good

python/xgboost.py

@@ -1,5 +1,7 @@
 # module for xgboost
 import ctypes 
+import numpy
+import scipy.sparse as scp
 
 # load in xgboost library
 xglib = ctypes.cdll.LoadLibrary('./libxgboostpy.so')
@@ -8,15 +10,57 @@ xglib = ctypes.cdll.LoadLibrary('./libxgboostpy.so')
 class REntry(ctypes.Structure):
     _fields_ = [("findex", ctypes.c_uint), ("fvalue", ctypes.c_float) ]
 
-
+# data matrix used in xgboost
 class DMatrix:
-    def __init__(self,fname = None):
+    # constructor
-        self.__handle = xglib.XGDMatrixCreate();
+    def __init__(self, data=None, label=None):
-        if fname != None:
+        self.handle = xglib.XGDMatrixCreate();
-            xglib.XGDMatrixLoad(self.__handle, ctypes.c_char_p(fname), 0)
+        if data == None:
+            return        
+        if type(data) is str:
+            xglib.XGDMatrixLoad(self.handle, ctypes.c_char_p(data), 1) 
+        elif type(data) is scp.csr_matrix:
+            self.__init_from_csr(data)
+        else:
+            try:
+                csr = scp.csr_matrix(data)
+                self.__init_from_csr(data)
+            except:
+                raise "DMatrix", "can not intialize DMatrix from"+type(data)                
+        if label != None:
+            self.set_label(label)
+
+    # convert data from csr matrix
+    def __init_from_csr(self,csr):
+        assert len(csr.indices) == len(csr.data)
+        xglib.XGDMatrixParseCSR( self.handle, 
+                                 ( ctypes.c_ulong  * len(csr.indptr) )(*csr.indptr),
+                                 ( ctypes.c_uint  * len(csr.indices) )(*csr.indices),
+                                 ( ctypes.c_float * len(csr.data) )(*csr.data),
+                                 len(csr.indptr), len(csr.data) )
+    # destructor
     def __del__(self):
-        xglib.XGDMatrixFree(self.__handle)
+        xglib.XGDMatrixFree(self.handle)
-
+    # load data from file 
-dmata = DMatrix('xx.buffer')
+    def load(self, fname):
-
+        xglib.XGDMatrixLoad(self.handle, ctypes.c_char_p(fname), 1)
+    # set label of dmatrix
+    def set_label(self, label):
+        xglib.XGDMatrixSetLabel(self.handle, (ctypes.c_float*len(label))(*label), len(label) );
+    # get label from dmatrix
+    def get_label(self):
+        GetLabel = xglib.XGDMatrixGetLabel
+        GetLabel.restype = ctypes.POINTER( ctypes.c_float )
+        length = ctypes.c_ulong()
+        labels = GetLabel(self.handle, ctypes.byref(length));
+        return [ labels[i] for i in xrange(length.value) ]
+    # append a row to DMatrix
+    def add_row(self, row):
+        xglib.XGDMatrixAddRow(self.handle, (REntry*len(row))(*row), len(row) );
+    
 
+mat = DMatrix('xx.buffer')
+lb = mat.get_label()
+print len(lb)
+mat.set_label(lb)
+mat.add_row( [(1,2), (3,4)] )

python/xgboost_python.cpp

@@ -18,6 +18,37 @@ namespace xgboost{
                 this->CacheLoad(fname, silent);
                 init_col_ = this->data.HaveColAccess();
             }
+            inline void AddRow( const XGEntry *data, size_t len ){
+                xgboost::booster::FMatrixS &mat = this->data;
+                mat.row_data_.resize( mat.row_ptr_.back() + len );
+                memcpy( &mat.row_data_[mat.row_ptr_.back()], data, sizeof(XGEntry)*len );
+                mat.row_ptr_.push_back( mat.row_ptr_.back() + len );
+            }
+            inline void ParseCSR( const size_t *indptr,
+                                  const unsigned *indices,
+                                  const float *data,
+                                  size_t nindptr,
+                                  size_t nelem ){
+                xgboost::booster::FMatrixS &mat = this->data;
+                mat.row_ptr_.resize( nindptr );
+                memcpy( &mat.row_ptr_[0], indptr, sizeof(size_t)*nindptr );
+                mat.row_data_.resize( nelem );
+                for( size_t i = 0; i < nelem; ++ i ){
+                    mat.row_data_[i] = XGEntry(indices[i], data[i]);
+                }
+            }
+            inline void SetLabel( const float *label, size_t len ){
+                this->info.labels.resize( len );
+                memcpy( &(this->info).labels[0], label, sizeof(float)*len );
+            }
+            inline const float* GetLabel( size_t* len ) const{
+                *len = this->info.labels.size();
+                return &(this->info.labels[0]);
+            }
+            inline void InitTrain(void){
+                if(!this->data.HaveColAccess()) this->data.InitData();
+                utils::Assert( this->data.NumRow() == this->info.labels.size(), "DMatrix: number of labels must match number of rows in matrix");
+            }
         };
     };
 };
@@ -25,17 +56,34 @@ namespace xgboost{
 using namespace xgboost::python;
 
 extern "C"{
-    void* XGDMatrixCreate(void){
+    void* XGDMatrixCreate( void ){
         return new DMatrix();
     }
-    void XGDMatrixFree(void *handle){
+    void XGDMatrixFree( void *handle ){
         delete static_cast<DMatrix*>(handle);
     }
-    void XGDMatrixLoad(void *handle, const char *fname, int silent){
+    void XGDMatrixLoad( void *handle, const char *fname, int silent ){
         static_cast<DMatrix*>(handle)->Load(fname, silent!=0);
     }
-    void XGDMatrixSaveBinary(void *handle, const char *fname, int silent){
+    void XGDMatrixSaveBinary( void *handle, const char *fname, int silent ){
         static_cast<DMatrix*>(handle)->SaveBinary(fname, silent!=0);
     }
+    void XGDMatrixAddRow( void *handle, const XGEntry *data, size_t len ){
+        static_cast<DMatrix*>(handle)->AddRow(data, len);
+    }
+    void XGDMatrixParseCSR( void *handle, 
+                            const size_t *indptr,
+                            const unsigned *indices,
+                            const float *data,
+                            size_t nindptr,
+                            size_t nelem ){
+        static_cast<DMatrix*>(handle)->ParseCSR(indptr, indices, data, nindptr, nelem);
+    }
+    void XGDMatrixSetLabel( void *handle, const float *label, size_t len ){
+        static_cast<DMatrix*>(handle)->SetLabel(label,len);        
+    }
+    const float* XGDMatrixGetLabel( const void *handle, size_t* len ){
+        return static_cast<const DMatrix*>(handle)->GetLabel(len);
+    }
 };
 

python/xgboost_python.h

@@ -34,14 +34,41 @@ extern "C"{
      * \param silent print statistics when saving
      */
     void XGDMatrixSaveBinary(void *handle, const char *fname, int silent);
+    /*! 
+     * \brief set matrix content from csr format
+     * \param handle a instance of data matrix
+     * \param indptr pointer to row 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
+     */
+    void XGDMatrixParseCSR( void *handle, 
+                            const size_t *indptr,
+                            const unsigned *indices,
+                            const float *data,
+                            size_t nindptr,
+                            size_t nelem );
+    /*! 
+     * \brief set label of the training matrix
+     * \param handle a instance of data matrix
+     * \param data array of row content 
+     * \param len length of array
+     */    
+    void XGDMatrixSetLabel( void *handle, const float *label, size_t len );        
+    /*! 
+     * \brief get label set from matrix
+     * \param handle a instance of data matrix
+     * \param len used to set result length
+     */
+    const float* XGDMatrixGetLabel( const void *handle, size_t* len );
     /*! 
      * \brief add row 
      * \param handle a instance of data matrix
-     * \param fname file name 
+     * \param data array of row content 
-     * \return a new data matrix
+     * \param len length of array
      */
-    void XGDMatrixPush(void *handle, const XGEntry *data, int len);
+    void XGDMatrixAddRow(void *handle, const XGEntry *data, size_t len);
-    
     /*! 
      * \brief create a booster
      */