# (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