223 lines
8.1 KiB
Python
223 lines
8.1 KiB
Python
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# This file is part of h5py, a Python interface to the HDF5 library.
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#
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# http://www.h5py.org
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#
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# Copyright 2008-2013 Andrew Collette and contributors
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#
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# License: Standard 3-clause BSD; see "license.txt" for full license terms
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# and contributor agreement.
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import sys
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import numpy as np
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from .common import ut, TestCase
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from h5py import File, Group, Dataset
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import h5py
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class BaseDataset(TestCase):
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"""
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data is a 3-dimensional dataset with dimensions [z, y, x]
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The z dimension is labeled. It does not have any attached scales.
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The y dimension is not labeled. It has one attached scale.
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The x dimension is labeled. It has two attached scales.
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data2 is a 3-dimensional dataset with no associated dimension scales.
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"""
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def setUp(self):
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self.f = File(self.mktemp(), 'w')
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self.f['data'] = np.ones((4, 3, 2), 'f')
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self.f['data2'] = np.ones((4, 3, 2), 'f')
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self.f['x1'] = np.ones((2), 'f')
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h5py.h5ds.set_scale(self.f['x1'].id)
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h5py.h5ds.attach_scale(self.f['data'].id, self.f['x1'].id, 2)
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self.f['x2'] = np.ones((2), 'f')
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h5py.h5ds.set_scale(self.f['x2'].id, b'x2 name')
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h5py.h5ds.attach_scale(self.f['data'].id, self.f['x2'].id, 2)
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self.f['y1'] = np.ones((3), 'f')
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h5py.h5ds.set_scale(self.f['y1'].id, b'y1 name')
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h5py.h5ds.attach_scale(self.f['data'].id, self.f['y1'].id, 1)
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self.f['z1'] = np.ones((4), 'f')
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h5py.h5ds.set_label(self.f['data'].id, 0, b'z')
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h5py.h5ds.set_label(self.f['data'].id, 2, b'x')
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def tearDown(self):
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if self.f:
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self.f.close()
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class TestH5DSBindings(BaseDataset):
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"""
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Feature: Datasets can be created from existing data
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"""
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def test_create_dimensionscale(self):
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""" Create a dimension scale from existing dataset """
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self.assertTrue(h5py.h5ds.is_scale(self.f['x1'].id))
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self.assertEqual(h5py.h5ds.get_scale_name(self.f['x1'].id), b'')
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self.assertEqual(self.f['x1'].attrs['CLASS'], b"DIMENSION_SCALE")
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self.assertEqual(h5py.h5ds.get_scale_name(self.f['x2'].id), b'x2 name')
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def test_attach_dimensionscale(self):
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self.assertTrue(
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h5py.h5ds.is_attached(self.f['data'].id, self.f['x1'].id, 2)
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)
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self.assertFalse(
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h5py.h5ds.is_attached(self.f['data'].id, self.f['x1'].id, 1))
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self.assertEqual(h5py.h5ds.get_num_scales(self.f['data'].id, 0), 0)
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self.assertEqual(h5py.h5ds.get_num_scales(self.f['data'].id, 1), 1)
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self.assertEqual(h5py.h5ds.get_num_scales(self.f['data'].id, 2), 2)
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def test_detach_dimensionscale(self):
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self.assertTrue(
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h5py.h5ds.is_attached(self.f['data'].id, self.f['x1'].id, 2)
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)
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h5py.h5ds.detach_scale(self.f['data'].id, self.f['x1'].id, 2)
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self.assertFalse(
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h5py.h5ds.is_attached(self.f['data'].id, self.f['x1'].id, 2)
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)
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self.assertEqual(h5py.h5ds.get_num_scales(self.f['data'].id, 2), 1)
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# TODO: update condition once the bug is fixed upstream
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@ut.skipUnless(
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h5py.version.hdf5_version_tuple > (2, 0, 0),
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"Reading non-existent label segfaults"
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)
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def test_label_dimensionscale(self):
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self.assertEqual(h5py.h5ds.get_label(self.f['data'].id, 0), b'z')
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self.assertEqual(h5py.h5ds.get_label(self.f['data'].id, 1), b'')
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self.assertEqual(h5py.h5ds.get_label(self.f['data'].id, 2), b'x')
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def test_iter_dimensionscales(self):
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def func(dsid):
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res = h5py.h5ds.get_scale_name(dsid)
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if res == b'x2 name':
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return dsid
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res = h5py.h5ds.iterate(self.f['data'].id, 2, func, 0)
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self.assertEqual(h5py.h5ds.get_scale_name(res), b'x2 name')
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class TestDimensionManager(BaseDataset):
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def test_make_scale(self):
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# test recreating or renaming an existing scale:
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self.f['x1'].make_scale(b'foobar')
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self.assertEqual(self.f['data'].dims[2]['foobar'], self.f['x1'])
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# test creating entirely new scale:
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self.f['data2'].make_scale(b'foobaz')
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self.f['data'].dims[2].attach_scale(self.f['data2'])
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self.assertEqual(self.f['data'].dims[2]['foobaz'], self.f['data2'])
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def test_get_dimension(self):
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with self.assertRaises(IndexError):
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self.f['data'].dims[3]
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def test_len(self):
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self.assertEqual(len(self.f['data'].dims), 3)
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self.assertEqual(len(self.f['data2'].dims), 3)
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def test_iter(self):
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dims = self.f['data'].dims
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self.assertEqual(
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[d for d in dims],
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[dims[0], dims[1], dims[2]]
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)
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def test_repr(self):
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ds = self.f.create_dataset('x', (2,3))
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self.assertIsInstance(repr(ds.dims), str)
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self.f.close()
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self.assertIsInstance(repr(ds.dims), str)
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class TestDimensionsHighLevel(BaseDataset):
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def test_len(self):
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self.assertEqual(len(self.f['data'].dims[0]), 0)
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self.assertEqual(len(self.f['data'].dims[1]), 1)
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self.assertEqual(len(self.f['data'].dims[2]), 2)
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self.assertEqual(len(self.f['data2'].dims[0]), 0)
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self.assertEqual(len(self.f['data2'].dims[1]), 0)
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self.assertEqual(len(self.f['data2'].dims[2]), 0)
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def test_get_label(self):
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self.assertEqual(self.f['data'].dims[2].label, 'x')
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self.assertEqual(self.f['data'].dims[1].label, '')
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self.assertEqual(self.f['data'].dims[0].label, 'z')
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self.assertEqual(self.f['data2'].dims[2].label, '')
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self.assertEqual(self.f['data2'].dims[1].label, '')
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self.assertEqual(self.f['data2'].dims[0].label, '')
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def test_set_label(self):
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self.f['data'].dims[0].label = 'foo'
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self.assertEqual(self.f['data'].dims[2].label, 'x')
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self.assertEqual(self.f['data'].dims[1].label, '')
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self.assertEqual(self.f['data'].dims[0].label, 'foo')
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def test_detach_scale(self):
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self.f['data'].dims[2].detach_scale(self.f['x1'])
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self.assertEqual(len(self.f['data'].dims[2]), 1)
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self.assertEqual(self.f['data'].dims[2][0], self.f['x2'])
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self.f['data'].dims[2].detach_scale(self.f['x2'])
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self.assertEqual(len(self.f['data'].dims[2]), 0)
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def test_attach_scale(self):
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self.f['x3'] = self.f['x2'][...]
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self.f['data'].dims[2].attach_scale(self.f['x3'])
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self.assertEqual(len(self.f['data'].dims[2]), 3)
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self.assertEqual(self.f['data'].dims[2][2], self.f['x3'])
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def test_get_dimension_scale(self):
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self.assertEqual(self.f['data'].dims[2][0], self.f['x1'])
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with self.assertRaises(RuntimeError):
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self.f['data2'].dims[2][0], self.f['x2']
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self.assertEqual(self.f['data'].dims[2][''], self.f['x1'])
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self.assertEqual(self.f['data'].dims[2]['x2 name'], self.f['x2'])
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def test_get_items(self):
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self.assertEqual(
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self.f['data'].dims[2].items(),
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[('', self.f['x1']), ('x2 name', self.f['x2'])]
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)
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def test_get_keys(self):
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self.assertEqual(self.f['data'].dims[2].keys(), ['', 'x2 name'])
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def test_get_values(self):
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self.assertEqual(
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self.f['data'].dims[2].values(),
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[self.f['x1'], self.f['x2']]
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)
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def test_iter(self):
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self.assertEqual([i for i in self.f['data'].dims[2]], ['', 'x2 name'])
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def test_repr(self):
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ds = self.f["data"]
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self.assertEqual(repr(ds.dims[2])[1:16], '"x" dimension 2')
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self.f.close()
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self.assertIsInstance(repr(ds.dims), str)
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def test_attributes(self):
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self.f["data2"].attrs["DIMENSION_LIST"] = self.f["data"].attrs[
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"DIMENSION_LIST"]
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self.assertEqual(len(self.f['data2'].dims[0]), 0)
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self.assertEqual(len(self.f['data2'].dims[1]), 1)
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self.assertEqual(len(self.f['data2'].dims[2]), 2)
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def test_is_scale(self):
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"""Test Dataset.is_scale property"""
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self.assertTrue(self.f['x1'].is_scale)
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self.assertTrue(self.f['x2'].is_scale)
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self.assertTrue(self.f['y1'].is_scale)
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self.assertFalse(self.f['z1'].is_scale)
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self.assertFalse(self.f['data'].is_scale)
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self.assertFalse(self.f['data2'].is_scale)
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