add create from csc

R-package/src/xgboost_R.cpp

@@ -7,7 +7,6 @@
 #include "wrapper/xgboost_wrapper.h"
 #include "src/utils/utils.h"
 #include "src/utils/omp.h"
-#include "src/utils/matrix_csr.h"
 using namespace std;
 using namespace xgboost;
 
@@ -91,37 +90,25 @@ extern "C" {
                                 SEXP indices,
                                 SEXP data) {
     _WrapperBegin();
-    const int *col_ptr = INTEGER(indptr);
+    const int *p_indptr = INTEGER(indptr);
-    const int *row_index = INTEGER(indices);
+    const int *p_indices = INTEGER(indices);
-    const double *col_data = REAL(data);
+    const double *p_data = REAL(data);
-    int ncol = length(indptr) - 1;
+    int nindptr = length(indptr);
     int ndata = length(data);
-    // transform into CSR format
+    std::vector<bst_ulong> col_ptr_(nindptr);
-    std::vector<bst_ulong> row_ptr;
+    std::vector<unsigned> indices_(ndata);
-    std::vector< std::pair<unsigned, float> > csr_data;
+    std::vector<float> data_(ndata);
-    utils::SparseCSRMBuilder<std::pair<unsigned,float>, false, bst_ulong> builder(row_ptr, csr_data);
+
-    builder.InitBudget();
+    for (int i = 0; i < nindptr; ++i) {
-    for (int i = 0; i < ncol; ++i) {
+      col_ptr_[i] = static_cast<bst_ulong>(p_indptr[i]);
-      for (int j = col_ptr[i]; j < col_ptr[i+1]; ++j) {
-        builder.AddBudget(row_index[j]);
-      }
     }
-    builder.InitStorage();
-    for (int i = 0; i < ncol; ++i) {
-      for (int j = col_ptr[i]; j < col_ptr[i+1]; ++j) {
-        builder.PushElem(row_index[j], std::make_pair(i, col_data[j]));
-      }
-    }
-    utils::Assert(csr_data.size() == static_cast<size_t>(ndata), "BUG CreateFromCSC");
-    std::vector<float> row_data(ndata);
-    std::vector<unsigned> col_index(ndata);
     #pragma omp parallel for schedule(static)
     for (int i = 0; i < ndata; ++i) {
-      col_index[i] = csr_data[i].first;
+      indices_[i] = static_cast<unsigned>(p_indices[i]);
-      row_data[i] = csr_data[i].second;      
+      data_[i] = static_cast<float>(p_data[i]);
     }
-    void *handle = XGDMatrixCreateFromCSR(BeginPtr(row_ptr), BeginPtr(col_index),
+    void *handle = XGDMatrixCreateFromCSC(BeginPtr(col_ptr_), BeginPtr(indices_),
-                                          BeginPtr(row_data), row_ptr.size(), ndata );
+                                          BeginPtr(data_), nindptr, ndata);
     SEXP ret = PROTECT(R_MakeExternalPtr(handle, R_NilValue, R_NilValue));
     R_RegisterCFinalizerEx(ret, _DMatrixFinalizer, TRUE);
     UNPROTECT(1);

demo/guide-python/basic_walkthrough.py

@@ -42,7 +42,7 @@ assert np.sum(np.abs(preds2-preds)) == 0
 
 ###
 # build dmatrix from scipy.sparse
-print ('start running example of build DMatrix from scipy.sparse')
+print ('start running example of build DMatrix from scipy.sparse CSR Matrix')
 labels = []
 row = []; col = []; dat = []
 i = 0
@@ -54,8 +54,14 @@ for l in open('../data/agaricus.txt.train'):
         row.append(i); col.append(int(k)); dat.append(float(v))
     i += 1
 csr = scipy.sparse.csr_matrix( (dat, (row,col)) )
-dtrain = xgb.DMatrix( csr )
+dtrain = xgb.DMatrix( csr, label = labels )
-dtrain.set_label(labels)
+watchlist  = [(dtest,'eval'), (dtrain,'train')]
+bst = xgb.train( param, dtrain, num_round, watchlist )
+
+print ('start running example of build DMatrix from scipy.sparse CSC Matrix')
+# we can also construct from csc matrix
+csc = scipy.sparse.csc_matrix( (dat, (row,col)) )
+dtrain = xgb.DMatrix(csc, label=labels)
 watchlist  = [(dtest,'eval'), (dtrain,'train')]
 bst = xgb.train( param, dtrain, num_round, watchlist )
 
@@ -63,8 +69,7 @@ print ('start running example of build DMatrix from numpy array')
 # NOTE: npymat is numpy array, we will convert it into scipy.sparse.csr_matrix in internal implementation
 # then convert to DMatrix
 npymat = csr.todense()
-dtrain = xgb.DMatrix( npymat)
+dtrain = xgb.DMatrix(npymat, label = labels)
-dtrain.set_label(labels)
 watchlist  = [(dtest,'eval'), (dtrain,'train')]
 bst = xgb.train( param, dtrain, num_round, watchlist )
 

wrapper/xgboost.py

@@ -22,6 +22,7 @@ xglib = ctypes.cdll.LoadLibrary(XGBOOST_PATH)
 # DMatrix functions
 xglib.XGDMatrixCreateFromFile.restype = ctypes.c_void_p
 xglib.XGDMatrixCreateFromCSR.restype = ctypes.c_void_p
+xglib.XGDMatrixCreateFromCSC.restype = ctypes.c_void_p
 xglib.XGDMatrixCreateFromMat.restype = ctypes.c_void_p
 xglib.XGDMatrixSliceDMatrix.restype = ctypes.c_void_p
 xglib.XGDMatrixGetFloatInfo.restype = ctypes.POINTER(ctypes.c_float)
@@ -66,6 +67,8 @@ class DMatrix:
                 xglib.XGDMatrixCreateFromFile(ctypes.c_char_p(data.encode('utf-8')), 0))
         elif isinstance(data, scp.csr_matrix):
             self.__init_from_csr(data)
+        elif isinstance(data, scp.csc_matrix):
+            self.__init_from_csc(data)            
         elif isinstance(data, numpy.ndarray) and len(data.shape) == 2:
             self.__init_from_npy2d(data, missing)
         else:
@@ -88,6 +91,15 @@ class DMatrix:
             (ctypes.c_float * len(csr.data))(*csr.data),
             len(csr.indptr), len(csr.data)))
 
+    def __init_from_csc(self, csc):
+        """convert data from csr matrix"""
+        assert len(csc.indices) == len(csc.data)
+        self.handle = ctypes.c_void_p(xglib.XGDMatrixCreateFromCSC(
+            (ctypes.c_ulong  * len(csc.indptr))(*csc.indptr),
+            (ctypes.c_uint * len(csc.indices))(*csc.indices),
+            (ctypes.c_float * len(csc.data))(*csc.data),
+            len(csc.indptr), len(csc.data)))
+
     def __init_from_npy2d(self,mat,missing):
         """convert data from numpy matrix"""
         data = numpy.array(mat.reshape(mat.size), dtype='float32')

wrapper/xgboost_wrapper.cpp

@@ -14,6 +14,7 @@ using namespace std;
 #include "../src/learner/learner-inl.hpp"
 #include "../src/io/io.h"
 #include "../src/utils/utils.h"
+#include "../src/utils/matrix_csr.h"
 #include "../src/io/simple_dmatrix-inl.hpp"
 
 using namespace xgboost;
@@ -102,6 +103,31 @@ extern "C"{
     mat.info.info.num_row = nindptr - 1;
     return p_mat;
   }
+  XGB_DLL void* XGDMatrixCreateFromCSC(const bst_ulong *col_ptr,
+                                       const unsigned *indices,
+                                       const float *data,
+                                       bst_ulong nindptr,
+                                       bst_ulong nelem) {
+    DMatrixSimple *p_mat = new DMatrixSimple();
+    DMatrixSimple &mat = *p_mat;
+    utils::SparseCSRMBuilder<RowBatch::Entry, false> builder(mat.row_ptr_, mat.row_data_);
+    builder.InitBudget();
+    bst_ulong ncol = nindptr - 1;
+    for (bst_ulong i = 0; i < ncol; ++i) {
+      for (unsigned j = col_ptr[i]; j < col_ptr[i+1]; ++j) {
+        builder.AddBudget(indices[j]);
+      }
+    }
+    builder.InitStorage();
+    for (bst_ulong i = 0; i < ncol; ++i) {
+      for (unsigned j = col_ptr[i]; j < col_ptr[i+1]; ++j) {
+        builder.PushElem(indices[j], RowBatch::Entry(static_cast<bst_uint>(i), data[j]));
+      }
+    }
+    mat.info.info.num_row = mat.row_ptr_.size() - 1;
+    mat.info.info.num_col = static_cast<size_t>(ncol);
+    return p_mat;
+  }
   void* XGDMatrixCreateFromMat(const float *data,
                                bst_ulong nrow,
                                bst_ulong ncol,

wrapper/xgboost_wrapper.h

@@ -22,7 +22,7 @@ extern "C" {
    * \return a loaded data matrix
    */
   XGB_DLL void* XGDMatrixCreateFromFile(const char *fname, int silent);
-  /*! 
+  /*!
    * \brief create a matrix content from csr format
    * \param indptr pointer to row headers
    * \param indices findex
@@ -36,6 +36,20 @@ extern "C" {
                                        const float *data,
                                        bst_ulong nindptr,
                                        bst_ulong nelem);
+  /*!
+   * \brief create a matrix content from CSC format
+   * \param col_ptr pointer to col headers
+   * \param indices findex
+   * \param data fvalue
+   * \param nindptr number of rows in the matix + 1 
+   * \param nelem number of nonzero elements in the matrix
+   * \return created dmatrix
+   */
+  XGB_DLL void* XGDMatrixCreateFromCSC(const bst_ulong *col_ptr,
+                                       const unsigned *indices,
+                                       const float *data,
+                                       bst_ulong nindptr,
+                                       bst_ulong nelem);  
   /*!
    * \brief create matrix content from dense matrix
    * \param data pointer to the data space