File size: 4,607 Bytes
2c3c408 | 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 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 | # quickstart_dimension_labels_sparse.py
#
# LICENSE
#
# The MIT License
#
# Copyright (c) 2023 TileDB, Inc.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
# DESCRIPTION
#
# Please refer to the TileDB and TileDB-Py documentation for more information:
# https://docs.tiledb.com/main/how-to
# https://tiledb-inc-tiledb.readthedocs-hosted.com/projects/tiledb-py/en/stable/python-api.html
#
# When run, this program will create a simple 2D sparse array with dimension labels, write
# some data to it, and read a slice of the data back.
import numpy as np
import tiledb
def create_array(uri: str):
"""Create array schema with dimension labels"""
dim1 = tiledb.Dim("index1", domain=(0, 5))
dim2 = tiledb.Dim("index2", domain=(0, 5))
dom = tiledb.Domain(dim1, dim2)
att = tiledb.Attr("values", dtype=np.int64)
dim_labels = {
0: {"x1": dim1.create_label_schema("increasing", np.float64, tile=6)},
1: {"x2": dim2.create_label_schema("increasing", np.float64, tile=6)},
}
schema = tiledb.ArraySchema(
domain=dom, attrs=(att,), dim_labels=dim_labels, sparse=True
)
tiledb.Array.create(uri, schema)
def write_array(uri: str):
"""Write attribute and label data to the array"""
# Use dimension label URIs to write directly to dimension label arrays.
schema = tiledb.ArraySchema.load(uri)
with tiledb.open(schema.dim_label("x1").uri, "w") as x1_array:
x1_array[:] = np.linspace(-1.0, 1.0, 6)
with tiledb.open(schema.dim_label("x2").uri, "w") as x2_array:
x2_array[:] = np.linspace(-1.0, 1.0, 6)
# Write a tridiagonal matrix.
coords1 = np.append(np.arange(1, 6), np.arange(5))
coords2 = np.append(np.arange(5), np.arange(1, 6))
data = np.append(np.arange(1, 6), -np.arange(1, 6))
with tiledb.open(uri, "w") as array:
array[coords1, coords2] = data
def read_array(uri: str):
"""Read the array from the dimension label"""
with tiledb.open(uri, "r") as array:
# Create a subarray and set label ranges.
subarray = tiledb.Subarray(array)
subarray.add_label_range("x1", (0.0, 1.0))
subarray.add_label_range("x2", (0.0, 1.0))
# Get data from the main array.
data = array.read_subarray(subarray)
# Read the labels.
x1_label = array.schema.dim_label("x1")
x2_label = array.schema.dim_label("x2")
with tiledb.open(x1_label.uri) as x1_array:
x1_coords = x1_array.multi_index[data["index1"]]
data["x1"] = x1_coords[x1_label.label_attr_name]
with tiledb.open(array.schema.dim_label("x2").uri) as x2_array:
x2_coords = x2_array.multi_index[data["index2"]]
data["x2"] = x2_coords[x2_label.label_attr_name]
print("Reading data where 0.0 <= x1 <= 2.0 and -2.0 <= x2 <= 0.0")
for name, value in data.items():
print(f" '{name}'={value}")
if __name__ == "__main__":
# Name of the array to create.
ARRAY_NAME = "quickstart_labels_sparse"
LIBVERSION = tiledb.libtiledb.version()
if LIBVERSION[0] == 2 and LIBVERSION[1] < 15:
print(
f"Dimension labels requires libtiledb version >= 2.15.0. Current version is"
f" {LIBVERSION[0]}.{LIBVERSION[1]}.{LIBVERSION[2]}"
)
else:
# Only create and write to the array if it doesn't already exist.
if tiledb.object_type(ARRAY_NAME) != "array":
create_array(ARRAY_NAME)
write_array(ARRAY_NAME)
# Read from the array and print output.
read_array(ARRAY_NAME)
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