fix numpy convert

LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2014 Tianqi Chen
+Copyright (c) 2014 by Tianqi Chen and Contributors 
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.

python/example/demo.py

@@ -68,7 +68,9 @@ for l in open('agaricus.txt.train'):
     i += 1
 
 csr = scipy.sparse.csr_matrix( (dat, (row,col)) )
+print 'haha'
 dtrain = xgb.DMatrix( csr )
+print 'set label'
 dtrain.set_label(labels)
 evallist  = [(dtest,'eval'), (dtrain,'train')]
 bst = xgb.train( param, dtrain, num_round, evallist )

python/xgboost.py

@@ -33,15 +33,16 @@ def ctypes2numpy( cptr, length ):
 # data matrix used in xgboost
 class DMatrix:
     # constructor
-    def __init__(self, data=None, label=None):
+    def __init__(self, data=None, label=None, missing=0.0):
         self.handle = xglib.XGDMatrixCreate()
         if data == None:
             return
         if isinstance(data,str):
-            xglib.XGDMatrixLoad(self.handle, ctypes.c_char_p(data), 1) 
+            xglib.XGDMatrixLoad(self.handle, ctypes.c_char_p(data), 1)             
-            
         elif isinstance(data,scp.csr_matrix):
             self.__init_from_csr(data)
+        elif isinstance(data, numpy.ndarray) and len(data.shape) == 2:
+            self.__init_from_npy2d(data, missing)
         else:
             try:
                 csr = scp.csr_matrix(data)
@@ -59,6 +60,12 @@ class DMatrix:
                                  ( ctypes.c_uint  * len(csr.indices) )(*csr.indices),
                                  ( ctypes.c_float * len(csr.data) )(*csr.data),
                                  len(csr.indptr), len(csr.data) )
+    # convert data from numpy matrix
+    def __init_from_npy2d(self,mat,missing):
+        data = numpy.array( mat.reshape(mat.size), dtype='float32' )
+        xglib.XGDMatrixParseMat( self.handle, 
+                                 data.ctypes.data_as(ctypes.POINTER(ctypes.c_float)), 
+                                 mat.shape[0], mat.shape[1], ctypes.c_float(missing) )
     # destructor
     def __del__(self):
         xglib.XGDMatrixFree(self.handle)    
@@ -103,7 +110,7 @@ class DMatrix:
 
 class Booster:
     """learner class """
-    def __init__(self, params, cache=[]):
+    def __init__(self, params={}, cache=[]):
         """ constructor, param: """    
         for d in cache:
             assert isinstance(d,DMatrix)

python/xgboost_python.cpp

@@ -52,6 +52,28 @@ namespace xgboost{
                 for( size_t i = 0; i < nelem; ++ i ){
                     mat.row_data_[i] = XGEntry(indices[i], data[i]);
                 }
+                this->data.InitData();
+                this->init_col_ = true;
+            }
+
+            inline void ParseMat( const float *data,
+                                  size_t nrow,
+                                  size_t ncol,
+                                  float  missing ){
+                xgboost::booster::FMatrixS &mat = this->data;
+                mat.Clear();
+                for( size_t i = 0; i < nrow; ++i, data += ncol ){
+                    size_t nelem = 0;
+                    for( size_t j = 0; j < ncol; ++j ){
+                        if( data[j] != missing ){                           
+                            mat.row_data_.push_back( XGEntry(j, data[j]) );
+                            ++ nelem;
+                        }
+                    }
+                    mat.row_ptr_.push_back( mat.row_ptr_.back() + nelem );
+                }
+                this->data.InitData();
+                this->init_col_ = true;
             }
             inline void SetLabel( const float *label, size_t len ){
                 this->info.labels.resize( len );
@@ -163,6 +185,13 @@ extern "C"{
                             size_t nelem ){
         static_cast<DMatrix*>(handle)->ParseCSR(indptr, indices, data, nindptr, nelem);
     }
+    void XGDMatrixParseMat( void *handle, 
+                            const float *data,
+                            size_t nrow,
+                            size_t ncol,
+                            float  missing ){
+      static_cast<DMatrix*>(handle)->ParseMat(data, nrow, ncol, missing);
+    }
     void XGDMatrixSetLabel( void *handle, const float *label, size_t len ){
         static_cast<DMatrix*>(handle)->SetLabel(label,len);        
     }

python/xgboost_python.h

@@ -49,6 +49,19 @@ extern "C"{
                             const float *data,
                             size_t nindptr,
                             size_t nelem );
+    /*! 
+     * \brief set matrix content from data content
+     * \param handle a instance of data matrix
+     * \param data pointer to the data space
+     * \param nrow number of rows
+     * \param ncol number columns
+     * \param missing which value to represent missing value
+     */
+    void XGDMatrixParseMat( void *handle, 
+                            const float *data,
+                            size_t nrow,
+                            size_t ncol,
+                            float  missing );
     /*! 
      * \brief set label of the training matrix
      * \param handle a instance of data matrix
@@ -74,9 +87,16 @@ extern "C"{
      * \brief get label set from matrix
      * \param handle a instance of data matrix
      * \param len used to set result length
-     * \return pointer to the row
+     * \return pointer to the label
      */
     const float* XGDMatrixGetLabel( const void *handle, size_t* len );
+    /*! 
+     * \brief get weight set from matrix
+     * \param handle a instance of data matrix
+     * \param len used to set result length
+     * \return pointer to the weight
+     */
+    const float* XGDMatrixGetWeight( const void *handle, size_t* len );
     /*! 
      * \brief clear all the records, including feature matrix and label
      * \param handle a instance of data matrix