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|
# (C) Copyright 2005-2025 Enthought, Inc., Austin, TX
# All rights reserved.
#
# This software is provided without warranty under the terms of the BSD
# license included in LICENSE.txt and may be redistributed only under
# the conditions described in the aforementioned license. The license
# is also available online at http://www.enthought.com/licenses/BSD.txt
#
# Thanks for using Enthought open source!
import os
from contextlib import closing
import unittest
from apptools._testing.optional_dependencies import (
numpy as np,
tables,
requires_numpy,
requires_tables,
)
if np is not None and tables is not None:
from ..file import H5File
from ..dict_node import H5DictNode
from ..table_node import H5TableNode
from .utils import open_h5file, temp_h5_file
H5_TEST_FILE = "_temp_test_filt.h5"
@requires_numpy
@requires_tables
class FileTestCase(unittest.TestCase):
def tearDown(self):
try:
os.remove(H5_TEST_FILE)
except OSError:
pass
def test_reopen(self):
h5 = H5File(H5_TEST_FILE, mode="w")
assert h5.is_open
h5.close()
assert not h5.is_open
h5.open()
assert h5.is_open
h5.close()
def test_open_from_pytables_object(self):
with closing(tables.File(H5_TEST_FILE, "w")) as pyt_file:
pyt_file.create_group("/", "my_group")
with open_h5file(pyt_file) as h5:
assert "/my_group" in h5
def test_open_from_closed_pytables_object(self):
with closing(tables.File(H5_TEST_FILE, "w")) as pyt_file:
pyt_file.create_group("/", "my_group")
pyt_file.close()
with open_h5file(pyt_file) as h5:
assert "/my_group" in h5
def test_create_array_with_H5File(self):
array = np.arange(3)
with open_h5file(H5_TEST_FILE, mode="w") as h5:
h5array = h5.create_array("/array", array)
# Test returned array
np.testing.assert_allclose(h5array, array)
# Test stored array
np.testing.assert_allclose(h5["/array"], array)
def test_create_array_with_H5Group(self):
array = np.arange(3)
node_path = "/tardigrade/array"
with open_h5file(H5_TEST_FILE, mode="w") as h5:
group = h5.create_group("/tardigrade")
h5array = group.create_array("array", array)
# Test returned array
np.testing.assert_allclose(h5array, array)
# Test stored array
np.testing.assert_allclose(h5[node_path], array)
def test_getitem_failure(self):
array = np.arange(3)
with open_h5file(H5_TEST_FILE, mode="w") as h5:
h5.create_array("/array", array)
with self.assertRaises(NameError):
h5["/not_there"]
def test_iteritems(self):
node_paths = ["/foo", "/bar", "/baz"]
array = np.arange(3)
with open_h5file(H5_TEST_FILE, mode="w") as h5:
for path in node_paths:
h5.create_array(path, array)
# We expect to see the root node when calling iteritems...
node_paths.append("/")
iter_paths = []
# 2to3 converts the iteritems blindly to items which is incorrect,
# so we resort to this ugliness.
items = getattr(h5, "iteritems")()
for path, node in items:
iter_paths.append(path)
assert set(node_paths) == set(iter_paths)
def test_create_plain_array_with_H5File(self):
with open_h5file(H5_TEST_FILE, mode="w") as h5:
h5array = h5.create_array("/array", np.arange(3), chunked=False)
assert isinstance(h5array, tables.Array)
assert not isinstance(h5array, tables.CArray)
def test_create_plain_array_with_H5Group(self):
with open_h5file(H5_TEST_FILE, mode="w") as h5:
h5array = h5.root.create_array(
"/array", np.arange(3), chunked=False
)
assert isinstance(h5array, tables.Array)
assert not isinstance(h5array, tables.CArray)
def test_create_chunked_array_with_H5File(self):
array = np.arange(3, dtype=np.uint8)
with open_h5file(H5_TEST_FILE, mode="w") as h5:
h5array = h5.create_array("/array", array, chunked=True)
np.testing.assert_allclose(h5array, array)
assert isinstance(h5array, tables.CArray)
def test_create_chunked_array_with_H5Group(self):
array = np.arange(3, dtype=np.uint8)
with open_h5file(H5_TEST_FILE, mode="w") as h5:
h5array = h5.root.create_array("/array", array, chunked=True)
np.testing.assert_allclose(h5array, array)
assert isinstance(h5array, tables.CArray)
def test_create_extendable_array_with_H5File(self):
array = np.arange(3, dtype=np.uint8)
with open_h5file(H5_TEST_FILE, mode="w") as h5:
h5array = h5.create_array("/array", array, extendable=True)
np.testing.assert_allclose(h5array, array)
assert isinstance(h5array, tables.EArray)
def test_create_extendable_array_with_H5Group(self):
array = np.arange(3, dtype=np.uint8)
with open_h5file(H5_TEST_FILE, mode="w") as h5:
h5array = h5.root.create_array("/array", array, extendable=True)
np.testing.assert_allclose(h5array, array)
assert isinstance(h5array, tables.EArray)
def test_str_and_repr(self):
array = np.arange(3)
with open_h5file(H5_TEST_FILE, mode="w") as h5:
h5.create_array("/array", array)
assert repr(h5) == repr(h5._h5)
assert str(h5) == str(h5._h5)
def test_shape_and_dtype(self):
array = np.ones((3, 4), dtype=np.uint8)
with open_h5file(H5_TEST_FILE, mode="w") as h5:
for node, chunked in (("/array", False), ("/carray", True)):
h5array = h5.create_array(
node, array.shape, dtype=array.dtype, chunked=chunked
)
assert h5array.dtype == array.dtype
assert h5array.shape == array.shape
def test_shape_only_raises(self):
shape = (3, 4)
with open_h5file(H5_TEST_FILE, mode="w") as h5:
with self.assertRaises(ValueError):
h5.create_array("/array", shape)
def test_create_duplicate_array_raises(self):
array = np.arange(3)
with open_h5file(H5_TEST_FILE, mode="w", delete_existing=False) as h5:
h5.create_array("/array", array)
with self.assertRaises(ValueError):
h5.create_array("/array", array)
def test_delete_existing_array_with_H5File(self):
old_array = np.arange(3)
new_array = np.ones(5)
with open_h5file(H5_TEST_FILE, mode="w", delete_existing=True) as h5:
h5.create_array("/array", old_array)
# New array with the same node name should delete old array
h5.create_array("/array", new_array)
np.testing.assert_allclose(h5["/array"], new_array)
def test_delete_existing_array_with_H5Group(self):
old_array = np.arange(3)
new_array = np.ones(5)
with open_h5file(H5_TEST_FILE, mode="w") as h5:
h5.create_array("/array", old_array)
# New array with the same node name should delete old array
h5.root.create_array("/array", new_array, delete_existing=True)
np.testing.assert_allclose(h5["/array"], new_array)
def test_delete_existing_dict_with_H5File(self):
old_dict = {"a": "Goose"}
new_dict = {"b": "Quail"}
with open_h5file(H5_TEST_FILE, mode="w", delete_existing=True) as h5:
h5.create_dict("/dict", old_dict)
# New dict with the same node name should delete old dict
h5.create_dict("/dict", new_dict)
assert h5["/dict"].data == new_dict
def test_delete_existing_dict_with_H5Group(self):
old_dict = {"a": "Goose"}
new_dict = {"b": "Quail"}
with open_h5file(H5_TEST_FILE, mode="w") as h5:
h5.create_dict("/dict", old_dict)
# New dict with the same node name should delete old dict
h5.root.create_dict("/dict", new_dict, delete_existing=True)
assert h5["/dict"].data == new_dict
def test_delete_existing_table_with_H5File(self):
old_description = [("Honk", "int"), ("Wink", "float")]
new_description = [("Toot", "float"), ("Pop", "int")]
with open_h5file(H5_TEST_FILE, mode="w", delete_existing=True) as h5:
h5.create_table("/table", old_description)
# New table with the same node name should delete old table
h5.create_table("/table", new_description)
tab = h5["/table"]
tab.append({"Pop": (1,), "Toot": (np.pi,)})
assert tab.ix[0][0] == np.pi
def test_delete_existing_table_with_H5Group(self):
old_description = [("Honk", "int"), ("Wink", "float")]
new_description = [("Toot", "float"), ("Pop", "int")]
with open_h5file(H5_TEST_FILE, mode="w") as h5:
h5.create_table("/table", old_description)
# New table with the same node name should delete old table
h5.root.create_table(
"/table", new_description, delete_existing=True
)
tab = h5["/table"]
tab.append({"Pop": (1,), "Toot": (np.pi,)})
assert tab.ix[0][0] == np.pi
def test_delete_existing_group_with_H5File(self):
with open_h5file(H5_TEST_FILE, mode="w", delete_existing=True) as h5:
h5.create_group("/group")
grp = h5["/group"]
grp.attrs["test"] = 4
assert grp.attrs["test"] == 4
h5.create_group("/group")
grp = h5["/group"]
grp.attrs["test"] = 6
assert grp.attrs["test"] == 6
def test_delete_existing_group_with_H5Group(self):
with open_h5file(H5_TEST_FILE, mode="w") as h5:
h5.create_group("/group")
grp = h5["/group"]
grp.attrs["test"] = 4
assert grp.attrs["test"] == 4
h5.root.create_group("/group", delete_existing=True)
grp = h5["/group"]
grp.attrs["test"] = 6
assert grp.attrs["test"] == 6
def test_remove_group_with_H5File(self):
with open_h5file(H5_TEST_FILE, mode="w", delete_existing=True) as h5:
h5.create_group("/group")
assert "/group" in h5
h5.remove_group("/group")
assert "/group" not in h5
def test_remove_group_with_H5Group(self):
node_path = "/waterbear/group"
with open_h5file(H5_TEST_FILE, mode="w", delete_existing=True) as h5:
group = h5.create_group("/waterbear")
group.create_group("group")
assert node_path in h5
group.remove_group("group")
assert node_path not in h5
def test_remove_group_with_remove_node(self):
node_path = "/group"
with open_h5file(H5_TEST_FILE, mode="w") as h5:
h5.create_group(node_path)
with self.assertRaises(ValueError):
# Groups should be removed w/ `remove_group`
h5.remove_node(node_path)
def test_remove_node_with_H5File(self):
with open_h5file(H5_TEST_FILE, mode="w", delete_existing=True) as h5:
h5.create_array("/array", np.arange(3))
assert "/array" in h5
h5.remove_node("/array")
assert "/array" not in h5
def test_remove_node_with_H5Group(self):
node_path = "/waterbear/array"
with open_h5file(H5_TEST_FILE, mode="w", delete_existing=True) as h5:
group = h5.create_group("/waterbear")
h5.create_array(node_path, np.arange(3))
assert node_path in h5
group.remove_node("array")
assert node_path not in h5
def test_read_mode_raises_on_nonexistent_file(self):
cm = open_h5file("_nonexistent_.h5", mode="r")
with self.assertRaises(IOError):
cm.__enter__()
cm = open_h5file("_nonexistent_.h5", mode="r+")
with self.assertRaises(IOError):
cm.__enter__()
def test_cleanup(self):
with open_h5file(H5_TEST_FILE, mode="w") as h5:
h5_pytables = h5._h5 # This reference gets deleted on close
assert not h5_pytables.isopen
def test_create_group_with_H5File(self):
with open_h5file(H5_TEST_FILE, mode="w") as h5:
h5.create_group("/group")
assert "/group" in h5
def test_create_group_with_H5Group(self):
with open_h5file(H5_TEST_FILE, mode="w") as h5:
group = h5["/"]
group.create_group("group")
assert "/group" in h5
def test_split_path(self):
path, node = H5File.split_path("/")
assert path == "/"
assert node == ""
path, node = H5File.split_path("/node")
assert path == "/"
assert node == "node"
path, node = H5File.split_path("/group/node")
assert path == "/group"
assert node == "node"
def test_join_path(self):
path = H5File.join_path("/", "a", "b", "c")
assert path == "/a/b/c"
path = H5File.join_path("a", "b/c")
assert path == "/a/b/c"
path = H5File.join_path("a", "/b", "/c")
assert path == "/a/b/c"
def test_auto_groups(self):
with open_h5file(H5_TEST_FILE, mode="w") as h5:
h5.auto_groups = True
h5.create_array("/group/array", np.arange(3))
assert "/group/array" in h5
def test_auto_groups_deep(self):
with open_h5file(H5_TEST_FILE, mode="w") as h5:
h5.auto_groups = True
h5.create_array("/group1/group2/array", np.arange(3))
assert "/group1/group2/array" in h5
def test_groups(self):
array = np.arange(3)
with open_h5file(H5_TEST_FILE, mode="w") as h5:
h5.create_array("/a/b/array", array)
group_a = h5["/a"]
# Check that __contains__ works for groups
assert "b" in group_a
assert "b/array" in group_a
group_b = group_a["b"]
# Check that __contains__ works for arrays
assert "array" in group_b
np.testing.assert_allclose(group_b["array"], array)
np.testing.assert_allclose(group_a["b/array"], array)
def test_group_attributes(self):
value_1 = "foo"
value_2 = "bar"
with open_h5file(H5_TEST_FILE, mode="w") as h5:
h5["/"].attrs["name"] = value_1
assert h5["/"].attrs["name"] == value_1
group = h5["/"]
# Make sure changes to the attribute consistent
group._h5_group._v_attrs["name"] = value_2
assert group.attrs["name"] == value_2
def test_group_properties(self):
with open_h5file(H5_TEST_FILE, mode="w", auto_groups=True) as h5:
h5.create_array("/group1/group2/array", np.arange(3))
h5.create_array("/group1/array1", np.arange(3))
assert h5["/group1"].name == "group1"
child_names = h5["/group1"].children_names
assert sorted(child_names) == sorted(["group2", "array1"])
sub_names = h5["/group1"].subgroup_names
assert sub_names == ["group2"]
assert h5["/group1"].root.name == "/"
assert h5["/group1/group2"].root.name == "/"
def test_iter_groups(self):
with open_h5file(H5_TEST_FILE, mode="w", auto_groups=True) as h5:
h5.create_array("/group1/array", np.arange(3))
h5.create_array("/group1/subgroup/deep_array", np.arange(3))
group = h5["/group1"]
assert set(n.name for n in group.iter_groups()) == set(
["subgroup"]
)
def test_mapping_interface_for_file(self):
with open_h5file(H5_TEST_FILE, mode="w", auto_groups=True) as h5:
array = h5.create_array("/array", np.arange(3))
h5.create_array("/group/deep_array", np.arange(3))
# `deep_array` isn't a direct descendent and isn't counted.
assert len(h5) == 2
assert "/group" in h5
assert "/array" in h5
np.testing.assert_allclose(h5["/array"], array)
assert set(n.name for n in h5) == set(["array", "group"])
def test_mapping_interface_for_group(self):
with open_h5file(H5_TEST_FILE, mode="w", auto_groups=True) as h5:
array = h5.create_array("/group1/array", np.arange(3))
h5.create_array("/group1/subgroup/deep_array", np.arange(3))
group = h5["/group1"]
# `deep_array` isn't a direct descendent and isn't counted.
assert len(group) == 2
assert "subgroup" in group
assert "array" in group
np.testing.assert_allclose(group["array"], array)
assert set(n.name for n in group) == set(["array", "subgroup"])
def test_group_str_and_repr(self):
with open_h5file(H5_TEST_FILE, mode="w") as h5:
group = h5["/"]
assert str(group) == str(group._h5_group)
assert repr(group) == repr(group._h5_group)
def test_attribute_translation(self):
value_1 = (1, 2, 3)
value_1_array = np.array(value_1)
with open_h5file(H5_TEST_FILE, mode="w") as h5:
h5["/"].attrs["name"] = value_1
assert isinstance(h5["/"].attrs["name"], np.ndarray)
np.testing.assert_allclose(h5["/"].attrs["name"], value_1_array)
def test_get_attribute(self):
with open_h5file(H5_TEST_FILE, mode="w") as h5:
attrs = h5["/"].attrs
attrs["name"] = "hello"
assert attrs.get("name") == attrs["name"]
def test_del_attribute(self):
with open_h5file(H5_TEST_FILE, mode="w") as h5:
attrs = h5["/"].attrs
attrs["name"] = "hello"
del attrs["name"]
assert "name" not in attrs
def test_get_attribute_default(self):
with open_h5file(H5_TEST_FILE, mode="w") as h5:
assert h5["/"].attrs.get("missing", "null") == "null"
def test_attribute_update(self):
with open_h5file(H5_TEST_FILE, mode="w") as h5:
attrs = h5["/"].attrs
attrs.update({"a": 1, "b": 2})
assert attrs["a"] == 1
assert attrs["b"] == 2
attrs.update({"b": 20, "c": 30})
assert attrs["b"] == 20
assert attrs["c"] == 30
def test_attribute_iteration_methods(self):
with open_h5file(H5_TEST_FILE, mode="w") as h5:
attrs = h5["/"].attrs
attrs["organ"] = "gallbladder"
attrs["count"] = 42
attrs["alpha"] = 0xFF
items = list(attrs.items())
assert all(isinstance(x, tuple) for x in items)
# unfold the pairs
keys, vals = [list(item) for item in zip(*items)]
assert keys == list(attrs.keys())
assert vals == list(attrs.values())
# Check that __iter__ is consistent
assert keys == list(iter(attrs))
assert len(attrs) == len(keys)
def test_bad_node_name(self):
with open_h5file(H5_TEST_FILE, mode="w") as h5:
with self.assertRaises(ValueError):
h5.create_array("/attrs", np.zeros(3))
def test_bad_group_name(self):
with open_h5file(H5_TEST_FILE, mode="w") as h5:
with self.assertRaises(ValueError):
h5.create_array("/attrs/array", np.zeros(3))
def test_create_dict_with_H5File(self):
data = {"a": 1}
with temp_h5_file() as h5:
h5.create_dict("/dict", data)
assert isinstance(h5["/dict"], H5DictNode)
assert h5["/dict"]["a"] == 1
def test_create_dict_with_H5Group(self):
node_path = "/bananas/dict"
data = {"a": 1}
with temp_h5_file() as h5:
group = h5.create_group("/bananas")
group.create_dict("dict", data)
assert isinstance(h5[node_path], H5DictNode)
assert h5[node_path]["a"] == 1
def test_create_table_with_H5File(self):
description = [("foo", "int"), ("bar", "float")]
with temp_h5_file() as h5:
h5.create_table("/table", description)
tab = h5["/table"]
assert isinstance(tab, H5TableNode)
tab.append({"foo": (1,), "bar": (np.pi,)})
assert tab.ix[0][0] == 1
assert tab.ix[0][1] == np.pi
h5.remove_node("/table")
assert "/table" not in h5
def test_create_table_with_H5Group(self):
node_path = "/rhinocerous/table"
description = [("foo", "int"), ("bar", "float")]
with temp_h5_file() as h5:
group = h5.create_group("/rhinocerous")
group.create_table("table", description)
tab = h5[node_path]
assert isinstance(tab, H5TableNode)
tab.append({"foo": (1,), "bar": (np.pi,)})
assert tab.ix[0][0] == 1
assert tab.ix[0][1] == np.pi
group.remove_node("table")
assert node_path not in h5
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