Remove the use of dmlc::JSONWriter, dmlc::Stream, and dmlc serializer (…

…#289)

include/treelite/annotator.h

@@ -1,5 +1,5 @@
 /*!
- * Copyright (c) 2017-2020 by Contributors
+ * Copyright (c) 2017-2021 by Contributors
  * \file annotator.h
  * \author Hyunsu Cho
  * \brief Branch annotation tools
@@ -9,7 +9,11 @@
 
 #include <treelite/tree.h>
 #include <treelite/data.h>
+#include <istream>
+#include <ostream>
 #include <vector>
+#include <cstdio>
+#include <cstdint>
 
 namespace treelite {
 
@@ -29,12 +33,12 @@ class BranchAnnotator {
    * \brief load branch annotation from a JSON file
    * \param fi input stream
    */
-  void Load(dmlc::Stream* fi);
+  void Load(std::istream& fi);
   /*!
    * \brief save branch annotation to a JSON file
    * \param fo output stream
    */
-  void Save(dmlc::Stream* fo) const;
+  void Save(std::ostream& fo) const;
   /*!
    * \brief fetch branch annotation.
    * Usage example:
@@ -48,12 +52,12 @@ class BranchAnnotator {
    * \endcode
    * \return branch annotation in 2D vector
    */
-  inline std::vector<std::vector<size_t>> Get() const {
-    return counts;
+  inline std::vector<std::vector<uint64_t>> Get() const {
+    return counts_;
   }
 
  private:
-  std::vector<std::vector<size_t>> counts;
+  std::vector<std::vector<uint64_t>> counts_;
 };
 
 }  // namespace treelite

include/treelite/tree.h

@@ -12,6 +12,7 @@
 #include <algorithm>
 #include <map>
 #include <memory>
+#include <ostream>
 #include <string>
 #include <vector>
 #include <utility>
@@ -27,14 +28,6 @@
 
 #define TREELITE_MAX_PRED_TRANSFORM_LENGTH 256
 
-/* Foward declarations */
-namespace dmlc {
-
-class Stream;
-float stof(const std::string& value, std::size_t* pos);
-
-}  // namespace dmlc
-
 namespace treelite {
 
 // Represent a frame in the Python buffer protocol (PEP 3118). We use a simplified representation
@@ -161,7 +154,7 @@ enum class TaskType : uint8_t {
 };
 
 /*! \brief Group of parameters that are dependent on the choice of the task type. */
-struct TaskParameter {
+struct TaskParam {
   enum class OutputType : uint8_t { kFloat = 0, kInt = 1 };
   /*! \brief The type of output from each leaf node. */
   OutputType output_type;
@@ -190,7 +183,7 @@ struct TaskParameter {
   unsigned int leaf_vector_size;
 };
 
-static_assert(std::is_pod<TaskParameter>::value, "TaskParameter must be POD type");
+static_assert(std::is_pod<TaskParam>::value, "TaskParameter must be POD type");
 
 /*! \brief in-memory representation of a decision tree */
 template <typename ThresholdType, typename LeafOutputType>
@@ -289,6 +282,9 @@ class Tree {
   ContiguousArray<uint32_t> matching_categories_;
   ContiguousArray<std::size_t> matching_categories_offset_;
 
+  template <typename WriterType, typename X, typename Y>
+  friend void SerializeTreeToJSON(WriterType& writer, const Tree<X, Y>& tree);
+
   // allocate a new node
   inline int AllocNode();
 
@@ -562,8 +558,6 @@ class Tree {
     node.gain_ = gain;
     node.gain_present_ = true;
   }
-
-  void ReferenceSerialize(dmlc::Stream* fo) const;
 };
 
 struct ModelParam {
@@ -656,7 +650,7 @@ class Model {
 
   virtual std::size_t GetNumTree() const = 0;
   virtual void SetTreeLimit(std::size_t limit) = 0;
-  virtual void ReferenceSerialize(dmlc::Stream* fo) const = 0;
+  virtual void SerializeToJSON(std::ostream& fo) const = 0;
 
   /* In-memory serialization, zero-copy */
   std::vector<PyBufferFrame> GetPyBuffer();
@@ -676,7 +670,7 @@ class Model {
   /*! \brief whether to average tree outputs */
   bool average_tree_output;
   /*! \brief Group of parameters that are specific to the particular task type */
-  TaskParameter task_param;
+  TaskParam task_param;
   /*! \brief extra parameters */
   ModelParam param;
 
@@ -712,7 +706,7 @@ class ModelImpl : public Model {
   ModelImpl(ModelImpl&&) noexcept = default;
   ModelImpl& operator=(ModelImpl&&) noexcept = default;
 
-  void ReferenceSerialize(dmlc::Stream* fo) const override;
+  void SerializeToJSON(std::ostream& fo) const override;
   inline std::size_t GetNumTree() const override {
     return trees.size();
   }

include/treelite/tree_impl.h

@@ -296,9 +296,9 @@ ModelParam::InitAllowUnknown(const Container& kwargs) {
                    TREELITE_MAX_PRED_TRANSFORM_LENGTH - 1);
       this->pred_transform[TREELITE_MAX_PRED_TRANSFORM_LENGTH - 1] = '\0';
     } else if (e.first == "sigmoid_alpha") {
-      this->sigmoid_alpha = dmlc::stof(e.second, nullptr);
+      this->sigmoid_alpha = std::stof(e.second, nullptr);
     } else if (e.first == "global_bias") {
-      this->global_bias = dmlc::stof(e.second, nullptr);
+      this->global_bias = std::stof(e.second, nullptr);
     }
   }
   return unknowns;

src/CMakeLists.txt

@@ -102,7 +102,7 @@ target_sources(objtreelite
     filesystem.cc
     optable.cc
     serializer.cc
-    reference_serializer.cc
+    json_serializer.cc
     ${PROJECT_SOURCE_DIR}/include/treelite/annotator.h
     ${PROJECT_SOURCE_DIR}/include/treelite/base.h
     ${PROJECT_SOURCE_DIR}/include/treelite/c_api.h

src/annotator.cc

@@ -8,7 +8,10 @@
 #include <treelite/annotator.h>
 #include <treelite/math.h>
 #include <treelite/omp.h>
-#include <dmlc/json.h>
+#include <rapidjson/istreamwrapper.h>
+#include <rapidjson/ostreamwrapper.h>
+#include <rapidjson/writer.h>
+#include <rapidjson/document.h>
 #include <dmlc/io.h>
 #include <limits>
 #include <cstdint>
@@ -23,7 +26,7 @@ union Entry {
 
 template <typename ElementType, typename ThresholdType, typename LeafOutputType>
 void Traverse_(const treelite::Tree<ThresholdType, LeafOutputType>& tree,
-               const Entry<ElementType>* data, int nid, size_t* out_counts) {
+               const Entry<ElementType>* data, int nid, uint64_t* out_counts) {
   ++out_counts[nid];
   if (!tree.IsLeaf(nid)) {
     const unsigned split_index = tree.SplitIndex(nid);
@@ -58,15 +61,15 @@ void Traverse_(const treelite::Tree<ThresholdType, LeafOutputType>& tree,
 
 template <typename ElementType, typename ThresholdType, typename LeafOutputType>
 void Traverse(const treelite::Tree<ThresholdType, LeafOutputType>& tree,
-              const Entry<ElementType>* data, size_t* out_counts) {
+              const Entry<ElementType>* data, uint64_t* out_counts) {
   Traverse_(tree, data, 0, out_counts);
 }
 
 template <typename ElementType, typename ThresholdType, typename LeafOutputType>
 inline void ComputeBranchLoopImpl(
     const treelite::ModelImpl<ThresholdType, LeafOutputType>& model,
     const treelite::DenseDMatrixImpl<ElementType>* dmat, size_t rbegin, size_t rend, int nthread,
-    const size_t* count_row_ptr, size_t* counts_tloc) {
+    const size_t* count_row_ptr, uint64_t* counts_tloc) {
   std::vector<Entry<ElementType>> inst(nthread * dmat->num_col, {-1});
   const size_t ntree = model.trees.size();
   CHECK_LE(rbegin, rend);
@@ -103,7 +106,7 @@ template <typename ElementType, typename ThresholdType, typename LeafOutputType>
 inline void ComputeBranchLoopImpl(
     const treelite::ModelImpl<ThresholdType, LeafOutputType>& model,
     const treelite::CSRDMatrixImpl<ElementType>* dmat, size_t rbegin, size_t rend, int nthread,
-    const size_t* count_row_ptr, size_t* counts_tloc) {
+    const size_t* count_row_ptr, uint64_t* counts_tloc) {
   std::vector<Entry<ElementType>> inst(nthread * dmat->num_col, {-1});
   const size_t ntree = model.trees.size();
   CHECK_LE(rbegin, rend);
@@ -136,7 +139,7 @@ class ComputeBranchLoopDispatcherWithDenseDMatrix {
   inline static void Dispatch(
       const treelite::ModelImpl<ThresholdType, LeafOutputType>& model,
       const treelite::DMatrix* dmat, size_t rbegin, size_t rend, int nthread,
-      const size_t* count_row_ptr, size_t* counts_tloc) {
+      const size_t* count_row_ptr, uint64_t* counts_tloc) {
     const auto* dmat_ = static_cast<const treelite::DenseDMatrixImpl<ElementType>*>(dmat);
     CHECK(dmat_) << "Dangling data matrix reference detected";
     ComputeBranchLoopImpl(model, dmat_, rbegin, rend, nthread, count_row_ptr, counts_tloc);
@@ -150,7 +153,7 @@ class ComputeBranchLoopDispatcherWithCSRDMatrix {
   inline static void Dispatch(
       const treelite::ModelImpl<ThresholdType, LeafOutputType>& model,
       const treelite::DMatrix* dmat, size_t rbegin, size_t rend, int nthread,
-      const size_t* count_row_ptr, size_t* counts_tloc) {
+      const size_t* count_row_ptr, uint64_t* counts_tloc) {
     const auto* dmat_ = static_cast<const treelite::CSRDMatrixImpl<ElementType>*>(dmat);
     CHECK(dmat_) << "Dangling data matrix reference detected";
     ComputeBranchLoopImpl(model, dmat_, rbegin, rend, nthread, count_row_ptr, counts_tloc);
@@ -161,7 +164,7 @@ template <typename ThresholdType, typename LeafOutputType>
 inline void ComputeBranchLoop(const treelite::ModelImpl<ThresholdType, LeafOutputType>& model,
                               const treelite::DMatrix* dmat, size_t rbegin,
                               size_t rend, int nthread, const size_t* count_row_ptr,
-                              size_t* counts_tloc) {
+                              uint64_t* counts_tloc) {
   switch (dmat->GetType()) {
   case treelite::DMatrixType::kDense: {
     treelite::DispatchWithTypeInfo<ComputeBranchLoopDispatcherWithDenseDMatrix>(
@@ -189,9 +192,9 @@ inline void
 AnnotateImpl(
     const treelite::ModelImpl<ThresholdType, LeafOutputType>& model,
     const treelite::DMatrix* dmat, int nthread, int verbose,
-    std::vector<std::vector<size_t>>* out_counts) {
-  std::vector<size_t> new_counts;
-  std::vector<size_t> counts_tloc;
+    std::vector<std::vector<uint64_t>>* out_counts) {
+  std::vector<uint64_t> new_counts;
+  std::vector<uint64_t> counts_tloc;
   std::vector<size_t> count_row_ptr;
 
   count_row_ptr = {0};
@@ -224,7 +227,7 @@ AnnotateImpl(
   }
 
   // change layout of counts
-  std::vector<std::vector<size_t>>& counts = *out_counts;
+  std::vector<std::vector<uint64_t>>& counts = *out_counts;
   for (size_t i = 0; i < ntree; ++i) {
     counts.emplace_back(&new_counts[count_row_ptr[i]], &new_counts[count_row_ptr[i + 1]]);
   }
@@ -234,22 +237,43 @@ void
 BranchAnnotator::Annotate(const Model& model, const DMatrix* dmat, int nthread, int verbose) {
   TypeInfo threshold_type = model.GetThresholdType();
   model.Dispatch([this, dmat, nthread, verbose, threshold_type](auto& handle) {
-    AnnotateImpl(handle, dmat, nthread, verbose, &this->counts);
+    AnnotateImpl(handle, dmat, nthread, verbose, &this->counts_);
   });
 }
 
 void
-BranchAnnotator::Load(dmlc::Stream* fi) {
-  dmlc::istream is(fi);
-  std::unique_ptr<dmlc::JSONReader> reader(new dmlc::JSONReader(&is));
-  reader->Read(&counts);
+BranchAnnotator::Load(std::istream& fi) {
+  rapidjson::IStreamWrapper is(fi);
+
+  rapidjson::Document doc;
+  doc.ParseStream(is);
+
+  std::string err_msg = "JSON file must contain a list of lists of integers";
+  CHECK(doc.IsArray()) << err_msg;
+  counts_.clear();
+  for (const auto& node_cnt : doc.GetArray()) {
+    CHECK(node_cnt.IsArray()) << err_msg;
+    counts_.emplace_back();
+    for (const auto& e : node_cnt.GetArray()) {
+      counts_.back().push_back(e.GetUint64());
+    }
+  }
 }
 
 void
-BranchAnnotator::Save(dmlc::Stream* fo) const {
-  dmlc::ostream os(fo);
-  std::unique_ptr<dmlc::JSONWriter> writer(new dmlc::JSONWriter(&os));
-  writer->Write(counts);
+BranchAnnotator::Save(std::ostream& fo) const {
+  rapidjson::OStreamWrapper os(fo);
+  rapidjson::Writer<rapidjson::OStreamWrapper> writer(os);
+
+  writer.StartArray();
+  for (const auto& node_cnt : counts_) {
+    writer.StartArray();
+    for (auto e : node_cnt) {
+      writer.Uint64(e);
+    }
+    writer.EndArray();
+  }
+  writer.EndArray();
 }
 
 }  // namespace treelite

src/c_api/c_api.cc

@@ -19,6 +19,8 @@
 #include <dmlc/io.h>
 #include <memory>
 #include <algorithm>
+#include <fstream>
+#include <cstdio>
 
 using namespace treelite;
 
@@ -51,8 +53,8 @@ int TreeliteAnnotationSave(AnnotationHandle handle,
                            const char* path) {
   API_BEGIN();
   const BranchAnnotator* annotator = static_cast<BranchAnnotator*>(handle);
-  std::unique_ptr<dmlc::Stream> fo(dmlc::Stream::Create(path, "w"));
-  annotator->Save(fo.get());
+  std::ofstream fo(path);
+  annotator->Save(fo);
   API_END();
 }
 

src/compiler/ast/ast.h

@@ -1,5 +1,5 @@
 /*!
- * Copyright (c) 2017-2020 by Contributors
+ * Copyright (c) 2017-2021 by Contributors
  * \file ast.h
  * \brief Definition for AST classes
  * \author Hyunsu Cho
@@ -14,6 +14,7 @@
 #include <string>
 #include <vector>
 #include <utility>
+#include <cstdint>
 
 namespace treelite {
 namespace compiler {
@@ -24,7 +25,7 @@ class ASTNode {
   std::vector<ASTNode*> children;
   int node_id;
   int tree_id;
-  dmlc::optional<size_t> data_count;
+  dmlc::optional<uint64_t> data_count;
   dmlc::optional<double> sum_hess;
   virtual std::string GetDump() const = 0;
   virtual ~ASTNode() = 0;  // force ASTNode to be abstract class

src/compiler/ast/builder.h

@@ -13,6 +13,7 @@
 #include <ostream>
 #include <utility>
 #include <memory>
+#include <cstdint>
 #include "./ast.h"
 
 namespace treelite {
@@ -58,7 +59,7 @@ class ASTBuilder {
   /* \brief replace split thresholds with integers */
   void QuantizeThresholds();
   /* \brief Load data counts from annotation file */
-  void LoadDataCounts(const std::vector<std::vector<size_t>>& counts);
+  void LoadDataCounts(const std::vector<std::vector<uint64_t>>& counts);
   /*
    * \brief Get a text representation of AST
    */