Use array interface for CSC matrix. (#8672)
* Use array interface for CSC matrix. Use array interface for CSC matrix and align the interface with CSR and dense. - Fix nthread issue in the R package DMatrix. - Unify the behavior of handling `missing` with other inputs. - Unify the behavior of handling `missing` around R, Python, Java, and Scala DMatrix. - Expose `num_non_missing` to the JVM interface. - Deprecate old CSR and CSC constructors.
This commit is contained in:
Jiaming Yuan
GitHub
@@ -1,31 +1,32 @@
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/**
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* Copyright 2014-2023 by XGBoost Contributors
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*/
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#include "xgboost/c_api.h"
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#include <rabit/c_api.h>
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#include <cstring>
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#include <fstream>
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#include <vector>
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#include <string>
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#include <memory>
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#include <string>
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#include <vector>
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#include "xgboost/base.h"
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#include "xgboost/data.h"
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#include "xgboost/host_device_vector.h"
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#include "xgboost/learner.h"
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#include "xgboost/c_api.h"
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#include "xgboost/logging.h"
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#include "xgboost/version_config.h"
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#include "xgboost/json.h"
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#include "xgboost/global_config.h"
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#include "c_api_error.h"
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#include "c_api_utils.h"
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#include "../collective/communicator-inl.h"
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#include "../common/io.h"
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#include "../common/charconv.h"
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#include "../common/io.h"
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#include "../data/adapter.h"
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#include "../data/simple_dmatrix.h"
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#include "c_api_error.h"
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#include "c_api_utils.h"
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#include "xgboost/base.h"
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#include "xgboost/data.h"
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#include "xgboost/global_config.h"
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#include "xgboost/host_device_vector.h"
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#include "xgboost/json.h"
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#include "xgboost/learner.h"
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#include "xgboost/logging.h"
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#include "xgboost/string_view.h" // StringView
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#include "xgboost/version_config.h"
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#if defined(XGBOOST_USE_FEDERATED)
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#include "../../plugin/federated/federated_server.h"
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@@ -58,6 +59,13 @@ void XGBBuildInfoDevice(Json *p_info) {
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} // namespace xgboost
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#endif
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namespace {
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void DeprecatedFunc(StringView old, StringView since, StringView replacement) {
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LOG(WARNING) << "`" << old << "` is deprecated since" << since << ", use `" << replacement
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<< "` instead.";
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}
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} // anonymous namespace
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XGB_DLL int XGBuildInfo(char const **out) {
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API_BEGIN();
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xgboost_CHECK_C_ARG_PTR(out);
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@@ -298,7 +306,7 @@ XGB_DLL int XGDeviceQuantileDMatrixCreateFromCallback(DataIterHandle iter, DMatr
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int nthread, int max_bin,
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DMatrixHandle *out) {
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API_BEGIN();
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LOG(WARNING) << __func__ << " is deprecated. Use `XGQuantileDMatrixCreateFromCallback` instead.";
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DeprecatedFunc(__func__, "1.7.0", "XGQuantileDMatrixCreateFromCallback");
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*out = new std::shared_ptr<xgboost::DMatrix>{
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xgboost::DMatrix::Create(iter, proxy, nullptr, reset, next, missing, nthread, max_bin)};
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API_END();
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@@ -398,14 +406,11 @@ XGB_DLL int XGProxyDMatrixSetDataCSR(DMatrixHandle handle, char const *indptr,
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// End Create from data iterator
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XGB_DLL int XGDMatrixCreateFromCSREx(const size_t* indptr,
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const unsigned* indices,
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const bst_float* data,
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size_t nindptr,
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size_t nelem,
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size_t num_col,
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DMatrixHandle* out) {
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XGB_DLL int XGDMatrixCreateFromCSREx(const size_t *indptr, const unsigned *indices,
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const bst_float *data, size_t nindptr, size_t nelem,
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size_t num_col, DMatrixHandle *out) {
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API_BEGIN();
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DeprecatedFunc(__func__, "2.0.0", "XGDMatrixCreateFromCSR");
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data::CSRAdapter adapter(indptr, indices, data, nindptr - 1, nelem, num_col);
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*out = new std::shared_ptr<DMatrix>(DMatrix::Create(&adapter, std::nan(""), 1));
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API_END();
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@@ -443,14 +448,29 @@ XGB_DLL int XGDMatrixCreateFromDense(char const *data,
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API_END();
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}
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XGB_DLL int XGDMatrixCreateFromCSCEx(const size_t* col_ptr,
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const unsigned* indices,
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const bst_float* data,
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size_t nindptr,
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size_t,
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size_t num_row,
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DMatrixHandle* out) {
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XGB_DLL int XGDMatrixCreateFromCSC(char const *indptr, char const *indices, char const *data,
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xgboost::bst_ulong nrow, char const *c_json_config,
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DMatrixHandle *out) {
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API_BEGIN();
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xgboost_CHECK_C_ARG_PTR(indptr);
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xgboost_CHECK_C_ARG_PTR(indices);
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xgboost_CHECK_C_ARG_PTR(data);
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data::CSCArrayAdapter adapter{StringView{indptr}, StringView{indices}, StringView{data}, nrow};
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xgboost_CHECK_C_ARG_PTR(c_json_config);
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auto config = Json::Load(StringView{c_json_config});
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float missing = GetMissing(config);
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auto n_threads = OptionalArg<Integer, int64_t>(config, "nthread", common::OmpGetNumThreads(0));
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xgboost_CHECK_C_ARG_PTR(out);
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*out = new std::shared_ptr<DMatrix>(DMatrix::Create(&adapter, missing, n_threads));
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API_END();
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}
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XGB_DLL int XGDMatrixCreateFromCSCEx(const size_t *col_ptr, const unsigned *indices,
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const bst_float *data, size_t nindptr, size_t, size_t num_row,
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DMatrixHandle *out) {
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API_BEGIN();
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DeprecatedFunc(__func__, "2.0.0", "XGDMatrixCreateFromCSC");
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data::CSCAdapter adapter(col_ptr, indices, data, nindptr - 1, num_row);
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xgboost_CHECK_C_ARG_PTR(out);
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*out = new std::shared_ptr<DMatrix>(DMatrix::Create(&adapter, std::nan(""), 1));
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@@ -1203,8 +1223,7 @@ XGB_DLL int XGBoosterGetModelRaw(BoosterHandle handle, xgboost::bst_ulong *out_l
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raw_str.resize(0);
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common::MemoryBufferStream fo(&raw_str);
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LOG(WARNING) << "`" << __func__
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<< "` is deprecated, please use `XGBoosterSaveModelToBuffer` instead.";
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DeprecatedFunc(__func__, "1.6.0", "XGBoosterSaveModelToBuffer");
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learner->Configure();
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learner->SaveModel(&fo);
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@@ -1,10 +1,11 @@
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/*!
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* Copyright (c) 2021-2022 by XGBoost Contributors
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/**
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* Copyright 2021-2023 by XGBoost Contributors
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*/
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#ifndef XGBOOST_C_API_C_API_UTILS_H_
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#define XGBOOST_C_API_C_API_UTILS_H_
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#include <algorithm>
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#include <cstddef>
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#include <functional>
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#include <memory> // std::shared_ptr
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#include <string>
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@@ -14,6 +15,7 @@
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#include "xgboost/data.h" // DMatrix
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#include "xgboost/json.h"
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#include "xgboost/learner.h"
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#include "xgboost/linalg.h" // ArrayInterfaceHandler
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#include "xgboost/logging.h"
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#include "xgboost/string_view.h" // StringView
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@@ -281,5 +283,55 @@ inline std::shared_ptr<DMatrix> CastDMatrixHandle(DMatrixHandle const handle) {
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CHECK(p_m) << msg;
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return p_m;
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}
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namespace detail {
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template <typename PtrT, typename I, typename T>
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void MakeSparseFromPtr(PtrT const *p_indptr, I const *p_indices, T const *p_data,
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std::size_t nindptr, std::string *indptr_str, std::string *indices_str,
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std::string *data_str) {
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auto ndata = static_cast<Integer::Int>(p_indptr[nindptr - 1]);
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// Construct array interfaces
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Json jindptr{Object{}};
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Json jindices{Object{}};
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Json jdata{Object{}};
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CHECK(p_indptr);
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jindptr["data"] =
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Array{std::vector<Json>{Json{reinterpret_cast<Integer::Int>(p_indptr)}, Json{true}}};
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jindptr["shape"] = std::vector<Json>{Json{nindptr}};
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jindptr["version"] = Integer{3};
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CHECK(p_indices);
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jindices["data"] =
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Array{std::vector<Json>{Json{reinterpret_cast<Integer::Int>(p_indices)}, Json{true}}};
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jindices["shape"] = std::vector<Json>{Json{ndata}};
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jindices["version"] = Integer{3};
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CHECK(p_data);
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jdata["data"] =
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Array{std::vector<Json>{Json{reinterpret_cast<Integer::Int>(p_data)}, Json{true}}};
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jdata["shape"] = std::vector<Json>{Json{ndata}};
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jdata["version"] = Integer{3};
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std::string pindptr_typestr =
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linalg::detail::ArrayInterfaceHandler::TypeChar<PtrT>() + std::to_string(sizeof(PtrT));
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std::string ind_typestr =
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linalg::detail::ArrayInterfaceHandler::TypeChar<I>() + std::to_string(sizeof(I));
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std::string data_typestr =
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linalg::detail::ArrayInterfaceHandler::TypeChar<T>() + std::to_string(sizeof(T));
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if (DMLC_LITTLE_ENDIAN) {
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jindptr["typestr"] = String{"<" + pindptr_typestr};
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jindices["typestr"] = String{"<" + ind_typestr};
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jdata["typestr"] = String{"<" + data_typestr};
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} else {
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jindptr["typestr"] = String{">" + pindptr_typestr};
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jindices["typestr"] = String{">" + ind_typestr};
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jdata["typestr"] = String{">" + data_typestr};
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}
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Json::Dump(jindptr, indptr_str);
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Json::Dump(jindices, indices_str);
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Json::Dump(jdata, data_str);
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}
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} // namespace detail
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} // namespace xgboost
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#endif // XGBOOST_C_API_C_API_UTILS_H_
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@@ -6,25 +6,25 @@
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#define XGBOOST_DATA_ADAPTER_H_
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#include <dmlc/data.h>
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#include <cstddef>
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#include <algorithm>
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#include <cstddef> // std::size_t
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#include <functional>
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#include <limits>
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#include <map>
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#include <memory>
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#include <string>
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#include <utility>
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#include <utility> // std::move
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#include <vector>
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#include <map>
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#include <algorithm>
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#include "xgboost/logging.h"
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#include "xgboost/base.h"
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#include "xgboost/data.h"
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#include "xgboost/span.h"
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#include "array_interface.h"
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#include "../c_api/c_api_error.h"
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#include "../common/math.h"
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#include "array_interface.h"
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#include "arrow-cdi.h"
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#include "xgboost/base.h"
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#include "xgboost/data.h"
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#include "xgboost/logging.h"
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#include "xgboost/span.h"
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#include "xgboost/string_view.h"
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namespace xgboost {
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namespace data {
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@@ -472,6 +472,84 @@ class CSCAdapter : public detail::SingleBatchDataIter<CSCAdapterBatch> {
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size_t num_columns_;
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};
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class CSCArrayAdapterBatch : public detail::NoMetaInfo {
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ArrayInterface<1> indptr_;
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ArrayInterface<1> indices_;
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ArrayInterface<1> values_;
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bst_row_t n_rows_;
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class Line {
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std::size_t column_idx_;
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ArrayInterface<1> row_idx_;
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ArrayInterface<1> values_;
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std::size_t offset_;
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public:
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Line(std::size_t idx, ArrayInterface<1> row_idx, ArrayInterface<1> values, std::size_t offset)
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: column_idx_{idx},
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row_idx_{std::move(row_idx)},
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values_{std::move(values)},
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offset_{offset} {}
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std::size_t Size() const { return values_.Shape(0); }
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COOTuple GetElement(std::size_t idx) const {
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return {TypedIndex<std::size_t, 1>{row_idx_}(offset_ + idx), column_idx_,
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values_(offset_ + idx)};
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}
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};
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public:
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static constexpr bool kIsRowMajor = false;
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CSCArrayAdapterBatch(ArrayInterface<1> indptr, ArrayInterface<1> indices,
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ArrayInterface<1> values, bst_row_t n_rows)
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: indptr_{std::move(indptr)},
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indices_{std::move(indices)},
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values_{std::move(values)},
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n_rows_{n_rows} {}
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std::size_t Size() const { return indptr_.n - 1; }
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Line GetLine(std::size_t idx) const {
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auto begin_no_stride = TypedIndex<std::size_t, 1>{indptr_}(idx);
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auto end_no_stride = TypedIndex<std::size_t, 1>{indptr_}(idx + 1);
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auto indices = indices_;
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auto values = values_;
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// Slice indices and values, stride remains unchanged since this is slicing by
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// specific index.
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auto offset = indices.strides[0] * begin_no_stride;
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indices.shape[0] = end_no_stride - begin_no_stride;
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values.shape[0] = end_no_stride - begin_no_stride;
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return Line{idx, indices, values, offset};
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}
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};
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/**
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* \brief CSC adapter with support for array interface.
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*/
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class CSCArrayAdapter : public detail::SingleBatchDataIter<CSCArrayAdapterBatch> {
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ArrayInterface<1> indptr_;
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ArrayInterface<1> indices_;
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ArrayInterface<1> values_;
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size_t num_rows_;
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CSCArrayAdapterBatch batch_;
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public:
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CSCArrayAdapter(StringView indptr, StringView indices, StringView values, std::size_t num_rows)
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: indptr_{indptr},
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indices_{indices},
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values_{values},
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num_rows_{num_rows},
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batch_{
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CSCArrayAdapterBatch{indptr_, indices_, values_, static_cast<bst_row_t>(num_rows_)}} {}
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// JVM package sends 0 as unknown
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size_t NumRows() const { return num_rows_ == 0 ? kAdapterUnknownSize : num_rows_; }
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size_t NumColumns() const { return indptr_.n - 1; }
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const CSCArrayAdapterBatch& Value() const override { return batch_; }
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};
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class DataTableAdapterBatch : public detail::NoMetaInfo {
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enum class DTType : std::uint8_t {
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kFloat32 = 0,
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@@ -945,31 +945,33 @@ DMatrix* DMatrix::Create(AdapterT* adapter, float missing, int nthread, const st
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return new data::SimpleDMatrix(adapter, missing, nthread);
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}
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template DMatrix* DMatrix::Create<data::DenseAdapter>(
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data::DenseAdapter* adapter, float missing, int nthread,
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const std::string& cache_prefix);
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template DMatrix* DMatrix::Create<data::ArrayAdapter>(
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data::ArrayAdapter* adapter, float missing, int nthread,
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const std::string& cache_prefix);
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template DMatrix* DMatrix::Create<data::CSRAdapter>(
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data::CSRAdapter* adapter, float missing, int nthread,
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const std::string& cache_prefix);
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template DMatrix* DMatrix::Create<data::CSCAdapter>(
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data::CSCAdapter* adapter, float missing, int nthread,
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const std::string& cache_prefix);
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template DMatrix* DMatrix::Create<data::DataTableAdapter>(
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data::DataTableAdapter* adapter, float missing, int nthread,
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const std::string& cache_prefix);
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template DMatrix* DMatrix::Create<data::FileAdapter>(
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data::FileAdapter* adapter, float missing, int nthread,
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const std::string& cache_prefix);
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template DMatrix* DMatrix::Create<data::CSRArrayAdapter>(
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data::CSRArrayAdapter* adapter, float missing, int nthread,
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const std::string& cache_prefix);
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template DMatrix *
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DMatrix::Create(data::IteratorAdapter<DataIterHandle, XGBCallbackDataIterNext,
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XGBoostBatchCSR> *adapter,
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float missing, int nthread, const std::string &cache_prefix);
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template DMatrix* DMatrix::Create<data::DenseAdapter>(data::DenseAdapter* adapter, float missing,
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std::int32_t nthread,
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const std::string& cache_prefix);
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template DMatrix* DMatrix::Create<data::ArrayAdapter>(data::ArrayAdapter* adapter, float missing,
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std::int32_t nthread,
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const std::string& cache_prefix);
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template DMatrix* DMatrix::Create<data::CSRAdapter>(data::CSRAdapter* adapter, float missing,
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std::int32_t nthread,
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const std::string& cache_prefix);
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template DMatrix* DMatrix::Create<data::CSCAdapter>(data::CSCAdapter* adapter, float missing,
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std::int32_t nthread,
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const std::string& cache_prefix);
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template DMatrix* DMatrix::Create<data::DataTableAdapter>(data::DataTableAdapter* adapter,
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float missing, std::int32_t nthread,
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const std::string& cache_prefix);
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template DMatrix* DMatrix::Create<data::FileAdapter>(data::FileAdapter* adapter, float missing,
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std::int32_t nthread,
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const std::string& cache_prefix);
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template DMatrix* DMatrix::Create<data::CSRArrayAdapter>(data::CSRArrayAdapter* adapter,
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float missing, std::int32_t nthread,
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const std::string& cache_prefix);
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template DMatrix* DMatrix::Create<data::CSCArrayAdapter>(data::CSCArrayAdapter* adapter,
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float missing, std::int32_t nthread,
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const std::string& cache_prefix);
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template DMatrix* DMatrix::Create(
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data::IteratorAdapter<DataIterHandle, XGBCallbackDataIterNext, XGBoostBatchCSR>* adapter,
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float missing, int nthread, const std::string& cache_prefix);
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template DMatrix* DMatrix::Create<data::RecordBatchesIterAdapter>(
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data::RecordBatchesIterAdapter* adapter, float missing, int nthread, const std::string&);
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@@ -1221,20 +1223,19 @@ void SparsePage::PushCSC(const SparsePage &batch) {
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self_offset = std::move(offset);
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}
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template uint64_t
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SparsePage::Push(const data::DenseAdapterBatch& batch, float missing, int nthread);
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template uint64_t
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SparsePage::Push(const data::ArrayAdapterBatch& batch, float missing, int nthread);
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template uint64_t
|
||||
SparsePage::Push(const data::CSRAdapterBatch& batch, float missing, int nthread);
|
||||
template uint64_t
|
||||
SparsePage::Push(const data::CSRArrayAdapterBatch& batch, float missing, int nthread);
|
||||
template uint64_t
|
||||
SparsePage::Push(const data::CSCAdapterBatch& batch, float missing, int nthread);
|
||||
template uint64_t
|
||||
SparsePage::Push(const data::DataTableAdapterBatch& batch, float missing, int nthread);
|
||||
template uint64_t
|
||||
SparsePage::Push(const data::FileAdapterBatch& batch, float missing, int nthread);
|
||||
template uint64_t SparsePage::Push(const data::DenseAdapterBatch& batch, float missing,
|
||||
int nthread);
|
||||
template uint64_t SparsePage::Push(const data::ArrayAdapterBatch& batch, float missing,
|
||||
int nthread);
|
||||
template uint64_t SparsePage::Push(const data::CSRAdapterBatch& batch, float missing, int nthread);
|
||||
template uint64_t SparsePage::Push(const data::CSRArrayAdapterBatch& batch, float missing,
|
||||
int nthread);
|
||||
template uint64_t SparsePage::Push(const data::CSCArrayAdapterBatch& batch, float missing,
|
||||
int nthread);
|
||||
template uint64_t SparsePage::Push(const data::CSCAdapterBatch& batch, float missing, int nthread);
|
||||
template uint64_t SparsePage::Push(const data::DataTableAdapterBatch& batch, float missing,
|
||||
int nthread);
|
||||
template uint64_t SparsePage::Push(const data::FileAdapterBatch& batch, float missing, int nthread);
|
||||
|
||||
namespace data {
|
||||
|
||||
|
||||
@@ -1,23 +1,23 @@
|
||||
/*!
|
||||
* Copyright 2014~2022 by XGBoost Contributors
|
||||
/**
|
||||
* Copyright 2014~2023 by XGBoost Contributors
|
||||
* \file simple_dmatrix.cc
|
||||
* \brief the input data structure for gradient boosting
|
||||
* \author Tianqi Chen
|
||||
*/
|
||||
#include <vector>
|
||||
#include "simple_dmatrix.h"
|
||||
|
||||
#include <algorithm>
|
||||
#include <limits>
|
||||
#include <type_traits>
|
||||
#include <algorithm>
|
||||
#include <vector>
|
||||
|
||||
#include "xgboost/data.h"
|
||||
#include "xgboost/c_api.h"
|
||||
|
||||
#include "simple_dmatrix.h"
|
||||
#include "./simple_batch_iterator.h"
|
||||
#include "../common/random.h"
|
||||
#include "../common/threading_utils.h"
|
||||
#include "./simple_batch_iterator.h"
|
||||
#include "adapter.h"
|
||||
#include "gradient_index.h"
|
||||
#include "xgboost/c_api.h"
|
||||
#include "xgboost/data.h"
|
||||
|
||||
namespace xgboost {
|
||||
namespace data {
|
||||
@@ -229,7 +229,9 @@ SimpleDMatrix::SimpleDMatrix(AdapterT* adapter, float missing, int nthread) {
|
||||
offset_vec.emplace_back(offset_vec.back());
|
||||
}
|
||||
} else {
|
||||
CHECK((std::is_same<AdapterT, CSCAdapter>::value)) << "Expecting CSCAdapter";
|
||||
CHECK((std::is_same<AdapterT, CSCAdapter>::value ||
|
||||
std::is_same<AdapterT, CSCArrayAdapter>::value))
|
||||
<< "Expecting CSCAdapter";
|
||||
info_.num_row_ = offset_vec.size() - 1;
|
||||
}
|
||||
} else {
|
||||
@@ -267,20 +269,14 @@ void SimpleDMatrix::SaveToLocalFile(const std::string& fname) {
|
||||
fo->Write(sparse_page_->data.HostVector());
|
||||
}
|
||||
|
||||
template SimpleDMatrix::SimpleDMatrix(DenseAdapter* adapter, float missing,
|
||||
int nthread);
|
||||
template SimpleDMatrix::SimpleDMatrix(ArrayAdapter* adapter, float missing,
|
||||
int nthread);
|
||||
template SimpleDMatrix::SimpleDMatrix(CSRAdapter* adapter, float missing,
|
||||
int nthread);
|
||||
template SimpleDMatrix::SimpleDMatrix(CSRArrayAdapter* adapter, float missing,
|
||||
int nthread);
|
||||
template SimpleDMatrix::SimpleDMatrix(CSCAdapter* adapter, float missing,
|
||||
int nthread);
|
||||
template SimpleDMatrix::SimpleDMatrix(DataTableAdapter* adapter, float missing,
|
||||
int nthread);
|
||||
template SimpleDMatrix::SimpleDMatrix(FileAdapter* adapter, float missing,
|
||||
int nthread);
|
||||
template SimpleDMatrix::SimpleDMatrix(DenseAdapter* adapter, float missing, int nthread);
|
||||
template SimpleDMatrix::SimpleDMatrix(ArrayAdapter* adapter, float missing, int nthread);
|
||||
template SimpleDMatrix::SimpleDMatrix(CSRAdapter* adapter, float missing, int nthread);
|
||||
template SimpleDMatrix::SimpleDMatrix(CSRArrayAdapter* adapter, float missing, int nthread);
|
||||
template SimpleDMatrix::SimpleDMatrix(CSCArrayAdapter* adapter, float missing, int nthread);
|
||||
template SimpleDMatrix::SimpleDMatrix(CSCAdapter* adapter, float missing, int nthread);
|
||||
template SimpleDMatrix::SimpleDMatrix(DataTableAdapter* adapter, float missing, int nthread);
|
||||
template SimpleDMatrix::SimpleDMatrix(FileAdapter* adapter, float missing, int nthread);
|
||||
template SimpleDMatrix::SimpleDMatrix(
|
||||
IteratorAdapter<DataIterHandle, XGBCallbackDataIterNext, XGBoostBatchCSR>
|
||||
*adapter,
|
||||
|
||||
Reference in New Issue
Block a user