# 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. """ import numpy as np from .common import ut, TestCase import h5py from h5py import h5s, h5t, h5d from h5py import File, MultiBlockSlice 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.ref_dtype) 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.regionref_dtype) 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 """ dt = np.dtype([('a', 'i'),('b', h5py.ref_dtype)]) 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.ref_dtype) 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.string_dtype(encoding='ascii')) 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]) def test_write(self): """Assigning to a 1D slice of a 2D dataset """ dset = self.f.create_dataset('x2', (10, 2)) x = np.zeros((10, 1)) dset[:, 0] = x[:, 0] with self.assertRaises(TypeError): dset[:, 1] = x 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=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=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, 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 """ self.assertArrayEqual(self.dset['a'], self.data['a']) def test_unicode_names(self): """ Unicode field names for for read and write """ self.assertArrayEqual(self.dset['a'], self.data['a']) self.dset['a'] = 42 data = self.data.copy() data['a'] = 42 self.assertArrayEqual(self.dset['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)) class TestMultiBlockSlice(BaseSlicing): def setUp(self): super(TestMultiBlockSlice, self).setUp() self.arr = np.arange(10) self.dset = self.f.create_dataset('x', data=self.arr) def test_default(self): # Default selects entire dataset as one block mbslice = MultiBlockSlice() self.assertEqual(mbslice.indices(10), (0, 1, 10, 1)) np.testing.assert_array_equal(self.dset[mbslice], self.arr) def test_default_explicit(self): mbslice = MultiBlockSlice(start=0, count=10, stride=1, block=1) self.assertEqual(mbslice.indices(10), (0, 1, 10, 1)) np.testing.assert_array_equal(self.dset[mbslice], self.arr) def test_start(self): mbslice = MultiBlockSlice(start=4) self.assertEqual(mbslice.indices(10), (4, 1, 6, 1)) np.testing.assert_array_equal(self.dset[mbslice], np.array([4, 5, 6, 7, 8, 9])) def test_count(self): mbslice = MultiBlockSlice(count=7) self.assertEqual(mbslice.indices(10), (0, 1, 7, 1)) np.testing.assert_array_equal( self.dset[mbslice], np.array([0, 1, 2, 3, 4, 5, 6]) ) def test_count_more_than_length_error(self): mbslice = MultiBlockSlice(count=11) with self.assertRaises(ValueError): mbslice.indices(10) def test_stride(self): mbslice = MultiBlockSlice(stride=2) self.assertEqual(mbslice.indices(10), (0, 2, 5, 1)) np.testing.assert_array_equal(self.dset[mbslice], np.array([0, 2, 4, 6, 8])) def test_stride_zero_error(self): with self.assertRaises(ValueError): # This would cause a ZeroDivisionError if not caught MultiBlockSlice(stride=0, block=0).indices(10) def test_stride_block_equal(self): mbslice = MultiBlockSlice(stride=2, block=2) self.assertEqual(mbslice.indices(10), (0, 2, 5, 2)) np.testing.assert_array_equal(self.dset[mbslice], self.arr) def test_block_more_than_stride_error(self): with self.assertRaises(ValueError): MultiBlockSlice(block=3) with self.assertRaises(ValueError): MultiBlockSlice(stride=2, block=3) def test_stride_more_than_block(self): mbslice = MultiBlockSlice(stride=3, block=2) self.assertEqual(mbslice.indices(10), (0, 3, 3, 2)) np.testing.assert_array_equal(self.dset[mbslice], np.array([0, 1, 3, 4, 6, 7])) def test_block_overruns_extent_error(self): # If fully described then must fit within extent mbslice = MultiBlockSlice(start=2, count=2, stride=5, block=4) with self.assertRaises(ValueError): mbslice.indices(10) def test_fully_described(self): mbslice = MultiBlockSlice(start=1, count=2, stride=5, block=4) self.assertEqual(mbslice.indices(10), (1, 5, 2, 4)) np.testing.assert_array_equal( self.dset[mbslice], np.array([1, 2, 3, 4, 6, 7, 8, 9]) ) def test_count_calculated(self): # If not given, count should be calculated to select as many full blocks as possible mbslice = MultiBlockSlice(start=1, stride=3, block=2) self.assertEqual(mbslice.indices(10), (1, 3, 3, 2)) np.testing.assert_array_equal(self.dset[mbslice], np.array([1, 2, 4, 5, 7, 8])) def test_zero_count_calculated_error(self): # In this case, there is no possible count to select even one block, so error mbslice = MultiBlockSlice(start=8, stride=4, block=3) with self.assertRaises(ValueError): mbslice.indices(10)