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| 1 | +# -*- coding: utf-8 -*- |
| 2 | +from __future__ import absolute_import, print_function, division |
| 3 | +import tempfile |
| 4 | +import os |
| 5 | +import shutil |
| 6 | + |
| 7 | + |
| 8 | +from nose.tools import eq_ as eq, assert_false, assert_raises, assert_true |
| 9 | +import numpy as np |
| 10 | +from numpy.testing import assert_array_equal |
| 11 | +from zarr import defaults |
| 12 | +from zarr.ext import PersistentArray |
| 13 | + |
| 14 | + |
| 15 | +def test_array_1d(): |
| 16 | + a = np.arange(1050) |
| 17 | + |
| 18 | + path = tempfile.mktemp() |
| 19 | + assert_false(os.path.exists(path)) |
| 20 | + |
| 21 | + # open for reading (does not exist) |
| 22 | + with assert_raises(ValueError): |
| 23 | + z = PersistentArray(path) |
| 24 | + with assert_raises(ValueError): |
| 25 | + z = PersistentArray(path, mode='r') |
| 26 | + # open for appending (does not exist) |
| 27 | + with assert_raises(ValueError): |
| 28 | + z = PersistentArray(path, mode='a') |
| 29 | + |
| 30 | + # open for writing |
| 31 | + z = PersistentArray(path, mode='w', shape=a.shape, chunks=100, |
| 32 | + dtype=a.dtype) |
| 33 | + |
| 34 | + # check directory creation |
| 35 | + assert_true(os.path.exists(path)) |
| 36 | + |
| 37 | + # check properties |
| 38 | + eq(a.shape, z.shape) |
| 39 | + eq(a.dtype, z.dtype) |
| 40 | + eq((100,), z.chunks) |
| 41 | + eq((11,), z.cdata.shape) |
| 42 | + eq(defaults.cname, z.cname) |
| 43 | + eq(defaults.clevel, z.clevel) |
| 44 | + eq(defaults.shuffle, z.shuffle) |
| 45 | + eq(a.nbytes, z.nbytes) |
| 46 | + eq(0, z.cbytes) |
| 47 | + |
| 48 | + # set data |
| 49 | + z[:] = a |
| 50 | + |
| 51 | + # check properties |
| 52 | + eq(a.nbytes, z.nbytes) |
| 53 | + eq(sum(c.cbytes for c in z.cdata.flat), z.cbytes) |
| 54 | + |
| 55 | + # check round-trip |
| 56 | + assert_array_equal(a, z[:]) |
| 57 | + assert_array_equal(a, z[...]) |
| 58 | + |
| 59 | + # check slicing |
| 60 | + assert_array_equal(a[:10], z[:10]) |
| 61 | + assert_array_equal(a[10:20], z[10:20]) |
| 62 | + assert_array_equal(a[-10:], z[-10:]) |
| 63 | + # ...across chunk boundaries... |
| 64 | + assert_array_equal(a[:110], z[:110]) |
| 65 | + assert_array_equal(a[190:310], z[190:310]) |
| 66 | + assert_array_equal(a[-110:], z[-110:]) |
| 67 | + |
| 68 | + # open for reading |
| 69 | + z2 = PersistentArray(path, mode='r') |
| 70 | + eq(a.shape, z2.shape) |
| 71 | + eq(a.dtype, z2.dtype) |
| 72 | + eq((100,), z2.chunks) |
| 73 | + eq((11,), z2.cdata.shape) |
| 74 | + eq(defaults.cname, z2.cname) |
| 75 | + eq(defaults.clevel, z2.clevel) |
| 76 | + eq(defaults.shuffle, z2.shuffle) |
| 77 | + eq(a.nbytes, z2.nbytes) |
| 78 | + eq(z.cbytes, z2.cbytes) |
| 79 | + |
| 80 | + # check data |
| 81 | + assert_array_equal(a, z2[:]) |
| 82 | + |
| 83 | + # check read-only |
| 84 | + with assert_raises(ValueError): |
| 85 | + z2[:] = 0 |
| 86 | + |
| 87 | + # open for appending |
| 88 | + z3 = PersistentArray(path, mode='a') |
| 89 | + eq(a.shape, z3.shape) |
| 90 | + eq(a.dtype, z3.dtype) |
| 91 | + eq((100,), z3.chunks) |
| 92 | + eq((11,), z3.cdata.shape) |
| 93 | + eq(defaults.cname, z3.cname) |
| 94 | + eq(defaults.clevel, z3.clevel) |
| 95 | + eq(defaults.shuffle, z3.shuffle) |
| 96 | + eq(a.nbytes, z3.nbytes) |
| 97 | + eq(z.cbytes, z3.cbytes) |
| 98 | + |
| 99 | + # check can write |
| 100 | + z3[:] = 0 |
| 101 | + |
| 102 | + # check effect of write |
| 103 | + assert_array_equal(np.zeros_like(a), z3[:]) |
| 104 | + assert_array_equal(np.zeros_like(a), z2[:]) |
| 105 | + assert_array_equal(np.zeros_like(a), z[:]) |
| 106 | + |
| 107 | + # tidy up |
| 108 | + shutil.rmtree(path) |
| 109 | + |
| 110 | + |
| 111 | +def test_array_1d_fill_value(): |
| 112 | + |
| 113 | + for fill_value in -1, 0, 1, 10: |
| 114 | + |
| 115 | + path = tempfile.mktemp() |
| 116 | + |
| 117 | + a = np.arange(1050) |
| 118 | + f = np.empty_like(a) |
| 119 | + f.fill(fill_value) |
| 120 | + z = PersistentArray(path, mode='w', shape=a.shape, chunks=100, |
| 121 | + fill_value=fill_value) |
| 122 | + z[190:310] = a[190:310] |
| 123 | + |
| 124 | + assert_array_equal(f[:190], z[:190]) |
| 125 | + assert_array_equal(a[190:310], z[190:310]) |
| 126 | + assert_array_equal(f[310:], z[310:]) |
| 127 | + |
| 128 | + z2 = PersistentArray(path, mode='r') |
| 129 | + |
| 130 | + assert_array_equal(f[:190], z2[:190]) |
| 131 | + assert_array_equal(a[190:310], z2[190:310]) |
| 132 | + assert_array_equal(f[310:], z2[310:]) |
| 133 | + |
| 134 | + shutil.rmtree(path) |
| 135 | + |
| 136 | + |
| 137 | +def test_array_2d(): |
| 138 | + |
| 139 | + a = np.arange(10000).reshape((1000, 10)) |
| 140 | + path = tempfile.mktemp() |
| 141 | + |
| 142 | + z = PersistentArray(path, mode='w', shape=a.shape, chunks=(100, 2), |
| 143 | + dtype=a.dtype) |
| 144 | + |
| 145 | + # check properties |
| 146 | + eq(a.shape, z.shape) |
| 147 | + eq(a.dtype, z.dtype) |
| 148 | + eq((100, 2), z.chunks) |
| 149 | + eq((10, 5), z.cdata.shape) |
| 150 | + eq(defaults.cname, z.cname) |
| 151 | + eq(defaults.clevel, z.clevel) |
| 152 | + eq(defaults.shuffle, z.shuffle) |
| 153 | + eq(a.nbytes, z.nbytes) |
| 154 | + eq(0, z.cbytes) |
| 155 | + |
| 156 | + # set data |
| 157 | + z[:] = a |
| 158 | + |
| 159 | + # check properties |
| 160 | + eq(a.nbytes, z.nbytes) |
| 161 | + eq(sum(c.cbytes for c in z.cdata.flat), z.cbytes) |
| 162 | + |
| 163 | + # check round-trip |
| 164 | + assert_array_equal(a, z[:]) |
| 165 | + assert_array_equal(a, z[...]) |
| 166 | + |
| 167 | + # check slicing |
| 168 | + assert_array_equal(a[:10], z[:10]) |
| 169 | + assert_array_equal(a[10:20], z[10:20]) |
| 170 | + assert_array_equal(a[-10:], z[-10:]) |
| 171 | + assert_array_equal(a[:, :2], z[:, :2]) |
| 172 | + assert_array_equal(a[:, 2:4], z[:, 2:4]) |
| 173 | + assert_array_equal(a[:, -2:], z[:, -2:]) |
| 174 | + assert_array_equal(a[:10, :2], z[:10, :2]) |
| 175 | + assert_array_equal(a[10:20, 2:4], z[10:20, 2:4]) |
| 176 | + assert_array_equal(a[-10:, -2:], z[-10:, -2:]) |
| 177 | + # ...across chunk boundaries... |
| 178 | + assert_array_equal(a[:110], z[:110]) |
| 179 | + assert_array_equal(a[190:310], z[190:310]) |
| 180 | + assert_array_equal(a[-110:], z[-110:]) |
| 181 | + assert_array_equal(a[:, :3], z[:, :3]) |
| 182 | + assert_array_equal(a[:, 3:7], z[:, 3:7]) |
| 183 | + assert_array_equal(a[:, -3:], z[:, -3:]) |
| 184 | + assert_array_equal(a[:110, :3], z[:110, :3]) |
| 185 | + assert_array_equal(a[190:310, 3:7], z[190:310, 3:7]) |
| 186 | + assert_array_equal(a[-110:, -3:], z[-110:, -3:]) |
| 187 | + |
| 188 | + # check open for reading |
| 189 | + z2 = PersistentArray(path, mode='r') |
| 190 | + |
| 191 | + # check properties |
| 192 | + eq(a.shape, z2.shape) |
| 193 | + eq(a.dtype, z2.dtype) |
| 194 | + eq((100, 2), z2.chunks) |
| 195 | + eq((10, 5), z2.cdata.shape) |
| 196 | + eq(defaults.cname, z2.cname) |
| 197 | + eq(defaults.clevel, z2.clevel) |
| 198 | + eq(defaults.shuffle, z2.shuffle) |
| 199 | + eq(a.nbytes, z2.nbytes) |
| 200 | + eq(z.cbytes, z2.cbytes) |
| 201 | + |
| 202 | + # check data |
| 203 | + assert_array_equal(a, z2[:]) |
| 204 | + assert_array_equal(a, z2[...]) |
| 205 | + |
| 206 | + # check slicing |
| 207 | + assert_array_equal(a[:10], z2[:10]) |
| 208 | + assert_array_equal(a[10:20], z2[10:20]) |
| 209 | + assert_array_equal(a[-10:], z2[-10:]) |
| 210 | + assert_array_equal(a[:, :2], z2[:, :2]) |
| 211 | + assert_array_equal(a[:, 2:4], z2[:, 2:4]) |
| 212 | + assert_array_equal(a[:, -2:], z2[:, -2:]) |
| 213 | + assert_array_equal(a[:10, :2], z2[:10, :2]) |
| 214 | + assert_array_equal(a[10:20, 2:4], z2[10:20, 2:4]) |
| 215 | + assert_array_equal(a[-10:, -2:], z2[-10:, -2:]) |
| 216 | + # ...across chunk boundaries... |
| 217 | + assert_array_equal(a[:110], z2[:110]) |
| 218 | + assert_array_equal(a[190:310], z2[190:310]) |
| 219 | + assert_array_equal(a[-110:], z2[-110:]) |
| 220 | + assert_array_equal(a[:, :3], z2[:, :3]) |
| 221 | + assert_array_equal(a[:, 3:7], z2[:, 3:7]) |
| 222 | + assert_array_equal(a[:, -3:], z2[:, -3:]) |
| 223 | + assert_array_equal(a[:110, :3], z2[:110, :3]) |
| 224 | + assert_array_equal(a[190:310, 3:7], z2[190:310, 3:7]) |
| 225 | + assert_array_equal(a[-110:, -3:], z2[-110:, -3:]) |
| 226 | + |
| 227 | + |
| 228 | +# TODO test resize |
| 229 | +# TODO test append |
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