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@tqchen
tqchen committed Jul 4, 2015
1 parent aba41d0 commit 1123253
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Showing 10 changed files with 178 additions and 143 deletions.
16 changes: 9 additions & 7 deletions src/data.h
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Original file line number Diff line number Diff line change
@@ -1,10 +1,12 @@
#ifndef XGBOOST_DATA_H
#define XGBOOST_DATA_H
/*!
* Copyright (c) 2014 by Contributors
* \file data.h
* \brief the input data structure for gradient boosting
* \author Tianqi Chen
*/
#ifndef XGBOOST_DATA_H_
#define XGBOOST_DATA_H_

#include <cstdio>
#include <vector>
#include "utils/utils.h"
Expand Down Expand Up @@ -32,7 +34,7 @@ struct bst_gpair {
bst_gpair(bst_float grad, bst_float hess) : grad(grad), hess(hess) {}
};

/*!
/*!
* \brief extra information that might needed by gbm and tree module
* these information are not necessarily presented, and can be empty
*/
Expand Down Expand Up @@ -102,7 +104,7 @@ struct RowBatch : public SparseBatch {
return Inst(data_ptr + ind_ptr[i], static_cast<bst_uint>(ind_ptr[i+1] - ind_ptr[i]));
}
};
/*!
/*!
* \brief read-only column batch, used to access columns,
* the columns are not required to be continuous
*/
Expand Down Expand Up @@ -131,7 +133,7 @@ class IFMatrix {
/*!\brief get column iterator */
virtual utils::IIterator<ColBatch> *ColIterator(void) = 0;
/*!
* \brief get the column iterator associated with FMatrix with subset of column features
* \brief get the column iterator associated with FMatrix with subset of column features
* \param fset is the list of column index set that must be contained in the returning Column iterator
* \return the column iterator, initialized so that it reads the elements in fset
*/
Expand All @@ -154,11 +156,11 @@ class IFMatrix {
/*! \brief get number of non-missing entries in column */
virtual size_t GetColSize(size_t cidx) const = 0;
/*! \brief get column density */
virtual float GetColDensity(size_t cidx) const = 0;
virtual float GetColDensity(size_t cidx) const = 0;
/*! \brief reference of buffered rowset */
virtual const std::vector<bst_uint> &buffered_rowset(void) const = 0;
// virtual destructor
virtual ~IFMatrix(void){}
};
} // namespace xgboost
#endif // XGBOOST_DATA_H
#endif // XGBOOST_DATA_H_
24 changes: 13 additions & 11 deletions src/io/dmlc_simple.cpp
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Original file line number Diff line number Diff line change
@@ -1,6 +1,8 @@
// Copyright by Contributors
#define _CRT_SECURE_NO_WARNINGS
#define _CRT_SECURE_NO_DEPRECATE
#define NOMINMAX
#include <string>
#include "../utils/io.h"

// implements a single no split version of DMLC
Expand All @@ -9,7 +11,7 @@
namespace xgboost {
namespace utils {
/*!
* \brief line split implementation from single FILE
* \brief line split implementation from single FILE
* simply returns lines of files, used for stdin
*/
class SingleFileSplit : public dmlc::InputSplit {
Expand All @@ -32,7 +34,7 @@ class SingleFileSplit : public dmlc::InputSplit {
}
virtual size_t Read(void *ptr, size_t size) {
return std::fread(ptr, 1, size, fp_);
}
}
virtual void Write(const void *ptr, size_t size) {
utils::Error("cannot do write in inputsplit");
}
Expand All @@ -47,13 +49,13 @@ class SingleFileSplit : public dmlc::InputSplit {
chunk_end_);
out_rec->dptr = chunk_begin_;
out_rec->size = next - chunk_begin_;
chunk_begin_ = next;
chunk_begin_ = next;
return true;
}
virtual bool NextChunk(Blob *out_chunk) {
if (chunk_begin_ == chunk_end_) {
if (!LoadChunk()) return false;
}
}
out_chunk->dptr = chunk_begin_;
out_chunk->size = chunk_end_ - chunk_begin_;
chunk_begin_ = chunk_end_;
Expand All @@ -64,8 +66,8 @@ class SingleFileSplit : public dmlc::InputSplit {
if (max_size <= overflow_.length()) {
*size = 0; return true;
}
if (overflow_.length() != 0) {
std::memcpy(buf, BeginPtr(overflow_), overflow_.length());
if (overflow_.length() != 0) {
std::memcpy(buf, BeginPtr(overflow_), overflow_.length());
}
size_t olen = overflow_.length();
overflow_.resize(0);
Expand All @@ -88,13 +90,13 @@ class SingleFileSplit : public dmlc::InputSplit {
return true;
}
}

protected:
inline const char* FindLastRecordBegin(const char *begin,
const char *end) {
if (begin == end) return begin;
for (const char *p = end - 1; p != begin; --p) {
if (*p == '\n' || *p == '\r') return p + 1;
if (*p == '\n' || *p == '\r') return p + 1;
}
return begin;
}
Expand Down Expand Up @@ -143,7 +145,7 @@ class StdFile : public dmlc::Stream {
public:
explicit StdFile(std::FILE *fp, bool use_stdio)
: fp(fp), use_stdio(use_stdio) {
}
}
virtual ~StdFile(void) {
this->Close();
}
Expand All @@ -154,7 +156,7 @@ class StdFile : public dmlc::Stream {
std::fwrite(ptr, size, 1, fp);
}
virtual void Seek(size_t pos) {
std::fseek(fp, static_cast<long>(pos), SEEK_SET);
std::fseek(fp, static_cast<long>(pos), SEEK_SET); // NOLINT(*)
}
virtual size_t Tell(void) {
return std::ftell(fp);
Expand Down Expand Up @@ -197,7 +199,7 @@ Stream *Stream::Create(const char *fname, const char * const mode, bool allow_nu
"to use hdfs, s3 or distributed version, compile with make dmlc=1";
utils::Check(strncmp(fname, "s3://", 5) != 0, msg);
utils::Check(strncmp(fname, "hdfs://", 7) != 0, msg);

std::FILE *fp = NULL;
bool use_stdio = false;
using namespace std;
Expand Down
9 changes: 5 additions & 4 deletions src/io/io.cpp
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Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
// Copyright 2014 by Contributors
#define _CRT_SECURE_NO_WARNINGS
#define _CRT_SECURE_NO_DEPRECATE
#define NOMINMAX
Expand All @@ -17,7 +18,7 @@ DataMatrix* LoadDataMatrix(const char *fname,
const char *cache_file) {
using namespace std;
std::string fname_ = fname;

const char *dlm = strchr(fname, '#');
if (dlm != NULL) {
utils::Check(strchr(dlm + 1, '#') == NULL,
Expand All @@ -29,7 +30,7 @@ DataMatrix* LoadDataMatrix(const char *fname,
cache_file = dlm +1;
}

if (cache_file == NULL) {
if (cache_file == NULL) {
if (!std::strcmp(fname, "stdin") ||
!std::strncmp(fname, "s3://", 5) ||
!std::strncmp(fname, "hdfs://", 7) ||
Expand All @@ -42,7 +43,7 @@ DataMatrix* LoadDataMatrix(const char *fname,
utils::FileStream fs(utils::FopenCheck(fname, "rb"));
utils::Check(fs.Read(&magic, sizeof(magic)) != 0, "invalid input file format");
fs.Seek(0);
if (magic == DMatrixSimple::kMagic) {
if (magic == DMatrixSimple::kMagic) {
DMatrixSimple *dmat = new DMatrixSimple();
dmat->LoadBinary(fs, silent, fname);
fs.Close();
Expand Down Expand Up @@ -81,7 +82,7 @@ DataMatrix* LoadDataMatrix(const char *fname,
}
}

void SaveDataMatrix(const DataMatrix &dmat, const char *fname, bool silent) {
void SaveDataMatrix(const DataMatrix &dmat, const char *fname, bool silent) {
if (dmat.magic == DMatrixSimple::kMagic) {
const DMatrixSimple *p_dmat = static_cast<const DMatrixSimple*>(&dmat);
p_dmat->SaveBinary(fname, silent);
Expand Down
11 changes: 6 additions & 5 deletions src/io/libsvm_parser.h
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@ namespace io {
/*! \brief page returned by libsvm parser */
struct LibSVMPage : public SparsePage {
std::vector<float> label;
// overload clear
// overload clear
inline void Clear() {
SparsePage::Clear();
label.clear();
Expand All @@ -35,7 +35,7 @@ struct LibSVMPage : public SparsePage {
*/
class LibSVMPageFactory {
public:
explicit LibSVMPageFactory()
LibSVMPageFactory()
: bytes_read_(0), at_head_(true) {
}
inline bool Init(void) {
Expand Down Expand Up @@ -85,7 +85,7 @@ class LibSVMPageFactory {
data->resize(nthread);
bytes_read_ += chunk.size;
utils::Assert(chunk.size != 0, "LibSVMParser.FileData");
char *head = reinterpret_cast<char*>(chunk.dptr);
char *head = reinterpret_cast<char*>(chunk.dptr);
#pragma omp parallel num_threads(nthread_)
{
// threadid
Expand Down Expand Up @@ -150,7 +150,7 @@ class LibSVMPageFactory {
}
return begin;
}

private:
// nthread
int nthread_;
Expand Down Expand Up @@ -199,12 +199,13 @@ class LibSVMParser : public utils::IIterator<LibSVMPage> {
inline size_t bytes_read(void) const {
return itr.get_factory().bytes_read();
}

private:
bool at_end_;
size_t data_ptr_;
std::vector<LibSVMPage> *data_;
utils::ThreadBuffer<std::vector<LibSVMPage>*, LibSVMPageFactory> itr;
};
};

} // namespace io
} // namespace xgboost
Expand Down
32 changes: 18 additions & 14 deletions src/io/page_dmatrix-inl.hpp
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Original file line number Diff line number Diff line change
@@ -1,11 +1,15 @@
#ifndef XGBOOST_IO_PAGE_DMATRIX_INL_HPP_
#define XGBOOST_IO_PAGE_DMATRIX_INL_HPP_
/*!
* Copyright (c) 2014 by Contributors
* \file page_dmatrix-inl.hpp
* row iterator based on sparse page
* \author Tianqi Chen
*/
#ifndef XGBOOST_IO_PAGE_DMATRIX_INL_HPP_
#define XGBOOST_IO_PAGE_DMATRIX_INL_HPP_

#include <vector>
#include <string>
#include <algorithm>
#include "../data.h"
#include "../utils/iterator.h"
#include "../utils/thread_buffer.h"
Expand Down Expand Up @@ -94,12 +98,12 @@ class DMatrixPageBase : public DataMatrix {
fbin.Close();
if (!silent) {
utils::Printf("DMatrixPage: %lux%lu is saved to %s\n",
static_cast<unsigned long>(mat.info.num_row()),
static_cast<unsigned long>(mat.info.num_col()), fname_);
static_cast<unsigned long>(mat.info.num_row()), // NOLINT(*)
static_cast<unsigned long>(mat.info.num_col()), fname_); // NOLINT(*)
}
}
/*! \brief load and initialize the iterator with fi */
inline void LoadBinary(utils::FileStream &fi,
inline void LoadBinary(utils::FileStream &fi, // NOLINT(*)
bool silent,
const char *fname_) {
this->set_cache_file(fname_);
Expand All @@ -114,8 +118,8 @@ class DMatrixPageBase : public DataMatrix {
iter_->Load(fs);
if (!silent) {
utils::Printf("DMatrixPage: %lux%lu matrix is loaded",
static_cast<unsigned long>(info.num_row()),
static_cast<unsigned long>(info.num_col()));
static_cast<unsigned long>(info.num_row()), // NOLINT(*)
static_cast<unsigned long>(info.num_col())); // NOLINT(*)
if (fname_ != NULL) {
utils::Printf(" from %s\n", fname_);
} else {
Expand All @@ -141,7 +145,7 @@ class DMatrixPageBase : public DataMatrix {
}
this->set_cache_file(cache_file);
std::string fname_row = std::string(cache_file) + ".row.blob";
utils::FileStream fo(utils::FopenCheck(fname_row.c_str(), "wb"));
utils::FileStream fo(utils::FopenCheck(fname_row.c_str(), "wb"));
SparsePage page;
size_t bytes_write = 0;
double tstart = rabit::utils::GetTime();
Expand Down Expand Up @@ -178,8 +182,8 @@ class DMatrixPageBase : public DataMatrix {
if (page.data.size() != 0) {
page.Save(&fo);
}
fo.Close();
iter_->Load(utils::FileStream(utils::FopenCheck(fname_row.c_str(), "rb")));
fo.Close();
iter_->Load(utils::FileStream(utils::FopenCheck(fname_row.c_str(), "rb")));
// save data matrix
utils::FileStream fs(utils::FopenCheck(cache_file, "wb"));
int tmagic = kMagic;
Expand All @@ -188,8 +192,8 @@ class DMatrixPageBase : public DataMatrix {
fs.Close();
if (!silent) {
utils::Printf("DMatrixPage: %lux%lu is parsed from %s\n",
static_cast<unsigned long>(info.num_row()),
static_cast<unsigned long>(info.num_col()),
static_cast<unsigned long>(info.num_row()), // NOLINT(*)
static_cast<unsigned long>(info.num_col()), // NOLINT(*)
uri);
}
}
Expand Down Expand Up @@ -241,12 +245,12 @@ class DMatrixHalfRAM : public DMatrixPageBase<0xffffab03> {
virtual IFMatrix *fmat(void) const {
return fmat_;
}
virtual void set_cache_file(const std::string &cache_file) {
virtual void set_cache_file(const std::string &cache_file) {
}
virtual void CheckMagic(int tmagic) {
utils::Check(tmagic == DMatrixPageBase<0xffffab02>::kMagic ||
tmagic == DMatrixPageBase<0xffffab03>::kMagic,
"invalid format,magic number mismatch");
"invalid format,magic number mismatch");
}
/*! \brief the real fmatrix */
IFMatrix *fmat_;
Expand Down
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