[PLUGIN] Add densify parser

dmlc-core

@@ -1 +1 @@
-Subproject commit c66d2ab2d30f55303b65b5ed9dc1f9ee04260f7e
+Subproject commit e0a18eb45cb9c6e7314dbd3328dda158e3a3486f

make/travis.mk

@@ -31,3 +31,4 @@ LIBJVM=$(JAVA_HOME)/jre/lib/amd64/server
 #
 XGB_PLUGINS += plugin/example/plugin.mk
 XGB_PLUGINS += plugin/lz4/plugin.mk
+XGB_PLUGINS += plugin/dense_libsvm/plugin.mk

plugin/dense_parser/dense_libsvm.cc

@@ -0,0 +1,85 @@
+/*!
+ * Copyright 2015 by Contributors
+ * \file dense_libsvm.cc
+ * \brief Plugin to load in libsvm, but fill all the missing entries with zeros.
+ *  This plugin is mainly used for benchmark purposes and do not need to be included.
+ */
+#include <dmlc/data.h>
+#include <memory>
+
+namespace dmlc {
+namespace data {
+
+template<typename IndexType>
+class DensifyParser : public dmlc::Parser<IndexType> {
+ public:
+  DensifyParser(dmlc::Parser<IndexType>* parser, uint32_t num_col)
+      : parser_(parser), num_col_(num_col) {
+  }
+
+  void BeforeFirst() override {
+    parser_->BeforeFirst();
+  }
+
+  bool Next() override {
+    if (!parser_->Next()) return false;
+    const RowBlock<IndexType>& batch = parser_->Value();
+    LOG(INFO) << batch.size;
+    dense_index_.resize(num_col_ * batch.size);
+    dense_value_.resize(num_col_ * batch.size);
+    std::fill(dense_value_.begin(), dense_value_.end(), 0.0f);
+    offset_.resize(batch.size + 1);
+    offset_[0] = 0;
+
+    for (size_t i = 0; i < batch.size; ++i) {
+      offset_[i + 1] = (i + 1) * num_col_;
+      Row<IndexType> row = batch[i];
+      for (uint32_t j = 0; j < num_col_; ++j) {
+        dense_index_[i * num_col_ + j] = j;
+      }
+      for (unsigned k = 0; k < row.length; ++k) {
+        uint32_t index = row.get_index(k);
+        CHECK_LT(index, num_col_)
+            << "Featuere index larger than num_col";
+        dense_value_[i * num_col_ + index]  = row.get_value(k);
+      }
+    }
+    out_ = batch;
+    out_.index = dmlc::BeginPtr(dense_index_);
+    out_.value = dmlc::BeginPtr(dense_value_);
+    out_.offset = dmlc::BeginPtr(offset_);
+    return true;
+  }
+
+  const dmlc::RowBlock<IndexType>& Value() const override {
+    return out_;
+  }
+
+  size_t BytesRead() const override {
+    return parser_->BytesRead();
+  }
+
+ private:
+  RowBlock<IndexType> out_;
+  std::unique_ptr<Parser<IndexType> > parser_;
+  uint32_t num_col_;
+  std::vector<size_t> offset_;
+  std::vector<IndexType> dense_index_;
+  std::vector<float> dense_value_;
+};
+
+template<typename IndexType>
+Parser<IndexType> *
+CreateDenseLibSVMParser(const std::string& path,
+                        const std::map<std::string, std::string>& args,
+                        unsigned part_index,
+                        unsigned num_parts) {
+  CHECK_NE(args.count("num_col"), 0) << "expect num_col in dense_libsvm";
+  return new DensifyParser<IndexType>(
+            Parser<IndexType>::Create(path.c_str(), part_index, num_parts, "libsvm"),
+           uint32_t(atoi(args.at("num_col").c_str())));
+}
+}  // namespace data
+
+DMLC_REGISTER_DATA_PARSER(uint32_t, dense_libsvm, data::CreateDenseLibSVMParser<uint32_t>);
+}  // namespace dmlc

plugin/dense_parser/plugin.mk

@@ -0,0 +1,2 @@
+PLUGIN_OBJS += build_plugin/dense_parser/dense_libsvm.o
+PLUGIN_LDFLAGS +=

src/data/data.cc

@@ -181,7 +181,7 @@ DMatrix* DMatrix::Load(const std::string& uri,
   std::string ftype = file_format;
   if (file_format == "auto") ftype = "libsvm";
   std::unique_ptr<dmlc::Parser<uint32_t> > parser(
-      dmlc::Parser<uint32_t>::Create(fname.c_str(), partid, npart, ftype.c_str()));
+      dmlc::Parser<uint32_t>::Create(fname.c_str(), partid, npart, file_format.c_str()));
   DMatrix* dmat = DMatrix::Create(parser.get(), cache_file);
   if (!silent) {
     LOG(CONSOLE) << dmat->info().num_row << 'x' << dmat->info().num_col << " matrix with "