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0675c0b697
* MDAL 0.5.90 : support for custom Logger and 1D meshes * [FEATURE] [MESH] Support rendering of 1D meshes, see https://github.com/qgis/QGIS-Enhancement-Proposals/issues/164 1D mesh consist of edges (edge is straight line segment with 2 vertices) and the data that is defined on either vertices or edges. Such data can be loaded by MDAL and rendered as mesh layer in QGIS.
232 lines
8.0 KiB
C++
232 lines
8.0 KiB
C++
/*
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MDAL - Mesh Data Abstraction Library (MIT License)
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Copyright (C) 2019 Peter Petrik (zilolv at gmail dot com)
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*/
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#ifndef MDAL_XDMF_HPP
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#define MDAL_XDMF_HPP
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#include <string>
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#include <vector>
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#include <memory>
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#include <iosfwd>
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#include <iostream>
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#include <fstream>
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#include <utility>
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#include "mdal_data_model.hpp"
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#include "mdal.h"
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#include "mdal_hdf5.hpp"
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#include "mdal_driver.hpp"
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#include "mdal_xml.hpp"
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namespace MDAL
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{
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/**
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* The XdmfDataset reads the data directly from HDF5 file
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* by usage of hyperslabs retrieval
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*
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* http://xdmf.org/index.php/XDMF_Model_and_Format#HyperSlab
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* HyperSlab consists of 3 rows: start, stride, and count
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* - Currently we do not support stride other than 1 (every element)
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* - Assumes BASEMENT 3.x format where the array is nFaces x 1
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*/
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struct HyperSlab
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{
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size_t startX = 0; // offset X
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size_t startY = 0; // offset Y
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size_t count = 0; // number of cells/vertices
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bool countInFirstColumn = true;
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bool isScalar;
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};
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/**
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* The XdmfDataset is simple vector or scalar dataset
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* where values are stored in one HD5 variable
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* and are lazy loaded on demand. Active flag is always ON.
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*
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* The definition is stored in XML file in format:
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*
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* <Attribute Name="water_surface" AttributeType="Scalar" Center="Cell">
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* <DataItem ItemType="HyperSlab" Dimensions="9 1" Type="HyperSlab">
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* <DataItem Dimensions="3 2" Format="XML"> 0 0 1 1 9 1 </DataItem>
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* <DataItem Dimensions="9 3" Format="HDF"> test.h5:/RESULTS/CellsAll/HydState/0000002 </DataItem>
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* </DataItem>
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* </Attribute>
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*/
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class XdmfDataset: public Dataset2D
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{
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public:
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XdmfDataset( DatasetGroup *grp,
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const HyperSlab &slab,
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const HdfDataset &valuesDs,
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MDAL::RelativeTimestamp time
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);
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~XdmfDataset() override;
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size_t scalarData( size_t indexStart, size_t count, double *buffer ) override;
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size_t vectorData( size_t indexStart, size_t count, double *buffer ) override;
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private:
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std::vector<hsize_t> offsets( size_t indexStart );
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std::vector<hsize_t> selections( size_t copyValues );
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HdfDataset mHdf5DatasetValues;
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HyperSlab mHyperSlab;
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};
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/**
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* The XdmfFunctionDataset is a function that
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* references two or three scalar XdmfDatasets
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* to create a vector or scalar dataset based on
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* referenced datasets. Active flag is always ON.
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*
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* Currently we do not use any fancy bison/flex based
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* expression parsing, just supporting few types of
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* most common function types:
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* - subtraction (A-B)
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* - join ( [A, B] vector)
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* - magnitude
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*
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* The definition is stored in XML file in format:
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*
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* <Attribute Name="..." AttributeType="Scalar" Center="Cell">
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* <DataItem ItemType="Function" Function="$0 - $1" Dimensions="9" >
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* <DataItem ItemType="HyperSlab" Type="HyperSlab">...</DataItem>
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* <DataItem ItemType="HyperSlab" Type="HyperSlab">...</DataItem>
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* </DataItem>
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* </Attribute>
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*/
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class XdmfFunctionDataset: public Dataset2D
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{
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public:
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enum FunctionType
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{
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Join = 1, //!< vector: [$0, $1] from 2 scalars
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Subtract, //!< scalar: $1 - $0, e.g. calculate relative depth
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Flow, //!< scalar: flow velocity (abs) = sqrt($0/($2-$3)*$0/($2-$3) + $1/($2-$3)*$1/($2-$3))
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};
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XdmfFunctionDataset( DatasetGroup *grp,
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FunctionType type,
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const RelativeTimestamp &time
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);
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~XdmfFunctionDataset() override;
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//! Adds reference XMDF dataset
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void addReferenceDataset( const HyperSlab &slab, const HdfDataset &hdfDataset, const RelativeTimestamp &time );
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//! Swaps first and second reference dataset
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void swap();
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size_t scalarData( size_t indexStart, size_t count, double *buffer ) override;
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size_t vectorData( size_t indexStart, size_t count, double *buffer ) override;
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private:
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size_t subtractFunction( size_t indexStart, size_t count, double *buffer );
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size_t flowFunction( size_t indexStart, size_t count, double *buffer );
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size_t joinFunction( size_t indexStart, size_t count, double *buffer );
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size_t extractRawData( size_t indexStart, size_t count, size_t nDatasets, std::vector<double> &buf );
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const FunctionType mType;
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std::vector<std::shared_ptr<XdmfDataset>> mReferenceDatasets;
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/**
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* "fake" base group for reference datasets.
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* This group is not exposed to public API and
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* it is just an implementation detail.
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*/
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DatasetGroup mBaseReferenceGroup;
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};
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class DriverXdmf: public Driver
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{
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public:
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/**
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* Driver for XDMF Files
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*
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* XDMF is combination of XML file with dataset metadata and
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* HDF5 file with actual data for the datasets
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*
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* full file specification http://xdmf.org/index.php/XDMF_Model_and_Format
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*
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* XDMF file can have data (vectors) stored in different ways. Currently we
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* only support format for BASEMENET 3.x solver
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*/
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DriverXdmf();
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~DriverXdmf( ) override;
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DriverXdmf *create() override;
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bool canReadDatasets( const std::string &uri ) override;
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void load( const std::string &datFile, Mesh *mesh ) override;
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private:
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/**
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Parses XML File with this structure, where data is specified as pointers to HDF in Attribute tags
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<?xml version="1.0" ?>
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<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
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<Xdmf Version="2.0">
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<Domain>
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<Topology> ... </Topology>
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<Geometry> ... </Geometry>
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<Grid GridType="Collection" Name="..." CollectionType="Temporal">
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<Grid GridType="Uniform" Name="Timestep">
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<Time TimeType="Single" Name="time = 0.000000" Value="0.000000"> </Time>
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<Topology></Topology>
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<Geometry GeometryType="XY" Reference="/Xdmf/Domain/Geometry[1]"></Geometry>
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<Attribute> ... </Attribute>
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</Grid>
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</Grid>
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<Domain>
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</Xdmf>
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*/
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DatasetGroups parseXdmfXml( );
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//! Finds a group with a name or creates a new group if does not exists
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std::shared_ptr<MDAL::DatasetGroup> findGroup( std::map< std::string, std::shared_ptr<MDAL::DatasetGroup> > &groups,
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const std::string &groupName,
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bool isScalar );
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/**
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* Parses scalar/vector definition for XDMF dataset, e.g.
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*
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* <DataItem ItemType="HyperSlab" Dimensions="9 1" Type="HyperSlab">
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* <DataItem Dimensions="3 2" Format="XML"> 0 1 1 1 9 1 </DataItem>
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* <DataItem Dimensions="9 3" Format="HDF"> test.h5:/RESULTS/CellsAll/HydState/0000002 </DataItem>
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* </DataItem>
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*/
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std::pair<HdfDataset, HyperSlab > parseXdmfDataset( const XMLFile &xmfFile, xmlNodePtr itemNod );
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//! Parses hypeslab specification from string
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HyperSlab parseHyperSlab( const std::string &str, size_t dimB );
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/**
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* Parses hyperslab specification from matrix in DataItem [Dimension] tag
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<DataItem ItemType="Uniform" Dimensions="3 3" Format="XML">
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0 0 0 1 1 1 18497 1 1
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</DataItem>
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*/
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HyperSlab parseHyperSlabNode( const XMLFile &xmfFile, xmlNodePtr node );
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/**
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* Parses hdf5 dataset from node
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<DataItem Dimensions="9 3" Format="HDF"> test.h5:/RESULTS/CellsAll/HydState/0000002 </DataItem>
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*/
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HdfDataset parseHdf5Node( const XMLFile &xmfFile, xmlNodePtr node );
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//! Extracts HDF5 filename and HDF5 Path from XML file dirname and fileName:hdfPath syntax
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void hdf5NamePath( const std::string &dataItemPath, std::string &filePath, std::string &hdf5Path );
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//! Parses 2d matrix from text, e.g. 3 2 -> [3, 2]. Verifies that it has 2 items
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std::vector<size_t> parseDimensions2D( const std::string &data );
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MDAL::Mesh *mMesh = nullptr;
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std::string mDatFile;
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std::map< std::string, std::shared_ptr<HdfFile> > mHdfFiles;
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};
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} // namespace MDAL
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#endif //MDAL_XDMF_HPP
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