# This file is part of h5py, a Python interface to the HDF5 library. # # http://www.h5py.org # # Copyright 2008-2013 Andrew Collette and contributors # # License: Standard 3-clause BSD; see "license.txt" for full license terms # and contributor agreement. """ Dataset slicing test module. Tests all supported slicing operations, including read/write and broadcasting operations. Does not test type conversion except for corner cases overlapping with slicing; for example, when selecting specific fields of a compound type. """ from __future__ import absolute_import import six import numpy as np from ..common import ut, TestCase import h5py from h5py import h5s, h5t, h5d from h5py.highlevel import File class BaseSlicing(TestCase): def setUp(self): self.f = File(self.mktemp(), 'w') def tearDown(self): if self.f: self.f.close() class TestSingleElement(BaseSlicing): """ Feature: Retrieving a single element works with NumPy semantics """ def test_single_index(self): """ Single-element selection with [index] yields array scalar """ dset = self.f.create_dataset('x', (1,), dtype='i1') out = dset[0] self.assertIsInstance(out, np.int8) def test_single_null(self): """ Single-element selection with [()] yields ndarray """ dset = self.f.create_dataset('x', (1,), dtype='i1') out = dset[()] self.assertIsInstance(out, np.ndarray) self.assertEqual(out.shape, (1,)) def test_scalar_index(self): """ Slicing with [...] yields scalar ndarray """ dset = self.f.create_dataset('x', shape=(), dtype='f') out = dset[...] self.assertIsInstance(out, np.ndarray) self.assertEqual(out.shape, ()) def test_scalar_null(self): """ Slicing with [()] yields array scalar """ dset = self.f.create_dataset('x', shape=(), dtype='i1') out = dset[()] self.assertIsInstance(out, np.int8) def test_compound(self): """ Compound scalar is numpy.void, not tuple (issue 135) """ dt = np.dtype([('a','i4'),('b','f8')]) v = np.ones((4,), dtype=dt) dset = self.f.create_dataset('foo', (4,), data=v) self.assertEqual(dset[0], v[0]) self.assertIsInstance(dset[0], np.void) class TestObjectIndex(BaseSlicing): """ Feature: numpy.object_ subtypes map to real Python objects """ def test_reference(self): """ Indexing a reference dataset returns a h5py.Reference instance """ dset = self.f.create_dataset('x', (1,), dtype=h5py.special_dtype(ref=h5py.Reference)) dset[0] = self.f.ref self.assertEqual(type(dset[0]), h5py.Reference) def test_regref(self): """ Indexing a region reference dataset returns a h5py.RegionReference """ dset1 = self.f.create_dataset('x', (10,10)) regref = dset1.regionref[...] dset2 = self.f.create_dataset('y', (1,), dtype=h5py.special_dtype(ref=h5py.RegionReference)) dset2[0] = regref self.assertEqual(type(dset2[0]), h5py.RegionReference) def test_reference_field(self): """ Compound types of which a reference is an element work right """ reftype = h5py.special_dtype(ref=h5py.Reference) dt = np.dtype([('a', 'i'),('b',reftype)]) dset = self.f.create_dataset('x', (1,), dtype=dt) dset[0] = (42, self.f['/'].ref) out = dset[0] self.assertEqual(type(out[1]), h5py.Reference) # isinstance does NOT work def test_scalar(self): """ Indexing returns a real Python object on scalar datasets """ dset = self.f.create_dataset('x', (), dtype=h5py.special_dtype(ref=h5py.Reference)) dset[()] = self.f.ref self.assertEqual(type(dset[()]), h5py.Reference) def test_bytestr(self): """ Indexing a byte string dataset returns a real python byte string """ dset = self.f.create_dataset('x', (1,), dtype=h5py.special_dtype(vlen=bytes)) dset[0] = b"Hello there!" self.assertEqual(type(dset[0]), bytes) class TestSimpleSlicing(TestCase): """ Feature: Simple NumPy-style slices (start:stop:step) are supported. """ def setUp(self): self.f = File(self.mktemp(), 'w') self.arr = np.arange(10) self.dset = self.f.create_dataset('x', data=self.arr) def tearDown(self): if self.f: self.f.close() def test_negative_stop(self): """ Negative stop indexes work as they do in NumPy """ self.assertArrayEqual(self.dset[2:-2], self.arr[2:-2]) class TestArraySlicing(BaseSlicing): """ Feature: Array types are handled appropriately """ def test_read(self): """ Read arrays tack array dimensions onto end of shape tuple """ dt = np.dtype('(3,)f8') dset = self.f.create_dataset('x',(10,),dtype=dt) self.assertEqual(dset.shape, (10,)) self.assertEqual(dset.dtype, dt) # Full read out = dset[...] self.assertEqual(out.dtype, np.dtype('f8')) self.assertEqual(out.shape, (10,3)) # Single element out = dset[0] self.assertEqual(out.dtype, np.dtype('f8')) self.assertEqual(out.shape, (3,)) # Range out = dset[2:8:2] self.assertEqual(out.dtype, np.dtype('f8')) self.assertEqual(out.shape, (3,3)) def test_write_broadcast(self): """ Array fill from constant is not supported (issue 211). """ dt = np.dtype('(3,)i') dset = self.f.create_dataset('x', (10,), dtype=dt) with self.assertRaises(TypeError): dset[...] = 42 def test_write_element(self): """ Write a single element to the array Issue 211. """ dt = np.dtype('(3,)f8') dset = self.f.create_dataset('x', (10,), dtype=dt) data = np.array([1,2,3.0]) dset[4] = data out = dset[4] self.assertTrue(np.all(out == data)) def test_write_slices(self): """ Write slices to array type """ dt = np.dtype('(3,)i') data1 = np.ones((2,), dtype=dt) data2 = np.ones((4,5), dtype=dt) dset = self.f.create_dataset('x', (10,9,11), dtype=dt) dset[0,0,2:4] = data1 self.assertArrayEqual(dset[0,0,2:4], data1) dset[3, 1:5, 6:11] = data2 self.assertArrayEqual(dset[3, 1:5, 6:11], data2) def test_roundtrip(self): """ Read the contents of an array and write them back Issue 211. """ dt = np.dtype('(3,)f8') dset = self.f.create_dataset('x', (10,), dtype=dt) out = dset[...] dset[...] = out self.assertTrue(np.all(dset[...] == out)) class TestZeroLengthSlicing(BaseSlicing): """ Slices resulting in empty arrays """ def test_slice_zero_length_dimension(self): """ Slice a dataset with a zero in its shape vector along the zero-length dimension """ for i, shape in enumerate([(0,), (0, 3), (0, 2, 1)]): dset = self.f.create_dataset('x%d'%i, shape, dtype=np.int, maxshape=(None,)*len(shape)) self.assertEqual(dset.shape, shape) out = dset[...] self.assertIsInstance(out, np.ndarray) self.assertEqual(out.shape, shape) out = dset[:] self.assertIsInstance(out, np.ndarray) self.assertEqual(out.shape, shape) if len(shape) > 1: out = dset[:, :1] self.assertIsInstance(out, np.ndarray) self.assertEqual(out.shape[:2], (0, 1)) def test_slice_other_dimension(self): """ Slice a dataset with a zero in its shape vector along a non-zero-length dimension """ for i, shape in enumerate([(3, 0), (1, 2, 0), (2, 0, 1)]): dset = self.f.create_dataset('x%d'%i, shape, dtype=np.int, maxshape=(None,)*len(shape)) self.assertEqual(dset.shape, shape) out = dset[:1] self.assertIsInstance(out, np.ndarray) self.assertEqual(out.shape, (1,)+shape[1:]) def test_slice_of_length_zero(self): """ Get a slice of length zero from a non-empty dataset """ for i, shape in enumerate([(3,), (2, 2,), (2, 1, 5)]): dset = self.f.create_dataset('x%d'%i, data=np.zeros(shape, np.int), maxshape=(None,)*len(shape)) self.assertEqual(dset.shape, shape) out = dset[1:1] self.assertIsInstance(out, np.ndarray) self.assertEqual(out.shape, (0,)+shape[1:]) class TestFieldNames(BaseSlicing): """ Field names for read & write """ dt = np.dtype([('a', 'f'), ('b', 'i'), ('c', 'f4')]) data = np.ones((100,), dtype=dt) def setUp(self): BaseSlicing.setUp(self) self.dset = self.f.create_dataset('x', (100,), dtype=self.dt) self.dset[...] = self.data def test_read(self): """ Test read with field selections (bytes and unicode) """ if six.PY2: # Byte strings are only allowed for field names on Py2 self.assertArrayEqual(self.dset[b'a'], self.data['a']) self.assertArrayEqual(self.dset[u'a'], self.data['a']) def test_unicode_names(self): """ Unicode field names for for read and write """ self.assertArrayEqual(self.dset[u'a'], self.data['a']) self.dset[u'a'] = 42 data = self.data.copy() data['a'] = 42 self.assertArrayEqual(self.dset[u'a'], data['a']) def test_write(self): """ Test write with field selections """ data2 = self.data.copy() data2['a'] *= 2 self.dset['a'] = data2 self.assertTrue(np.all(self.dset[...] == data2)) data2['b'] *= 4 self.dset['b'] = data2 self.assertTrue(np.all(self.dset[...] == data2)) data2['a'] *= 3 data2['c'] *= 3 self.dset['a','c'] = data2 self.assertTrue(np.all(self.dset[...] == data2)) def test_write_noncompound(self): """ Test write with non-compound source (single-field) """ data2 = self.data.copy() data2['b'] = 1.0 self.dset['b'] = 1.0 self.assertTrue(np.all(self.dset[...] == data2))