isotree 0.3.0 → 0.4.0
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- checksums.yaml +4 -4
- data/CHANGELOG.md +9 -0
- data/LICENSE.txt +2 -2
- data/README.md +1 -1
- data/lib/isotree/version.rb +1 -1
- data/lib/isotree.rb +3 -3
- data/vendor/isotree/LICENSE +1 -1
- data/vendor/isotree/README.md +5 -5
- data/vendor/isotree/include/isotree.hpp +5 -0
- data/vendor/isotree/inst/COPYRIGHTS +70 -0
- data/vendor/isotree/src/RcppExports.cpp +130 -66
- data/vendor/isotree/src/Rwrapper.cpp +831 -346
- data/vendor/isotree/src/c_interface.cpp +6 -1
- data/vendor/isotree/src/crit.hpp +4 -0
- data/vendor/isotree/src/digamma.hpp +184 -0
- data/vendor/isotree/src/dist.hpp +2 -2
- data/vendor/isotree/src/fit_model.hpp +2 -2
- data/vendor/isotree/src/helpers_iforest.hpp +1 -0
- data/vendor/isotree/src/impute.hpp +40 -12
- data/vendor/isotree/src/isotree.hpp +19 -10
- data/vendor/isotree/src/mult.hpp +1 -1
- data/vendor/isotree/src/oop_interface.cpp +7 -5
- data/vendor/isotree/src/python_helpers.hpp +10 -30
- data/vendor/isotree/src/robinmap/README.md +1 -1
- data/vendor/isotree/src/robinmap/include/tsl/robin_hash.h +29 -10
- data/vendor/isotree/src/serialize.cpp +32 -16
- data/vendor/isotree/src/sql.cpp +2 -2
- data/vendor/isotree/src/utils.hpp +15 -37
- data/vendor/isotree/src/xoshiro.hpp +3 -7
- metadata +7 -6
@@ -40,7 +40,7 @@
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* International Conference on Knowledge Discovery & Data Mining. 2018.
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*
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* BSD 2-Clause License
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-
* Copyright (c) 2019-
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* Copyright (c) 2019-2023, David Cortes
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* All rights reserved.
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are met:
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@@ -64,12 +64,10 @@
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#include <Rcpp.h>
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#include <Rcpp/unwindProtect.h>
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// [[Rcpp::plugins(unwindProtect)]]
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#include <Rinternals.h>
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#include <R_ext/Altrep.h>
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#
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#define FOR_R
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#endif
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#include <type_traits>
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/* This is the package's header */
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#include "isotree.hpp"
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@@ -87,7 +85,7 @@
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so it's not enough to just include 'isotree_exportable.hpp' and let
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the templates be instantiated elsewhere. */
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#define throw_mem_err() Rcpp::
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#define throw_mem_err() throw Rcpp::exception("Error: insufficient memory. Try smaller sample sizes and fewer trees.\n")
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SEXP alloc_RawVec(void *data)
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{
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@@ -148,9 +146,9 @@ Rcpp::RawVector serialize_cpp_obj(const Model *model_outputs)
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{
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size_t serialized_size = determine_serialized_size(*model_outputs);
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if (unlikely(!serialized_size))
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Rcpp::
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throw Rcpp::exception("Unexpected error.");
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if (unlikely(serialized_size > (size_t)std::numeric_limits<R_xlen_t>::max()))
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Rcpp::
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throw Rcpp::exception("Resulting model is too large for R to handle.");
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Rcpp::RawVector out = Rcpp::unwindProtect(alloc_RawVec, (void*)&serialized_size);
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char *out_ = (char*)RAW(out);
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serialize_isotree(*model_outputs, out_);
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@@ -195,11 +193,279 @@ SEXP deserialize_Indexer(Rcpp::RawVector src)
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}
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// [[Rcpp::export(rng = false)]]
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-
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SEXP serialize_IsoForest_from_ptr(SEXP R_ptr)
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{
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const IsoForest* model = (const IsoForest*)R_ExternalPtrAddr(R_ptr);
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return serialize_cpp_obj<IsoForest>(model);
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}
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// [[Rcpp::export(rng = false)]]
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SEXP serialize_ExtIsoForest_from_ptr(SEXP R_ptr)
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{
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const ExtIsoForest* model = (const ExtIsoForest*)R_ExternalPtrAddr(R_ptr);
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return serialize_cpp_obj<ExtIsoForest>(model);
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}
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// [[Rcpp::export(rng = false)]]
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SEXP serialize_Imputer_from_ptr(SEXP R_ptr)
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{
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const Imputer* model = (const Imputer*)R_ExternalPtrAddr(R_ptr);
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return serialize_cpp_obj<Imputer>(model);
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}
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// [[Rcpp::export(rng = false)]]
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SEXP serialize_Indexer_from_ptr(SEXP R_ptr)
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{
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const TreesIndexer* model = (const TreesIndexer*)R_ExternalPtrAddr(R_ptr);
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return serialize_cpp_obj<TreesIndexer>(model);
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}
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// [[Rcpp::export(rng = false)]]
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Rcpp::LogicalVector check_null_ptr_model_internal(SEXP ptr_model)
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{
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return Rcpp::LogicalVector(R_ExternalPtrAddr(ptr_model) == NULL);
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}
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static R_altrep_class_t altrepped_pointer_IsoForest;
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static R_altrep_class_t altrepped_pointer_ExtIsoForest;
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static R_altrep_class_t altrepped_pointer_Imputer;
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static R_altrep_class_t altrepped_pointer_TreesIndexer;
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static R_altrep_class_t altrepped_pointer_NullPointer;
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template <class Model>
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R_altrep_class_t get_altrep_obj_class()
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{
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if (std::is_same<Model, IsoForest>::value) return altrepped_pointer_IsoForest;
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if (std::is_same<Model, ExtIsoForest>::value) return altrepped_pointer_ExtIsoForest;
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if (std::is_same<Model, Imputer>::value) return altrepped_pointer_Imputer;
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if (std::is_same<Model, TreesIndexer>::value) return altrepped_pointer_TreesIndexer;
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throw Rcpp::exception("Internal error. Please open a bug report.");
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}
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R_xlen_t altrepped_pointer_length(SEXP obj)
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{
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return 1;
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}
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SEXP get_element_from_altrepped_obj(SEXP R_altrepped_obj, R_xlen_t idx)
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{
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return R_altrep_data1(R_altrepped_obj);
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}
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template <class Model>
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void delete_model_from_R_ptr(SEXP R_ptr)
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{
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Model *cpp_ptr = (Model*)R_ExternalPtrAddr(R_ptr);
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delete cpp_ptr;
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R_SetExternalPtrAddr(R_ptr, nullptr);
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R_ClearExternalPtr(R_ptr);
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}
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template <class Model>
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SEXP get_altrepped_pointer(void *void_ptr)
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{
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SEXP R_ptr_name = PROTECT(Rf_mkString("ptr"));
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SEXP R_ptr_class = PROTECT(Rf_mkString("isotree_altrepped_handle"));
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SEXP R_ptr = PROTECT(R_MakeExternalPtr(nullptr, R_NilValue, R_NilValue));
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SEXP out = PROTECT(R_new_altrep(get_altrep_obj_class<Model>(), R_NilValue, R_NilValue));
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std::unique_ptr<Model> *ptr = (std::unique_ptr<Model>*)void_ptr;
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R_SetExternalPtrAddr(R_ptr, ptr->get());
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R_RegisterCFinalizerEx(R_ptr, delete_model_from_R_ptr<Model>, TRUE);
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ptr->release();
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R_set_altrep_data1(out, R_ptr);
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Rf_setAttrib(out, R_NamesSymbol, R_ptr_name);
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Rf_setAttrib(out, R_ClassSymbol, R_ptr_class);
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UNPROTECT(4);
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return out;
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}
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template <class Model>
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SEXP serialize_altrepped_pointer(SEXP altrepped_obj)
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{
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try {
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Model *cpp_ptr = (Model*)R_ExternalPtrAddr(R_altrep_data1(altrepped_obj));
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R_xlen_t state_size = determine_serialized_size(*cpp_ptr);
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SEXP R_state = PROTECT(Rf_allocVector(RAWSXP, state_size));
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serialize_isotree(*cpp_ptr, (char*)RAW(R_state));
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UNPROTECT(1);
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return R_state;
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}
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catch (const std::exception &ex) {
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Rf_error("%s\n", ex.what());
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}
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return R_NilValue; /* <- won't be reached */
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}
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template <class Model>
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SEXP deserialize_altrepped_pointer(SEXP cls, SEXP R_state)
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{
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SEXP R_ptr_name = PROTECT(Rf_mkString("ptr"));
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SEXP R_ptr_class = PROTECT(Rf_mkString("isotree_altrepped_handle"));
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SEXP R_ptr = PROTECT(R_MakeExternalPtr(nullptr, R_NilValue, R_NilValue));
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SEXP out = PROTECT(R_new_altrep(get_altrep_obj_class<Model>(), R_NilValue, R_NilValue));
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try {
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std::unique_ptr<Model> model(new Model());
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const char *inp = (const char*)RAW(R_state);
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deserialize_isotree(*model, inp);
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R_SetExternalPtrAddr(R_ptr, model.get());
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R_RegisterCFinalizerEx(R_ptr, delete_model_from_R_ptr<Model>, TRUE);
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model.release();
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}
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catch (const std::exception &ex) {
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Rf_error("%s\n", ex.what());
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}
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R_set_altrep_data1(out, R_ptr);
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Rf_setAttrib(out, R_NamesSymbol, R_ptr_name);
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Rf_setAttrib(out, R_ClassSymbol, R_ptr_class);
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UNPROTECT(4);
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return out;
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}
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template <class Model>
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SEXP duplicate_altrepped_pointer(SEXP altrepped_obj, Rboolean deep)
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{
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SEXP R_ptr_name = PROTECT(Rf_mkString("ptr"));
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SEXP R_ptr_class = PROTECT(Rf_mkString("isotree_altrepped_handle"));
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SEXP out = PROTECT(R_new_altrep(get_altrep_obj_class<Model>(), R_NilValue, R_NilValue));
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if (!deep) {
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R_set_altrep_data1(out, R_altrep_data1(altrepped_obj));
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}
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else {
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SEXP R_ptr = PROTECT(R_MakeExternalPtr(nullptr, R_NilValue, R_NilValue));
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try {
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std::unique_ptr<Model> new_obj(new Model());
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Model *cpp_ptr = (Model*)R_ExternalPtrAddr(R_altrep_data1(altrepped_obj));
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*new_obj = *cpp_ptr;
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R_SetExternalPtrAddr(R_ptr, new_obj.get());
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R_RegisterCFinalizerEx(R_ptr, delete_model_from_R_ptr<Model>, TRUE);
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new_obj.release();
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}
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catch (const std::exception &ex) {
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Rf_error("%s\n", ex.what());
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}
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R_set_altrep_data1(out, R_ptr);
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UNPROTECT(1);
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}
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Rf_setAttrib(out, R_NamesSymbol, R_ptr_name);
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Rf_setAttrib(out, R_NamesSymbol, R_ptr_class);
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UNPROTECT(3);
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return out;
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}
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SEXP get_altrepped_null_pointer()
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{
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SEXP R_ptr_name = PROTECT(Rf_mkString("ptr"));
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SEXP R_ptr_class = PROTECT(Rf_mkString("isotree_altrepped_handle"));
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SEXP R_ptr = PROTECT(R_MakeExternalPtr(nullptr, R_NilValue, R_NilValue));
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SEXP out = PROTECT(R_new_altrep(altrepped_pointer_NullPointer, R_ptr, R_NilValue));
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Rf_setAttrib(out, R_NamesSymbol, R_ptr_name);
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Rf_setAttrib(out, R_ClassSymbol, R_ptr_class);
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UNPROTECT(4);
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return out;
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}
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SEXP safe_get_altrepped_null_pointer(void *unused)
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{
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return get_altrepped_null_pointer();
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}
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SEXP serialize_altrepped_null(SEXP altrepped_obj)
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{
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return Rf_allocVector(RAWSXP, 0);
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}
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SEXP deserialize_altrepped_null(SEXP cls, SEXP R_state)
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{
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return get_altrepped_null_pointer();
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}
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SEXP duplicate_altrepped_pointer(SEXP altrepped_obj, Rboolean deep)
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{
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return get_altrepped_null_pointer();
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}
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Rboolean inspect_altrepped_pointer(SEXP x, int pre, int deep, int pvec, void (*inspect_subtree)(SEXP, int, int, int))
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{
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Rcpp::Rcout << "Altrepped pointer [address:" << R_ExternalPtrAddr(R_altrep_data1(x)) << "]\n";
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return TRUE;
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}
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template <class Model>
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Model* get_pointer_from_altrep(SEXP altrepped_obj)
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{
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return (Model*)R_ExternalPtrAddr(R_altrep_data1(altrepped_obj));
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}
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template <class Model>
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Model* get_pointer_from_xptr(SEXP R_ptr)
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{
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return (Model*)R_ExternalPtrAddr(R_ptr);
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}
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// [[Rcpp::init]]
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void init_altrepped_vectors(DllInfo* dll)
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{
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altrepped_pointer_IsoForest = R_make_altlist_class("altrepped_pointer_IsoForest", "isotree", dll);
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R_set_altrep_Length_method(altrepped_pointer_IsoForest, altrepped_pointer_length);
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R_set_altrep_Inspect_method(altrepped_pointer_IsoForest, inspect_altrepped_pointer);
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R_set_altrep_Serialized_state_method(altrepped_pointer_IsoForest, serialize_altrepped_pointer<IsoForest>);
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R_set_altrep_Unserialize_method(altrepped_pointer_IsoForest, deserialize_altrepped_pointer<IsoForest>);
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R_set_altrep_Duplicate_method(altrepped_pointer_IsoForest, duplicate_altrepped_pointer<IsoForest>);
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R_set_altlist_Elt_method(altrepped_pointer_IsoForest, get_element_from_altrepped_obj);
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altrepped_pointer_ExtIsoForest = R_make_altlist_class("altrepped_pointer_ExtIsoForest", "isotree", dll);
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R_set_altrep_Length_method(altrepped_pointer_ExtIsoForest, altrepped_pointer_length);
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R_set_altrep_Inspect_method(altrepped_pointer_ExtIsoForest, inspect_altrepped_pointer);
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R_set_altrep_Serialized_state_method(altrepped_pointer_ExtIsoForest, serialize_altrepped_pointer<ExtIsoForest>);
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R_set_altrep_Unserialize_method(altrepped_pointer_ExtIsoForest, deserialize_altrepped_pointer<ExtIsoForest>);
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R_set_altrep_Duplicate_method(altrepped_pointer_ExtIsoForest, duplicate_altrepped_pointer<ExtIsoForest>);
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R_set_altlist_Elt_method(altrepped_pointer_ExtIsoForest, get_element_from_altrepped_obj);
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altrepped_pointer_Imputer = R_make_altlist_class("altrepped_pointer_Imputer", "isotree", dll);
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R_set_altrep_Length_method(altrepped_pointer_Imputer, altrepped_pointer_length);
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R_set_altrep_Inspect_method(altrepped_pointer_Imputer, inspect_altrepped_pointer);
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+
R_set_altrep_Serialized_state_method(altrepped_pointer_Imputer, serialize_altrepped_pointer<Imputer>);
|
448
|
+
R_set_altrep_Unserialize_method(altrepped_pointer_Imputer, deserialize_altrepped_pointer<Imputer>);
|
449
|
+
R_set_altrep_Duplicate_method(altrepped_pointer_Imputer, duplicate_altrepped_pointer<Imputer>);
|
450
|
+
R_set_altlist_Elt_method(altrepped_pointer_Imputer, get_element_from_altrepped_obj);
|
451
|
+
|
452
|
+
altrepped_pointer_TreesIndexer = R_make_altlist_class("altrepped_pointer_TreesIndexer", "isotree", dll);
|
453
|
+
R_set_altrep_Length_method(altrepped_pointer_TreesIndexer, altrepped_pointer_length);
|
454
|
+
R_set_altrep_Inspect_method(altrepped_pointer_TreesIndexer, inspect_altrepped_pointer);
|
455
|
+
R_set_altrep_Serialized_state_method(altrepped_pointer_TreesIndexer, serialize_altrepped_pointer<TreesIndexer>);
|
456
|
+
R_set_altrep_Unserialize_method(altrepped_pointer_TreesIndexer, deserialize_altrepped_pointer<TreesIndexer>);
|
457
|
+
R_set_altrep_Duplicate_method(altrepped_pointer_TreesIndexer, duplicate_altrepped_pointer<TreesIndexer>);
|
458
|
+
R_set_altlist_Elt_method(altrepped_pointer_TreesIndexer, get_element_from_altrepped_obj);
|
459
|
+
|
460
|
+
altrepped_pointer_NullPointer = R_make_altlist_class("altrepped_pointer_NullPointer", "isotree", dll);
|
461
|
+
R_set_altrep_Length_method(altrepped_pointer_NullPointer, altrepped_pointer_length);
|
462
|
+
R_set_altrep_Inspect_method(altrepped_pointer_NullPointer, inspect_altrepped_pointer);
|
463
|
+
R_set_altrep_Serialized_state_method(altrepped_pointer_NullPointer, serialize_altrepped_null);
|
464
|
+
R_set_altrep_Unserialize_method(altrepped_pointer_NullPointer, deserialize_altrepped_null);
|
465
|
+
R_set_altrep_Duplicate_method(altrepped_pointer_NullPointer, duplicate_altrepped_pointer);
|
466
|
+
R_set_altlist_Elt_method(altrepped_pointer_NullPointer, get_element_from_altrepped_obj);
|
467
|
+
}
|
468
|
+
|
203
469
|
double* set_R_nan_as_C_nan(double *x, size_t n, std::vector<double> &v, int nthreads)
|
204
470
|
{
|
205
471
|
v.assign(x, x + n);
|
@@ -223,6 +489,13 @@ double* set_R_nan_as_C_nan(double *x, size_t n, int nthreads)
|
|
223
489
|
return x;
|
224
490
|
}
|
225
491
|
|
492
|
+
TreesIndexer* get_indexer_ptr_from_R_obj(SEXP indexer_R_ptr)
|
493
|
+
{
|
494
|
+
TreesIndexer *out = get_pointer_from_xptr<TreesIndexer>(indexer_R_ptr);
|
495
|
+
if (out && out->indices.empty()) out = nullptr;
|
496
|
+
return out;
|
497
|
+
}
|
498
|
+
|
226
499
|
// [[Rcpp::export(rng = false)]]
|
227
500
|
Rcpp::List fit_model(Rcpp::NumericVector X_num, Rcpp::IntegerVector X_cat, Rcpp::IntegerVector ncat,
|
228
501
|
Rcpp::NumericVector Xc, Rcpp::IntegerVector Xc_ind, Rcpp::IntegerVector Xc_indptr,
|
@@ -242,7 +515,7 @@ Rcpp::List fit_model(Rcpp::NumericVector X_num, Rcpp::IntegerVector X_cat, Rcpp:
|
|
242
515
|
Rcpp::CharacterVector missing_action, bool all_perm,
|
243
516
|
bool build_imputer, bool output_imputations, size_t min_imp_obs,
|
244
517
|
Rcpp::CharacterVector depth_imp, Rcpp::CharacterVector weigh_imp_rows,
|
245
|
-
int random_seed, bool use_long_double, int nthreads)
|
518
|
+
int random_seed, bool use_long_double, int nthreads, bool lazy_serialization)
|
246
519
|
{
|
247
520
|
double* numeric_data_ptr = NULL;
|
248
521
|
int* categ_data_ptr = NULL;
|
@@ -384,18 +657,37 @@ Rcpp::List fit_model(Rcpp::NumericVector X_num, Rcpp::IntegerVector X_cat, Rcpp:
|
|
384
657
|
}
|
385
658
|
|
386
659
|
Rcpp::List outp = Rcpp::List::create(
|
387
|
-
|
388
|
-
|
389
|
-
|
390
|
-
|
391
|
-
|
392
|
-
|
393
|
-
|
394
|
-
|
395
|
-
|
396
|
-
Rcpp::_["err"] = Rcpp::LogicalVector::create(1)
|
660
|
+
Rcpp::_["depths"] = depths,
|
661
|
+
Rcpp::_["tmat"] = tmat,
|
662
|
+
Rcpp::_["dmat"] = dmat,
|
663
|
+
Rcpp::_["model"] = R_NilValue,
|
664
|
+
Rcpp::_["imputer"] = R_NilValue,
|
665
|
+
Rcpp::_["indexer"] = R_NilValue,
|
666
|
+
Rcpp::_["imputed_num"] = R_NilValue,
|
667
|
+
Rcpp::_["imputed_cat"] = R_NilValue,
|
668
|
+
Rcpp::_["err"] = Rcpp::LogicalVector::create(1)
|
397
669
|
);
|
398
670
|
|
671
|
+
Rcpp::List model_lst_nonlazy = Rcpp::List::create(
|
672
|
+
Rcpp::_["ptr"] = R_NilValue,
|
673
|
+
Rcpp::_["ser"] = R_NilValue
|
674
|
+
);
|
675
|
+
|
676
|
+
Rcpp::List imputer_lst_nonlazy = Rcpp::List::create(
|
677
|
+
Rcpp::_["ptr"] = Rcpp::XPtr<void*>(nullptr, false),
|
678
|
+
Rcpp::_["ser"] = R_NilValue
|
679
|
+
);
|
680
|
+
|
681
|
+
if (lazy_serialization) {
|
682
|
+
outp["indexer"] = get_altrepped_null_pointer();
|
683
|
+
}
|
684
|
+
else {
|
685
|
+
outp["indexer"] = Rcpp::List::create(
|
686
|
+
Rcpp::_["ptr"] = Rcpp::XPtr<void*>(nullptr, false),
|
687
|
+
Rcpp::_["ser"] = R_NilValue
|
688
|
+
);
|
689
|
+
}
|
690
|
+
|
399
691
|
std::unique_ptr<IsoForest> model_ptr(nullptr);
|
400
692
|
std::unique_ptr<ExtIsoForest> ext_model_ptr(nullptr);
|
401
693
|
std::unique_ptr<Imputer> imputer_ptr(nullptr);
|
@@ -408,9 +700,7 @@ Rcpp::List fit_model(Rcpp::NumericVector X_num, Rcpp::IntegerVector X_cat, Rcpp:
|
|
408
700
|
if (build_imputer)
|
409
701
|
imputer_ptr = std::unique_ptr<Imputer>(new Imputer());
|
410
702
|
|
411
|
-
int ret_val
|
412
|
-
try {
|
413
|
-
ret_val =
|
703
|
+
int ret_val =
|
414
704
|
fit_iforest(model_ptr.get(), ext_model_ptr.get(),
|
415
705
|
numeric_data_ptr, ncols_numeric,
|
416
706
|
categ_data_ptr, ncols_categ, ncat_ptr,
|
@@ -432,14 +722,21 @@ Rcpp::List fit_model(Rcpp::NumericVector X_num, Rcpp::IntegerVector X_cat, Rcpp:
|
|
432
722
|
all_perm, imputer_ptr.get(), min_imp_obs,
|
433
723
|
depth_imp_C, weigh_imp_rows_C, output_imputations,
|
434
724
|
(uint64_t) random_seed, use_long_double, nthreads);
|
435
|
-
}
|
436
|
-
catch (std::bad_alloc &e) {
|
437
|
-
throw_mem_err();
|
438
|
-
}
|
439
|
-
Rcpp::checkUserInterrupt();
|
440
725
|
|
726
|
+
Rcpp::checkUserInterrupt(); /* <- nothing is returned in this case */
|
727
|
+
/* Note to self: the procedure has its own interrupt checker, so when an interrupt
|
728
|
+
signal is triggered, first it will print a message about it, then re-issue the
|
729
|
+
signal, then check for interrupt through Rcpp's, which will return nothing to
|
730
|
+
the outside and will not raise any error. In this case, at least the user will
|
731
|
+
see the error message. Note that Rcpp's interrupt non-return, unlike R's, triggers
|
732
|
+
stack unwinding for C++ objects. */
|
733
|
+
|
734
|
+
/* Note to self: since the function for fitting the model uses the C++ exception system,
|
735
|
+
and the stop signals are translated into Rcpp stops, this section below should not
|
736
|
+
be reachable anyhow. */
|
441
737
|
if (ret_val == EXIT_FAILURE)
|
442
738
|
{
|
739
|
+
Rcpp::Rcerr << "Unexpected error" << std::endl;
|
443
740
|
return Rcpp::unwindProtect(safe_errlist, nullptr);
|
444
741
|
}
|
445
742
|
|
@@ -447,63 +744,66 @@ Rcpp::List fit_model(Rcpp::NumericVector X_num, Rcpp::IntegerVector X_cat, Rcpp:
|
|
447
744
|
tmat_to_dense(tmat_ptr, dmat_ptr, nrows, standardize_dist? 0. : std::numeric_limits<double>::infinity());
|
448
745
|
|
449
746
|
bool serialization_failed = false;
|
450
|
-
|
451
|
-
|
747
|
+
|
748
|
+
if (lazy_serialization)
|
749
|
+
{
|
750
|
+
if (ndim == 1) {
|
751
|
+
outp["model"] = Rcpp::unwindProtect(get_altrepped_pointer<IsoForest>, (void*)&model_ptr);
|
752
|
+
}
|
753
|
+
else {
|
754
|
+
outp["model"] = Rcpp::unwindProtect(get_altrepped_pointer<ExtIsoForest>, (void*)&ext_model_ptr);
|
755
|
+
}
|
756
|
+
|
757
|
+
if (build_imputer) {
|
758
|
+
outp["imputer"] = Rcpp::unwindProtect(get_altrepped_pointer<Imputer>, (void*)&imputer_ptr);
|
759
|
+
}
|
760
|
+
else {
|
761
|
+
outp["imputer"] = Rcpp::unwindProtect(safe_get_altrepped_null_pointer, nullptr);
|
762
|
+
}
|
763
|
+
}
|
764
|
+
|
765
|
+
else
|
766
|
+
{
|
767
|
+
Rcpp::RawVector serialized_obj;
|
768
|
+
/* Note to self: the serialization functions use unwind protection internally. */
|
452
769
|
if (ndim == 1)
|
453
770
|
serialized_obj = serialize_cpp_obj(model_ptr.get());
|
454
771
|
else
|
455
772
|
serialized_obj = serialize_cpp_obj(ext_model_ptr.get());
|
456
|
-
}
|
457
|
-
catch (std::bad_alloc &e) {
|
458
|
-
throw_mem_err();
|
459
|
-
}
|
460
|
-
if (unlikely(!serialized_obj.size())) serialization_failed = true;
|
461
|
-
if (unlikely(serialization_failed)) {
|
462
|
-
if (ndim == 1)
|
463
|
-
model_ptr.reset();
|
464
|
-
else
|
465
|
-
ext_model_ptr.reset();
|
466
|
-
}
|
467
773
|
|
468
|
-
|
469
|
-
|
470
|
-
|
774
|
+
if (unlikely(!serialized_obj.size())) serialization_failed = true;
|
775
|
+
if (unlikely(serialization_failed)) {
|
776
|
+
throw Rcpp::exception("Error: insufficient memory\n");
|
777
|
+
}
|
778
|
+
|
779
|
+
model_lst_nonlazy["ser"] = serialized_obj;
|
471
780
|
if (ndim == 1) {
|
472
|
-
|
781
|
+
model_lst_nonlazy["ptr"] = Rcpp::unwindProtect(safe_XPtr<IsoForest>, model_ptr.get());
|
473
782
|
model_ptr.release();
|
474
783
|
}
|
475
784
|
else {
|
476
|
-
|
785
|
+
model_lst_nonlazy["ptr"] = Rcpp::unwindProtect(safe_XPtr<ExtIsoForest>, ext_model_ptr.get());
|
477
786
|
ext_model_ptr.release();
|
478
787
|
}
|
479
|
-
} else
|
480
|
-
outp["ptr"] = R_NilValue;
|
481
788
|
|
482
|
-
|
483
|
-
|
484
|
-
|
485
|
-
outp["imp_ser"] = serialize_cpp_obj(imputer_ptr.get());
|
486
|
-
}
|
487
|
-
catch (std::bad_alloc &e) {
|
488
|
-
throw_mem_err();
|
489
|
-
}
|
490
|
-
if (!Rf_xlength(outp["imp_ser"]))
|
789
|
+
outp["model"] = model_lst_nonlazy;
|
790
|
+
|
791
|
+
if (build_imputer)
|
491
792
|
{
|
492
|
-
|
493
|
-
|
494
|
-
|
495
|
-
|
496
|
-
|
497
|
-
|
498
|
-
|
499
|
-
outp["ptr"] = R_NilValue;
|
500
|
-
} else {
|
501
|
-
outp["imp_ptr"] = Rcpp::unwindProtect(safe_XPtr<Imputer>, imputer_ptr.get());
|
793
|
+
imputer_lst_nonlazy["ser"] = serialize_cpp_obj(imputer_ptr.get());
|
794
|
+
if (!Rf_xlength(imputer_lst_nonlazy["ser"]))
|
795
|
+
{
|
796
|
+
throw Rcpp::exception("Error: insufficient memory\n");
|
797
|
+
}
|
798
|
+
|
799
|
+
imputer_lst_nonlazy["ptr"] = Rcpp::unwindProtect(safe_XPtr<Imputer>, imputer_ptr.get());
|
502
800
|
imputer_ptr.release();
|
503
801
|
}
|
802
|
+
|
803
|
+
outp["imputer"] = imputer_lst_nonlazy;
|
504
804
|
}
|
505
805
|
|
506
|
-
if (output_imputations
|
806
|
+
if (output_imputations)
|
507
807
|
{
|
508
808
|
outp["imputed_num"] = Xcpp;
|
509
809
|
outp["imputed_cat"] = X_cat;
|
@@ -534,12 +834,13 @@ void fit_tree(SEXP model_R_ptr, Rcpp::RawVector serialized_obj, Rcpp::RawVector
|
|
534
834
|
Rcpp::NumericVector ref_X_num, Rcpp::IntegerVector ref_X_cat,
|
535
835
|
Rcpp::NumericVector ref_Xc, Rcpp::IntegerVector ref_Xc_ind, Rcpp::IntegerVector ref_Xc_indptr,
|
536
836
|
uint64_t random_seed, bool use_long_double,
|
537
|
-
Rcpp::List &model_cpp_obj_update, Rcpp::List &model_params_update
|
837
|
+
Rcpp::List &model_cpp_obj_update, Rcpp::List &model_params_update,
|
838
|
+
bool is_altrepped)
|
538
839
|
{
|
539
840
|
Rcpp::List out = Rcpp::List::create(
|
540
|
-
Rcpp::_["
|
541
|
-
Rcpp::_["
|
542
|
-
Rcpp::_["
|
841
|
+
Rcpp::_["model_ser"] = R_NilValue,
|
842
|
+
Rcpp::_["imputer_ser"] = R_NilValue,
|
843
|
+
Rcpp::_["indexer_ser"] = R_NilValue
|
543
844
|
);
|
544
845
|
|
545
846
|
Rcpp::IntegerVector ntrees_plus1 = Rcpp::IntegerVector::create(Rf_asInteger(model_params_update["ntrees"]) + 1);
|
@@ -674,10 +975,7 @@ void fit_tree(SEXP model_R_ptr, Rcpp::RawVector serialized_obj, Rcpp::RawVector
|
|
674
975
|
if (build_imputer)
|
675
976
|
imputer_ptr = static_cast<Imputer*>(R_ExternalPtrAddr(imp_R_ptr));
|
676
977
|
|
677
|
-
|
678
|
-
indexer_ptr = static_cast<TreesIndexer*>(R_ExternalPtrAddr(indexer_R_ptr));
|
679
|
-
if (indexer_ptr != NULL && indexer_ptr->indices.empty())
|
680
|
-
indexer_ptr = NULL;
|
978
|
+
indexer_ptr = get_indexer_ptr_from_R_obj(indexer_R_ptr);
|
681
979
|
|
682
980
|
size_t old_ntrees = (ndim == 1)? (model_ptr->trees.size()) : (ext_model_ptr->hplanes.size());
|
683
981
|
|
@@ -706,6 +1004,9 @@ void fit_tree(SEXP model_R_ptr, Rcpp::RawVector serialized_obj, Rcpp::RawVector
|
|
706
1004
|
|
707
1005
|
Rcpp::RawVector new_serialized, new_imp_serialized, new_ind_serialized;
|
708
1006
|
size_t new_size;
|
1007
|
+
|
1008
|
+
if (is_altrepped) goto dont_serialize;
|
1009
|
+
|
709
1010
|
try
|
710
1011
|
{
|
711
1012
|
if (ndim == 1)
|
@@ -719,7 +1020,7 @@ void fit_tree(SEXP model_R_ptr, Rcpp::RawVector serialized_obj, Rcpp::RawVector
|
|
719
1020
|
new_serialized = resize_vec(serialized_obj, new_size);
|
720
1021
|
char *temp = (char*)RAW(new_serialized);
|
721
1022
|
incremental_serialize_isotree(*model_ptr, temp);
|
722
|
-
out["
|
1023
|
+
out["model_ser"] = new_serialized;
|
723
1024
|
}
|
724
1025
|
|
725
1026
|
catch (std::runtime_error &e) {
|
@@ -729,7 +1030,7 @@ void fit_tree(SEXP model_R_ptr, Rcpp::RawVector serialized_obj, Rcpp::RawVector
|
|
729
1030
|
|
730
1031
|
else {
|
731
1032
|
serialize_anew_singlevar:
|
732
|
-
out["
|
1033
|
+
out["model_ser"] = serialize_cpp_obj(model_ptr);
|
733
1034
|
}
|
734
1035
|
}
|
735
1036
|
|
@@ -744,7 +1045,7 @@ void fit_tree(SEXP model_R_ptr, Rcpp::RawVector serialized_obj, Rcpp::RawVector
|
|
744
1045
|
new_serialized = resize_vec(serialized_obj, new_size);
|
745
1046
|
char *temp = (char*)RAW(new_serialized);
|
746
1047
|
incremental_serialize_isotree(*ext_model_ptr, temp);
|
747
|
-
out["
|
1048
|
+
out["model_ser"] = new_serialized;
|
748
1049
|
}
|
749
1050
|
|
750
1051
|
catch (std::runtime_error &e) {
|
@@ -754,7 +1055,7 @@ void fit_tree(SEXP model_R_ptr, Rcpp::RawVector serialized_obj, Rcpp::RawVector
|
|
754
1055
|
|
755
1056
|
else {
|
756
1057
|
serialize_anew_ext:
|
757
|
-
out["
|
1058
|
+
out["model_ser"] = serialize_cpp_obj(ext_model_ptr);
|
758
1059
|
}
|
759
1060
|
}
|
760
1061
|
|
@@ -769,7 +1070,7 @@ void fit_tree(SEXP model_R_ptr, Rcpp::RawVector serialized_obj, Rcpp::RawVector
|
|
769
1070
|
new_imp_serialized = resize_vec(serialized_imputer, new_size);
|
770
1071
|
char *temp = (char*)RAW(new_imp_serialized);
|
771
1072
|
incremental_serialize_isotree(*imputer_ptr, temp);
|
772
|
-
out["
|
1073
|
+
out["imputer_ser"] = new_imp_serialized;
|
773
1074
|
}
|
774
1075
|
|
775
1076
|
catch (std::runtime_error &e) {
|
@@ -779,7 +1080,7 @@ void fit_tree(SEXP model_R_ptr, Rcpp::RawVector serialized_obj, Rcpp::RawVector
|
|
779
1080
|
|
780
1081
|
else {
|
781
1082
|
serialize_anew_imp:
|
782
|
-
out["
|
1083
|
+
out["imputer_ser"] = serialize_cpp_obj(imputer_ptr);
|
783
1084
|
}
|
784
1085
|
}
|
785
1086
|
|
@@ -794,7 +1095,7 @@ void fit_tree(SEXP model_R_ptr, Rcpp::RawVector serialized_obj, Rcpp::RawVector
|
|
794
1095
|
new_ind_serialized = resize_vec(serialized_indexer, new_size);
|
795
1096
|
char *temp = (char*)RAW(new_ind_serialized);
|
796
1097
|
incremental_serialize_isotree(*indexer_ptr, temp);
|
797
|
-
out["
|
1098
|
+
out["indexer_ser"] = new_ind_serialized;
|
798
1099
|
}
|
799
1100
|
|
800
1101
|
catch (std::runtime_error &e) {
|
@@ -804,7 +1105,7 @@ void fit_tree(SEXP model_R_ptr, Rcpp::RawVector serialized_obj, Rcpp::RawVector
|
|
804
1105
|
|
805
1106
|
else {
|
806
1107
|
serialize_anew_ind:
|
807
|
-
out["
|
1108
|
+
out["indexer_ser"] = serialize_cpp_obj(indexer_ptr);
|
808
1109
|
}
|
809
1110
|
}
|
810
1111
|
}
|
@@ -822,11 +1123,27 @@ void fit_tree(SEXP model_R_ptr, Rcpp::RawVector serialized_obj, Rcpp::RawVector
|
|
822
1123
|
throw;
|
823
1124
|
}
|
824
1125
|
|
825
|
-
|
826
|
-
|
827
|
-
|
828
|
-
|
829
|
-
|
1126
|
+
{
|
1127
|
+
Rcpp::List model_lst = model_cpp_obj_update["model"];
|
1128
|
+
model_lst["ser"] = out["model_ser"];
|
1129
|
+
model_cpp_obj_update["model"] = model_lst;
|
1130
|
+
|
1131
|
+
if (build_imputer)
|
1132
|
+
{
|
1133
|
+
Rcpp::List imputer_lst = model_cpp_obj_update["imputer"];
|
1134
|
+
imputer_lst["ser"] = out["imputer_ser"];
|
1135
|
+
model_cpp_obj_update["imputer"] = imputer_lst;
|
1136
|
+
}
|
1137
|
+
|
1138
|
+
if (indexer_ptr)
|
1139
|
+
{
|
1140
|
+
Rcpp::List indexer_lst = model_cpp_obj_update["indexer"];
|
1141
|
+
indexer_lst["ser"] = out["indexer_ser"];
|
1142
|
+
model_cpp_obj_update["indexer"] = indexer_lst;
|
1143
|
+
}
|
1144
|
+
}
|
1145
|
+
|
1146
|
+
dont_serialize:
|
830
1147
|
model_params_update["ntrees"] = ntrees_plus1;
|
831
1148
|
}
|
832
1149
|
|
@@ -880,14 +1197,10 @@ void predict_iso(SEXP model_R_ptr, bool is_extended,
|
|
880
1197
|
IsoForest* model_ptr = NULL;
|
881
1198
|
ExtIsoForest* ext_model_ptr = NULL;
|
882
1199
|
if (is_extended)
|
883
|
-
ext_model_ptr =
|
1200
|
+
ext_model_ptr = get_pointer_from_xptr<ExtIsoForest>(model_R_ptr);
|
884
1201
|
else
|
885
|
-
model_ptr =
|
886
|
-
TreesIndexer* indexer =
|
887
|
-
if (!Rf_isNull(indexer_R_ptr) && R_ExternalPtrAddr(indexer_R_ptr) != NULL)
|
888
|
-
indexer = static_cast<TreesIndexer*>(R_ExternalPtrAddr(indexer_R_ptr));
|
889
|
-
if (indexer != NULL && indexer->indices.empty())
|
890
|
-
indexer = NULL;
|
1202
|
+
model_ptr = get_pointer_from_xptr<IsoForest>(model_R_ptr);
|
1203
|
+
TreesIndexer* indexer = get_indexer_ptr_from_R_obj(indexer_R_ptr);
|
891
1204
|
|
892
1205
|
MissingAction missing_action = is_extended?
|
893
1206
|
ext_model_ptr->missing_action
|
@@ -951,17 +1264,13 @@ void dist_iso(SEXP model_R_ptr, SEXP indexer_R_ptr,
|
|
951
1264
|
|
952
1265
|
IsoForest* model_ptr = NULL;
|
953
1266
|
ExtIsoForest* ext_model_ptr = NULL;
|
954
|
-
TreesIndexer* indexer =
|
1267
|
+
TreesIndexer* indexer = get_indexer_ptr_from_R_obj(indexer_R_ptr);
|
955
1268
|
if (is_extended)
|
956
|
-
ext_model_ptr =
|
1269
|
+
ext_model_ptr = get_pointer_from_xptr<ExtIsoForest>(model_R_ptr);
|
957
1270
|
else
|
958
|
-
model_ptr =
|
959
|
-
if (!Rf_isNull(indexer_R_ptr) && R_ExternalPtrAddr(indexer_R_ptr) != NULL)
|
960
|
-
indexer = static_cast<TreesIndexer*>(R_ExternalPtrAddr(indexer_R_ptr));
|
961
|
-
if (indexer != NULL && (indexer->indices.empty() || (!as_kernel && indexer->indices.front().node_distances.empty())))
|
962
|
-
indexer = NULL;
|
1271
|
+
model_ptr = get_pointer_from_xptr<IsoForest>(model_R_ptr);
|
963
1272
|
|
964
|
-
if (use_reference_points && indexer
|
1273
|
+
if (use_reference_points && indexer && !indexer->indices.front().reference_points.empty()) {
|
965
1274
|
tmat_ptr = NULL;
|
966
1275
|
dmat_ptr = NULL;
|
967
1276
|
rmat_ptr = REAL(rmat);
|
@@ -1044,11 +1353,13 @@ Rcpp::List impute_iso(SEXP model_R_ptr, SEXP imputer_R_ptr, bool is_extended,
|
|
1044
1353
|
IsoForest* model_ptr = NULL;
|
1045
1354
|
ExtIsoForest* ext_model_ptr = NULL;
|
1046
1355
|
if (is_extended)
|
1047
|
-
ext_model_ptr =
|
1356
|
+
ext_model_ptr = get_pointer_from_xptr<ExtIsoForest>(model_R_ptr);
|
1048
1357
|
else
|
1049
|
-
model_ptr =
|
1358
|
+
model_ptr = get_pointer_from_xptr<IsoForest>(model_R_ptr);
|
1359
|
+
|
1360
|
+
Imputer* imputer_ptr = get_pointer_from_xptr<Imputer>(imputer_R_ptr);
|
1050
1361
|
|
1051
|
-
|
1362
|
+
if (!imputer_ptr) throw Rcpp::exception("Error: requested missing value imputation, but model was built without imputer.\n");
|
1052
1363
|
|
1053
1364
|
|
1054
1365
|
impute_missing_values(numeric_data_ptr, categ_data_ptr, true,
|
@@ -1064,85 +1375,154 @@ Rcpp::List impute_iso(SEXP model_R_ptr, SEXP imputer_R_ptr, bool is_extended,
|
|
1064
1375
|
}
|
1065
1376
|
|
1066
1377
|
// [[Rcpp::export(rng = false)]]
|
1067
|
-
void drop_imputer(
|
1378
|
+
void drop_imputer(bool is_altrepped, bool free_cpp,
|
1379
|
+
SEXP lst_imputer, Rcpp::List lst_cpp_objects, Rcpp::List lst_params)
|
1068
1380
|
{
|
1069
|
-
|
1070
|
-
|
1071
|
-
|
1072
|
-
|
1381
|
+
SEXP FalseObj = PROTECT(Rf_ScalarLogical(0));
|
1382
|
+
SEXP blank_ptr = PROTECT(R_MakeExternalPtr(nullptr, R_NilValue, R_NilValue));
|
1383
|
+
SEXP altrepped_null = PROTECT(get_altrepped_null_pointer());
|
1384
|
+
|
1385
|
+
if (is_altrepped) {
|
1386
|
+
|
1387
|
+
if (free_cpp) {
|
1388
|
+
SEXP imp_R_ptr = R_altrep_data1(lst_imputer);
|
1389
|
+
Imputer* imputer_ptr = (Imputer*)R_ExternalPtrAddr(imp_R_ptr);
|
1390
|
+
delete imputer_ptr;
|
1391
|
+
R_SetExternalPtrAddr(imp_R_ptr, nullptr);
|
1392
|
+
R_ClearExternalPtr(imp_R_ptr);
|
1393
|
+
}
|
1394
|
+
|
1395
|
+
lst_cpp_objects["imputer"] = altrepped_null;
|
1396
|
+
|
1397
|
+
}
|
1398
|
+
|
1399
|
+
else {
|
1400
|
+
|
1401
|
+
if (free_cpp) {
|
1402
|
+
SEXP imp_R_ptr = VECTOR_ELT(lst_imputer, 0);
|
1403
|
+
Imputer* imputer_ptr = get_pointer_from_xptr<Imputer>(imp_R_ptr);
|
1404
|
+
delete imputer_ptr;
|
1405
|
+
R_SetExternalPtrAddr(imp_R_ptr, nullptr);
|
1406
|
+
R_ClearExternalPtr(imp_R_ptr);
|
1407
|
+
SET_VECTOR_ELT(lst_imputer, 0, imp_R_ptr);
|
1408
|
+
}
|
1073
1409
|
|
1074
|
-
|
1075
|
-
|
1410
|
+
SET_VECTOR_ELT(lst_imputer, 0, blank_ptr);
|
1411
|
+
SET_VECTOR_ELT(lst_imputer, 1, R_NilValue);
|
1412
|
+
}
|
1413
|
+
|
1414
|
+
lst_params["build_imputer"] = FalseObj;
|
1415
|
+
UNPROTECT(3);
|
1076
1416
|
}
|
1077
1417
|
|
1078
1418
|
// [[Rcpp::export(rng = false)]]
|
1079
|
-
void drop_indexer(
|
1419
|
+
void drop_indexer(bool is_altrepped, bool free_cpp,
|
1420
|
+
SEXP lst_indexer, Rcpp::List lst_cpp_objects, Rcpp::List lst_metadata)
|
1080
1421
|
{
|
1081
|
-
|
1082
|
-
|
1083
|
-
|
1084
|
-
|
1085
|
-
|
1422
|
+
SEXP empty_str = PROTECT(Rf_allocVector(STRSXP, 0));
|
1423
|
+
SEXP blank_ptr = PROTECT(R_MakeExternalPtr(nullptr, R_NilValue, R_NilValue));
|
1424
|
+
SEXP altrepped_null = PROTECT(get_altrepped_null_pointer());
|
1425
|
+
|
1426
|
+
if (is_altrepped) {
|
1427
|
+
|
1428
|
+
if (free_cpp) {
|
1429
|
+
SEXP ind_R_ptr = R_altrep_data1(lst_indexer);
|
1430
|
+
TreesIndexer* indexer_ptr = (TreesIndexer*)R_ExternalPtrAddr(ind_R_ptr);
|
1431
|
+
delete indexer_ptr;
|
1432
|
+
R_SetExternalPtrAddr(ind_R_ptr, nullptr);
|
1433
|
+
R_ClearExternalPtr(ind_R_ptr);
|
1434
|
+
}
|
1435
|
+
|
1436
|
+
lst_cpp_objects["indexer"] = altrepped_null;
|
1437
|
+
}
|
1438
|
+
|
1439
|
+
else {
|
1440
|
+
|
1441
|
+
if (free_cpp) {
|
1442
|
+
SEXP ind_R_ptr = VECTOR_ELT(lst_indexer, 0);
|
1443
|
+
TreesIndexer* indexer_ptr = get_pointer_from_xptr<TreesIndexer>(ind_R_ptr);
|
1444
|
+
delete indexer_ptr;
|
1445
|
+
R_SetExternalPtrAddr(ind_R_ptr, nullptr);
|
1446
|
+
R_ClearExternalPtr(ind_R_ptr);
|
1447
|
+
SET_VECTOR_ELT(lst_indexer, 0, ind_R_ptr);
|
1448
|
+
}
|
1449
|
+
|
1450
|
+
SET_VECTOR_ELT(lst_indexer, 0, blank_ptr);
|
1451
|
+
SET_VECTOR_ELT(lst_indexer, 1, R_NilValue);
|
1452
|
+
}
|
1086
1453
|
|
1087
|
-
|
1088
|
-
|
1454
|
+
lst_metadata["reference_names"] = empty_str;
|
1455
|
+
UNPROTECT(3);
|
1089
1456
|
}
|
1090
1457
|
|
1091
1458
|
// [[Rcpp::export(rng = false)]]
|
1092
|
-
void drop_reference_points(Rcpp::List
|
1459
|
+
void drop_reference_points(bool is_altrepped, SEXP lst_indexer, Rcpp::List lst_cpp_objects, Rcpp::List lst_metadata)
|
1093
1460
|
{
|
1094
|
-
|
1095
|
-
|
1096
|
-
|
1097
|
-
|
1098
|
-
|
1099
|
-
|
1100
|
-
|
1101
|
-
|
1102
|
-
|
1103
|
-
|
1104
|
-
|
1105
|
-
|
1106
|
-
|
1107
|
-
|
1108
|
-
}
|
1109
|
-
if (indexer_ptr->indices.front().reference_points.empty()) {
|
1110
|
-
lst_modify2["reference_names"] = empty_char;
|
1111
|
-
return;
|
1461
|
+
SEXP empty_str = PROTECT(Rf_allocVector(STRSXP, 0));
|
1462
|
+
|
1463
|
+
if (is_altrepped)
|
1464
|
+
{
|
1465
|
+
SEXP ind_R_ptr = R_altrep_data1(lst_indexer);
|
1466
|
+
TreesIndexer* indexer_ptr = (TreesIndexer*)R_ExternalPtrAddr(ind_R_ptr);
|
1467
|
+
if (!indexer_ptr) return;
|
1468
|
+
|
1469
|
+
for (auto &tree : indexer_ptr->indices)
|
1470
|
+
{
|
1471
|
+
tree.reference_points.clear();
|
1472
|
+
tree.reference_indptr.clear();
|
1473
|
+
tree.reference_mapping.clear();
|
1474
|
+
}
|
1112
1475
|
}
|
1113
1476
|
|
1114
|
-
|
1115
|
-
for (auto &tree : new_indexer->indices)
|
1477
|
+
else
|
1116
1478
|
{
|
1117
|
-
|
1118
|
-
|
1119
|
-
|
1479
|
+
SEXP ind_R_ptr = VECTOR_ELT(lst_indexer, 0);
|
1480
|
+
TreesIndexer* indexer_ptr = get_pointer_from_xptr<TreesIndexer>(ind_R_ptr);
|
1481
|
+
if (!indexer_ptr) return;
|
1482
|
+
|
1483
|
+
std::unique_ptr<TreesIndexer> new_indexer(new TreesIndexer(*indexer_ptr));
|
1484
|
+
for (auto &tree : new_indexer->indices)
|
1485
|
+
{
|
1486
|
+
tree.reference_points.clear();
|
1487
|
+
tree.reference_indptr.clear();
|
1488
|
+
tree.reference_mapping.clear();
|
1489
|
+
}
|
1490
|
+
|
1491
|
+
SET_VECTOR_ELT(lst_indexer, 1, serialize_cpp_obj(new_indexer.get()));
|
1492
|
+
*indexer_ptr = std::move(*new_indexer);
|
1493
|
+
new_indexer.release();
|
1120
1494
|
}
|
1121
|
-
|
1122
|
-
|
1123
|
-
|
1124
|
-
lst_modify["ind_ser"] = ind_ser;
|
1125
|
-
lst_modify2["reference_names"] = empty_char;
|
1495
|
+
|
1496
|
+
lst_metadata["reference_names"] = empty_str;
|
1497
|
+
UNPROTECT(1);
|
1126
1498
|
}
|
1127
1499
|
|
1128
1500
|
// [[Rcpp::export(rng = false)]]
|
1129
1501
|
Rcpp::List subset_trees
|
1130
1502
|
(
|
1131
1503
|
SEXP model_R_ptr, SEXP imputer_R_ptr, SEXP indexer_R_ptr,
|
1132
|
-
bool is_extended, bool
|
1504
|
+
bool is_extended, bool is_altrepped,
|
1133
1505
|
Rcpp::IntegerVector trees_take
|
1134
1506
|
)
|
1135
1507
|
{
|
1136
|
-
bool has_indexer = !Rf_isNull(indexer_R_ptr) && R_ExternalPtrAddr(indexer_R_ptr) != NULL;
|
1137
|
-
|
1138
1508
|
Rcpp::List out = Rcpp::List::create(
|
1509
|
+
Rcpp::_["model"] = R_NilValue,
|
1510
|
+
Rcpp::_["imputer"] = R_NilValue,
|
1511
|
+
Rcpp::_["indexer"] = R_NilValue
|
1512
|
+
);
|
1513
|
+
Rcpp::List lst_model = Rcpp::List::create(
|
1139
1514
|
Rcpp::_["ptr"] = R_NilValue,
|
1140
|
-
Rcpp::_["
|
1141
|
-
|
1142
|
-
|
1143
|
-
Rcpp::_["
|
1144
|
-
Rcpp::_["
|
1515
|
+
Rcpp::_["ser"] = R_NilValue
|
1516
|
+
);
|
1517
|
+
Rcpp::List lst_imputer = Rcpp::List::create(
|
1518
|
+
Rcpp::_["ptr"] = Rcpp::XPtr<void*>(nullptr, false),
|
1519
|
+
Rcpp::_["ser"] = R_NilValue
|
1145
1520
|
);
|
1521
|
+
Rcpp::List lst_indexer = Rcpp::List::create(
|
1522
|
+
Rcpp::_["ptr"] = Rcpp::XPtr<void*>(nullptr, false),
|
1523
|
+
Rcpp::_["ser"] = R_NilValue
|
1524
|
+
);
|
1525
|
+
|
1146
1526
|
|
1147
1527
|
IsoForest* model_ptr = NULL;
|
1148
1528
|
ExtIsoForest* ext_model_ptr = NULL;
|
@@ -1161,16 +1541,15 @@ Rcpp::List subset_trees
|
|
1161
1541
|
model_ptr = static_cast<IsoForest*>(R_ExternalPtrAddr(model_R_ptr));
|
1162
1542
|
new_model_ptr = std::unique_ptr<IsoForest>(new IsoForest());
|
1163
1543
|
}
|
1164
|
-
|
1165
1544
|
|
1166
|
-
|
1167
|
-
|
1168
|
-
new_imputer_ptr
|
1545
|
+
imputer_ptr = static_cast<Imputer*>(R_ExternalPtrAddr(imputer_R_ptr));
|
1546
|
+
if (imputer_ptr) {
|
1547
|
+
new_imputer_ptr = std::unique_ptr<Imputer>(new Imputer());
|
1169
1548
|
}
|
1170
1549
|
|
1171
|
-
|
1172
|
-
|
1173
|
-
new_indexer_ptr
|
1550
|
+
indexer_ptr = static_cast<TreesIndexer*>(R_ExternalPtrAddr(indexer_R_ptr));
|
1551
|
+
if (indexer_ptr) {
|
1552
|
+
new_indexer_ptr = std::unique_ptr<TreesIndexer>(new TreesIndexer());
|
1174
1553
|
}
|
1175
1554
|
|
1176
1555
|
std::unique_ptr<size_t[]> trees_take_(new size_t[trees_take.size()]);
|
@@ -1184,31 +1563,49 @@ Rcpp::List subset_trees
|
|
1184
1563
|
trees_take_.get(), trees_take.size());
|
1185
1564
|
trees_take_.reset();
|
1186
1565
|
|
1187
|
-
if (
|
1188
|
-
|
1566
|
+
if (is_altrepped)
|
1567
|
+
{
|
1568
|
+
out["model"] = is_extended?
|
1569
|
+
Rcpp::unwindProtect(get_altrepped_pointer<ExtIsoForest>, (void*)&new_ext_model_ptr)
|
1570
|
+
:
|
1571
|
+
Rcpp::unwindProtect(get_altrepped_pointer<IsoForest>, (void*)&new_model_ptr);
|
1572
|
+
out["imputer"] = imputer_ptr?
|
1573
|
+
Rcpp::unwindProtect(get_altrepped_pointer<Imputer>, (void*)&new_imputer_ptr)
|
1574
|
+
:
|
1575
|
+
Rcpp::unwindProtect(safe_get_altrepped_null_pointer, nullptr);
|
1576
|
+
out["indexer"] = indexer_ptr?
|
1577
|
+
Rcpp::unwindProtect(get_altrepped_pointer<TreesIndexer>, (void*)&new_indexer_ptr)
|
1578
|
+
:
|
1579
|
+
Rcpp::unwindProtect(safe_get_altrepped_null_pointer, nullptr);
|
1580
|
+
}
|
1581
|
+
|
1189
1582
|
else
|
1190
|
-
|
1191
|
-
|
1192
|
-
|
1193
|
-
|
1194
|
-
out["ind_ser"] = serialize_cpp_obj(new_indexer_ptr.get());
|
1583
|
+
{
|
1584
|
+
lst_model["ser"] = is_extended? serialize_cpp_obj(new_ext_model_ptr.get()) : serialize_cpp_obj(new_model_ptr.get());
|
1585
|
+
if (imputer_ptr) lst_imputer["ser"] = serialize_cpp_obj(new_imputer_ptr.get());
|
1586
|
+
if (indexer_ptr) lst_indexer["ser"] = serialize_cpp_obj(new_indexer_ptr.get());
|
1195
1587
|
|
1196
|
-
|
1197
|
-
|
1588
|
+
lst_model["ptr"] = is_extended?
|
1589
|
+
Rcpp::unwindProtect(safe_XPtr<ExtIsoForest>, new_ext_model_ptr.get())
|
1590
|
+
:
|
1591
|
+
Rcpp::unwindProtect(safe_XPtr<IsoForest>, new_model_ptr.get());
|
1198
1592
|
new_model_ptr.release();
|
1593
|
+
|
1594
|
+
if (imputer_ptr) {
|
1595
|
+
lst_imputer["ptr"] = Rcpp::unwindProtect(safe_XPtr<Imputer>, new_imputer_ptr.get());
|
1596
|
+
new_imputer_ptr.release();
|
1597
|
+
}
|
1598
|
+
|
1599
|
+
if (indexer_ptr) {
|
1600
|
+
lst_indexer["ptr"] = Rcpp::unwindProtect(safe_XPtr<TreesIndexer>, new_indexer_ptr.get());
|
1601
|
+
new_indexer_ptr.release();
|
1602
|
+
}
|
1603
|
+
|
1604
|
+
out["model"] = lst_model;
|
1605
|
+
out["imputer"] = lst_imputer;
|
1606
|
+
out["indexer"] = lst_indexer;
|
1199
1607
|
}
|
1200
|
-
|
1201
|
-
out["ptr"] = Rcpp::unwindProtect(safe_XPtr<ExtIsoForest>, new_ext_model_ptr.get());
|
1202
|
-
new_ext_model_ptr.release();
|
1203
|
-
}
|
1204
|
-
if (has_imputer) {
|
1205
|
-
out["imp_ptr"] = Rcpp::unwindProtect(safe_XPtr<Imputer>, new_imputer_ptr.get());
|
1206
|
-
new_imputer_ptr.release();
|
1207
|
-
}
|
1208
|
-
if (has_indexer) {
|
1209
|
-
out["indexer"] = Rcpp::unwindProtect(safe_XPtr<TreesIndexer>, new_indexer_ptr.get());
|
1210
|
-
new_indexer_ptr.release();
|
1211
|
-
}
|
1608
|
+
|
1212
1609
|
return out;
|
1213
1610
|
}
|
1214
1611
|
|
@@ -1251,12 +1648,12 @@ Rcpp::List get_n_nodes(SEXP model_R_ptr, bool is_extended, int nthreads)
|
|
1251
1648
|
ExtIsoForest* ext_model_ptr = NULL;
|
1252
1649
|
if (is_extended)
|
1253
1650
|
{
|
1254
|
-
ext_model_ptr =
|
1651
|
+
ext_model_ptr = get_pointer_from_xptr<ExtIsoForest>(model_R_ptr);
|
1255
1652
|
ntrees = ext_model_ptr->hplanes.size();
|
1256
1653
|
}
|
1257
1654
|
else
|
1258
1655
|
{
|
1259
|
-
model_ptr =
|
1656
|
+
model_ptr = get_pointer_from_xptr<IsoForest>(model_R_ptr);
|
1260
1657
|
ntrees = model_ptr->trees.size();
|
1261
1658
|
}
|
1262
1659
|
|
@@ -1282,65 +1679,52 @@ void append_trees_from_other(SEXP model_R_ptr, SEXP other_R_ptr,
|
|
1282
1679
|
Rcpp::RawVector serialized_imputer,
|
1283
1680
|
Rcpp::RawVector serialized_indexer,
|
1284
1681
|
Rcpp::List &model_cpp_obj_update,
|
1285
|
-
Rcpp::List &model_params_update
|
1682
|
+
Rcpp::List &model_params_update,
|
1683
|
+
bool is_altrepped)
|
1286
1684
|
{
|
1287
|
-
if ((!Rf_isNull(imp_R_ptr) && R_ExternalPtrAddr(imp_R_ptr) != NULL)
|
1288
|
-
&&
|
1289
|
-
!(!Rf_isNull(oimp_R_ptr) && R_ExternalPtrAddr(oimp_R_ptr) != NULL))
|
1290
|
-
{
|
1291
|
-
Rcpp::stop("Model to append trees to has imputer, but model to append from doesn't. Try dropping the imputer.\n");
|
1292
|
-
}
|
1293
|
-
if ((!Rf_isNull(ind_R_ptr) && R_ExternalPtrAddr(ind_R_ptr) != NULL)
|
1294
|
-
&&
|
1295
|
-
!(!Rf_isNull(oind_R_ptr) && R_ExternalPtrAddr(oind_R_ptr) != NULL))
|
1296
|
-
{
|
1297
|
-
Rcpp::stop("Model to append trees to has indexer, but model to append from doesn't. Try dropping the indexer.\n");
|
1298
|
-
}
|
1299
|
-
|
1300
1685
|
Rcpp::List out = Rcpp::List::create(
|
1301
|
-
Rcpp::_["
|
1302
|
-
Rcpp::_["
|
1303
|
-
Rcpp::_["
|
1686
|
+
Rcpp::_["model_ser"] = R_NilValue,
|
1687
|
+
Rcpp::_["imputer_ser"] = R_NilValue,
|
1688
|
+
Rcpp::_["indexer_ser"] = R_NilValue
|
1304
1689
|
);
|
1305
1690
|
|
1306
1691
|
Rcpp::IntegerVector ntrees_new = Rcpp::IntegerVector::create(Rf_asInteger(model_params_update["ntrees"]));
|
1307
1692
|
|
1308
|
-
IsoForest* model_ptr =
|
1309
|
-
IsoForest* other_ptr =
|
1310
|
-
ExtIsoForest* ext_model_ptr =
|
1311
|
-
ExtIsoForest* ext_other_ptr =
|
1312
|
-
Imputer* imputer_ptr =
|
1313
|
-
Imputer* oimputer_ptr =
|
1314
|
-
TreesIndexer* indexer_ptr =
|
1315
|
-
TreesIndexer* oindexer_ptr =
|
1693
|
+
IsoForest* model_ptr = nullptr;
|
1694
|
+
IsoForest* other_ptr = nullptr;
|
1695
|
+
ExtIsoForest* ext_model_ptr = nullptr;
|
1696
|
+
ExtIsoForest* ext_other_ptr = nullptr;
|
1697
|
+
Imputer* imputer_ptr = static_cast<Imputer*>(R_ExternalPtrAddr(imp_R_ptr));
|
1698
|
+
Imputer* oimputer_ptr = static_cast<Imputer*>(R_ExternalPtrAddr(oimp_R_ptr));
|
1699
|
+
TreesIndexer* indexer_ptr = get_indexer_ptr_from_R_obj(ind_R_ptr);
|
1700
|
+
TreesIndexer* oindexer_ptr = get_indexer_ptr_from_R_obj(oind_R_ptr);
|
1316
1701
|
size_t old_ntrees;
|
1317
1702
|
|
1318
1703
|
if (is_extended) {
|
1319
1704
|
ext_model_ptr = static_cast<ExtIsoForest*>(R_ExternalPtrAddr(model_R_ptr));
|
1320
1705
|
ext_other_ptr = static_cast<ExtIsoForest*>(R_ExternalPtrAddr(other_R_ptr));
|
1321
1706
|
old_ntrees = ext_model_ptr->hplanes.size();
|
1707
|
+
if (ext_model_ptr == ext_other_ptr) {
|
1708
|
+
throw Rcpp::exception("Error: attempting to append trees from one model to itself.");
|
1709
|
+
}
|
1322
1710
|
} else {
|
1323
1711
|
model_ptr = static_cast<IsoForest*>(R_ExternalPtrAddr(model_R_ptr));
|
1324
1712
|
other_ptr = static_cast<IsoForest*>(R_ExternalPtrAddr(other_R_ptr));
|
1325
1713
|
old_ntrees = model_ptr->trees.size();
|
1714
|
+
if (model_ptr == other_ptr) {
|
1715
|
+
throw Rcpp::exception("Error: attempting to append trees from one model to itself.");
|
1716
|
+
}
|
1326
1717
|
}
|
1327
1718
|
|
1328
|
-
if (
|
1329
|
-
|
1330
|
-
R_ExternalPtrAddr(oimp_R_ptr) != NULL)
|
1331
|
-
{
|
1332
|
-
imputer_ptr = static_cast<Imputer*>(R_ExternalPtrAddr(imp_R_ptr));
|
1333
|
-
oimputer_ptr = static_cast<Imputer*>(R_ExternalPtrAddr(oimp_R_ptr));
|
1719
|
+
if (imputer_ptr && !oimputer_ptr) {
|
1720
|
+
throw Rcpp::exception("Model to append trees to has imputer, but model to append from doesn't. Try dropping the imputer.\n");
|
1334
1721
|
}
|
1335
1722
|
|
1336
|
-
if (
|
1337
|
-
|
1338
|
-
R_ExternalPtrAddr(oind_R_ptr) != NULL)
|
1339
|
-
{
|
1340
|
-
indexer_ptr = static_cast<TreesIndexer*>(R_ExternalPtrAddr(ind_R_ptr));
|
1341
|
-
oindexer_ptr = static_cast<TreesIndexer*>(R_ExternalPtrAddr(oind_R_ptr));
|
1723
|
+
if (indexer_ptr && !oindexer_ptr) {
|
1724
|
+
throw Rcpp::exception("Model to append trees to has indexer, but model to append from doesn't. Try dropping the indexer.\n");
|
1342
1725
|
}
|
1343
1726
|
|
1727
|
+
|
1344
1728
|
merge_models(model_ptr, other_ptr,
|
1345
1729
|
ext_model_ptr, ext_other_ptr,
|
1346
1730
|
imputer_ptr, oimputer_ptr,
|
@@ -1348,6 +1732,9 @@ void append_trees_from_other(SEXP model_R_ptr, SEXP other_R_ptr,
|
|
1348
1732
|
|
1349
1733
|
Rcpp::RawVector new_serialized, new_imp_serialized, new_ind_serialized;
|
1350
1734
|
size_t new_size;
|
1735
|
+
|
1736
|
+
if (is_altrepped) goto dont_serialize;
|
1737
|
+
|
1351
1738
|
try
|
1352
1739
|
{
|
1353
1740
|
if (!is_extended)
|
@@ -1361,7 +1748,7 @@ void append_trees_from_other(SEXP model_R_ptr, SEXP other_R_ptr,
|
|
1361
1748
|
new_serialized = resize_vec(serialized_obj, new_size);
|
1362
1749
|
char *temp = (char*)RAW(new_serialized);
|
1363
1750
|
incremental_serialize_isotree(*model_ptr, temp);
|
1364
|
-
out["
|
1751
|
+
out["model_ser"] = new_serialized;
|
1365
1752
|
}
|
1366
1753
|
|
1367
1754
|
catch (std::runtime_error &e) {
|
@@ -1371,7 +1758,7 @@ void append_trees_from_other(SEXP model_R_ptr, SEXP other_R_ptr,
|
|
1371
1758
|
|
1372
1759
|
else {
|
1373
1760
|
serialize_anew_singlevar:
|
1374
|
-
out["
|
1761
|
+
out["model_ser"] = serialize_cpp_obj(model_ptr);
|
1375
1762
|
}
|
1376
1763
|
}
|
1377
1764
|
|
@@ -1386,7 +1773,7 @@ void append_trees_from_other(SEXP model_R_ptr, SEXP other_R_ptr,
|
|
1386
1773
|
new_serialized = resize_vec(serialized_obj, new_size);
|
1387
1774
|
char *temp = (char*)RAW(new_serialized);
|
1388
1775
|
incremental_serialize_isotree(*ext_model_ptr, temp);
|
1389
|
-
out["
|
1776
|
+
out["model_ser"] = new_serialized;
|
1390
1777
|
}
|
1391
1778
|
|
1392
1779
|
catch (std::runtime_error &e) {
|
@@ -1396,11 +1783,11 @@ void append_trees_from_other(SEXP model_R_ptr, SEXP other_R_ptr,
|
|
1396
1783
|
|
1397
1784
|
else {
|
1398
1785
|
serialize_anew_ext:
|
1399
|
-
out["
|
1786
|
+
out["model_ser"] = serialize_cpp_obj(ext_model_ptr);
|
1400
1787
|
}
|
1401
1788
|
}
|
1402
1789
|
|
1403
|
-
if (imputer_ptr
|
1790
|
+
if (imputer_ptr)
|
1404
1791
|
{
|
1405
1792
|
if (serialized_imputer.size() &&
|
1406
1793
|
check_can_undergo_incremental_serialization(*imputer_ptr, (char*)RAW(serialized_imputer)))
|
@@ -1411,7 +1798,7 @@ void append_trees_from_other(SEXP model_R_ptr, SEXP other_R_ptr,
|
|
1411
1798
|
new_imp_serialized = resize_vec(serialized_imputer, new_size);
|
1412
1799
|
char *temp = (char*)RAW(new_imp_serialized);
|
1413
1800
|
incremental_serialize_isotree(*imputer_ptr, temp);
|
1414
|
-
out["
|
1801
|
+
out["imputer_ser"] = new_imp_serialized;
|
1415
1802
|
}
|
1416
1803
|
|
1417
1804
|
catch (std::runtime_error &e) {
|
@@ -1421,11 +1808,11 @@ void append_trees_from_other(SEXP model_R_ptr, SEXP other_R_ptr,
|
|
1421
1808
|
|
1422
1809
|
else {
|
1423
1810
|
serialize_anew_imp:
|
1424
|
-
out["
|
1811
|
+
out["imputer_ser"] = serialize_cpp_obj(imputer_ptr);
|
1425
1812
|
}
|
1426
1813
|
}
|
1427
1814
|
|
1428
|
-
if (indexer_ptr
|
1815
|
+
if (indexer_ptr)
|
1429
1816
|
{
|
1430
1817
|
if (serialized_indexer.size() &&
|
1431
1818
|
check_can_undergo_incremental_serialization(*indexer_ptr, (char*)RAW(serialized_indexer)))
|
@@ -1436,7 +1823,7 @@ void append_trees_from_other(SEXP model_R_ptr, SEXP other_R_ptr,
|
|
1436
1823
|
new_ind_serialized = resize_vec(serialized_indexer, new_size);
|
1437
1824
|
char *temp = (char*)RAW(new_ind_serialized);
|
1438
1825
|
incremental_serialize_isotree(*indexer_ptr, temp);
|
1439
|
-
out["
|
1826
|
+
out["indexer_ser"] = new_ind_serialized;
|
1440
1827
|
}
|
1441
1828
|
|
1442
1829
|
catch (std::runtime_error &e) {
|
@@ -1446,7 +1833,7 @@ void append_trees_from_other(SEXP model_R_ptr, SEXP other_R_ptr,
|
|
1446
1833
|
|
1447
1834
|
else {
|
1448
1835
|
serialize_anew_ind:
|
1449
|
-
out["
|
1836
|
+
out["indexer_ser"] = serialize_cpp_obj(indexer_ptr);
|
1450
1837
|
}
|
1451
1838
|
}
|
1452
1839
|
}
|
@@ -1458,18 +1845,34 @@ void append_trees_from_other(SEXP model_R_ptr, SEXP other_R_ptr,
|
|
1458
1845
|
else
|
1459
1846
|
ext_model_ptr->hplanes.resize(old_ntrees);
|
1460
1847
|
|
1461
|
-
if (imputer_ptr
|
1848
|
+
if (imputer_ptr)
|
1462
1849
|
imputer_ptr->imputer_tree.resize(old_ntrees);
|
1463
|
-
if (indexer_ptr
|
1850
|
+
if (indexer_ptr)
|
1464
1851
|
indexer_ptr->indices.resize(old_ntrees);
|
1465
1852
|
throw;
|
1466
1853
|
}
|
1467
1854
|
|
1468
|
-
|
1469
|
-
|
1470
|
-
|
1471
|
-
|
1472
|
-
|
1855
|
+
{
|
1856
|
+
Rcpp::List model_lst = model_cpp_obj_update["model"];
|
1857
|
+
model_lst["ser"] = out["model_ser"];
|
1858
|
+
model_cpp_obj_update["model"] = model_lst;
|
1859
|
+
|
1860
|
+
if (imputer_ptr)
|
1861
|
+
{
|
1862
|
+
Rcpp::List imputer_lst = model_cpp_obj_update["imputer"];
|
1863
|
+
imputer_lst["ser"] = out["imputer_ser"];
|
1864
|
+
model_cpp_obj_update["imputer"] = imputer_lst;
|
1865
|
+
}
|
1866
|
+
|
1867
|
+
if (indexer_ptr)
|
1868
|
+
{
|
1869
|
+
Rcpp::List indexer_lst = model_cpp_obj_update["indexer"];
|
1870
|
+
indexer_lst["ser"] = out["indexer_ser"];
|
1871
|
+
model_cpp_obj_update["indexer"] = indexer_lst;
|
1872
|
+
}
|
1873
|
+
}
|
1874
|
+
|
1875
|
+
dont_serialize:
|
1473
1876
|
*(INTEGER(ntrees_new)) = is_extended? ext_model_ptr->hplanes.size() : model_ptr->trees.size();
|
1474
1877
|
model_params_update["ntrees"] = ntrees_new;
|
1475
1878
|
}
|
@@ -1551,14 +1954,12 @@ Rcpp::CharacterVector model_to_sql_with_select_from(SEXP model_R_ptr, bool is_ex
|
|
1551
1954
|
}
|
1552
1955
|
|
1553
1956
|
// [[Rcpp::export(rng = false)]]
|
1554
|
-
Rcpp::List copy_cpp_objects(SEXP model_R_ptr, bool is_extended, SEXP imp_R_ptr,
|
1957
|
+
Rcpp::List copy_cpp_objects(SEXP model_R_ptr, bool is_extended, SEXP imp_R_ptr, SEXP ind_R_ptr, bool lazy_serialization)
|
1555
1958
|
{
|
1556
|
-
bool has_indexer = !Rf_isNull(ind_R_ptr) && R_ExternalPtrAddr(ind_R_ptr) != NULL;
|
1557
|
-
|
1558
1959
|
Rcpp::List out = Rcpp::List::create(
|
1559
|
-
Rcpp::_["
|
1560
|
-
Rcpp::_["
|
1561
|
-
Rcpp::_["indexer"] =
|
1960
|
+
Rcpp::_["model"] = Rcpp::XPtr<void*>(nullptr, false),
|
1961
|
+
Rcpp::_["imputer"] = Rcpp::XPtr<void*>(nullptr, false),
|
1962
|
+
Rcpp::_["indexer"] = Rcpp::XPtr<void*>(nullptr, false)
|
1562
1963
|
);
|
1563
1964
|
|
1564
1965
|
IsoForest* model_ptr = NULL;
|
@@ -1569,9 +1970,9 @@ Rcpp::List copy_cpp_objects(SEXP model_R_ptr, bool is_extended, SEXP imp_R_ptr,
|
|
1569
1970
|
ext_model_ptr = static_cast<ExtIsoForest*>(R_ExternalPtrAddr(model_R_ptr));
|
1570
1971
|
else
|
1571
1972
|
model_ptr = static_cast<IsoForest*>(R_ExternalPtrAddr(model_R_ptr));
|
1572
|
-
if (
|
1973
|
+
if (R_ExternalPtrAddr(imp_R_ptr))
|
1573
1974
|
imputer_ptr = static_cast<Imputer*>(R_ExternalPtrAddr(imp_R_ptr));
|
1574
|
-
if (
|
1975
|
+
if (R_ExternalPtrAddr(ind_R_ptr))
|
1575
1976
|
indexer_ptr = static_cast<TreesIndexer*>(R_ExternalPtrAddr(ind_R_ptr));
|
1576
1977
|
|
1577
1978
|
std::unique_ptr<IsoForest> copy_model(new IsoForest());
|
@@ -1579,84 +1980,115 @@ Rcpp::List copy_cpp_objects(SEXP model_R_ptr, bool is_extended, SEXP imp_R_ptr,
|
|
1579
1980
|
std::unique_ptr<Imputer> copy_imputer(new Imputer());
|
1580
1981
|
std::unique_ptr<TreesIndexer> copy_indexer(new TreesIndexer());
|
1581
1982
|
|
1582
|
-
if (model_ptr
|
1983
|
+
if (model_ptr)
|
1583
1984
|
*copy_model = *model_ptr;
|
1584
|
-
if (ext_model_ptr
|
1985
|
+
if (ext_model_ptr)
|
1585
1986
|
*copy_ext_model = *ext_model_ptr;
|
1586
|
-
if (imputer_ptr
|
1987
|
+
if (imputer_ptr)
|
1587
1988
|
*copy_imputer = *imputer_ptr;
|
1588
|
-
if (indexer_ptr
|
1989
|
+
if (indexer_ptr)
|
1589
1990
|
*copy_indexer = *indexer_ptr;
|
1590
1991
|
|
1591
|
-
if (
|
1592
|
-
|
1593
|
-
|
1594
|
-
|
1595
|
-
|
1596
|
-
|
1597
|
-
|
1598
|
-
|
1599
|
-
|
1600
|
-
|
1601
|
-
|
1992
|
+
if (lazy_serialization)
|
1993
|
+
{
|
1994
|
+
if (is_extended) {
|
1995
|
+
out["model"] = Rcpp::unwindProtect(get_altrepped_pointer<ExtIsoForest>, (void*)©_ext_model);
|
1996
|
+
}
|
1997
|
+
else {
|
1998
|
+
out["model"] = Rcpp::unwindProtect(get_altrepped_pointer<IsoForest>, (void*)©_model);
|
1999
|
+
}
|
2000
|
+
|
2001
|
+
if (imputer_ptr) {
|
2002
|
+
out["imputer"] = Rcpp::unwindProtect(get_altrepped_pointer<Imputer>, (void*)©_imputer);
|
2003
|
+
}
|
2004
|
+
else {
|
2005
|
+
out["imputer"] = Rcpp::unwindProtect(safe_get_altrepped_null_pointer, nullptr);
|
2006
|
+
}
|
2007
|
+
|
2008
|
+
if (indexer_ptr) {
|
2009
|
+
out["indexer"] = Rcpp::unwindProtect(get_altrepped_pointer<TreesIndexer>, (void*)©_indexer);
|
2010
|
+
}
|
2011
|
+
else {
|
2012
|
+
out["indexer"] = Rcpp::unwindProtect(safe_get_altrepped_null_pointer, nullptr);
|
2013
|
+
}
|
1602
2014
|
}
|
1603
|
-
|
1604
|
-
|
1605
|
-
|
2015
|
+
|
2016
|
+
else
|
2017
|
+
{
|
2018
|
+
if (is_extended) {
|
2019
|
+
out["model"] = Rcpp::unwindProtect(safe_XPtr<ExtIsoForest>, copy_ext_model.get());
|
2020
|
+
copy_ext_model.release();
|
2021
|
+
}
|
2022
|
+
else {
|
2023
|
+
out["model"] = Rcpp::unwindProtect(safe_XPtr<IsoForest>, copy_model.get());
|
2024
|
+
copy_model.release();
|
2025
|
+
}
|
2026
|
+
if (imputer_ptr) {
|
2027
|
+
out["imputer"] = Rcpp::unwindProtect(safe_XPtr<Imputer>, copy_imputer.get());
|
2028
|
+
copy_imputer.release();
|
2029
|
+
}
|
2030
|
+
if (indexer_ptr) {
|
2031
|
+
out["indexer"] = Rcpp::unwindProtect(safe_XPtr<TreesIndexer>, copy_indexer.get());
|
2032
|
+
copy_indexer.release();
|
2033
|
+
}
|
1606
2034
|
}
|
2035
|
+
|
1607
2036
|
return out;
|
1608
2037
|
}
|
1609
2038
|
|
1610
2039
|
// [[Rcpp::export(rng = false)]]
|
1611
|
-
void build_tree_indices(Rcpp::List
|
2040
|
+
void build_tree_indices(Rcpp::List lst_cpp_objects, SEXP ptr_model, bool is_altrepped, bool is_extended, bool with_distances, int nthreads)
|
1612
2041
|
{
|
1613
|
-
Rcpp::
|
1614
|
-
|
2042
|
+
Rcpp::List lst_out = Rcpp::List::create(
|
2043
|
+
Rcpp::_["ptr"] = R_NilValue,
|
2044
|
+
Rcpp::_["ser"] = R_NilValue
|
2045
|
+
);
|
1615
2046
|
std::unique_ptr<TreesIndexer> indexer(new TreesIndexer());
|
1616
2047
|
|
1617
2048
|
if (!is_extended) {
|
1618
2049
|
build_tree_indices(*indexer,
|
1619
|
-
*static_cast<IsoForest*>(R_ExternalPtrAddr(
|
2050
|
+
*static_cast<IsoForest*>(R_ExternalPtrAddr(ptr_model)),
|
1620
2051
|
nthreads,
|
1621
2052
|
with_distances);
|
1622
2053
|
}
|
1623
2054
|
else {
|
1624
2055
|
build_tree_indices(*indexer,
|
1625
|
-
*static_cast<ExtIsoForest*>(R_ExternalPtrAddr(
|
2056
|
+
*static_cast<ExtIsoForest*>(R_ExternalPtrAddr(ptr_model)),
|
1626
2057
|
nthreads,
|
1627
2058
|
with_distances);
|
1628
2059
|
}
|
1629
2060
|
|
1630
|
-
|
1631
|
-
|
1632
|
-
|
1633
|
-
|
1634
|
-
|
2061
|
+
if (is_altrepped) {
|
2062
|
+
lst_cpp_objects["indexer"] = Rcpp::unwindProtect(get_altrepped_pointer<TreesIndexer>, (void*)&indexer);
|
2063
|
+
}
|
2064
|
+
|
2065
|
+
else {
|
2066
|
+
lst_out["ser"] = serialize_cpp_obj(indexer.get());
|
2067
|
+
lst_out["ptr"] = Rcpp::unwindProtect(safe_XPtr<TreesIndexer>, indexer.get());
|
2068
|
+
indexer.release();
|
2069
|
+
lst_cpp_objects["indexer"] = lst_out;
|
1635
2070
|
}
|
1636
|
-
|
1637
|
-
lst_modify["ind_ser"] = ind_ser;
|
1638
|
-
lst_modify["indexer"] = empty_lst["indexer"];
|
1639
|
-
indexer.release();
|
1640
2071
|
}
|
1641
2072
|
|
1642
2073
|
// [[Rcpp::export(rng = false)]]
|
1643
2074
|
bool check_node_indexer_has_distances(SEXP indexer_R_ptr)
|
1644
2075
|
{
|
1645
|
-
|
1646
|
-
|
1647
|
-
TreesIndexer *indexer = static_cast<TreesIndexer*>(R_ExternalPtrAddr(indexer_R_ptr));
|
1648
|
-
if (indexer->indices.empty()) return false;
|
2076
|
+
const TreesIndexer *indexer = (const TreesIndexer*)R_ExternalPtrAddr(indexer_R_ptr);
|
2077
|
+
if (!indexer) return false;
|
1649
2078
|
return !indexer->indices.front().node_distances.empty();
|
1650
2079
|
}
|
1651
2080
|
|
1652
2081
|
// [[Rcpp::export(rng = false)]]
|
1653
|
-
void set_reference_points(Rcpp::List
|
2082
|
+
void set_reference_points(Rcpp::List lst_cpp_objects, SEXP ptr_model, SEXP ind_R_ptr, bool is_altrepped,
|
2083
|
+
Rcpp::List lst_metadata, SEXP rnames, bool is_extended,
|
1654
2084
|
Rcpp::NumericVector X_num, Rcpp::IntegerVector X_cat,
|
1655
2085
|
Rcpp::NumericVector Xc, Rcpp::IntegerVector Xc_ind, Rcpp::IntegerVector Xc_indptr,
|
1656
2086
|
size_t nrows, int nthreads, bool with_distances)
|
1657
2087
|
{
|
1658
|
-
Rcpp::
|
1659
|
-
|
2088
|
+
Rcpp::List lst_out = Rcpp::List::create(
|
2089
|
+
Rcpp::_["ptr"] = R_NilValue,
|
2090
|
+
Rcpp::_["ser"] = R_NilValue
|
2091
|
+
);
|
1660
2092
|
|
1661
2093
|
double* numeric_data_ptr = NULL;
|
1662
2094
|
int* categ_data_ptr = NULL;
|
@@ -1682,14 +2114,13 @@ void set_reference_points(Rcpp::List lst_modify, Rcpp::List lst_modify2, SEXP rn
|
|
1682
2114
|
Xc_indptr_ptr = INTEGER(Xc_indptr);
|
1683
2115
|
}
|
1684
2116
|
|
1685
|
-
IsoForest* model_ptr =
|
1686
|
-
ExtIsoForest* ext_model_ptr =
|
1687
|
-
TreesIndexer* indexer =
|
2117
|
+
IsoForest* model_ptr = nullptr;
|
2118
|
+
ExtIsoForest* ext_model_ptr = nullptr;
|
2119
|
+
TreesIndexer* indexer = static_cast<TreesIndexer*>(R_ExternalPtrAddr(ind_R_ptr));
|
1688
2120
|
if (is_extended)
|
1689
|
-
ext_model_ptr = static_cast<ExtIsoForest*>(R_ExternalPtrAddr(
|
2121
|
+
ext_model_ptr = static_cast<ExtIsoForest*>(R_ExternalPtrAddr(ptr_model));
|
1690
2122
|
else
|
1691
|
-
model_ptr = static_cast<IsoForest*>(R_ExternalPtrAddr(
|
1692
|
-
indexer = indexer_R_ptr.get();
|
2123
|
+
model_ptr = static_cast<IsoForest*>(R_ExternalPtrAddr(ptr_model));
|
1693
2124
|
|
1694
2125
|
MissingAction missing_action = is_extended?
|
1695
2126
|
ext_model_ptr->missing_action
|
@@ -1701,9 +2132,18 @@ void set_reference_points(Rcpp::List lst_modify, Rcpp::List lst_modify2, SEXP rn
|
|
1701
2132
|
if (Xc.size()) Xc_ptr = set_R_nan_as_C_nan(Xc_ptr, Xc.size(), Xcpp, nthreads);
|
1702
2133
|
}
|
1703
2134
|
|
1704
|
-
std::unique_ptr<TreesIndexer> new_indexer(new TreesIndexer(*indexer));
|
2135
|
+
std::unique_ptr<TreesIndexer> new_indexer(is_altrepped? nullptr : (new TreesIndexer(*indexer)));
|
2136
|
+
TreesIndexer *indexer_use = is_altrepped? indexer : new_indexer.get();
|
1705
2137
|
|
1706
|
-
|
2138
|
+
/* Note: if using an altrepped pointer, the indexer is modified in-place. If that fails,
|
2139
|
+
it will end up overwitten, with the previous references taken away. OTOH, if using
|
2140
|
+
a pointer + serialized, and it fails, it should not overwrite anything, and thus
|
2141
|
+
should not re-assign here immediately. */
|
2142
|
+
if (is_altrepped) {
|
2143
|
+
lst_metadata["reference_names"] = rnames;
|
2144
|
+
}
|
2145
|
+
|
2146
|
+
set_reference_points(model_ptr, ext_model_ptr, indexer_use,
|
1707
2147
|
with_distances,
|
1708
2148
|
numeric_data_ptr, categ_data_ptr,
|
1709
2149
|
true, (size_t)0, (size_t)0,
|
@@ -1711,39 +2151,41 @@ void set_reference_points(Rcpp::List lst_modify, Rcpp::List lst_modify2, SEXP rn
|
|
1711
2151
|
(double*)NULL, (int*)NULL, (int*)NULL,
|
1712
2152
|
nrows, nthreads);
|
1713
2153
|
|
1714
|
-
|
1715
|
-
|
1716
|
-
|
1717
|
-
|
1718
|
-
|
2154
|
+
if (!is_altrepped) {
|
2155
|
+
lst_out["ser"] = serialize_cpp_obj(new_indexer.get());
|
2156
|
+
*indexer = std::move(*new_indexer);
|
2157
|
+
lst_metadata["reference_names"] = rnames;
|
2158
|
+
}
|
1719
2159
|
}
|
1720
2160
|
|
1721
2161
|
// [[Rcpp::export(rng = false)]]
|
1722
2162
|
bool check_node_indexer_has_references(SEXP indexer_R_ptr)
|
1723
2163
|
{
|
1724
|
-
|
1725
|
-
|
1726
|
-
|
1727
|
-
if (indexer->indices.empty())
|
1728
|
-
return false;
|
1729
|
-
if (indexer->indices.front().reference_points.empty())
|
1730
|
-
return false;
|
1731
|
-
else
|
1732
|
-
return true;
|
2164
|
+
const TreesIndexer *indexer = (const TreesIndexer*)R_ExternalPtrAddr(indexer_R_ptr);
|
2165
|
+
if (!indexer) return false;
|
2166
|
+
return !(indexer->indices.front().reference_points.empty());
|
1733
2167
|
}
|
1734
2168
|
|
1735
2169
|
// [[Rcpp::export(rng = false)]]
|
1736
2170
|
int get_num_references(SEXP indexer_R_ptr)
|
1737
2171
|
{
|
1738
|
-
TreesIndexer *indexer = static_cast<TreesIndexer*>(R_ExternalPtrAddr(indexer_R_ptr));
|
1739
|
-
if (indexer
|
2172
|
+
const TreesIndexer *indexer = static_cast<const TreesIndexer*>(R_ExternalPtrAddr(indexer_R_ptr));
|
2173
|
+
if (!indexer || indexer->indices.empty()) return 0;
|
1740
2174
|
return indexer->indices.front().reference_points.size();
|
1741
2175
|
}
|
1742
2176
|
|
1743
2177
|
// [[Rcpp::export(rng = false)]]
|
1744
|
-
SEXP
|
2178
|
+
SEXP get_null_R_pointer_internal(bool altrepped)
|
1745
2179
|
{
|
1746
|
-
|
2180
|
+
if (!altrepped) {
|
2181
|
+
return R_MakeExternalPtr(nullptr, R_NilValue, R_NilValue);
|
2182
|
+
}
|
2183
|
+
else {
|
2184
|
+
SEXP R_ptr = PROTECT(R_MakeExternalPtr(nullptr, R_NilValue, R_NilValue));
|
2185
|
+
SEXP out = PROTECT(R_new_altrep(altrepped_pointer_NullPointer, R_ptr, R_NilValue));
|
2186
|
+
UNPROTECT(2);
|
2187
|
+
return out;
|
2188
|
+
}
|
1747
2189
|
}
|
1748
2190
|
|
1749
2191
|
/* This library will use different code paths for opening a file path
|
@@ -1852,18 +2294,30 @@ void serialize_to_file
|
|
1852
2294
|
}
|
1853
2295
|
|
1854
2296
|
// [[Rcpp::export]]
|
1855
|
-
Rcpp::List deserialize_from_file(Rcpp::CharacterVector fname)
|
2297
|
+
Rcpp::List deserialize_from_file(Rcpp::CharacterVector fname, bool lazy_serialization)
|
1856
2298
|
{
|
1857
2299
|
Rcpp::List out = Rcpp::List::create(
|
1858
|
-
Rcpp::_["
|
1859
|
-
Rcpp::_["
|
1860
|
-
Rcpp::_["imp_ptr"] = R_NilValue,
|
1861
|
-
Rcpp::_["imp_ser"] = R_NilValue,
|
2300
|
+
Rcpp::_["model"] = R_NilValue,
|
2301
|
+
Rcpp::_["imputer"] = R_NilValue,
|
1862
2302
|
Rcpp::_["indexer"] = R_NilValue,
|
1863
|
-
Rcpp::_["ind_ser"] = R_NilValue,
|
1864
2303
|
Rcpp::_["metadata"] = R_NilValue
|
1865
2304
|
);
|
1866
2305
|
|
2306
|
+
if (!lazy_serialization) {
|
2307
|
+
out["model"] = Rcpp::List::create(
|
2308
|
+
Rcpp::_["ptr"] = Rcpp::XPtr<void*>(nullptr, false),
|
2309
|
+
Rcpp::_["ser"] = R_NilValue
|
2310
|
+
);
|
2311
|
+
out["imputer"] = Rcpp::List::create(
|
2312
|
+
Rcpp::_["ptr"] = Rcpp::XPtr<void*>(nullptr, false),
|
2313
|
+
Rcpp::_["ser"] = R_NilValue
|
2314
|
+
);
|
2315
|
+
out["indexer"] = Rcpp::List::create(
|
2316
|
+
Rcpp::_["ptr"] = Rcpp::XPtr<void*>(nullptr, false),
|
2317
|
+
Rcpp::_["ser"] = R_NilValue
|
2318
|
+
);
|
2319
|
+
}
|
2320
|
+
|
1867
2321
|
FileOpener file_(fname[0], "rb");
|
1868
2322
|
FILE *input_file = file_.get_handle();
|
1869
2323
|
|
@@ -1928,30 +2382,61 @@ Rcpp::List deserialize_from_file(Rcpp::CharacterVector fname)
|
|
1928
2382
|
ptr_metadata
|
1929
2383
|
);
|
1930
2384
|
|
1931
|
-
if (
|
1932
|
-
|
1933
|
-
|
1934
|
-
|
1935
|
-
|
1936
|
-
|
1937
|
-
|
1938
|
-
|
2385
|
+
if (lazy_serialization)
|
2386
|
+
{
|
2387
|
+
if (has_IsoForest)
|
2388
|
+
out["model"] = Rcpp::unwindProtect(get_altrepped_pointer<IsoForest>, &model);
|
2389
|
+
else
|
2390
|
+
out["model"] = Rcpp::unwindProtect(get_altrepped_pointer<ExtIsoForest>, &model_ext);
|
2391
|
+
|
2392
|
+
if (has_Imputer)
|
2393
|
+
out["imputer"] = Rcpp::unwindProtect(get_altrepped_pointer<Imputer>, &imputer);
|
2394
|
+
else
|
2395
|
+
out["imputer"] = Rcpp::unwindProtect(safe_get_altrepped_null_pointer, nullptr);
|
1939
2396
|
|
1940
|
-
|
1941
|
-
|
1942
|
-
|
1943
|
-
|
1944
|
-
else {
|
1945
|
-
out["ptr"] = Rcpp::unwindProtect(safe_XPtr<ExtIsoForest>, model_ext.get());
|
1946
|
-
model_ext.release();
|
1947
|
-
}
|
1948
|
-
if (has_Imputer) {
|
1949
|
-
out["imp_ptr"] = Rcpp::unwindProtect(safe_XPtr<Imputer>, imputer.get());
|
1950
|
-
imputer.release();
|
2397
|
+
if (has_Imputer)
|
2398
|
+
out["indexer"] = Rcpp::unwindProtect(get_altrepped_pointer<TreesIndexer>, &indexer);
|
2399
|
+
else
|
2400
|
+
out["indexer"] = Rcpp::unwindProtect(safe_get_altrepped_null_pointer, nullptr);
|
1951
2401
|
}
|
1952
|
-
|
1953
|
-
|
1954
|
-
|
2402
|
+
|
2403
|
+
else
|
2404
|
+
{
|
2405
|
+
Rcpp::List tmp_model = out["model"];
|
2406
|
+
Rcpp::List tmp_imputer = out["imputer"];
|
2407
|
+
Rcpp::List tmp_indexer = out["indexer"];
|
2408
|
+
|
2409
|
+
if (has_IsoForest)
|
2410
|
+
tmp_model["ser"] = serialize_cpp_obj(model.get());
|
2411
|
+
else
|
2412
|
+
tmp_model["ser"] = serialize_cpp_obj(model_ext.get());
|
2413
|
+
|
2414
|
+
if (has_Imputer)
|
2415
|
+
tmp_imputer["ser"] = serialize_cpp_obj(imputer.get());
|
2416
|
+
|
2417
|
+
if (has_Indexer)
|
2418
|
+
tmp_indexer["ser"] = serialize_cpp_obj(indexer.get());
|
2419
|
+
|
2420
|
+
if (has_IsoForest) {
|
2421
|
+
tmp_model["ptr"] = Rcpp::unwindProtect(safe_XPtr<IsoForest>, model.get());
|
2422
|
+
model.release();
|
2423
|
+
}
|
2424
|
+
else {
|
2425
|
+
tmp_model["ptr"] = Rcpp::unwindProtect(safe_XPtr<ExtIsoForest>, model_ext.get());
|
2426
|
+
model_ext.release();
|
2427
|
+
}
|
2428
|
+
if (has_Imputer) {
|
2429
|
+
tmp_imputer["ptr"] = Rcpp::unwindProtect(safe_XPtr<Imputer>, imputer.get());
|
2430
|
+
imputer.release();
|
2431
|
+
}
|
2432
|
+
if (has_Indexer) {
|
2433
|
+
tmp_indexer["ptr"] = Rcpp::unwindProtect(safe_XPtr<TreesIndexer>, indexer.get());
|
2434
|
+
indexer.release();
|
2435
|
+
}
|
2436
|
+
|
2437
|
+
out["model"] = tmp_model;
|
2438
|
+
out["imputer"] = tmp_imputer;
|
2439
|
+
out["indexer"] = tmp_indexer;
|
1955
2440
|
}
|
1956
2441
|
|
1957
2442
|
return out;
|
@@ -2473,12 +2958,12 @@ Rcpp::IntegerMatrix get_null_int_mat()
|
|
2473
2958
|
int get_ntrees(SEXP model_R_ptr, bool is_extended)
|
2474
2959
|
{
|
2475
2960
|
if (is_extended) {
|
2476
|
-
ExtIsoForest* ext_model_ptr = static_cast<ExtIsoForest*>(R_ExternalPtrAddr(model_R_ptr));
|
2961
|
+
const ExtIsoForest* ext_model_ptr = static_cast<const ExtIsoForest*>(R_ExternalPtrAddr(model_R_ptr));
|
2477
2962
|
return ext_model_ptr->hplanes.size();
|
2478
2963
|
}
|
2479
2964
|
|
2480
2965
|
else {
|
2481
|
-
IsoForest* model_ptr = static_cast<IsoForest*>(R_ExternalPtrAddr(model_R_ptr));
|
2966
|
+
const IsoForest* model_ptr = static_cast<const IsoForest*>(R_ExternalPtrAddr(model_R_ptr));
|
2482
2967
|
return model_ptr->trees.size();
|
2483
2968
|
}
|
2484
2969
|
}
|