Cleanup str roundtrip using ctypes
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sinhrks
parent
bad4a27b9f
commit
bb6b7ded55
@ -21,16 +21,66 @@ class XGBoostError(Exception):
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"""Error throwed by xgboost trainer."""
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pass
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PY3 = (sys.version_info[0] == 3)
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if sys.version_info[0] == 3:
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if PY3:
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# pylint: disable=invalid-name, redefined-builtin
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STRING_TYPES = str,
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unicode = str
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else:
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# pylint: disable=invalid-name
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STRING_TYPES = basestring,
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def from_pystr_to_cstr(data):
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"""Convert a list of Python str to C pointer
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Parameters
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----------
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data : list
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list of str
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"""
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if isinstance(data, list):
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pointers = (ctypes.c_char_p * len(data))()
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if PY3:
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data = [bytes(d, 'utf-8') for d in data]
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else:
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data = [d.encode('utf-8') if isinstance(d, unicode) else d
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for d in data]
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pointers[:] = data
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return pointers
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else:
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# copy from above when we actually use it
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raise NotImplementedError
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def from_cstr_to_pystr(data, length):
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"""Revert C pointer to Python str
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Parameters
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----------
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data : ctypes pointer
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pointer to data
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length : ctypes pointer
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pointer to length of data
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"""
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if PY3:
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res = []
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for i in range(length.value):
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try:
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res.append(str(data[i].decode('ascii')))
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except UnicodeDecodeError:
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res.append(str(data[i].decode('utf-8')))
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else:
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res = []
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for i in range(length.value):
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try:
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res.append(str(data[i].decode('ascii')))
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except UnicodeDecodeError:
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res.append(unicode(data[i].decode('utf-8')))
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return res
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def find_lib_path():
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"""Load find the path to xgboost dynamic library files.
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@ -787,21 +837,12 @@ class Booster(object):
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sarr = ctypes.POINTER(ctypes.c_char_p)()
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if self.feature_names is not None and fmap == '':
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flen = int(len(self.feature_names))
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fname = (ctypes.c_char_p * flen)()
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ftype = (ctypes.c_char_p * flen)()
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fname = from_pystr_to_cstr(self.feature_names)
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# supports quantitative type only
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# {'q': quantitative, 'i': indicator}
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if sys.version_info[0] == 3:
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features = [bytes(f, 'utf-8') for f in self.feature_names]
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types = [bytes('q', 'utf-8')] * flen
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else:
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features = [f.encode('utf-8') if isinstance(f, unicode) else f
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for f in self.feature_names]
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types = ['q'] * flen
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fname[:] = features
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ftype[:] = types
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ftype = from_pystr_to_cstr(['q'] * flen)
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_check_call(_LIB.XGBoosterDumpModelWithFeatures(self.handle,
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flen,
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fname,
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@ -815,13 +856,7 @@ class Booster(object):
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int(with_stats),
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ctypes.byref(length),
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ctypes.byref(sarr)))
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res = []
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for i in range(length.value):
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try:
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res.append(str(sarr[i].decode('ascii')))
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except UnicodeDecodeError:
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res.append(unicode(sarr[i].decode('utf-8')))
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res = from_cstr_to_pystr(sarr, length)
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return res
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def get_fscore(self, fmap=''):
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@ -6,106 +6,125 @@ import unittest
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dpath = 'demo/data/'
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class TestBasic(unittest.TestCase):
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def test_basic(self):
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dtrain = xgb.DMatrix(dpath + 'agaricus.txt.train')
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dtest = xgb.DMatrix(dpath + 'agaricus.txt.test')
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param = {'max_depth':2, 'eta':1, 'silent':1, 'objective':'binary:logistic' }
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# specify validations set to watch performance
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watchlist = [(dtest,'eval'), (dtrain,'train')]
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num_round = 2
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bst = xgb.train(param, dtrain, num_round, watchlist)
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# this is prediction
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preds = bst.predict(dtest)
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labels = dtest.get_label()
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err = sum(1 for i in range(len(preds)) if int(preds[i]>0.5)!=labels[i]) / float(len(preds))
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# error must be smaller than 10%
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assert err < 0.1
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# save dmatrix into binary buffer
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dtest.save_binary('dtest.buffer')
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# save model
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bst.save_model('xgb.model')
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# load model and data in
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bst2 = xgb.Booster(model_file='xgb.model')
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dtest2 = xgb.DMatrix('dtest.buffer')
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preds2 = bst2.predict(dtest2)
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# assert they are the same
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assert np.sum(np.abs(preds2-preds)) == 0
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def test_dmatrix_init(self):
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data = np.random.randn(5, 5)
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# different length
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self.assertRaises(ValueError, xgb.DMatrix, data,
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feature_names=list('abcdef'))
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# contains duplicates
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self.assertRaises(ValueError, xgb.DMatrix, data,
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feature_names=['a', 'b', 'c', 'd', 'd'])
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# contains symbol
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self.assertRaises(ValueError, xgb.DMatrix, data,
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feature_names=['a', 'b', 'c', 'd', 'e=1'])
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def test_feature_names(self):
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data = np.random.randn(100, 5)
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target = np.array([0, 1] * 50)
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cases = [['Feature1', 'Feature2', 'Feature3', 'Feature4', 'Feature5'],
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[u'要因1', u'要因2', u'要因3', u'要因4', u'要因5']]
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for features in cases:
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dm = xgb.DMatrix(data, label=target,
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feature_names=features)
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assert dm.feature_names == features
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assert dm.num_row() == 100
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assert dm.num_col() == 5
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params={'objective': 'multi:softprob',
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'eval_metric': 'mlogloss',
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'eta': 0.3,
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'num_class': 3}
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bst = xgb.train(params, dm, num_boost_round=10)
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scores = bst.get_fscore()
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assert list(sorted(k for k in scores)) == features
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dummy = np.random.randn(5, 5)
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dm = xgb.DMatrix(dummy, feature_names=features)
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bst.predict(dm)
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# different feature name must raises error
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dm = xgb.DMatrix(dummy, feature_names=list('abcde'))
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self.assertRaises(ValueError, bst.predict, dm)
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def test_load_file_invalid(self):
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self.assertRaises(ValueError, xgb.Booster,
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model_file='incorrect_path')
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def test_plotting(self):
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bst2 = xgb.Booster(model_file='xgb.model')
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# plotting
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def test_basic():
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dtrain = xgb.DMatrix(dpath + 'agaricus.txt.train')
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dtest = xgb.DMatrix(dpath + 'agaricus.txt.test')
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param = {'max_depth':2, 'eta':1, 'silent':1, 'objective':'binary:logistic' }
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# specify validations set to watch performance
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watchlist = [(dtest,'eval'), (dtrain,'train')]
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num_round = 2
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bst = xgb.train(param, dtrain, num_round, watchlist)
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# this is prediction
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preds = bst.predict(dtest)
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labels = dtest.get_label()
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err = sum(1 for i in range(len(preds)) if int(preds[i]>0.5)!=labels[i]) / float(len(preds))
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# error must be smaller than 10%
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assert err < 0.1
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import matplotlib
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matplotlib.use('Agg')
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# save dmatrix into binary buffer
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dtest.save_binary('dtest.buffer')
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# save model
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bst.save_model('xgb.model')
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# load model and data in
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bst2 = xgb.Booster(model_file='xgb.model')
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dtest2 = xgb.DMatrix('dtest.buffer')
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preds2 = bst2.predict(dtest2)
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# assert they are the same
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assert np.sum(np.abs(preds2-preds)) == 0
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from matplotlib.axes import Axes
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from graphviz import Digraph
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def test_feature_names():
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data = np.random.randn(100, 5)
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target = np.array([0, 1] * 50)
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ax = xgb.plot_importance(bst2)
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assert isinstance(ax, Axes)
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assert ax.get_title() == 'Feature importance'
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assert ax.get_xlabel() == 'F score'
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assert ax.get_ylabel() == 'Features'
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assert len(ax.patches) == 4
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cases = [['Feature1', 'Feature2', 'Feature3', 'Feature4', 'Feature5'],
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[u'要因1', u'要因2', u'要因3', u'要因4', u'要因5']]
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for features in cases:
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dm = xgb.DMatrix(data, label=target,
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feature_names=features)
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assert dm.feature_names == features
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assert dm.num_row() == 100
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assert dm.num_col() == 5
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params={'objective': 'multi:softprob',
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'eval_metric': 'mlogloss',
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'eta': 0.3,
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'num_class': 3}
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bst = xgb.train(params, dm, num_boost_round=10)
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scores = bst.get_fscore()
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assert list(sorted(k for k in scores)) == features
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ax = xgb.plot_importance(bst2, color='r',
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title='t', xlabel='x', ylabel='y')
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assert isinstance(ax, Axes)
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assert ax.get_title() == 't'
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assert ax.get_xlabel() == 'x'
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assert ax.get_ylabel() == 'y'
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assert len(ax.patches) == 4
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for p in ax.patches:
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assert p.get_facecolor() == (1.0, 0, 0, 1.0) # red
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def test_plotting():
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bst2 = xgb.Booster(model_file='xgb.model')
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# plotting
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ax = xgb.plot_importance(bst2, color=['r', 'r', 'b', 'b'],
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title=None, xlabel=None, ylabel=None)
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assert isinstance(ax, Axes)
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assert ax.get_title() == ''
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assert ax.get_xlabel() == ''
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assert ax.get_ylabel() == ''
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assert len(ax.patches) == 4
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assert ax.patches[0].get_facecolor() == (1.0, 0, 0, 1.0) # red
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assert ax.patches[1].get_facecolor() == (1.0, 0, 0, 1.0) # red
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assert ax.patches[2].get_facecolor() == (0, 0, 1.0, 1.0) # blue
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assert ax.patches[3].get_facecolor() == (0, 0, 1.0, 1.0) # blue
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import matplotlib
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matplotlib.use('Agg')
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g = xgb.to_graphviz(bst2, num_trees=0)
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assert isinstance(g, Digraph)
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ax = xgb.plot_tree(bst2, num_trees=0)
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assert isinstance(ax, Axes)
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from matplotlib.axes import Axes
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from graphviz import Digraph
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ax = xgb.plot_importance(bst2)
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assert isinstance(ax, Axes)
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assert ax.get_title() == 'Feature importance'
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assert ax.get_xlabel() == 'F score'
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assert ax.get_ylabel() == 'Features'
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assert len(ax.patches) == 4
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ax = xgb.plot_importance(bst2, color='r',
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title='t', xlabel='x', ylabel='y')
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assert isinstance(ax, Axes)
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assert ax.get_title() == 't'
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assert ax.get_xlabel() == 'x'
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assert ax.get_ylabel() == 'y'
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assert len(ax.patches) == 4
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for p in ax.patches:
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assert p.get_facecolor() == (1.0, 0, 0, 1.0) # red
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ax = xgb.plot_importance(bst2, color=['r', 'r', 'b', 'b'],
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title=None, xlabel=None, ylabel=None)
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assert isinstance(ax, Axes)
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assert ax.get_title() == ''
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assert ax.get_xlabel() == ''
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assert ax.get_ylabel() == ''
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assert len(ax.patches) == 4
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assert ax.patches[0].get_facecolor() == (1.0, 0, 0, 1.0) # red
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assert ax.patches[1].get_facecolor() == (1.0, 0, 0, 1.0) # red
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assert ax.patches[2].get_facecolor() == (0, 0, 1.0, 1.0) # blue
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assert ax.patches[3].get_facecolor() == (0, 0, 1.0, 1.0) # blue
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g = xgb.to_graphviz(bst2, num_trees=0)
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assert isinstance(g, Digraph)
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ax = xgb.plot_tree(bst2, num_trees=0)
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assert isinstance(ax, Axes)
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