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import csv
import os
import tempfile
import warnings
import numpy as np
import pytest
import scipy.sparse
from hypothesis import given, settings, strategies
from scipy.sparse import csr_matrix, rand
import xgboost as xgb
from xgboost import testing as tm
from xgboost.core import DataSplitMode
from xgboost.testing.data import np_dtypes, run_base_margin_info
dpath = "demo/data/"
rng = np.random.RandomState(1994)
class TestDMatrix:
def test_warn_missing(self):
from xgboost import data
with pytest.warns(UserWarning):
data._warn_unused_missing("uri", 4)
with warnings.catch_warnings():
warnings.simplefilter("error")
data._warn_unused_missing("uri", None)
data._warn_unused_missing("uri", np.nan)
with warnings.catch_warnings():
warnings.simplefilter("error")
x = rng.randn(10, 10)
y = rng.randn(10)
xgb.DMatrix(x, y, missing=4)
def test_dmatrix_numpy_init(self):
data = np.random.randn(5, 5)
dm = xgb.DMatrix(data)
assert dm.num_row() == 5
assert dm.num_col() == 5
data = np.array([[1, 2], [3, 4]])
dm = xgb.DMatrix(data)
assert dm.num_row() == 2
assert dm.num_col() == 2
# 0d array
with pytest.raises(ValueError):
xgb.DMatrix(np.array(1))
# 1d array
with pytest.raises(ValueError):
xgb.DMatrix(np.array([1, 2, 3]))
# 3d array
data = np.random.randn(5, 5, 5)
with pytest.raises(ValueError):
xgb.DMatrix(data)
# object dtype
data = np.array([["a", "b"], ["c", "d"]])
with pytest.raises(ValueError):
xgb.DMatrix(data)
def test_np_view(self):
# Sliced Float32 array
y = np.array([12, 34, 56], np.float32)[::2]
from_view = xgb.DMatrix(np.array([[]]), label=y).get_label()
from_array = xgb.DMatrix(np.array([[]]), label=y + 0).get_label()
assert from_view.shape == from_array.shape
assert (from_view == from_array).all()
# Sliced UInt array
z = np.array([12, 34, 56], np.uint32)[::2]
dmat = xgb.DMatrix(np.array([[]]))
dmat.set_uint_info("group", z)
from_view = dmat.get_uint_info("group_ptr")
dmat = xgb.DMatrix(np.array([[]]))
dmat.set_uint_info("group", z + 0)
from_array = dmat.get_uint_info("group_ptr")
assert from_view.shape == from_array.shape
assert (from_view == from_array).all()
def test_slice(self):
X = rng.randn(100, 100)
y = rng.randint(low=0, high=3, size=100).astype(np.float32)
d = xgb.DMatrix(X, y)
np.testing.assert_equal(d.get_label(), y)
fw = rng.uniform(size=100).astype(np.float32)
d.set_info(feature_weights=fw)
# base margin is per-class in multi-class classifier
base_margin = rng.randn(100, 3).astype(np.float32)
d.set_base_margin(base_margin)
np.testing.assert_allclose(d.get_base_margin().reshape(100, 3), base_margin)
ridxs = [1, 2, 3, 4, 5, 6]
sliced = d.slice(ridxs)
# Slicing works with label and other meta info fields
np.testing.assert_equal(sliced.get_label(), y[1:7])
np.testing.assert_equal(sliced.get_float_info("feature_weights"), fw)
np.testing.assert_equal(sliced.get_base_margin(), base_margin[1:7, :].flatten())
np.testing.assert_equal(
sliced.get_base_margin(), sliced.get_float_info("base_margin")
)
# Slicing a DMatrix results into a DMatrix that's equivalent to a DMatrix that's
# constructed from the corresponding NumPy slice
d2 = xgb.DMatrix(X[1:7, :], y[1:7])
d2.set_base_margin(base_margin[1:7, :])
eval_res = {}
_ = xgb.train(
{"num_class": 3, "objective": "multi:softprob", "eval_metric": "mlogloss"},
d,
num_boost_round=2,
evals=[(d2, "d2"), (sliced, "sliced")],
evals_result=eval_res,
)
np.testing.assert_equal(
eval_res["d2"]["mlogloss"], eval_res["sliced"]["mlogloss"]
)
ridxs_arr = np.array(ridxs)[1:] # handles numpy slice correctly
sliced = d.slice(ridxs_arr)
np.testing.assert_equal(sliced.get_label(), y[2:7])
def test_feature_names_slice(self):
data = np.random.randn(5, 5)
# different length
with pytest.raises(ValueError):
xgb.DMatrix(data, feature_names=list("abcdef"))
# contains duplicates
with pytest.raises(ValueError):
xgb.DMatrix(data, feature_names=["a", "b", "c", "d", "d"])
# contains symbol
with pytest.raises(ValueError):
xgb.DMatrix(data, feature_names=["a", "b", "c", "d", "e<1"])
dm = xgb.DMatrix(data)
dm.feature_names = list("abcde")
assert dm.feature_names == list("abcde")
assert dm.slice([0, 1]).num_col() == dm.num_col()
assert dm.slice([0, 1]).feature_names == dm.feature_names
with pytest.raises(ValueError, match=r"Duplicates found: \[.*'bar'.*\]"):
dm.feature_names = ["bar"] * (data.shape[1] - 2) + ["a", "b"]
dm.feature_types = list("qiqiq")
assert dm.feature_types == list("qiqiq")
with pytest.raises(ValueError):
dm.feature_types = list("abcde")
# reset
dm.feature_names = None
dm.feature_types = None
assert dm.feature_names is None
assert dm.feature_types is None
def test_feature_names(self):
data = np.random.randn(100, 5)
target = np.array([0, 1] * 50)
cases = [
["Feature1", "Feature2", "Feature3", "Feature4", "Feature5"],
["要因1", "要因2", "要因3", "要因4", "要因5"],
]
for features in cases:
dm = xgb.DMatrix(data, label=target, feature_names=features)
assert dm.feature_names == features
assert dm.num_row() == 100
assert dm.num_col() == 5
params = {
"objective": "multi:softprob",
"eval_metric": "mlogloss",
"eta": 0.3,
"num_class": 3,
}
bst = xgb.train(params, dm, num_boost_round=10)
scores = bst.get_fscore()
assert list(sorted(k for k in scores)) == features
dummy = np.random.randn(5, 5)
dm = xgb.DMatrix(dummy, feature_names=features)
bst.predict(dm)
# different feature name must raises error
dm = xgb.DMatrix(dummy, feature_names=list("abcde"))
with pytest.raises(ValueError):
bst.predict(dm)
@pytest.mark.skipif(**tm.no_pandas())
def test_save_binary(self):
import pandas as pd
with tempfile.TemporaryDirectory() as tmpdir:
path = os.path.join(tmpdir, "m.dmatrix")
data = pd.DataFrame({"a": [0, 1], "b": [2, 3], "c": [4, 5]})
m0 = xgb.DMatrix(data.loc[:, ["a", "b"]], data["c"])
assert m0.feature_names == ["a", "b"]
m0.save_binary(path)
m1 = xgb.DMatrix(path)
assert m0.feature_names == m1.feature_names
assert m0.feature_types == m1.feature_types
def test_get_info(self):
dtrain, _ = tm.load_agaricus(__file__)
dtrain.get_float_info("label")
dtrain.get_float_info("weight")
dtrain.get_float_info("base_margin")
dtrain.get_uint_info("group_ptr")
group_len = np.array([2, 3, 4])
dtrain.set_group(group_len)
np.testing.assert_equal(group_len, dtrain.get_group())
def test_qid(self):
rows = 100
cols = 10
X, y = rng.randn(rows, cols), rng.randn(rows)
qid = rng.randint(low=0, high=10, size=rows, dtype=np.uint32)
qid = np.sort(qid)
Xy = xgb.DMatrix(X, y)
Xy.set_info(qid=qid)
group_ptr = Xy.get_uint_info("group_ptr")
assert group_ptr[0] == 0
assert group_ptr[-1] == rows
def test_feature_weights(self):
kRows = 10
kCols = 50
rng = np.random.RandomState(1994)
fw = rng.uniform(size=kCols)
X = rng.randn(kRows, kCols)
m = xgb.DMatrix(X)
m.set_info(feature_weights=fw)
np.testing.assert_allclose(fw, m.get_float_info("feature_weights"))
# Handle empty
m.set_info(feature_weights=np.empty((0,)))
assert m.get_float_info("feature_weights").shape[0] == 0
fw -= 1
with pytest.raises(ValueError):
m.set_info(feature_weights=fw)
def test_sparse_dmatrix_csr(self):
nrow = 100
ncol = 1000
x = rand(nrow, ncol, density=0.0005, format="csr", random_state=rng)
assert x.indices.max() < ncol
x.data[:] = 1
dtrain = xgb.DMatrix(x, label=rng.binomial(1, 0.3, nrow))
assert (dtrain.num_row(), dtrain.num_col()) == (nrow, ncol)
watchlist = [(dtrain, "train")]
param = {"max_depth": 3, "objective": "binary:logistic"}
bst = xgb.train(param, dtrain, 5, evals=watchlist)
bst.predict(dtrain)
i32 = csr_matrix((x.data.astype(np.int32), x.indices, x.indptr), shape=x.shape)
f32 = csr_matrix(
(i32.data.astype(np.float32), x.indices, x.indptr), shape=x.shape
)
di32 = xgb.DMatrix(i32)
df32 = xgb.DMatrix(f32)
dense = xgb.DMatrix(f32.toarray(), missing=0)
with tempfile.TemporaryDirectory() as tmpdir:
path = os.path.join(tmpdir, "f32.dmatrix")
df32.save_binary(path)
with open(path, "rb") as fd:
df32_buffer = np.array(fd.read())
path = os.path.join(tmpdir, "f32.dmatrix")
di32.save_binary(path)
with open(path, "rb") as fd:
di32_buffer = np.array(fd.read())
path = os.path.join(tmpdir, "dense.dmatrix")
dense.save_binary(path)
with open(path, "rb") as fd:
dense_buffer = np.array(fd.read())
np.testing.assert_equal(df32_buffer, di32_buffer)
np.testing.assert_equal(df32_buffer, dense_buffer)
def test_sparse_dmatrix_csc(self):
nrow = 1000
ncol = 100
x = rand(nrow, ncol, density=0.0005, format="csc", random_state=rng)
assert x.indices.max() < nrow - 1
x.data[:] = 1
dtrain = xgb.DMatrix(x, label=rng.binomial(1, 0.3, nrow))
assert (dtrain.num_row(), dtrain.num_col()) == (nrow, ncol)
watchlist = [(dtrain, "train")]
param = {"max_depth": 3, "objective": "binary:logistic"}
bst = xgb.train(param, dtrain, 5, evals=watchlist)
bst.predict(dtrain)
def test_unknown_data(self):
class Data:
pass
with pytest.raises(TypeError):
with pytest.warns(UserWarning):
d = Data()
xgb.DMatrix(d)
from scipy import sparse
rng = np.random.RandomState(1994)
X = rng.rand(10, 10)
y = rng.rand(10)
X = sparse.dok_matrix(X)
with pytest.warns(UserWarning, match="dok_matrix"):
Xy = xgb.DMatrix(X, y)
assert Xy.num_row() == 10
assert Xy.num_col() == 10
@pytest.mark.skipif(**tm.no_pandas())
def test_np_categorical(self):
n_features = 10
X, y = tm.make_categorical(10, n_features, n_categories=4, onehot=False)
X = X.values.astype(np.float32)
feature_types = ["c"] * n_features
assert isinstance(X, np.ndarray)
Xy = xgb.DMatrix(X, y, feature_types=feature_types)
np.testing.assert_equal(np.array(Xy.feature_types), np.array(feature_types))
def test_scipy_categorical(self):
from scipy import sparse
n_features = 10
X, y = tm.make_categorical(10, n_features, n_categories=4, onehot=False)
X = X.values.astype(np.float32)
feature_types = ["c"] * n_features
X[1, 3] = np.nan
X[2, 4] = np.nan
X = sparse.csr_matrix(X)
Xy = xgb.DMatrix(X, y, feature_types=feature_types)
np.testing.assert_equal(np.array(Xy.feature_types), np.array(feature_types))
X = sparse.csc_matrix(X)
Xy = xgb.DMatrix(X, y, feature_types=feature_types)
np.testing.assert_equal(np.array(Xy.feature_types), np.array(feature_types))
X = sparse.coo_matrix(X)
Xy = xgb.DMatrix(X, y, feature_types=feature_types)
np.testing.assert_equal(np.array(Xy.feature_types), np.array(feature_types))
def test_uri_categorical(self):
path = os.path.join(dpath, "agaricus.txt.train")
feature_types = ["q"] * 5 + ["c"] + ["q"] * 120
Xy = xgb.DMatrix(
path + "?indexing_mode=1&format=libsvm", feature_types=feature_types
)
np.testing.assert_equal(np.array(Xy.feature_types), np.array(feature_types))
def test_base_margin(self) -> None:
run_base_margin_info(np.asarray, xgb.DMatrix, "cpu")
@given(
strategies.integers(0, 1000),
strategies.integers(0, 100),
strategies.fractions(0, 1),
)
@settings(deadline=None, print_blob=True)
def test_to_csr(self, n_samples, n_features, sparsity) -> None:
if n_samples == 0 or n_features == 0 or sparsity == 1.0:
csr = scipy.sparse.csr_matrix(np.empty((0, 0)))
else:
csr = tm.make_sparse_regression(n_samples, n_features, sparsity, False)[
0
].astype(np.float32)
m = xgb.DMatrix(data=csr)
ret = m.get_data()
np.testing.assert_equal(csr.indptr, ret.indptr)
np.testing.assert_equal(csr.data, ret.data)
np.testing.assert_equal(csr.indices, ret.indices)
def test_dtypes(self) -> None:
n_samples = 128
n_features = 16
for orig, x in np_dtypes(n_samples, n_features):
m0 = xgb.DMatrix(orig)
m1 = xgb.DMatrix(x)
assert tm.predictor_equal(m0, m1)
@pytest.mark.skipif(tm.is_windows(), reason="Rabit does not run on windows")
class TestDMatrixColumnSplit:
def test_numpy(self):
def verify_numpy():
data = np.random.randn(5, 5)
dm = xgb.DMatrix(data, data_split_mode=DataSplitMode.COL)
assert dm.num_row() == 5
assert dm.num_col() == 5 * xgb.collective.get_world_size()
assert dm.feature_names is None
assert dm.feature_types is None
tm.run_with_rabit(world_size=3, test_fn=verify_numpy)
def test_numpy_feature_names(self):
def verify_numpy_feature_names():
world_size = xgb.collective.get_world_size()
data = np.random.randn(5, 5)
feature_names = [f"feature{x}" for x in range(5)]
feature_types = ["float"] * 5
dm = xgb.DMatrix(
data,
feature_names=feature_names,
feature_types=feature_types,
data_split_mode=DataSplitMode.COL,
)
assert dm.num_row() == 5
assert dm.num_col() == 5 * world_size
assert len(dm.feature_names) == 5 * world_size
assert dm.feature_names == tm.column_split_feature_names(
feature_names, world_size
)
assert len(dm.feature_types) == 5 * world_size
assert dm.feature_types == ["float"] * 5 * world_size
tm.run_with_rabit(world_size=3, test_fn=verify_numpy_feature_names)
def test_csr(self):
def verify_csr():
indptr = np.array([0, 2, 3, 6])
indices = np.array([0, 2, 2, 0, 1, 2])
data = np.array([1, 2, 3, 4, 5, 6])
X = scipy.sparse.csr_matrix((data, indices, indptr), shape=(3, 3))
dtrain = xgb.DMatrix(X, data_split_mode=DataSplitMode.COL)
assert dtrain.num_row() == 3
assert dtrain.num_col() == 3 * xgb.collective.get_world_size()
tm.run_with_rabit(world_size=3, test_fn=verify_csr)
def test_csc(self):
def verify_csc():
row = np.array([0, 2, 2, 0, 1, 2])
col = np.array([0, 0, 1, 2, 2, 2])
data = np.array([1, 2, 3, 4, 5, 6])
X = scipy.sparse.csc_matrix((data, (row, col)), shape=(3, 3))
dtrain = xgb.DMatrix(X, data_split_mode=DataSplitMode.COL)
assert dtrain.num_row() == 3
assert dtrain.num_col() == 3 * xgb.collective.get_world_size()
tm.run_with_rabit(world_size=3, test_fn=verify_csc)
def test_coo(self):
def verify_coo():
row = np.array([0, 2, 2, 0, 1, 2])
col = np.array([0, 0, 1, 2, 2, 2])
data = np.array([1, 2, 3, 4, 5, 6])
X = scipy.sparse.coo_matrix((data, (row, col)), shape=(3, 3))
dtrain = xgb.DMatrix(X, data_split_mode=DataSplitMode.COL)
assert dtrain.num_row() == 3
assert dtrain.num_col() == 3 * xgb.collective.get_world_size()
tm.run_with_rabit(world_size=3, test_fn=verify_coo)
def test_uri(self):
def verify_uri():
rank = xgb.collective.get_rank()
with tempfile.TemporaryDirectory() as tmpdir:
filename = os.path.join(tmpdir, f"test_data_{rank}.csv")
data = np.random.rand(5, 5)
with open(filename, mode="w", newline="") as file:
writer = csv.writer(file)
for row in data:
writer.writerow(row)
dtrain = xgb.DMatrix(
f"{filename}?format=csv", data_split_mode=DataSplitMode.COL
)
assert dtrain.num_row() == 5
assert dtrain.num_col() == 5 * xgb.collective.get_world_size()
tm.run_with_rabit(world_size=3, test_fn=verify_uri)
def test_list(self):
def verify_list():
data = [
[1, 2, 3, 4, 5],
[6, 7, 8, 9, 10],
[11, 12, 13, 14, 15],
[16, 17, 18, 19, 20],
[21, 22, 23, 24, 25],
]
dm = xgb.DMatrix(data, data_split_mode=DataSplitMode.COL)
assert dm.num_row() == 5
assert dm.num_col() == 5 * xgb.collective.get_world_size()
tm.run_with_rabit(world_size=3, test_fn=verify_list)
def test_tuple(self):
def verify_tuple():
data = (
(1, 2, 3, 4, 5),
(6, 7, 8, 9, 10),
(11, 12, 13, 14, 15),
(16, 17, 18, 19, 20),
(21, 22, 23, 24, 25),
)
dm = xgb.DMatrix(data, data_split_mode=DataSplitMode.COL)
assert dm.num_row() == 5
assert dm.num_col() == 5 * xgb.collective.get_world_size()
tm.run_with_rabit(world_size=3, test_fn=verify_tuple)
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