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import numpy as np
import pytest
import tiledb
from tiledb.tests.common import DiskTestCase
class DimensionLabelTestCase(DiskTestCase):
def test_dim_label_schema(self):
dim_label_schema1 = tiledb.DimLabelSchema(
"decreasing", label_dtype=np.float64, dim_dtype=np.int32
)
filter = tiledb.FilterList()
dim_label_schema2 = tiledb.DimLabelSchema(
"increasing",
label_dtype=np.float32,
dim_dtype=np.int64,
dim_tile=20,
label_filters=filter,
)
assert dim_label_schema1.label_order == "decreasing"
assert dim_label_schema1.label_dtype == np.float64
assert dim_label_schema1.dim_dtype == np.int32
assert dim_label_schema1.dim_tile is None
assert dim_label_schema1.label_filters is None
assert dim_label_schema2.label_order == "increasing"
assert dim_label_schema2.label_dtype == np.float32
assert dim_label_schema2.dim_dtype == np.int64
assert dim_label_schema2.dim_tile == 20
assert dim_label_schema2.label_filters == filter
def test_dim_label_schema_from_dim(self):
dim = tiledb.Dim("dim", domain=(1, 10), dtype=np.int32, tile=10)
dim_label_schema3 = dim.create_label_schema("decreasing", np.int32, tile=2)
filter = tiledb.FilterList()
dim_label_schema2 = dim.create_label_schema(
order="increasing", dtype=np.float32, tile=5, filters=filter
)
dim_label_schema1 = dim.create_label_schema("decreasing", np.float64, tile=None)
assert dim_label_schema1.label_order == "decreasing"
assert dim_label_schema1.label_dtype == np.float64
assert dim_label_schema1.dim_dtype == np.int32
assert dim_label_schema1.dim_tile == 10
assert dim_label_schema1.label_filters is None
assert dim_label_schema3.label_order == "decreasing"
assert dim_label_schema3.label_dtype == np.int32
assert dim_label_schema3.dim_dtype == np.int32
assert dim_label_schema3.dim_tile == 2
assert dim_label_schema3.label_filters is None
assert dim_label_schema2.label_order == "increasing"
assert dim_label_schema2.label_dtype == np.float32
assert dim_label_schema2.dim_dtype == np.int32
assert dim_label_schema2.dim_tile == 5
assert dim_label_schema2.label_filters == filter
assert dim.tile == 10
@pytest.mark.skipif(
tiledb.libtiledb.version()[0] == 2 and tiledb.libtiledb.version()[1] < 15,
reason="dimension labels requires libtiledb version 2.15 or greater",
)
def test_add_to_array_schema(self):
dim = tiledb.Dim("dim", domain=(1, 10))
dom = tiledb.Domain(dim)
att = tiledb.Attr("val", dtype=np.uint64)
filters = tiledb.FilterList([tiledb.ZstdFilter(10)])
dim_labels = {
0: {
"l1": tiledb.DimLabelSchema(
"increasing",
label_dtype=np.float64,
dim_dtype=dim.dtype,
dim_tile=10,
label_filters=filters,
)
}
}
schema = tiledb.ArraySchema(domain=dom, attrs=(att,), dim_labels=dim_labels)
assert schema.has_dim_label("l1")
assert not schema.has_dim_label("fake_name")
# Check the dimension label properties
dim_label = schema.dim_label("l1")
assert dim_label.dtype == np.float64
assert not dim_label.isvar
assert not dim_label.isascii
# Create array check values in dimension label schema
uri = self.path("array_with_label")
tiledb.Array.create(uri, schema)
# Load the array schema for the dimension label
base_array_schema = tiledb.ArraySchema.load(uri)
dim_label = base_array_schema.dim_label("l1")
label_array_schema = tiledb.ArraySchema.load(dim_label.uri)
# Chack the array schema for the dimension label
label_dim = label_array_schema.domain.dim(0)
assert label_dim.tile == 10
assert label_dim.dtype == np.uint64
label_attr = label_array_schema.attr(dim_label.label_attr_name)
assert label_attr.dtype == np.float64
assert label_attr.filters == filters
@pytest.mark.skipif(
tiledb.libtiledb.version()[0] == 2 and tiledb.libtiledb.version()[1] < 15,
reason="dimension labels requires libtiledb version 2.15 or greater",
)
def test_add_to_array_schema_out_of_bounds(self):
dim = tiledb.Dim("label", domain=(1, 10))
dom = tiledb.Domain(dim)
att = tiledb.Attr("val", dtype=np.uint64)
dim_labels = {
2: {
"l1": tiledb.DimLabelSchema(
"increasing", label_dtype=dim.dtype, dim_dtype=dim.dtype
)
}
}
with pytest.raises(tiledb.TileDBError):
tiledb.ArraySchema(domain=dom, attrs=(att,), dim_labels=dim_labels)
@pytest.mark.skipif(
tiledb.libtiledb.version()[0] == 2 and tiledb.libtiledb.version()[1] < 15,
reason="dimension labels requires libtiledb version 2.15 or greater",
)
def test_add_to_array_schema_dim_dtype_mismatch(self):
dim = tiledb.Dim("label", domain=(1, 10))
dom = tiledb.Domain(dim)
att = tiledb.Attr("val", dtype=np.uint64)
dim_labels = {
2: {
"label": tiledb.DimLabelSchema(
"increasing", label_dtype=dim.dtype, dim_dtype=np.int32
)
}
}
with pytest.raises(tiledb.TileDBError):
tiledb.ArraySchema(domain=dom, attrs=(att,), dim_labels=dim_labels)
@pytest.mark.skipif(
tiledb.libtiledb.version()[0] == 2 and tiledb.libtiledb.version()[1] < 15,
reason="dimension labels requires libtiledb version 2.15 or greater",
)
@pytest.mark.parametrize("var", [True, False])
def test_dimension_label_round_trip_dense_array(self, var):
# Create array schema with dimension labels
dim = tiledb.Dim("d1", domain=(1, 10))
dom = tiledb.Domain(dim)
att = tiledb.Attr("a1", dtype=np.int64)
dim_labels = {0: {"l1": dim.create_label_schema("increasing", np.int64)}}
if var:
dim_labels = {0: {"l1": dim.create_label_schema("increasing", np.bytes_)}}
schema = tiledb.ArraySchema(domain=dom, attrs=(att,), dim_labels=dim_labels)
# Create array
uri = self.path("dense_array_with_label")
tiledb.Array.create(uri, schema)
# Write data to the array and the label
attr_data = np.arange(1, 11)
label_data = np.arange(-9, 10, 2)
if var:
label_data = np.array(
[str(chr(ord("a") + c) * (10 - c)).encode("utf-8") for c in range(10)]
)
with tiledb.open(uri, "w") as array:
array[:] = {"a1": attr_data, "l1": label_data}
# Load the array schema and get the URI of the dimension label
schema = tiledb.ArraySchema.load(uri)
dim_label = schema.dim_label("l1")
# Read and check the data directly from the dimension label
with tiledb.open(dim_label.uri, "r") as L1:
output_data = L1[:]
output_label_data = output_data[dim_label.label_attr_name]
np.testing.assert_array_equal(output_label_data, label_data)
# Read and check the data using label indexer on parent array
with tiledb.open(uri, "r") as array:
indexer = array.label_index(["l1"])
# Read full array
result = indexer[label_data[0] : label_data[-1]]
np.testing.assert_array_equal(result["a1"], attr_data)
np.testing.assert_array_equal(result["l1"], label_data)
# Read each individual index
for index in range(10):
label_index = label_data[index]
result = indexer[label_index:label_index]
assert result["a1"][0] == attr_data[index]
assert result["l1"][0] == label_index
for index in range(10):
label_index = label_data[index:]
result = indexer[label_index[0] : label_index[-1]]
np.testing.assert_array_equal(result["a1"], attr_data[index:])
np.testing.assert_array_equal(result["l1"], label_index)
@pytest.mark.skipif(
tiledb.libtiledb.version()[0] == 2 and tiledb.libtiledb.version()[1] < 15,
reason="dimension labels requires libtiledb version 2.15 or greater",
)
@pytest.mark.parametrize("var", [True, False])
def test_dimension_label_round_trip_multidim_dense_array(self, var):
# Create array schema with dimension labels
dim1 = tiledb.Dim("x_index", domain=(1, 8))
dim2 = tiledb.Dim("y_index", domain=(1, 8))
dom = tiledb.Domain(dim1, dim2)
att = tiledb.Attr("value", dtype=np.int64)
dim_labels = {
0: {
"x1": dim1.create_label_schema(
"increasing", np.float64 if not var else "U"
),
"x2": dim1.create_label_schema("decreasing", np.int64),
},
1: {
"y1": dim2.create_label_schema("increasing", np.int64),
},
}
schema = tiledb.ArraySchema(domain=dom, attrs=(att,), dim_labels=dim_labels)
# Create array
uri = self.path("dense_array_with_label")
tiledb.Array.create(uri, schema)
# Write data to the array and the label
attr_data = np.reshape(np.arange(1, 65), (8, 8))
x1_data = np.linspace(-1.0, 1.0, 8)
if var:
x1_data = np.array(
[str(chr(ord("a") + c - 1) * c).encode("utf-8") for c in range(1, 9)]
)
x2_data = np.arange(8, 0, -1)
y1_data = np.arange(9, 17)
with tiledb.open(uri, "w") as array:
array[:, :] = {
"value": attr_data,
"x1": x1_data,
"y1": y1_data,
"x2": x2_data,
}
# Test querying by label
with tiledb.open(uri, "r") as array:
# Read full array: labels on both ranges
result = array.label_index(["x1", "y1"])[x1_data[0] : x1_data[-1], 9:17]
np.testing.assert_array_equal(result["value"], attr_data)
np.testing.assert_array_equal(result["x1"], x1_data)
np.testing.assert_array_equal(result["y1"], y1_data)
assert "x2" not in result
# Read full array: label only on first range
result = array.label_index(["x2"])[0:8]
np.testing.assert_array_equal(result["value"], attr_data)
np.testing.assert_array_equal(result["x2"], x2_data)
assert "x1" not in result
assert "y1" not in result
# Read full array: Label only on second range
result = array.label_index(["y1"])[:, 9:17]
np.testing.assert_array_equal(result["value"], attr_data)
np.testing.assert_array_equal(result["y1"], y1_data)
assert "x1" not in result
assert "x2" not in result
# Check conflicting labels are not allowed
with pytest.raises(tiledb.TileDBError):
array.label_index(["x1", "x2"])
@pytest.mark.skipif(
tiledb.libtiledb.version()[0] == 2 and tiledb.libtiledb.version()[1] < 15,
reason="dimension labels requires libtiledb version 2.15 or greater",
)
@pytest.mark.parametrize("var", [True, False])
def test_dimension_label_round_trip_sparse_array(self, var):
# Create array schema with dimension labels
dim = tiledb.Dim("index", domain=(1, 10))
dom = tiledb.Domain(dim)
att = tiledb.Attr("value", dtype=np.int64)
dim_labels = {
0: {
"l1": dim.create_label_schema(
"increasing", np.int64 if not var else "ascii"
)
}
}
schema = tiledb.ArraySchema(
domain=dom, attrs=(att,), dim_labels=dim_labels, sparse=True
)
# Create array
uri = self.path("sparse_array_with_label")
tiledb.Array.create(uri, schema)
# Write data to the array and the label
index_data = np.arange(1, 11)
attr_data = np.arange(11, 21)
label_data = np.arange(-10, 0)
if var:
label_data = np.array(
[str(chr(ord("a") + c) * (10 - c)).encode("utf-8") for c in range(10)]
)
with tiledb.open(uri, "w") as array:
array[index_data] = {"value": attr_data, "l1": label_data}
# Load the array schema and get the URI of the dimension label
schema = tiledb.ArraySchema.load(uri)
dim_label = schema.dim_label("l1")
# Read and check the data directly from the dimension label
with tiledb.open(dim_label.uri, "r") as label1:
output_label_data = label1[:][dim_label.label_attr_name]
np.testing.assert_array_equal(output_label_data, label_data)
@pytest.mark.skipif(
tiledb.libtiledb.version()[0] == 2 and tiledb.libtiledb.version()[1] < 15,
reason="dimension labels requires libtiledb version 2.15 or greater",
)
def test_dimension_label_round_trip_dense_var(self):
# Create array schema with dimension labels
dims = [
tiledb.Dim("d1", domain=(1, 10), dtype=np.int64),
tiledb.Dim("d2", domain=(1, 10), dtype=np.int64),
]
dom = tiledb.Domain(*dims)
att = tiledb.Attr("value", var=True, dtype="S")
dim_labels = {
0: {
"l1": dims[0].create_label_schema("increasing", np.float32),
},
1: {
"l2": dims[1].create_label_schema("decreasing", np.int32),
"l3": dims[1].create_label_schema("increasing", np.bytes_),
},
}
schema = tiledb.ArraySchema(
domain=dom, attrs=(att,), dim_labels=dim_labels, sparse=False
)
# Create array
uri = self.path("dense_array_with_var_label2")
tiledb.Array.create(uri, schema)
# Write data to the array and the label
attr_data = np.array(
[
[str(chr(ord("z") - c) * (10 - c)).encode("utf-8") for c in range(10)]
for i in range(10)
]
)
l1_data = np.arange(10, dtype=np.float32)
l2_data = np.arange(10, 0, -1, dtype=np.int32)
l3_data = np.array(
[str(chr(ord("a") + c) * (c + 1)).encode("utf-8") for c in range(10)]
)
with tiledb.open(uri, "w") as array:
array[:, :] = {
"value": attr_data,
"l1": l1_data,
"l2": l2_data,
"l3": l3_data,
}
# Load the array schema and get the URI of the dimension label
schema = tiledb.ArraySchema.load(uri)
for label_name, label_data in {
"l1": l1_data,
"l2": l2_data,
"l3": l3_data,
}.items():
dim_label = schema.dim_label(label_name)
# Read and check the data directly from the dimension label
with tiledb.open(dim_label.uri, "r") as label:
output_label_data = label[:][dim_label.label_attr_name]
np.testing.assert_array_equal(output_label_data, label_data)
with tiledb.open(uri, "r") as array:
indexer = array.label_index([label_name])
lower = min(label_data[0], label_data[-1])
upper = max(label_data[0], label_data[-1])
if label_name == "l1":
all_data = indexer[lower:upper]
else:
all_data = indexer[:, lower:upper]
np.testing.assert_array_equal(all_data[label_name], label_data)
np.testing.assert_array_equal(all_data["value"], attr_data)
# Slice array with varying sizes.
for index in range(10):
label_index = label_data[index:]
lower = min(label_index[0], label_index[-1])
upper = max(label_index[0], label_index[-1])
if label_name == "l1":
result = indexer[lower:upper]
# Check against dim1
np.testing.assert_array_equal(
result["value"], attr_data[index:, :]
)
else:
result = indexer[:, lower:upper]
# Check against dim2
np.testing.assert_array_equal(
result["value"], attr_data[:, index:]
)
np.testing.assert_array_equal(result[label_name], label_index)
@pytest.mark.skipif(
tiledb.libtiledb.version()[0] == 2 and tiledb.libtiledb.version()[1] < 15,
reason="dimension labels requires libtiledb version 2.15 or greater",
)
def test_dimension_label_on_query(self):
uri = self.path("query_label_index")
dim1 = tiledb.Dim("d1", domain=(1, 4))
dim2 = tiledb.Dim("d2", domain=(1, 3))
dom = tiledb.Domain(dim1, dim2)
att = tiledb.Attr("a1", dtype=np.int64)
dim_labels = {
0: {"l1": dim1.create_label_schema("decreasing", np.int64)},
1: {
"l2": dim2.create_label_schema("increasing", np.int64),
"l3": dim2.create_label_schema("increasing", np.float64),
},
}
schema = tiledb.ArraySchema(domain=dom, attrs=(att,), dim_labels=dim_labels)
tiledb.Array.create(uri, schema)
a1_data = np.reshape(np.arange(1, 13), (4, 3))
l1_data = np.arange(4, 0, -1)
l2_data = np.arange(-1, 2)
l3_data = np.linspace(0, 1.0, 3)
with tiledb.open(uri, "w") as A:
A[:] = {"a1": a1_data, "l1": l1_data, "l2": l2_data, "l3": l3_data}
with tiledb.open(uri, "r") as A:
np.testing.assert_equal(
A.query().label_index(["l1"])[3:4],
OrderedDict(
{"l1": np.array([4, 3]), "a1": np.array([[1, 2, 3], [4, 5, 6]])}
),
)
np.testing.assert_equal(
A.query().label_index(["l1", "l3"])[2, 0.5:1.0],
OrderedDict(
{
"l3": np.array([0.5, 1.0]),
"l1": np.array([2]),
"a1": np.array([[8, 9]]),
}
),
)
np.testing.assert_equal(
A.query().label_index(["l2"])[:, -1:0],
OrderedDict(
{
"l2": np.array([-1, 0]),
"a1": np.array([[1, 2], [4, 5], [7, 8], [10, 11]]),
},
),
)
np.testing.assert_equal(
A.query().label_index(["l3"])[:, 0.5:1.0],
OrderedDict(
{
"l3": np.array([0.5, 1.0]),
"a1": np.array([[2, 3], [5, 6], [8, 9], [11, 12]]),
},
),
)
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