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Unverified Commit 67dc1197 authored by Minjie Wang's avatar Minjie Wang Committed by GitHub
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[Refactor] Use object system for all CAPIs (#716) 

* WIP: using object system for graph

* c++ side refactoring done; compiled

* remove stale apis

* fix bug in DGLGraphCreate; passed test_graph.py

* fix bug in python modify; passed utest for pytorch/cpu

* fix lint

* address comments
parent b0d9e7aa
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include/dgl/graph.h
View file @ 67dc1197
......@@ -12,6 +12,7 @@
#include <cstdint>
#include <utility>
#include <tuple>
#include <memory>
#include "graph_interface.h"
......@@ -19,21 +20,9 @@ namespace dgl {
class Graph;
class GraphOp;
typedef std::shared_ptr<Graph> MutableGraphPtr;
/*!
* \brief Base dgl graph index class.
*
* DGL's graph is directed. Vertices are integers enumerated from zero.
*
* Removal of vertices/edges is not allowed. Instead, the graph can only be "cleared"
* by removing all the vertices and edges.
*
* When calling functions supporing multiple edges (e.g. AddEdges, HasEdges),
* the input edges are represented by two id arrays for source and destination
* vertex ids. In the general case, the two arrays should have the same length.
* If the length of src id array is one, it represents one-many connections.
* If the length of dst id array is one, it represents many-one connections.
*/
/*! \brief Mutable graph based on adjacency list. */
class Graph: public GraphInterface {
public:
/*! \brief default constructor */
......@@ -305,15 +294,6 @@ class Graph: public GraphInterface {
*/
Subgraph EdgeSubgraph(IdArray eids, bool preserve_nodes = false) const override;
/*!
* \brief Return a new graph with all the edges reversed.
*
* The returned graph preserves the vertex and edge index in the original graph.
*
* \return the reversed graph
*/
GraphPtr Reverse() const override;
/*!
* \brief Return the successor vector
* \param vid The vertex id.
......@@ -358,16 +338,6 @@ class Graph: public GraphInterface {
return DGLIdIters(data, data + size);
}
/*!
* \brief Reset the data in the graph and move its data to the returned graph object.
* \return a raw pointer to the graph object.
*/
GraphInterface *Reset() override {
Graph* gptr = new Graph();
*gptr = std::move(*this);
return gptr;
}
/*!
* \brief Get the adjacency matrix of the graph.
*
......@@ -379,6 +349,17 @@ class Graph: public GraphInterface {
*/
std::vector<IdArray> GetAdj(bool transpose, const std::string &fmt) const override;
/*! \brief Create an empty graph */
static MutableGraphPtr Create(bool multigraph = false) {
return std::make_shared<Graph>(multigraph);
}
/*! \brief Create from coo */
static MutableGraphPtr CreateFromCOO(
int64_t num_nodes, IdArray src_ids, IdArray dst_ids, bool multigraph = false) {
return std::make_shared<Graph>(src_ids, dst_ids, num_nodes, multigraph);
}
protected:
friend class GraphOp;
/*! \brief Internal edge list type */
......
include/dgl/graph_interface.h
View file @ 67dc1197
......@@ -11,13 +11,11 @@
#include <utility>
#include <algorithm>
#include "./runtime/object.h"
#include "array.h"
namespace dgl {
struct Subgraph;
struct NodeFlow;
const dgl_id_t DGL_INVALID_ID = static_cast<dgl_id_t>(-1);
/*!
......@@ -51,6 +49,15 @@ class DGLIdIters {
const dgl_id_t *begin_{nullptr}, *end_{nullptr};
};
/* \brief structure used to represent a list of edges */
typedef struct {
/* \brief the two endpoints and the id of the edge */
IdArray src, dst, id;
} EdgeArray;
// forward declaration
struct Subgraph;
class GraphRef;
class GraphInterface;
typedef std::shared_ptr<GraphInterface> GraphPtr;
......@@ -58,15 +65,15 @@ typedef std::shared_ptr<GraphInterface> GraphPtr;
* \brief dgl graph index interface.
*
* DGL's graph is directed. Vertices are integers enumerated from zero.
*
* When calling functions supporing multiple edges (e.g. AddEdges, HasEdges),
* the input edges are represented by two id arrays for source and destination
* vertex ids. In the general case, the two arrays should have the same length.
* If the length of src id array is one, it represents one-many connections.
* If the length of dst id array is one, it represents many-one connections.
*/
class GraphInterface {
class GraphInterface : public runtime::Object {
public:
/* \brief structure used to represent a list of edges */
typedef struct {
/* \brief the two endpoints and the id of the edge */
IdArray src, dst, id;
} EdgeArray;
virtual ~GraphInterface() = default;
/*!
......@@ -293,15 +300,6 @@ class GraphInterface {
*/
virtual Subgraph EdgeSubgraph(IdArray eids, bool preserve_nodes = false) const = 0;
/*!
* \brief Return a new graph with all the edges reversed.
*
* The returned graph preserves the vertex and edge index in the original graph.
*
* \return the reversed graph
*/
virtual GraphPtr Reverse() const = 0;
/*!
* \brief Return the successor vector
* \param vid The vertex id.
......@@ -330,12 +328,6 @@ class GraphInterface {
*/
virtual DGLIdIters InEdgeVec(dgl_id_t vid) const = 0;
/*!
* \brief Reset the data in the graph and move its data to the returned graph object.
* \return a raw pointer to the graph object.
*/
virtual GraphInterface *Reset() = 0;
/*!
* \brief Get the adjacency matrix of the graph.
*
......@@ -353,8 +345,14 @@ class GraphInterface {
* \return a vector of IdArrays.
*/
virtual std::vector<IdArray> GetAdj(bool transpose, const std::string &fmt) const = 0;
static constexpr const char* _type_key = "graph.Graph";
DGL_DECLARE_OBJECT_TYPE_INFO(GraphInterface, runtime::Object);
};
// Define GraphRef
DGL_DEFINE_OBJECT_REF(GraphRef, GraphInterface);
/*! \brief Subgraph data structure */
struct Subgraph {
/*! \brief The graph. */
......
include/dgl/graph_op.h
View file @ 67dc1197
......@@ -14,6 +14,15 @@ namespace dgl {
class GraphOp {
public:
/*!
* \brief Return a new graph with all the edges reversed.
*
* The returned graph preserves the vertex and edge index in the original graph.
*
* \return the reversed graph
*/
static GraphPtr Reverse(GraphPtr graph);
/*!
* \brief Return the line graph.
*
......@@ -25,7 +34,7 @@ class GraphOp {
* \param backtracking Whether the backtracking edges are included or not
* \return the line graph
*/
static Graph LineGraph(const Graph* graph, bool backtracking);
static GraphPtr LineGraph(GraphPtr graph, bool backtracking);
/*!
* \brief Return a disjoint union of the input graphs.
......@@ -36,10 +45,13 @@ class GraphOp {
* they have 5, 6, 7 nodes respectively. Then node#2 of g2 will become node#7
* in the result graph. Edge ids are re-assigned similarly.
*
* The input list must be either ALL mutable graphs or ALL immutable graphs.
* The returned graph type is also determined by the input graph type.
*
* \param graphs A list of input graphs to be unioned.
* \return the disjoint union of the graphs
*/
static Graph DisjointUnion(std::vector<const Graph*> graphs);
static GraphPtr DisjointUnion(std::vector<GraphPtr> graphs);
/*!
* \brief Partition the graph into several subgraphs.
......@@ -47,12 +59,15 @@ class GraphOp {
* This is a reverse operation of DisjointUnion. The graph will be partitioned
* into num graphs. This requires the given number of partitions to evenly
* divides the number of nodes in the graph.
*
* If the input graph is mutable, the result graphs are mutable.
* If the input graph is immutable, the result graphs are immutable.
*
* \param graph The graph to be partitioned.
* \param num The number of partitions.
* \return a list of partitioned graphs
*/
static std::vector<Graph> DisjointPartitionByNum(const Graph* graph, int64_t num);
static std::vector<GraphPtr> DisjointPartitionByNum(GraphPtr graph, int64_t num);
/*!
* \brief Partition the graph into several subgraphs.
......@@ -60,54 +75,15 @@ class GraphOp {
* This is a reverse operation of DisjointUnion. The graph will be partitioned
* based on the given sizes. This requires the sum of the given sizes is equal
* to the number of nodes in the graph.
*
* If the input graph is mutable, the result graphs are mutable.
* If the input graph is immutable, the result graphs are immutable.
*
* \param graph The graph to be partitioned.
* \param sizes The number of partitions.
* \return a list of partitioned graphs
*/
static std::vector<Graph> DisjointPartitionBySizes(const Graph* graph, IdArray sizes);
/*!
* \brief Return a readonly disjoint union of the input graphs.
*
* The new readonly graph will include all the nodes/edges in the given graphs.
* Nodes/Edges will be relabled in the given sequence order by batching over CSR Graphs.
* For example, giving input [g1, g2, g3], where
* they have 5, 6, 7 nodes respectively. Then node#2 of g2 will become node#7
* in the result graph. Edge ids are re-assigned similarly.
*
* \param ImmutableGraph A list of input graphs to be unioned.
* \return the disjoint union of the ImmutableGraph
*/
static ImmutableGraph DisjointUnion(std::vector<const ImmutableGraph*> graphs);
/*!
* \brief Partition the ImmutableGraph into several immutable subgraphs.
*
* This is a reverse operation of DisjointUnion. The graph will be partitioned
* into num graphs. This requires the given number of partitions to evenly
* divides the number of nodes in the graph.
*
* \param graph The ImmutableGraph to be partitioned.
* \param num The number of partitions.
* \return a list of partitioned ImmutableGraph
*/
static std::vector<ImmutableGraph> DisjointPartitionByNum(const ImmutableGraph *graph,
int64_t num);
/*!
* \brief Partition the ImmutableGraph into several immutable subgraphs.
*
* This is a reverse operation of DisjointUnion. The graph will be partitioned
* based on the given sizes. This requires the sum of the given sizes is equal
* to the number of nodes in the graph.
*
* \param graph The ImmutableGraph to be partitioned.
* \param sizes The number of partitions.
* \return a list of partitioned ImmutableGraph
*/
static std::vector<ImmutableGraph> DisjointPartitionBySizes(const ImmutableGraph *batched_graph,
IdArray sizes);
static std::vector<GraphPtr> DisjointPartitionBySizes(GraphPtr graph, IdArray sizes);
/*!
* \brief Map vids in the parent graph to the vids in the subgraph.
......@@ -143,7 +119,7 @@ class GraphOp {
* \param graph The input graph.
* \return a new immutable simple graph with no multi-edge.
*/
static ImmutableGraph ToSimpleGraph(const GraphInterface* graph);
static GraphPtr ToSimpleGraph(GraphPtr graph);
/*!
* \brief Convert the graph to a mutable bidirected graph.
......@@ -155,14 +131,14 @@ class GraphOp {
* \param graph The input graph.
* \return a new mutable bidirected graph.
*/
static Graph ToBidirectedMutableGraph(const GraphInterface* graph);
static GraphPtr ToBidirectedMutableGraph(GraphPtr graph);
/*!
* \brief Same as BidirectedMutableGraph except that the returned graph is immutable.
* \param graph The input graph.
* \return a new immutable bidirected graph.
*/
static ImmutableGraph ToBidirectedImmutableGraph(const GraphInterface* graph);
static GraphPtr ToBidirectedImmutableGraph(GraphPtr graph);
};
} // namespace dgl
......
include/dgl/heterograph_interface.h
View file @ 67dc1197
......@@ -38,14 +38,6 @@ typedef std::shared_ptr<HeteroGraphInterface> HeteroGraphPtr;
*/
class HeteroGraphInterface {
public:
/* \brief structure used to represent a list of edges */
// TODO(minjie): move this data structure outside of class definition so
// it can be shared by Graph and HeteroGraph.
typedef struct {
/* \brief the two endpoints and the id of the edge */
IdArray src, dst, id;
} EdgeArray;
virtual ~HeteroGraphInterface() = default;
////////////////////////// query/operations on meta graph ////////////////////////
......@@ -112,7 +104,7 @@ class HeteroGraphInterface {
/*! \return a 0-1 array indicating whether the given vertices are in the graph.*/
virtual BoolArray HasVertices(dgl_type_t vtype, IdArray vids) const {
const auto len = vids->shape[0];
BoolArray rst = NewBoolArray(len);
BoolArray rst = aten::NewBoolArray(len);
const dgl_id_t* vid_data = static_cast<dgl_id_t*>(vids->data);
dgl_id_t* rst_data = static_cast<dgl_id_t*>(rst->data);
for (int64_t i = 0; i < len; ++i) {
......@@ -129,7 +121,7 @@ class HeteroGraphInterface {
const auto srclen = src_ids->shape[0];
const auto dstlen = dst_ids->shape[0];
const auto rstlen = std::max(srclen, dstlen);
BoolArray rst = NewBoolArray(rstlen);
BoolArray rst = aten::NewBoolArray(rstlen);
dgl_id_t* rst_data = static_cast<dgl_id_t*>(rst->data);
const dgl_id_t* src_data = static_cast<dgl_id_t*>(src_ids->data);
const dgl_id_t* dst_data = static_cast<dgl_id_t*>(dst_ids->data);
......@@ -341,12 +333,6 @@ class HeteroGraphInterface {
*/
virtual DGLIdIters InEdgeVec(dgl_type_t etype, dgl_id_t vid) const = 0;
/*!
* \brief Reset the data in the graph and move its data to the returned graph object.
* \return a raw pointer to the graph object.
*/
virtual HeteroGraphInterface *Reset() = 0;
/*!
* \brief Get the adjacency matrix of the graph.
*
......
include/dgl/immutable_graph.h
View file @ 67dc1197
......@@ -23,6 +23,9 @@ class COO;
typedef std::shared_ptr<CSR> CSRPtr;
typedef std::shared_ptr<COO> COOPtr;
class ImmutableGraph;
typedef std::shared_ptr<ImmutableGraph> ImmutableGraphPtr;
/*!
* \brief Graph class stored using CSR structure.
*/
......@@ -167,10 +170,6 @@ class CSR : public GraphInterface {
return {};
}
GraphPtr Reverse() const override {
return Transpose();
}
DGLIdIters SuccVec(dgl_id_t vid) const override;
DGLIdIters OutEdgeVec(dgl_id_t vid) const override;
......@@ -187,12 +186,6 @@ class CSR : public GraphInterface {
return DGLIdIters(nullptr, nullptr);
}
GraphInterface *Reset() override {
CSR* gptr = new CSR();
*gptr = std::move(*this);
return gptr;
}
std::vector<IdArray> GetAdj(bool transpose, const std::string &fmt) const override {
CHECK(!transpose && fmt == "csr") << "Not valid adj format request.";
return {adj_.indptr, adj_.indices, adj_.data};
......@@ -256,7 +249,7 @@ class CSR : public GraphInterface {
aten::CSRMatrix adj_;
// whether the graph is a multi-graph
LazyObject<bool> is_multigraph_;
Lazy<bool> is_multigraph_;
// The name of the shared memory to store data.
// If it's empty, data isn't stored in shared memory.
......@@ -416,10 +409,6 @@ class COO : public GraphInterface {
Subgraph EdgeSubgraph(IdArray eids, bool preserve_nodes = false) const override;
GraphPtr Reverse() const override {
return Transpose();
}
DGLIdIters SuccVec(dgl_id_t vid) const override {
LOG(FATAL) << "COO graph does not support efficient SuccVec."
<< " Please use CSR graph or AdjList graph instead.";
......@@ -444,12 +433,6 @@ class COO : public GraphInterface {
return DGLIdIters(nullptr, nullptr);
}
GraphInterface *Reset() override {
COO* gptr = new COO();
*gptr = std::move(*this);
return gptr;
}
std::vector<IdArray> GetAdj(bool transpose, const std::string &fmt) const override {
CHECK(fmt == "coo") << "Not valid adj format request.";
if (transpose) {
......@@ -517,7 +500,7 @@ class COO : public GraphInterface {
aten::COOMatrix adj_;
/*! \brief whether the graph is a multi-graph */
LazyObject<bool> is_multigraph_;
Lazy<bool> is_multigraph_;
};
/*!
......@@ -840,21 +823,6 @@ class ImmutableGraph: public GraphInterface {
*/
Subgraph EdgeSubgraph(IdArray eids, bool preserve_nodes = false) const override;
/*!
* \brief Return a new graph with all the edges reversed.
*
* The returned graph preserves the vertex and edge index in the original graph.
*
* \return the reversed graph
*/
GraphPtr Reverse() const override {
if (coo_) {
return GraphPtr(new ImmutableGraph(out_csr_, in_csr_, coo_->Transpose()));
} else {
return GraphPtr(new ImmutableGraph(out_csr_, in_csr_));
}
}
/*!
* \brief Return the successor vector
* \param vid The vertex id.
......@@ -891,16 +859,6 @@ class ImmutableGraph: public GraphInterface {
return GetInCSR()->OutEdgeVec(vid);
}
/*!
* \brief Reset the data in the graph and move its data to the returned graph object.
* \return a raw pointer to the graph object.
*/
GraphInterface *Reset() override {
ImmutableGraph* gptr = new ImmutableGraph();
*gptr = std::move(*this);
return gptr;
}
/*!
* \brief Get the adjacency matrix of the graph.
*
......@@ -921,6 +879,35 @@ class ImmutableGraph: public GraphInterface {
/* !\brief Return coo. If not exist, create from csr.*/
COOPtr GetCOO() const;
/*! \brief Create an immutable graph from CSR. */
static ImmutableGraphPtr CreateFromCSR(
IdArray indptr, IdArray indices, IdArray edge_ids, const std::string &edge_dir);
static ImmutableGraphPtr CreateFromCSR(
IdArray indptr, IdArray indices, IdArray edge_ids,
bool multigraph, const std::string &edge_dir);
static ImmutableGraphPtr CreateFromCSR(
IdArray indptr, IdArray indices, IdArray edge_ids,
const std::string &edge_dir, const std::string &shared_mem_name);
static ImmutableGraphPtr CreateFromCSR(
IdArray indptr, IdArray indices, IdArray edge_ids,
bool multigraph, const std::string &edge_dir,
const std::string &shared_mem_name);
static ImmutableGraphPtr CreateFromCSR(
const std::string &shared_mem_name, size_t num_vertices,
size_t num_edges, bool multigraph,
const std::string &edge_dir);
/*! \brief Create an immutable graph from COO. */
static ImmutableGraphPtr CreateFromCOO(
int64_t num_vertices, IdArray src, IdArray dst);
static ImmutableGraphPtr CreateFromCOO(
int64_t num_vertices, IdArray src, IdArray dst, bool multigraph);
/*!
* \brief Convert the given graph to an immutable graph.
*
......@@ -930,14 +917,14 @@ class ImmutableGraph: public GraphInterface {
* \param graph The input graph.
* \return an immutable graph object.
*/
static ImmutableGraph ToImmutable(const GraphInterface* graph);
static ImmutableGraphPtr ToImmutable(GraphPtr graph);
/*!
* \brief Copy the data to another context.
* \param ctx The target context.
* \return The graph under another context.
*/
ImmutableGraph CopyTo(const DLContext& ctx) const;
static ImmutableGraphPtr CopyTo(ImmutableGraphPtr g, const DLContext& ctx);
/*!
* \brief Copy data to shared memory.
......@@ -945,85 +932,24 @@ class ImmutableGraph: public GraphInterface {
* \param name The name of the shared memory.
* \return The graph in the shared memory
*/
ImmutableGraph CopyToSharedMem(const std::string &edge_dir, const std::string &name) const;
static ImmutableGraphPtr CopyToSharedMem(
ImmutableGraphPtr g, const std::string &edge_dir, const std::string &name);
/*!
* \brief Convert the graph to use the given number of bits for storage.
* \param bits The new number of integer bits (32 or 64).
* \return The graph with new bit size storage.
*/
ImmutableGraph AsNumBits(uint8_t bits) const;
/*! \brief Create an immutable graph from CSR. */
static ImmutableGraph CreateFromCSR(IdArray indptr, IdArray indices, IdArray edge_ids,
const std::string &edge_dir) {
CSRPtr csr(new CSR(indptr, indices, edge_ids));
if (edge_dir == "in") {
return ImmutableGraph(csr, nullptr);
} else if (edge_dir == "out") {
return ImmutableGraph(nullptr, csr);
} else {
LOG(FATAL) << "Unknown edge direction: " << edge_dir;
return ImmutableGraph();
}
}
static ImmutableGraph CreateFromCSR(IdArray indptr, IdArray indices, IdArray edge_ids,
bool multigraph, const std::string &edge_dir) {
CSRPtr csr(new CSR(indptr, indices, edge_ids, multigraph));
if (edge_dir == "in") {
return ImmutableGraph(csr, nullptr);
} else if (edge_dir == "out") {
return ImmutableGraph(nullptr, csr);
} else {
LOG(FATAL) << "Unknown edge direction: " << edge_dir;
return ImmutableGraph();
}
}
static ImmutableGraph CreateFromCSR(IdArray indptr, IdArray indices, IdArray edge_ids,
const std::string &edge_dir,
const std::string &shared_mem_name) {
CSRPtr csr(new CSR(indptr, indices, edge_ids, GetSharedMemName(shared_mem_name, edge_dir)));
if (edge_dir == "in") {
return ImmutableGraph(csr, nullptr, shared_mem_name);
} else if (edge_dir == "out") {
return ImmutableGraph(nullptr, csr, shared_mem_name);
} else {
LOG(FATAL) << "Unknown edge direction: " << edge_dir;
return ImmutableGraph();
}
}
static ImmutableGraphPtr AsNumBits(ImmutableGraphPtr g, uint8_t bits);
static ImmutableGraph CreateFromCSR(IdArray indptr, IdArray indices, IdArray edge_ids,
bool multigraph, const std::string &edge_dir,
const std::string &shared_mem_name) {
CSRPtr csr(new CSR(indptr, indices, edge_ids, multigraph,
GetSharedMemName(shared_mem_name, edge_dir)));
if (edge_dir == "in") {
return ImmutableGraph(csr, nullptr, shared_mem_name);
} else if (edge_dir == "out") {
return ImmutableGraph(nullptr, csr, shared_mem_name);
} else {
LOG(FATAL) << "Unknown edge direction: " << edge_dir;
return ImmutableGraph();
}
}
static ImmutableGraph CreateFromCSR(const std::string &shared_mem_name, size_t num_vertices,
size_t num_edges, bool multigraph,
const std::string &edge_dir) {
CSRPtr csr(new CSR(GetSharedMemName(shared_mem_name, edge_dir), num_vertices, num_edges,
multigraph));
if (edge_dir == "in") {
return ImmutableGraph(csr, nullptr, shared_mem_name);
} else if (edge_dir == "out") {
return ImmutableGraph(nullptr, csr, shared_mem_name);
} else {
LOG(FATAL) << "Unknown edge direction: " << edge_dir;
return ImmutableGraph();
}
}
/*!
* \brief Return a new graph with all the edges reversed.
*
* The returned graph preserves the vertex and edge index in the original graph.
*
* \return the reversed graph
*/
ImmutableGraphPtr Reverse() const;
protected:
/* !\brief internal default constructor */
......@@ -1041,10 +967,6 @@ class ImmutableGraph: public GraphInterface {
this->shared_mem_name_ = shared_mem_name;
}
static std::string GetSharedMemName(const std::string &name, const std::string &edge_dir) {
return name + "_" + edge_dir;
}
/* !\brief return pointer to any available graph structure */
GraphPtr AnyGraph() const {
if (in_csr_) {
......
include/dgl/lazy.h
View file @ 67dc1197
......@@ -17,16 +17,16 @@ namespace dgl {
* The object is currently not threaad safe.
*/
template <typename T>
class LazyObject {
class Lazy {
public:
/*!\brief default constructor to construct a lazy object */
LazyObject() {}
Lazy() {}
/*!\brief constructor to construct an object with given value (non-lazy case) */
explicit LazyObject(const T& val): ptr_(new T(val)) {}
explicit Lazy(const T& val): ptr_(new T(val)) {}
/*!\brief destructor */
~LazyObject() = default;
~Lazy() = default;
/*!
* \brief Get the value of this object. If the object has not been instantiated,
......
include/dgl/nodeflow.h
View file @ 67dc1197
......@@ -9,6 +9,7 @@
#include <vector>
#include <string>
#include "./runtime/object.h"
#include "graph_interface.h"
namespace dgl {
......@@ -23,7 +24,7 @@ class ImmutableGraph;
* in a more compact format. We store extra information,
* such as the node and edge mapping from the NodeFlow graph to the parent graph.
*/
struct NodeFlow {
struct NodeFlowObject : public runtime::Object {
/*! \brief The graph. */
GraphPtr graph;
/*!
......@@ -42,6 +43,20 @@ struct NodeFlow {
* \brief The edge mapping from the NodeFlow graph to the parent graph.
*/
IdArray edge_mapping;
static constexpr const char* _type_key = "graph.NodeFlow";
DGL_DECLARE_OBJECT_TYPE_INFO(NodeFlowObject, runtime::Object);
};
// Define NodeFlow as the reference class of NodeFlowObject
class NodeFlow : public runtime::ObjectRef {
public:
DGL_DEFINE_OBJECT_REF_METHODS(NodeFlow, runtime::ObjectRef, NodeFlowObject);
/*! \brief create a new nodeflow reference */
static NodeFlow Create() {
return NodeFlow(std::make_shared<NodeFlowObject>());
}
};
/*!
......
include/dgl/runtime/container.h
View file @ 67dc1197
......@@ -314,6 +314,10 @@ class List : public ObjectRef {
inline bool empty() const {
return size() == 0;
}
/*! \brief Copy the content to a vector */
inline std::vector<T> ToVector() const {
return std::vector<T>(begin(), end());
}
/*! \brief specify container obj */
using ContainerType = ListObject;
......
include/dgl/runtime/object.h
View file @ 67dc1197
......@@ -192,10 +192,10 @@ class ObjectRef {
* For example:
*
* // This class is an abstract class and cannot create instances
* class SomeBaseClass : public Node {
* class SomeBaseClass : public Object {
* public:
* static constexpr const char* _type_key = "some_base";
* DGL_DECLARE_BASE_OBJECT_INFO(SomeBaseClass, Node);
* DGL_DECLARE_BASE_OBJECT_INFO(SomeBaseClass, Object);
* };
*
* // Child class that allows instantiation
......@@ -219,6 +219,29 @@ class ObjectRef {
return Parent::_DerivedFrom(tid); \
}
/*! \brief Macro to generate common object reference class method definition */
#define DGL_DEFINE_OBJECT_REF_METHODS(TypeName, BaseTypeName, ObjectName) \
TypeName() {} \
explicit TypeName(std::shared_ptr<runtime::Object> obj): BaseTypeName(obj) {} \
const ObjectName* operator->() const { \
return static_cast<const ObjectName*>(obj_.get()); \
} \
ObjectName* operator->() { \
return static_cast<ObjectName*>(obj_.get()); \
} \
std::shared_ptr<ObjectName> sptr() const { \
return CHECK_NOTNULL(std::dynamic_pointer_cast<ObjectName>(obj_)); \
} \
operator bool() const { return this->defined(); } \
using ContainerType = ObjectName;
/*! \brief Macro to generate object reference class definition */
#define DGL_DEFINE_OBJECT_REF(TypeName, ObjectName) \
class TypeName : public ::dgl::runtime::ObjectRef { \
public: \
DGL_DEFINE_OBJECT_REF_METHODS(TypeName, ::dgl::runtime::ObjectRef, ObjectName); \
};
// implementations of inline functions after this
template<typename T>
inline bool Object::is_type() const {
......
python/dgl/_ffi/_ctypes/object.py
View file @ 67dc1197
......@@ -61,11 +61,6 @@ class ObjectBase(object):
"'%s' object has no attribute '%s'" % (str(type(self)), name))
return RETURN_SWITCH[ret_type_code.value](ret_val)
def __setattr__(self, name, value):
if name != 'handle':
raise AttributeError('Set attribute is not allowed for DGL object.')
object.__setattr__(self, name, value)
def __init_handle_by_constructor__(self, fconstructor, *args):
"""Initialize the handle by calling constructor function.
......
python/dgl/contrib/sampling/randomwalk.py
View file @ 67dc1197
......@@ -35,7 +35,7 @@ def random_walk(g, seeds, num_traces, num_hops):
if len(seeds) == 0:
return utils.toindex([]).tousertensor()
seeds = utils.toindex(seeds).todgltensor()
traces = _CAPI_DGLRandomWalk(g._graph._handle,
traces = _CAPI_DGLRandomWalk(g._graph,
seeds, int(num_traces), int(num_hops))
return F.zerocopy_from_dlpack(traces.to_dlpack())
......@@ -109,7 +109,7 @@ def random_walk_with_restart(
return []
seeds = utils.toindex(seeds).todgltensor()
traces = _CAPI_DGLRandomWalkWithRestart(
g._graph._handle, seeds, restart_prob, int(max_nodes_per_seed),
g._graph, seeds, restart_prob, int(max_nodes_per_seed),
int(max_visit_counts), int(max_frequent_visited_nodes))
return _split_traces(traces)
......@@ -161,7 +161,7 @@ def bipartite_single_sided_random_walk_with_restart(
return []
seeds = utils.toindex(seeds).todgltensor()
traces = _CAPI_DGLBipartiteSingleSidedRandomWalkWithRestart(
g._graph._handle, seeds, restart_prob, int(max_nodes_per_seed),
g._graph, seeds, restart_prob, int(max_nodes_per_seed),
int(max_visit_counts), int(max_frequent_visited_nodes))
return _split_traces(traces)
......
python/dgl/contrib/sampling/sampler.py
View file @ 67dc1197
......@@ -10,7 +10,6 @@ from ..._ffi.function import _init_api
from ... import utils
from ...nodeflow import NodeFlow
from ... import backend as F
from ...utils import unwrap_to_ptr_list
try:
import Queue as queue
......@@ -310,8 +309,8 @@ class NeighborSampler(NodeFlowSampler):
self._neighbor_type = neighbor_type
def fetch(self, current_nodeflow_index):
handles = unwrap_to_ptr_list(_CAPI_UniformSampling(
self.g.c_handle,
nfobjs = _CAPI_UniformSampling(
self.g._graph,
self.seed_nodes.todgltensor(),
current_nodeflow_index, # start batch id
self.batch_size, # batch size
......@@ -319,8 +318,8 @@ class NeighborSampler(NodeFlowSampler):
self._expand_factor,
self._num_hops,
self._neighbor_type,
self._add_self_loop))
nflows = [NodeFlow(self.g, hdl) for hdl in handles]
self._add_self_loop)
nflows = [NodeFlow(self.g, obj) for obj in nfobjs]
return nflows
......@@ -395,15 +394,15 @@ class LayerSampler(NodeFlowSampler):
self._layer_sizes = utils.toindex(layer_sizes)
def fetch(self, current_nodeflow_index):
handles = unwrap_to_ptr_list(_CAPI_LayerSampling(
self.g.c_handle,
nfobjs = _CAPI_LayerSampling(
self.g._graph,
self.seed_nodes.todgltensor(),
current_nodeflow_index, # start batch id
self.batch_size, # batch size
self._num_workers, # num batches
self._layer_sizes.todgltensor(),
self._neighbor_type))
nflows = [NodeFlow(self.g, hdl) for hdl in handles]
self._neighbor_type)
nflows = [NodeFlow(self.g, obj) for obj in nfobjs]
return nflows
def create_full_nodeflow(g, num_layers, add_self_loop=False):
......
python/dgl/graph.py
View file @ 67dc1197
......@@ -38,11 +38,6 @@ class DGLBaseGraph(object):
def __init__(self, graph):
self._graph = graph
@property
def c_handle(self):
"""The C handle for the graph."""
return self._graph._handle
def number_of_nodes(self):
"""Return the number of nodes in the graph.
......
python/dgl/graph_index.py
View file @ 67dc1197
"""Module for graph index class definition."""
from __future__ import absolute_import
import ctypes
import numpy as np
import networkx as nx
import scipy
from ._ffi.base import c_array
from ._ffi.object import register_object, ObjectBase
from ._ffi.function import _init_api
from .base import DGLError
from . import backend as F
from . import utils
GraphIndexHandle = ctypes.c_void_p
class BoolFlag(object):
"""Bool flag with unknown value"""
BOOL_UNKNOWN = -1
BOOL_FALSE = 0
BOOL_TRUE = 1
class GraphIndex(object):
@register_object('graph.Graph')
class GraphIndex(ObjectBase):
"""Graph index object.
Parameters
----------
handle : GraphIndexHandle
Handler
Note
----
Do not create GraphIndex directly, you can create graph index object using
following functions:
- `dgl.graph_index.from_edge_list`
- `dgl.graph_index.from_scipy_sparse_matrix`
- `dgl.graph_index.from_networkx`
- `dgl.graph_index.from_shared_mem_csr_matrix`
- `dgl.graph_index.from_csr`
- `dgl.graph_index.from_coo`
"""
def __init__(self, handle):
self._handle = handle
self._multigraph = None # python-side cache of the flag
self._readonly = None # python-side cache of the flag
self._cache = {}
def __del__(self):
"""Free this graph index object."""
if hasattr(self, '_handle'):
_CAPI_DGLGraphFree(self._handle)
def __new__(cls):
obj = ObjectBase.__new__(cls)
obj._multigraph = None # python-side cache of the flag
obj._readonly = None # python-side cache of the flag
obj._cache = {}
return obj
def __getstate__(self):
src, dst, _ = self.edges()
......@@ -59,18 +60,14 @@ class GraphIndex(object):
self._readonly = readonly
if multigraph is None:
multigraph = BoolFlag.BOOL_UNKNOWN
self._handle = _CAPI_DGLGraphCreate(
self.__init_handle_by_constructor__(
_CAPI_DGLGraphCreate,
src.todgltensor(),
dst.todgltensor(),
int(multigraph),
int(num_nodes),
readonly)
@property
def handle(self):
"""Get the CAPI handle."""
return self._handle
def add_nodes(self, num):
"""Add nodes.
......@@ -79,7 +76,7 @@ class GraphIndex(object):
num : int
Number of nodes to be added.
"""
_CAPI_DGLGraphAddVertices(self._handle, int(num))
_CAPI_DGLGraphAddVertices(self, int(num))
self.clear_cache()
def add_edge(self, u, v):
......@@ -92,7 +89,7 @@ class GraphIndex(object):
v : int
The dst node.
"""
_CAPI_DGLGraphAddEdge(self._handle, u, v)
_CAPI_DGLGraphAddEdge(self, u, v)
self.clear_cache()
def add_edges(self, u, v):
......@@ -107,12 +104,12 @@ class GraphIndex(object):
"""
u_array = u.todgltensor()
v_array = v.todgltensor()
_CAPI_DGLGraphAddEdges(self._handle, u_array, v_array)
_CAPI_DGLGraphAddEdges(self, u_array, v_array)
self.clear_cache()
def clear(self):
"""Clear the graph."""
_CAPI_DGLGraphClear(self._handle)
_CAPI_DGLGraphClear(self)
self.clear_cache()
def clear_cache(self):
......@@ -128,7 +125,7 @@ class GraphIndex(object):
True if it is a multigraph, False otherwise.
"""
if self._multigraph is None:
self._multigraph = bool(_CAPI_DGLGraphIsMultigraph(self._handle))
self._multigraph = bool(_CAPI_DGLGraphIsMultigraph(self))
return self._multigraph
def is_readonly(self):
......@@ -140,7 +137,7 @@ class GraphIndex(object):
True if it is a read-only graph, False otherwise.
"""
if self._readonly is None:
self._readonly = bool(_CAPI_DGLGraphIsReadonly(self._handle))
self._readonly = bool(_CAPI_DGLGraphIsReadonly(self))
return self._readonly
def readonly(self, readonly_state=True):
......@@ -165,7 +162,7 @@ class GraphIndex(object):
int
The number of nodes
"""
return _CAPI_DGLGraphNumVertices(self._handle)
return _CAPI_DGLGraphNumVertices(self)
def number_of_edges(self):
"""Return the number of edges.
......@@ -175,7 +172,7 @@ class GraphIndex(object):
int
The number of edges
"""
return _CAPI_DGLGraphNumEdges(self._handle)
return _CAPI_DGLGraphNumEdges(self)
def has_node(self, vid):
"""Return true if the node exists.
......@@ -190,7 +187,7 @@ class GraphIndex(object):
bool
True if the node exists, False otherwise.
"""
return bool(_CAPI_DGLGraphHasVertex(self._handle, int(vid)))
return bool(_CAPI_DGLGraphHasVertex(self, int(vid)))
def has_nodes(self, vids):
"""Return true if the nodes exist.
......@@ -206,7 +203,7 @@ class GraphIndex(object):
0-1 array indicating existence
"""
vid_array = vids.todgltensor()
return utils.toindex(_CAPI_DGLGraphHasVertices(self._handle, vid_array))
return utils.toindex(_CAPI_DGLGraphHasVertices(self, vid_array))
def has_edge_between(self, u, v):
"""Return true if the edge exists.
......@@ -223,7 +220,7 @@ class GraphIndex(object):
bool
True if the edge exists, False otherwise
"""
return bool(_CAPI_DGLGraphHasEdgeBetween(self._handle, int(u), int(v)))
return bool(_CAPI_DGLGraphHasEdgeBetween(self, int(u), int(v)))
def has_edges_between(self, u, v):
"""Return true if the edge exists.
......@@ -242,7 +239,7 @@ class GraphIndex(object):
"""
u_array = u.todgltensor()
v_array = v.todgltensor()
return utils.toindex(_CAPI_DGLGraphHasEdgesBetween(self._handle, u_array, v_array))
return utils.toindex(_CAPI_DGLGraphHasEdgesBetween(self, u_array, v_array))
def predecessors(self, v, radius=1):
"""Return the predecessors of the node.
......@@ -260,7 +257,7 @@ class GraphIndex(object):
Array of predecessors
"""
return utils.toindex(_CAPI_DGLGraphPredecessors(
self._handle, int(v), int(radius)))
self, int(v), int(radius)))
def successors(self, v, radius=1):
"""Return the successors of the node.
......@@ -278,7 +275,7 @@ class GraphIndex(object):
Array of successors
"""
return utils.toindex(_CAPI_DGLGraphSuccessors(
self._handle, int(v), int(radius)))
self, int(v), int(radius)))
def edge_id(self, u, v):
"""Return the id array of all edges between u and v.
......@@ -295,7 +292,7 @@ class GraphIndex(object):
utils.Index
The edge id array.
"""
return utils.toindex(_CAPI_DGLGraphEdgeId(self._handle, int(u), int(v)))
return utils.toindex(_CAPI_DGLGraphEdgeId(self, int(u), int(v)))
def edge_ids(self, u, v):
"""Return a triplet of arrays that contains the edge IDs.
......@@ -318,7 +315,7 @@ class GraphIndex(object):
"""
u_array = u.todgltensor()
v_array = v.todgltensor()
edge_array = _CAPI_DGLGraphEdgeIds(self._handle, u_array, v_array)
edge_array = _CAPI_DGLGraphEdgeIds(self, u_array, v_array)
src = utils.toindex(edge_array(0))
dst = utils.toindex(edge_array(1))
......@@ -344,7 +341,7 @@ class GraphIndex(object):
The edge ids.
"""
eid_array = eid.todgltensor()
edge_array = _CAPI_DGLGraphFindEdges(self._handle, eid_array)
edge_array = _CAPI_DGLGraphFindEdges(self, eid_array)
src = utils.toindex(edge_array(0))
dst = utils.toindex(edge_array(1))
......@@ -370,10 +367,10 @@ class GraphIndex(object):
The edge ids.
"""
if len(v) == 1:
edge_array = _CAPI_DGLGraphInEdges_1(self._handle, int(v[0]))
edge_array = _CAPI_DGLGraphInEdges_1(self, int(v[0]))
else:
v_array = v.todgltensor()
edge_array = _CAPI_DGLGraphInEdges_2(self._handle, v_array)
edge_array = _CAPI_DGLGraphInEdges_2(self, v_array)
src = utils.toindex(edge_array(0))
dst = utils.toindex(edge_array(1))
eid = utils.toindex(edge_array(2))
......@@ -397,10 +394,10 @@ class GraphIndex(object):
The edge ids.
"""
if len(v) == 1:
edge_array = _CAPI_DGLGraphOutEdges_1(self._handle, int(v[0]))
edge_array = _CAPI_DGLGraphOutEdges_1(self, int(v[0]))
else:
v_array = v.todgltensor()
edge_array = _CAPI_DGLGraphOutEdges_2(self._handle, v_array)
edge_array = _CAPI_DGLGraphOutEdges_2(self, v_array)
src = utils.toindex(edge_array(0))
dst = utils.toindex(edge_array(1))
eid = utils.toindex(edge_array(2))
......@@ -430,7 +427,7 @@ class GraphIndex(object):
"""
if order is None:
order = ""
edge_array = _CAPI_DGLGraphEdges(self._handle, order)
edge_array = _CAPI_DGLGraphEdges(self, order)
src = edge_array(0)
dst = edge_array(1)
eid = edge_array(2)
......@@ -452,7 +449,7 @@ class GraphIndex(object):
int
The in degree.
"""
return _CAPI_DGLGraphInDegree(self._handle, int(v))
return _CAPI_DGLGraphInDegree(self, int(v))
def in_degrees(self, v):
"""Return the in degrees of the nodes.
......@@ -468,7 +465,7 @@ class GraphIndex(object):
The in degree array.
"""
v_array = v.todgltensor()
return utils.toindex(_CAPI_DGLGraphInDegrees(self._handle, v_array))
return utils.toindex(_CAPI_DGLGraphInDegrees(self, v_array))
def out_degree(self, v):
"""Return the out degree of the node.
......@@ -483,7 +480,7 @@ class GraphIndex(object):
int
The out degree.
"""
return _CAPI_DGLGraphOutDegree(self._handle, int(v))
return _CAPI_DGLGraphOutDegree(self, int(v))
def out_degrees(self, v):
"""Return the out degrees of the nodes.
......@@ -499,7 +496,7 @@ class GraphIndex(object):
The out degree array.
"""
v_array = v.todgltensor()
return utils.toindex(_CAPI_DGLGraphOutDegrees(self._handle, v_array))
return utils.toindex(_CAPI_DGLGraphOutDegrees(self, v_array))
def node_subgraph(self, v):
"""Return the induced node subgraph.
......@@ -515,9 +512,9 @@ class GraphIndex(object):
The subgraph index.
"""
v_array = v.todgltensor()
rst = _CAPI_DGLGraphVertexSubgraph(self._handle, v_array)
rst = _CAPI_DGLGraphVertexSubgraph(self, v_array)
induced_edges = utils.toindex(rst(2))
gidx = GraphIndex(rst(0))
gidx = rst(0)
return SubgraphIndex(gidx, self, v, induced_edges)
def node_subgraphs(self, vs_arr):
......@@ -556,9 +553,9 @@ class GraphIndex(object):
The subgraph index.
"""
e_array = e.todgltensor()
rst = _CAPI_DGLGraphEdgeSubgraph(self._handle, e_array, preserve_nodes)
rst = _CAPI_DGLGraphEdgeSubgraph(self, e_array, preserve_nodes)
induced_nodes = utils.toindex(rst(1))
gidx = GraphIndex(rst(0))
gidx = rst(0)
return SubgraphIndex(gidx, self, induced_nodes, e)
@utils.cached_member(cache='_cache', prefix='scipy_adj')
......@@ -588,7 +585,7 @@ class GraphIndex(object):
if not isinstance(transpose, bool):
raise DGLError('Expect bool value for "transpose" arg,'
' but got %s.' % (type(transpose)))
rst = _CAPI_DGLGraphGetAdj(self._handle, transpose, fmt)
rst = _CAPI_DGLGraphGetAdj(self, transpose, fmt)
if fmt == "csr":
indptr = utils.toindex(rst(0)).tonumpy()
indices = utils.toindex(rst(1)).tonumpy()
......@@ -631,9 +628,9 @@ class GraphIndex(object):
The first element of the tuple is the shuffle order for outward graph
The second element of the tuple is the shuffle order for inward graph
"""
csr = _CAPI_DGLGraphGetAdj(self._handle, True, "csr")
csr = _CAPI_DGLGraphGetAdj(self, True, "csr")
order = csr(2)
rev_csr = _CAPI_DGLGraphGetAdj(self._handle, False, "csr")
rev_csr = _CAPI_DGLGraphGetAdj(self, False, "csr")
rev_order = rev_csr(2)
return utils.toindex(order), utils.toindex(rev_order)
......@@ -665,7 +662,7 @@ class GraphIndex(object):
raise DGLError('Expect bool value for "transpose" arg,'
' but got %s.' % (type(transpose)))
fmt = F.get_preferred_sparse_format()
rst = _CAPI_DGLGraphGetAdj(self._handle, transpose, fmt)
rst = _CAPI_DGLGraphGetAdj(self, transpose, fmt)
if fmt == "csr":
indptr = F.copy_to(utils.toindex(rst(0)).tousertensor(), ctx)
indices = F.copy_to(utils.toindex(rst(1)).tousertensor(), ctx)
......@@ -794,8 +791,7 @@ class GraphIndex(object):
GraphIndex
The line graph of this graph.
"""
handle = _CAPI_DGLGraphLineGraph(self._handle, backtracking)
return GraphIndex(handle)
return _CAPI_DGLGraphLineGraph(self, backtracking)
def to_immutable(self):
"""Convert this graph index to an immutable one.
......@@ -805,8 +801,7 @@ class GraphIndex(object):
GraphIndex
An immutable graph index.
"""
handle = _CAPI_DGLToImmutable(self._handle)
return GraphIndex(handle)
return _CAPI_DGLToImmutable(self)
def ctx(self):
"""Return the context of this graph index.
......@@ -816,7 +811,7 @@ class GraphIndex(object):
DGLContext
The context of the graph.
"""
return _CAPI_DGLGraphContext(self._handle)
return _CAPI_DGLGraphContext(self)
def copy_to(self, ctx):
"""Copy this immutable graph index to the given device context.
......@@ -833,8 +828,7 @@ class GraphIndex(object):
GraphIndex
The graph index on the given device context.
"""
handle = _CAPI_DGLImmutableGraphCopyTo(self._handle, ctx.device_type, ctx.device_id)
return GraphIndex(handle)
return _CAPI_DGLImmutableGraphCopyTo(self, ctx.device_type, ctx.device_id)
def copyto_shared_mem(self, edge_dir, shared_mem_name):
"""Copy this immutable graph index to shared memory.
......@@ -853,8 +847,7 @@ class GraphIndex(object):
GraphIndex
The graph index on the given device context.
"""
handle = _CAPI_DGLImmutableGraphCopyToSharedMem(self._handle, edge_dir, shared_mem_name)
return GraphIndex(handle)
return _CAPI_DGLImmutableGraphCopyToSharedMem(self, edge_dir, shared_mem_name)
def nbits(self):
"""Return the number of integer bits used in the storage (32 or 64).
......@@ -864,7 +857,7 @@ class GraphIndex(object):
int
The number of bits.
"""
return _CAPI_DGLGraphNumBits(self._handle)
return _CAPI_DGLGraphNumBits(self)
def bits_needed(self):
"""Return the number of integer bits needed to represent the graph
......@@ -894,8 +887,7 @@ class GraphIndex(object):
GraphIndex
The graph index stored using the given number of bits.
"""
handle = _CAPI_DGLImmutableGraphAsNumBits(self._handle, int(bits))
return GraphIndex(handle)
return _CAPI_DGLImmutableGraphAsNumBits(self, int(bits))
class SubgraphIndex(object):
"""Internal subgraph data structure.
......@@ -955,19 +947,17 @@ def from_coo(num_nodes, src, dst, is_multigraph, readonly):
if is_multigraph is None:
is_multigraph = BoolFlag.BOOL_UNKNOWN
if readonly:
handle = _CAPI_DGLGraphCreate(
gidx = _CAPI_DGLGraphCreate(
src.todgltensor(),
dst.todgltensor(),
int(is_multigraph),
int(num_nodes),
readonly)
gidx = GraphIndex(handle)
else:
if is_multigraph is BoolFlag.BOOL_UNKNOWN:
# TODO(minjie): better behavior in the future
is_multigraph = BoolFlag.BOOL_FALSE
handle = _CAPI_DGLGraphCreateMutable(bool(is_multigraph))
gidx = GraphIndex(handle)
gidx = _CAPI_DGLGraphCreateMutable(bool(is_multigraph))
gidx.add_nodes(num_nodes)
gidx.add_edges(src, dst)
return gidx
......@@ -993,13 +983,13 @@ def from_csr(indptr, indices, is_multigraph,
indices = utils.toindex(indices)
if is_multigraph is None:
is_multigraph = BoolFlag.BOOL_UNKNOWN
handle = _CAPI_DGLGraphCSRCreate(
gidx = _CAPI_DGLGraphCSRCreate(
indptr.todgltensor(),
indices.todgltensor(),
shared_mem_name,
int(is_multigraph),
direction)
return GraphIndex(handle)
return gidx
def from_shared_mem_csr_matrix(shared_mem_name,
num_nodes, num_edges, edge_dir,
......@@ -1017,12 +1007,12 @@ def from_shared_mem_csr_matrix(shared_mem_name,
edge_dir : string
the edge direction. The supported option is "in" and "out".
"""
handle = _CAPI_DGLGraphCSRCreateMMap(
gidx = _CAPI_DGLGraphCSRCreateMMap(
shared_mem_name,
int(num_nodes), int(num_edges),
is_multigraph,
edge_dir)
return GraphIndex(handle)
return gidx
def from_networkx(nx_graph, readonly):
"""Convert from networkx graph.
......@@ -1175,10 +1165,7 @@ def disjoint_union(graphs):
GraphIndex
The disjoint union
"""
inputs = c_array(GraphIndexHandle, [gr._handle for gr in graphs])
inputs = ctypes.cast(inputs, ctypes.c_void_p)
handle = _CAPI_DGLDisjointUnion(inputs, len(graphs))
return GraphIndex(handle)
return _CAPI_DGLDisjointUnion(list(graphs))
def disjoint_partition(graph, num_or_size_splits):
"""Partition the graph disjointly.
......@@ -1202,17 +1189,13 @@ def disjoint_partition(graph, num_or_size_splits):
"""
if isinstance(num_or_size_splits, utils.Index):
rst = _CAPI_DGLDisjointPartitionBySizes(
graph._handle,
graph,
num_or_size_splits.todgltensor())
else:
rst = _CAPI_DGLDisjointPartitionByNum(
graph._handle,
graph,
int(num_or_size_splits))
graphs = []
for val in rst.asnumpy():
handle = ctypes.cast(int(val), ctypes.c_void_p)
graphs.append(GraphIndex(handle))
return graphs
return rst
def create_graph_index(graph_data, multigraph, readonly):
"""Create a graph index object.
......@@ -1236,8 +1219,7 @@ def create_graph_index(graph_data, multigraph, readonly):
raise Exception("can't create an empty immutable graph")
if multigraph is None:
multigraph = False
handle = _CAPI_DGLGraphCreateMutable(multigraph)
return GraphIndex(handle)
return _CAPI_DGLGraphCreateMutable(multigraph)
elif isinstance(graph_data, (list, tuple)):
# edge list
return from_edge_list(graph_data, multigraph, readonly)
......
python/dgl/kernel.py
View file @ 67dc1197
......@@ -139,7 +139,7 @@ def binary_op_reduce(reducer, op, G, A_target, B_target, A, B, out,
if out_rows is None:
out_rows = empty([])
_CAPI_DGLKernelBinaryOpReduce(
reducer, op, G._handle,
reducer, op, G,
int(A_target), int(B_target),
A, B, out,
A_rows, B_rows, out_rows)
......@@ -203,7 +203,7 @@ def backward_lhs_binary_op_reduce(
if out_rows is None:
out_rows = empty([])
_CAPI_DGLKernelBackwardLhsBinaryOpReduce(
reducer, op, G._handle,
reducer, op, G,
int(A_target), int(B_target),
A_rows, B_rows, out_rows,
A, B, out,
......@@ -268,7 +268,7 @@ def backward_rhs_binary_op_reduce(
if out_rows is None:
out_rows = empty([])
_CAPI_DGLKernelBackwardRhsBinaryOpReduce(
reducer, op, G._handle,
reducer, op, G,
int(A_target), int(B_target),
A_rows, B_rows, out_rows,
A, B, out,
......@@ -365,7 +365,7 @@ def copy_reduce(reducer, G, target,
if out_rows is None:
out_rows = empty([])
_CAPI_DGLKernelCopyReduce(
reducer, G._handle, int(target),
reducer, G, int(target),
X, out, X_rows, out_rows)
# pylint: disable=invalid-name
......@@ -407,7 +407,7 @@ def backward_copy_reduce(reducer, G, target,
if out_rows is None:
out_rows = empty([])
_CAPI_DGLKernelBackwardCopyReduce(
reducer, G._handle, int(target),
reducer, G, int(target),
X, out, grad_out, grad_X,
X_rows, out_rows)
......
python/dgl/network.py
View file @ 67dc1197
......@@ -3,7 +3,6 @@ from __future__ import absolute_import
from ._ffi.function import _init_api
from .nodeflow import NodeFlow
from .utils import unwrap_to_ptr_list
from . import utils
_init_api("dgl.network")
......@@ -64,14 +63,14 @@ def _send_nodeflow(sender, nodeflow, recv_id):
recv_id : int
Receiver ID
"""
graph_handle = nodeflow._graph._handle
gidx = nodeflow._graph
node_mapping = nodeflow._node_mapping.todgltensor()
edge_mapping = nodeflow._edge_mapping.todgltensor()
layers_offsets = utils.toindex(nodeflow._layer_offsets).todgltensor()
flows_offsets = utils.toindex(nodeflow._block_offsets).todgltensor()
_CAPI_SenderSendSubgraph(sender,
int(recv_id),
graph_handle,
gidx,
node_mapping,
edge_mapping,
layers_offsets,
......@@ -137,5 +136,5 @@ def _recv_nodeflow(receiver, graph):
else:
raise RuntimeError('Got unexpected control code {}'.format(res))
else:
hdl = unwrap_to_ptr_list(res)
return NodeFlow(graph, hdl[0])
# res is of type List<NodeFlowObject>
return NodeFlow(graph, res[0])
python/dgl/nodeflow.py
View file @ 67dc1197
"""Class for NodeFlow data structure."""
from __future__ import absolute_import
import ctypes
from ._ffi.object import register_object, ObjectBase
from ._ffi.function import _init_api
from .base import ALL, is_all, DGLError
from . import backend as F
from .frame import Frame, FrameRef
from .graph import DGLBaseGraph
from .graph_index import GraphIndex, transform_ids
from .graph_index import transform_ids
from .runtime import ir, scheduler, Runtime
from . import utils
from .view import LayerView, BlockView
__all__ = ['NodeFlow']
NodeFlowHandle = ctypes.c_void_p
@register_object('graph.NodeFlow')
class NodeFlowObject(ObjectBase):
"""NodeFlow object"""
@property
def graph(self):
"""The graph structure of this nodeflow.
Returns
-------
GraphIndex
"""
return _CAPI_NodeFlowGetGraph(self)
@property
def layer_offsets(self):
"""The offsets of each layer.
Returns
-------
NDArray
"""
return _CAPI_NodeFlowGetLayerOffsets(self)
@property
def block_offsets(self):
"""The offsets of each block.
Returns
-------
NDArray
"""
return _CAPI_NodeFlowGetBlockOffsets(self)
@property
def node_mapping(self):
"""Mapping array from nodeflow node id to parent graph
Returns
-------
NDArray
"""
return _CAPI_NodeFlowGetNodeMapping(self)
@property
def edge_mapping(self):
"""Mapping array from nodeflow edge id to parent graph
Returns
-------
NDArray
"""
return _CAPI_NodeFlowGetEdgeMapping(self)
class NodeFlow(DGLBaseGraph):
"""The NodeFlow class stores the sampling results of Neighbor
......@@ -36,25 +87,16 @@ class NodeFlow(DGLBaseGraph):
----------
parent : DGLGraph
The parent graph.
handle : NodeFlowHandle
The handle to the underlying C structure.
nfobj : NodeFlowObject
The nodeflow object
"""
def __init__(self, parent, handle):
# NOTE(minjie): handle is a pointer to the underlying C++ structure
# defined in include/dgl/sampler.h. The constructor will save
# all its members in the python side and destroy the handler
# afterwards. One can view the given handle object as a transient
# argument pack to construct this python class.
# TODO(minjie): We should use TVM's Node system as a cleaner solution later.
super(NodeFlow, self).__init__(GraphIndex(_CAPI_NodeFlowGetGraph(handle)))
def __init__(self, parent, nfobj):
super(NodeFlow, self).__init__(nfobj.graph)
self._parent = parent
self._node_mapping = utils.toindex(_CAPI_NodeFlowGetNodeMapping(handle))
self._edge_mapping = utils.toindex(_CAPI_NodeFlowGetEdgeMapping(handle))
self._layer_offsets = utils.toindex(
_CAPI_NodeFlowGetLayerOffsets(handle)).tonumpy()
self._block_offsets = utils.toindex(
_CAPI_NodeFlowGetBlockOffsets(handle)).tonumpy()
_CAPI_NodeFlowFree(handle)
self._node_mapping = utils.toindex(nfobj.node_mapping)
self._edge_mapping = utils.toindex(nfobj.edge_mapping)
self._layer_offsets = utils.toindex(nfobj.layer_offsets).tonumpy()
self._block_offsets = utils.toindex(nfobj.block_offsets).tonumpy()
# node/edge frames
self._node_frames = [FrameRef(Frame(num_rows=self.layer_size(i))) \
for i in range(self.num_layers)]
......@@ -293,6 +335,7 @@ class NodeFlow(DGLBaseGraph):
The parent node id array.
"""
nid = utils.toindex(nid)
# TODO(minjie): should not directly use []
return self._node_mapping.tousertensor()[nid.tousertensor()]
def map_to_parent_eid(self, eid):
......@@ -309,6 +352,7 @@ class NodeFlow(DGLBaseGraph):
The parent edge id array.
"""
eid = utils.toindex(eid)
# TODO(minjie): should not directly use []
return self._edge_mapping.tousertensor()[eid.tousertensor()]
def map_from_parent_nid(self, layer_id, parent_nids, remap_local=False):
......@@ -418,6 +462,7 @@ class NodeFlow(DGLBaseGraph):
assert layer_id + 1 < len(self._layer_offsets)
start = self._layer_offsets[layer_id]
end = self._layer_offsets[layer_id + 1]
# TODO(minjie): should not directly use []
return self._node_mapping.tousertensor()[start:end]
def block_eid(self, block_id):
......@@ -456,6 +501,7 @@ class NodeFlow(DGLBaseGraph):
block_id = self._get_block_id(block_id)
start = self._block_offsets[block_id]
end = self._block_offsets[block_id + 1]
# TODO(minjie): should not directly use []
ret = self._edge_mapping.tousertensor()[start:end]
# If `add_self_loop` is enabled, the returned parent eid can be -1.
# We have to make sure this case doesn't happen.
......@@ -487,7 +533,7 @@ class NodeFlow(DGLBaseGraph):
"""
block_id = self._get_block_id(block_id)
layer0_size = self._layer_offsets[block_id + 1] - self._layer_offsets[block_id]
rst = _CAPI_NodeFlowGetBlockAdj(self._graph._handle, "coo",
rst = _CAPI_NodeFlowGetBlockAdj(self._graph, "coo",
int(layer0_size),
int(self._layer_offsets[block_id + 1]),
int(self._layer_offsets[block_id + 2]),
......@@ -523,7 +569,7 @@ class NodeFlow(DGLBaseGraph):
fmt = F.get_preferred_sparse_format()
# We need to extract two layers.
layer0_size = self._layer_offsets[block_id + 1] - self._layer_offsets[block_id]
rst = _CAPI_NodeFlowGetBlockAdj(self._graph._handle, fmt,
rst = _CAPI_NodeFlowGetBlockAdj(self._graph, fmt,
int(layer0_size),
int(self._layer_offsets[block_id + 1]),
int(self._layer_offsets[block_id + 2]),
......
python/dgl/transform.py
View file @ 67dc1197
"""Module for graph transformation methods."""
from ._ffi.function import _init_api
from .graph import DGLGraph
from .graph_index import GraphIndex
from .batched_graph import BatchedDGLGraph
__all__ = ['line_graph', 'reverse', 'to_simple_graph', 'to_bidirected']
......@@ -121,8 +120,8 @@ def to_simple_graph(g):
DGLGraph
A simple graph.
"""
newgidx = GraphIndex(_CAPI_DGLToSimpleGraph(g._graph.handle))
return DGLGraph(newgidx, readonly=True)
gidx = _CAPI_DGLToSimpleGraph(g._graph)
return DGLGraph(gidx, readonly=True)
def to_bidirected(g, readonly=True):
"""Convert the graph to a bidirected graph.
......@@ -165,9 +164,9 @@ def to_bidirected(g, readonly=True):
(tensor([0, 1, 1, 0, 0]), tensor([0, 0, 0, 1, 1]))
"""
if readonly:
newgidx = GraphIndex(_CAPI_DGLToBidirectedImmutableGraph(g._graph.handle))
newgidx = _CAPI_DGLToBidirectedImmutableGraph(g._graph)
else:
newgidx = GraphIndex(_CAPI_DGLToBidirectedMutableGraph(g._graph.handle))
newgidx = _CAPI_DGLToBidirectedMutableGraph(g._graph)
return DGLGraph(newgidx)
_init_api("dgl.transform")
python/dgl/traversal.py
View file @ 67dc1197
......@@ -39,9 +39,9 @@ def bfs_nodes_generator(graph, source, reverse=False):
>>> list(dgl.bfs_nodes_generator(g, 0))
[tensor([0]), tensor([1]), tensor([2, 3]), tensor([4, 5])]
"""
ghandle = graph._graph._handle
gidx = graph._graph
source = utils.toindex(source)
ret = _CAPI_DGLBFSNodes(ghandle, source.todgltensor(), reverse)
ret = _CAPI_DGLBFSNodes(gidx, source.todgltensor(), reverse)
all_nodes = utils.toindex(ret(0)).tousertensor()
# TODO(minjie): how to support directly creating python list
sections = utils.toindex(ret(1)).tonumpy().tolist()
......@@ -79,9 +79,9 @@ def bfs_edges_generator(graph, source, reverse=False):
>>> list(dgl.bfs_edges_generator(g, 0))
[tensor([0]), tensor([1, 2]), tensor([4, 5])]
"""
ghandle = graph._graph._handle
gidx = graph._graph
source = utils.toindex(source)
ret = _CAPI_DGLBFSEdges(ghandle, source.todgltensor(), reverse)
ret = _CAPI_DGLBFSEdges(gidx, source.todgltensor(), reverse)
all_edges = utils.toindex(ret(0)).tousertensor()
# TODO(minjie): how to support directly creating python list
sections = utils.toindex(ret(1)).tonumpy().tolist()
......@@ -116,8 +116,8 @@ def topological_nodes_generator(graph, reverse=False):
>>> list(dgl.topological_nodes_generator(g))
[tensor([0]), tensor([1]), tensor([2]), tensor([3, 4]), tensor([5])]
"""
ghandle = graph._graph._handle
ret = _CAPI_DGLTopologicalNodes(ghandle, reverse)
gidx = graph._graph
ret = _CAPI_DGLTopologicalNodes(gidx, reverse)
all_nodes = utils.toindex(ret(0)).tousertensor()
# TODO(minjie): how to support directly creating python list
sections = utils.toindex(ret(1)).tonumpy().tolist()
......@@ -160,9 +160,9 @@ def dfs_edges_generator(graph, source, reverse=False):
>>> list(dgl.dfs_edges_generator(g, 0))
[tensor([0]), tensor([1]), tensor([3]), tensor([5]), tensor([4])]
"""
ghandle = graph._graph._handle
gidx = graph._graph
source = utils.toindex(source)
ret = _CAPI_DGLDFSEdges(ghandle, source.todgltensor(), reverse)
ret = _CAPI_DGLDFSEdges(gidx, source.todgltensor(), reverse)
all_edges = utils.toindex(ret(0)).tousertensor()
# TODO(minjie): how to support directly creating python list
sections = utils.toindex(ret(1)).tonumpy().tolist()
......@@ -231,10 +231,10 @@ def dfs_labeled_edges_generator(
(tensor([0]), tensor([1]), tensor([3]), tensor([5]), tensor([4]), tensor([2])),
(tensor([0]), tensor([0]), tensor([0]), tensor([0]), tensor([0]), tensor([2]))
"""
ghandle = graph._graph._handle
gidx = graph._graph
source = utils.toindex(source)
ret = _CAPI_DGLDFSLabeledEdges(
ghandle,
gidx,
source.todgltensor(),
reverse,
has_reverse_edge,
......
python/dgl/utils.py
View file @ 67dc1197
"""Utility module."""
from __future__ import absolute_import, division
import ctypes
from collections.abc import Mapping, Iterable
from functools import wraps
import numpy as np
from . import _api_internal
from .base import DGLError
from . import backend as F
from . import ndarray as nd
......@@ -534,30 +532,6 @@ def get_edata_name(g, name):
name += '_'
return name
def unwrap_to_ptr_list(wrapper):
"""Convert the internal vector wrapper to a python list of ctypes.c_void_p.
The wrapper will be destroyed after this function.
Parameters
----------
wrapper : ctypes.c_void_p
The handler to the wrapper.
Returns
-------
list of ctypes.c_void_p
A python list of void pointers.
"""
size = _api_internal._GetVectorWrapperSize(wrapper)
if size == 0:
return []
data = _api_internal._GetVectorWrapperData(wrapper)
data = ctypes.cast(data, ctypes.POINTER(ctypes.c_void_p * size))
rst = [ctypes.c_void_p(x) for x in data.contents]
_api_internal._FreeVectorWrapper(wrapper)
return rst
def to_dgl_context(ctx):
"""Convert a backend context to DGLContext"""
device_type = nd.DGLContext.STR2MASK[F.device_type(ctx)]
......
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