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
@@ -1,5 +1,5 @@
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/*
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Copyright (c) 2014-2022 by Contributors
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/**
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Copyright (c) 2014-2023 by Contributors
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Licensed under the Apache License, Version 2.0 (the "License");
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you may not use this file except in compliance with the License.
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You may obtain a copy of the License at
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@@ -12,18 +12,23 @@
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limitations under the License.
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*/
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#include "./xgboost4j.h"
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#include <rabit/c_api.h>
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#include <xgboost/base.h>
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#include <xgboost/c_api.h>
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#include <xgboost/json.h>
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#include <xgboost/logging.h>
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#include <cstddef>
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#include <cstdint>
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#include <limits>
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#include <rabit/c_api.h>
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#include <xgboost/c_api.h>
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#include <xgboost/base.h>
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#include <xgboost/logging.h>
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#include <xgboost/json.h>
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#include "./xgboost4j.h"
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#include <cstring>
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#include <vector>
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#include <limits>
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#include <string>
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#include <type_traits>
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#include <vector>
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#include "../../../src/c_api/c_api_utils.h"
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#define JVM_CHECK_CALL(__expr) \
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{ \
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@@ -219,58 +224,89 @@ JNIEXPORT jint JNICALL Java_ml_dmlc_xgboost4j_java_XGBoostJNI_XGDMatrixCreateFro
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return ret;
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}
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/*
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* Class: ml_dmlc_xgboost4j_java_XGBoostJNI
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* Method: XGDMatrixCreateFromCSREx
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* Signature: ([J[I[FI[J)I
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namespace {
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/**
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* \brief Create from sparse matrix.
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*
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* \param maker Indirect call to XGBoost C function for creating CSC and CSR.
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*
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* \return Status
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*/
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JNIEXPORT jint JNICALL Java_ml_dmlc_xgboost4j_java_XGBoostJNI_XGDMatrixCreateFromCSREx
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(JNIEnv *jenv, jclass jcls, jlongArray jindptr, jintArray jindices, jfloatArray jdata, jint jcol, jlongArray jout) {
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template <typename Fn>
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jint MakeJVMSparseInput(JNIEnv *jenv, jlongArray jindptr, jintArray jindices, jfloatArray jdata,
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jfloat jmissing, jint jnthread, Fn &&maker, jlongArray jout) {
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DMatrixHandle result;
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jlong* indptr = jenv->GetLongArrayElements(jindptr, 0);
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jint* indices = jenv->GetIntArrayElements(jindices, 0);
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jfloat* data = jenv->GetFloatArrayElements(jdata, 0);
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bst_ulong nindptr = (bst_ulong)jenv->GetArrayLength(jindptr);
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bst_ulong nelem = (bst_ulong)jenv->GetArrayLength(jdata);
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jint ret = (jint) XGDMatrixCreateFromCSREx((size_t const *)indptr,
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(unsigned int const *)indices,
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(float const *)data,
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nindptr, nelem, jcol, &result);
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jlong *indptr = jenv->GetLongArrayElements(jindptr, nullptr);
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jint *indices = jenv->GetIntArrayElements(jindices, nullptr);
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jfloat *data = jenv->GetFloatArrayElements(jdata, nullptr);
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bst_ulong nindptr = static_cast<bst_ulong>(jenv->GetArrayLength(jindptr));
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bst_ulong nelem = static_cast<bst_ulong>(jenv->GetArrayLength(jdata));
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std::string sindptr, sindices, sdata;
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CHECK_EQ(indptr[nindptr - 1], nelem);
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using IndPtrT = std::conditional_t<std::is_convertible<jlong *, long *>::value, long, long long>;
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using IndT =
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std::conditional_t<std::is_convertible<jint *, std::int32_t *>::value, std::int32_t, long>;
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xgboost::detail::MakeSparseFromPtr(
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static_cast<IndPtrT const *>(indptr), static_cast<IndT const *>(indices),
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static_cast<float const *>(data), nindptr, &sindptr, &sindices, &sdata);
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xgboost::Json jconfig{xgboost::Object{}};
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auto missing = static_cast<float>(jmissing);
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auto n_threads = static_cast<std::int32_t>(jnthread);
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// Construct configuration
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jconfig["nthread"] = xgboost::Integer{n_threads};
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jconfig["missing"] = xgboost::Number{missing};
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std::string config;
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xgboost::Json::Dump(jconfig, &config);
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jint ret = maker(sindptr.c_str(), sindices.c_str(), sdata.c_str(), config.c_str(), &result);
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JVM_CHECK_CALL(ret);
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setHandle(jenv, jout, result);
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//Release
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// Release
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jenv->ReleaseLongArrayElements(jindptr, indptr, 0);
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jenv->ReleaseIntArrayElements(jindices, indices, 0);
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jenv->ReleaseFloatArrayElements(jdata, data, 0);
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return ret;
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}
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} // anonymous namespace
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/*
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* Class: ml_dmlc_xgboost4j_java_XGBoostJNI
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* Method: XGDMatrixCreateFromCSCEx
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* Signature: ([J[I[FI[J)I
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* Method: XGDMatrixCreateFromCSR
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* Signature: ([J[I[FIFI[J)I
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*/
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JNIEXPORT jint JNICALL Java_ml_dmlc_xgboost4j_java_XGBoostJNI_XGDMatrixCreateFromCSCEx
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(JNIEnv *jenv, jclass jcls, jlongArray jindptr, jintArray jindices, jfloatArray jdata, jint jrow, jlongArray jout) {
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DMatrixHandle result;
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jlong* indptr = jenv->GetLongArrayElements(jindptr, NULL);
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jint* indices = jenv->GetIntArrayElements(jindices, 0);
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jfloat* data = jenv->GetFloatArrayElements(jdata, NULL);
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bst_ulong nindptr = (bst_ulong)jenv->GetArrayLength(jindptr);
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bst_ulong nelem = (bst_ulong)jenv->GetArrayLength(jdata);
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JNIEXPORT jint JNICALL Java_ml_dmlc_xgboost4j_java_XGBoostJNI_XGDMatrixCreateFromCSR(
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JNIEnv *jenv, jclass jcls, jlongArray jindptr, jintArray jindices, jfloatArray jdata, jint jcol,
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jfloat jmissing, jint jnthread, jlongArray jout) {
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using CSTR = char const *;
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return MakeJVMSparseInput(
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jenv, jindptr, jindices, jdata, jmissing, jnthread,
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[&](CSTR sindptr, CSTR sindices, CSTR sdata, CSTR sconfig, DMatrixHandle *result) {
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return XGDMatrixCreateFromCSR(sindptr, sindices, sdata, static_cast<std::int32_t>(jcol),
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sconfig, result);
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},
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jout);
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}
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jint ret = (jint) XGDMatrixCreateFromCSCEx((size_t const *)indptr,
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(unsigned int const *)indices,
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(float const *)data,
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nindptr, nelem, jrow, &result);
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JVM_CHECK_CALL(ret);
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setHandle(jenv, jout, result);
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//release
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jenv->ReleaseLongArrayElements(jindptr, indptr, 0);
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jenv->ReleaseIntArrayElements(jindices, indices, 0);
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jenv->ReleaseFloatArrayElements(jdata, data, 0);
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return ret;
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/*
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* Class: ml_dmlc_xgboost4j_java_XGBoostJNI
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* Method: XGDMatrixCreateFromCSC
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* Signature: ([J[I[FIFI[J)I
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*/
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JNIEXPORT jint JNICALL Java_ml_dmlc_xgboost4j_java_XGBoostJNI_XGDMatrixCreateFromCSC(
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JNIEnv *jenv, jclass jcls, jlongArray jindptr, jintArray jindices, jfloatArray jdata, jint jrow,
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jfloat jmissing, jint jnthread, jlongArray jout) {
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using CSTR = char const *;
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return MakeJVMSparseInput(
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jenv, jindptr, jindices, jdata, jmissing, jnthread,
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[&](CSTR sindptr, CSTR sindices, CSTR sdata, CSTR sconfig, DMatrixHandle *result) {
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return XGDMatrixCreateFromCSC(sindptr, sindices, sdata, static_cast<bst_ulong>(jrow),
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sconfig, result);
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},
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jout);
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}
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/*
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@@ -459,6 +495,23 @@ JNIEXPORT jint JNICALL Java_ml_dmlc_xgboost4j_java_XGBoostJNI_XGDMatrixNumRow
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return ret;
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}
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/*
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* Class: ml_dmlc_xgboost4j_java_XGBoostJNI
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* Method: XGDMatrixNumNonMissing
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* Signature: (J[J)I
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*/
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JNIEXPORT jint JNICALL Java_ml_dmlc_xgboost4j_java_XGBoostJNI_XGDMatrixNumNonMissing(
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JNIEnv *jenv, jclass, jlong jhandle, jlongArray jout) {
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DMatrixHandle handle = reinterpret_cast<DMatrixHandle>(jhandle);
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CHECK(handle);
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bst_ulong result[1];
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auto ret = static_cast<jint>(XGDMatrixNumNonMissing(handle, result));
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jlong jresult[1]{static_cast<jlong>(result[0])};
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jenv->SetLongArrayRegion(jout, 0, 1, jresult);
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JVM_CHECK_CALL(ret);
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return ret;
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}
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/*
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* Class: ml_dmlc_xgboost4j_java_XGBoostJNI
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* Method: XGBoosterCreate
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