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Fix #4163: always copy sliced data (#4165)

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* Revert "Accept numpy array view. (#4147)"

This reverts commit a985a99cf0.

* Fix #4163: always copy sliced data

* Remove print() from the test; check shape equality

* Check if 'base' attribute exists

* Fix lint

* Address reviewer comment

* Fix lint
This commit is contained in:
Philip Hyunsu Cho
2019-02-20 14:46:34 -08:00
committed by GitHub
parent cecbe0cf71
commit 2aaae2e7bb
6 changed files with 76 additions and 146 deletions
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72
python-package/xgboost/core.py
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@@ -219,17 +219,6 @@ def c_array(ctype, values):
return (ctype * len(values))(*values)
def _get_length_and_stride(data):
"Return length and stride of 1-D data."
if isinstance(data, np.ndarray) and data.base is not None:
length = len(data.base)
stride = data.strides[0] // data.dtype.itemsize
else:
length = len(data)
stride = 1
return length, stride
PANDAS_DTYPE_MAPPER = {'int8': 'int', 'int16': 'int', 'int32': 'int', 'int64': 'int',
'uint8': 'int', 'uint16': 'int', 'uint32': 'int', 'uint64': 'int',
'float16': 'float', 'float32': 'float', 'float64': 'float',
@@ -595,14 +584,16 @@ class DMatrix(object):
data: numpy array
The array of data to be set
"""
if getattr(data, 'base', None) is not None and \
data.base is not None and isinstance(data, np.ndarray) \
and isinstance(data.base, np.ndarray) and (not data.flags.c_contiguous):
self.set_float_info_npy2d(field, data)
return
c_data = c_array(ctypes.c_float, data)
length, stride = _get_length_and_stride(data)
_check_call(_LIB.XGDMatrixSetFloatInfoStrided(
self.handle,
c_str(field),
c_data,
c_bst_ulong(stride),
c_bst_ulong(length)))
_check_call(_LIB.XGDMatrixSetFloatInfo(self.handle,
c_str(field),
c_data,
c_bst_ulong(len(data))))
def set_float_info_npy2d(self, field, data):
"""Set float type property into the DMatrix
@@ -616,15 +607,19 @@ class DMatrix(object):
data: numpy array
The array of data to be set
"""
data = np.array(data, copy=False, dtype=np.float32)
if getattr(data, 'base', None) is not None and \
data.base is not None and isinstance(data, np.ndarray) \
and isinstance(data.base, np.ndarray) and (not data.flags.c_contiguous):
warnings.warn("Use subset (sliced data) of np.ndarray is not recommended " +
"because it will generate extra copies and increase memory consumption")
data = np.array(data, copy=True, dtype=np.float32)
else:
data = np.array(data, copy=False, dtype=np.float32)
c_data = data.ctypes.data_as(ctypes.POINTER(ctypes.c_float))
length, stride = _get_length_and_stride(data)
_check_call(_LIB.XGDMatrixSetFloatInfoStrided(
self.handle,
c_str(field),
c_data,
c_bst_ulong(stride),
c_bst_ulong(length)))
_check_call(_LIB.XGDMatrixSetFloatInfo(self.handle,
c_str(field),
c_data,
c_bst_ulong(len(data))))
def set_uint_info(self, field, data):
"""Set uint type property into the DMatrix.
@@ -637,15 +632,18 @@ class DMatrix(object):
data: numpy array
The array of data to be set
"""
data = np.array(data, copy=False, dtype=ctypes.c_uint)
c_data = c_array(ctypes.c_uint, data)
length, stride = _get_length_and_stride(data)
_check_call(_LIB.XGDMatrixSetUIntInfoStrided(
self.handle,
c_str(field),
c_data,
c_bst_ulong(stride),
c_bst_ulong(length)))
if getattr(data, 'base', None) is not None and \
data.base is not None and isinstance(data, np.ndarray) \
and isinstance(data.base, np.ndarray) and (not data.flags.c_contiguous):
warnings.warn("Use subset (sliced data) of np.ndarray is not recommended " +
"because it will generate extra copies and increase memory consumption")
data = np.array(data, copy=True, dtype=ctypes.c_uint)
else:
data = np.array(data, copy=False, dtype=ctypes.c_uint)
_check_call(_LIB.XGDMatrixSetUIntInfo(self.handle,
c_str(field),
c_array(ctypes.c_uint, data),
c_bst_ulong(len(data))))
def save_binary(self, fname, silent=True):
"""Save DMatrix to an XGBoost buffer.
@@ -741,7 +739,9 @@ class DMatrix(object):
group : array like
Group size of each group
"""
self.set_uint_info('group', group)
_check_call(_LIB.XGDMatrixSetGroup(self.handle,
c_array(ctypes.c_uint, group),
c_bst_ulong(len(group))))
def get_label(self):
"""Get the label of the DMatrix.