims.size() == 2)
{
if (dims[0] == this->Dimension[0] && dims[1] == this->Dimension[1])
{
inqVars.insert(std::pair<std::string, VarType>(arrayName, VarType::PointData));
}
else if (dims[0] == this->Dimension[0] - 1 && dims[1] == this->Dimension[1] - 1)
{
inqVars.insert(std::pair<std::string, VarType>(arrayName, VarType::CellData));
}
}
else if (dims.size() == 3)
{
if (dims[0] == this->Dimension[0] && dims[1] == this->Dimension[1] &&
dims[2] == this->Dimension[2])
{
inqVars.insert(std::pair<std::string, VarType>(arrayName, VarType::PointData));
}
else if (dims[0] == this->Dimension[0] - 1 && dims[1] == this->Dimension[1] - 1 &&
dims[2] == this->Dimension[2] - 1)
{
inqVars.insert(std::pair<std::string, VarType>(arrayName, VarType::CellData));
}
}
else
{
vtkWarningMacro("The dimension of array " << arrayName << " is not supported. Skipping");
}
}
}
this->Impl->InquiredVars = inqVars;
}
//------------------------------------------------------------------------------
void vtkADIOS2CoreImageReader::ReadImageBlocks(vtkMultiBlockDataSet* mbds)
{
try
{
// One adios block is mapped to one vtk image data.
size_t blockExtentI{ 0 };
for (size_t blockI = this->Impl->BlockStart;
blockI < this->Impl->BlockStart + this->Impl->BlockCount; blockI++)
{
vtkNew<vtkImageData> outputImage;
outputImage->SetOrigin(this->Origin);
outputImage->SetSpacing(this->Spacing);
const auto& extents = this->Impl->BlockExtents[blockExtentI++];
if (this->IsColumnMajor)
{
outputImage->SetExtent(
extents[0], extents[1], extents[2], extents[3], extents[4], extents[5]);
}
else
{
outputImage->SetExtent(
extents[4], extents[5], extents[2], extents[3], extents[0], extents[1]);
}
// The index of mbds starts from 0
mbds->SetBlock(static_cast<unsigned int>(blockI - this->Impl->BlockStart), outputImage);
// Fetch all datas for current image
for (const auto& iter : this->Impl->InquiredVars)
{
std::string varName = iter.first;
if (this->Impl->AvailVars.find(varName) == this->Impl->AvailVars.end())
{
vtkErrorMacro("Inquire variable " << varName << " cannot be found in the provided file");
continue;
}
// TODO: Add validation for inquire variable's dimensions
std::string typeStr = this->FetchTypeStringFromVarName(varName);
if (typeStr.empty())
{
vtkErrorMacro("Cannot find a type for " << varName << " invalid name is provided");
continue;
}
vtkSmartPointer<vtkAbstractArray> dataArray;
// Use the adios_types_map in adios2 code base to generate types
if (typeStr == "string")
{ // vtkStringArray uses vtkStdString instead of std::string. So we manually
// do the work here
auto varADIOS2 = this->Impl->AdiosIO.InquireVariable<std::string>(varName);
varADIOS2.SetBlockSelection(blockI);
varADIOS2.SetStepSelection({ this->Impl->RequestStep, 1 });
vtkNew<vtkStringArray> array;
dataArray = array;
array->SetNumberOfComponents(1);
array->SetName(varName.c_str());
array->SetNumberOfTuples(static_cast<vtkIdType>(varADIOS2.SelectionSize()));
this->Impl->BpReader.Get(varADIOS2, dynamic_cast<std::string*>(array->GetPointer(0)));
}
else if (typeStr == "char")
{
dataArray = this->PopulateDataArrayFromVar<char, NativeToVTKType>(varName, blockI);
}
else if (typeStr == "int8_t")
{
dataArray = this->PopulateDataArrayFromVar<int8_t, NativeToVTKType>(varName, blockI);
}
else if (typeStr == "uint8_t")
{
dataArray = this->PopulateDataArrayFromVar<uint8_t, NativeToVTKType>(varName, blockI);
}
else if (typeStr == "int16_t")
{
dataArray = this->PopulateDataArrayFromVar<int16_t, NativeToVTKType>(varName, blockI);
}
else if (typeStr == "uint16_t")
{
dataArray = this->PopulateDataArrayFromVar<uint16_t, NativeToVTKType>(varName, blockI);
}
else if (typeStr == "int32_t")
{
dataArray = this->PopulateDataArrayFromVar<int32_t, NativeToVTKType>(varName, blockI);
}
else if (typeStr == "uint32_t")
{
dataArray = this->PopulateDataArrayFromVar<uint32_t, NativeToVTKType>(varName, blockI);
}
else if (typeStr == "int64_t")
{
dataArray = this->PopulateDataArrayFromVar<int64_t, NativeToVTKType>(varName, blockI);
}
else if (typeStr == "uint64_t")
{
dataArray = this->PopulateDataArrayFromVar<uint64_t, NativeToVTKType>(varName, blockI);
}
else if (typeStr == "float")
{
dataArray = this->PopulateDataArrayFromVar<float, NativeToVTKType>(varName, blockI);
}
else if (typeStr == "double")
{
dataArray = this->PopulateDataArrayFromVar<double, NativeToVTKType>(varName, blockI);
}
else if (typeStr == "long double")
{
vtkWarningMacro(<< "ADIOS2 type long double is not supported yet. Skipping array "
<< varName);
continue;
}
else if (typeStr == "float complex")
{
vtkWarningMacro(<< "ADIOS2 type float complex is not supported yet. Skipping array "
<< varName);
continue;
}
else if (typeStr == "double complex")
{
vtkWarningMacro(<< "ADIOS2 type double complex is not supported yet. Skipping array "
<< varName);
continue;
}
if (dataArray && iter.second == VarType::CellData)
{
outputImage->GetCellData()->AddArray(dataArray);
}
else if (dataArray && iter.second == VarType::PointData)
{
outputImage->GetPointData()->AddArray(dataArray);
}
// Set active scalars if possible
if (this->Impl->ActiveScalar.first == varName)
{
if (this->Impl->ActiveScalar.second == vtkADIOS2CoreImageReader::VarType::CellData)
{
outputImage->GetCellData()->SetActiveScalars(varName.c_str());
}
else
{
outputImage->GetPointData()->SetActiveScalars(varName.c_str());
}
}
dataArray->Delete();
}
}
this->Impl->BpReader.PerformGets();
}
catch (std::exception& e)
{
vtkErrorMacro(<< e.what());
}
}
//------------------------------------------------------------------------------
bool vtkADIOS2CoreImageReader::GatherTimeSteps()
{
std::string typeStr = this->FetchTypeStringFromVarName(this->TimeStepArray);
if (typeStr.empty())
{
vtkErrorMacro(
"Cannot find a type for time step " << this->TimeStepArray << " invalid name is provided");
return false;
}
// FIXME: adios2 IO object returns an template dependent class instance instead of
// a pointer or template independent object. Without using std::variant,
// if statements are used to overcome the limitation
// Use the adios_types_map in adios2 code base to generate types
// It's a safe assumption that the type of time array should be one of the following types.
if (typeStr == "int8_t")
{
this->GatherTimeStepsFromADIOSTimeArray<int8_t>();
}
else if (typeStr == "uint8_t")
{
this->GatherTimeStepsFromADIOSTimeArray<uint8_t>();
}
else if (typeStr == "int16_t")
{
this->GatherTimeStepsFromADIOSTimeArray<int16_t>();
}
else if (typeStr == "uint16_t")
{
this->GatherTimeStepsFromADIOSTimeArray<uint16_t>();
}
else if (typeStr == "int32_t")
{
this->GatherTimeStepsFromADIOSTimeArray<int32_t>();
}
else if (typeStr == "uint32_t")
{
this->GatherTimeStepsFromADIOSTimeArray<uint32_t>();
}
else if (typeStr == "int64_t")
{
this->GatherTimeStepsFromADIOSTimeArray<uint64_t>();
}
else if (typeStr == "float")
{
this->GatherTimeStepsFromADIOSTimeArray<float>();
}
else if (typeStr == "double")
{
this->GatherTimeStepsFromADIOSTimeArray<double>();
}
else
{
vtkErrorMacro("Type " << typeStr << " is not supported yet as a time array type in VTK");
return false;
}
return true;
}
//------------------------------------------------------------------------------
template <typename T>
void vtkADIOS2CoreImageReader::CalculateWorkDistribution(const std::string& varName)
{
this->Impl->BlockExtents.clear();
auto var = this->Impl->AdiosIO.InquireVariable<T>(varName);
size_t blockNum = this->Impl->BpReader.BlocksInfo(var, this->Impl->RequestStep).size();
#if VTK_MODULE_ENABLE_VTK_ParallelMPI
size_t rank = static_cast<size_t>(this->Controller->GetLocalProcessId());
size_t procs = static_cast<size_t>(this->Controller->GetNumberOfProcesses());
#else
size_t rank{ 0 }, procs{ 1 };
#endif
// Decide how many blocks that current process shall read
this->Impl->BlockCount = blockNum / procs;
size_t leftOver = blockNum % procs;
if (rank < leftOver)
{
this->Impl->BlockCount++;
this->Impl->BlockStart = rank * (this->Impl->BlockCount);
}
else
{
this->Impl->BlockStart =
leftOver * (this->Impl->BlockCount + 1) + (rank - leftOver) * this->Impl->BlockCount;
}
// Calculate the extent for each block
for (size_t i = this->Impl->BlockStart; i < this->Impl->BlockStart + this->Impl->BlockCount; i++)
{
auto start = this->Impl->BpReader.BlocksInfo(var, this->Impl->RequestStep)[i].Start;
auto count = this->Impl->BpReader.BlocksInfo(var, this->Impl->RequestStep)[i].Count;
if (start.size() == 3 && count.size() == 3)
{
// Use the DimensionArray var to init workdistribution
// in most cases it's probably not necessary, but it's possible that arrays can have
// different block dimensions, in which case we don't want to just blindly grab the first
// array that's in the ArraySelection
auto iter = this->Impl->InquiredVars.find(this->DimensionArray);
if (iter == this->Impl->InquiredVars.end())
{
vtkErrorMacro("Cannot find DimensionArray " << this->DimensionArray << " in InquiredVars");
return;
}
int offSet = iter->second == VarType::PointData ? -1 : 0;
this->Impl->BlockExtents.push_back(
{ static_cast<int>(start[0]), static_cast<int>(start[0] + count[0]) + offSet,
static_cast<int>(start[1]), static_cast<int>(start[1] + count[1]) + offSet,
static_cast<int>(start[2]), static_cast<int>(start[2] + count[2]) + offSet });
}
else if (start.size() == 2 && count.size() == 2)
{
auto iter = this->Impl->InquiredVars.find(this->DimensionArray);
if (iter == this->Impl->InquiredVars.end())
{
vtkErrorMacro("Cannot find DimensionArray " << this->DimensionArray << " in InquiredVars");
return;
}
int offSet = iter->second == VarType::PointData ? -1 : 0;
this->Impl->BlockExtents.push_back(
{ static_cast<int>(start[0]), static_cast<int>(start[0] + count[0]) + offSet,
static_cast<int>(start[1]), static_cast<int>(start[1] + count[1]) + offSet, 0, 1 });
}
else
{
this->Impl->BlockExtents.push_back({});
}
}
}
//------------------------------------------------------------------------------
template <typename T, template <typename...> class U>
vtkSmartPointer<vtkAbstractArray> vtkADIOS2CoreImageReader::PopulateDataArrayFromVar(
const std::string& varName, size_t blockIndex)
{
vtkSmartPointer<vtkAbstractArray> array = vtkDataArray::CreateDataArray(U<T>::VTKType);
try
{
auto varADIOS2 = this->Impl->AdiosIO.InquireVariable<T>(varName);
varADIOS2.SetStepSelection({ this->Impl->RequestStep, 1 });
varADIOS2.SetBlockSelection(blockIndex);
array->SetNumberOfComponents(1);
array->SetName(varName.c_str());
array->SetNumberOfTuples(static_cast<vtkIdType>(varADIOS2.SelectionSize()));
this->Impl->BpReader.Get(varADIOS2, static_cast<T*>(array->GetVoidPointer(0)));
}
catch (const std::exception& ex)
{
vtkErrorMacro("Fail to populate data array from variable " << varName << ex.what());
}
return array;
}
//------------------------------------------------------------------------------
template <typename T>
void vtkADIOS2CoreImageReader::GatherTimeStepsFromADIOSTimeArray()
{
try
{
auto varADIOS2 = this->Impl->AdiosIO.InquireVariable<T>(this->TimeStepArray);
size_t nSteps = varADIOS2.Steps();
size_t stepsStart = varADIOS2.StepsStart();
std::vector<int> dims = parseDimensions(this->Impl->AvailVars[this->TimeStepArray]["Shape"]);
int multiplication{ 1 };
std::for_each(dims.begin(), dims.end(), [&multiplication](int v) { multiplication *= v; });
this->Impl->TimeSteps.clear();
// A temporary vector to hold time steps since ADIOS requires the variable and array should have
// same type
std::vector<T> tempTimeSteps(nSteps, 0);
if (multiplication == 1 || multiplication == static_cast<int>(nSteps))
{
// From Chuck: We should be able to read all steps at once but because of an ADIOS2 bug
// we can only read one at a time
for (size_t s = 0; s < nSteps; ++s)
{
varADIOS2.SetStepSelection({ stepsStart + s, 1 });
this->Impl->BpReader.Get(varADIOS2, tempTimeSteps.data() + s);
}
this->Impl->BpReader.PerformGets();
for (const auto v : tempTimeSteps)
{
this->Impl->TimeSteps.push_back(static_cast<double>(v));
}
}
else
{
for (int i = 0; i < static_cast<int>(nSteps); i++)
{
this->Impl->TimeSteps.push_back(static_cast<double>(stepsStart + i));
}
}
this->Impl->TimeStepsReverseMap.clear();
for (size_t i = 0; i < this->Impl->TimeSteps.size(); ++i)
{
this->Impl->TimeStepsReverseMap[this->Impl->TimeSteps[i]] = i;
}
}
catch (const std::exception& ex)
{
vtkErrorMacro("Fail to gather time steps from time array " << this->TimeStepArray << ex.what());
}
}
VTK_ABI_NAMESPACE_END
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