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# -*- coding: utf-8 -*-
# Copyright © 2019, German Neuroinformatics Node (G-Node)
#
# All rights reserved.
#
# Redistribution and use in section and binary forms, with or without
# modification, are permitted under the terms of the BSD License. See
# LICENSE file in the root of the Project.
import os
import unittest
import numpy as np
import nixio as nix
from .tmp import TempDir
class TestDataView(unittest.TestCase):
def setUp(self):
self.tmpdir = TempDir("dvtest")
self.testfilename = os.path.join(self.tmpdir.path, "dvtest.nix")
self.file = nix.File.open(self.testfilename, nix.FileMode.Overwrite)
self.data = np.random.random_sample((40, 80))
block = self.file.create_block("testblock", "nix.test.block")
block.create_data_array("data", "nix.test.data", data=self.data)
def tearDown(self):
del self.file.blocks[0]
self.file.close()
self.tmpdir.cleanup()
def test_data_view_read(self):
da = self.file.blocks[0].data_arrays[0]
dv = da.get_slice((10, 3), extents=(1, 3))
np.testing.assert_almost_equal(dv[:], da[10:11, 3:6])
def test_data_view_read_2d_str_array(self):
numbers = ["one", "two", "three", "four", "five", "six", "seven", "eight", "nine", "ten"]
data = np.empty((10, 4), dtype=str)
for i in range(10):
for j in range(4):
data[i, j] = " ".join([numbers[i], numbers[j]])
da = self.file.blocks[0].create_data_array("str_2d_array", "test", dtype=nix.DataType.String, data=data)
da.append_set_dimension()
da.append_set_dimension()
dv = da.get_slice((0, 0), extents=(10, 4))
npeq = np.testing.assert_equal
npeq(dv.shape, da.shape)
npeq(dv[:], data)
for d in dv[:]:
assert("numpy.str_" not in str(type(d)))
def test_data_view_fancy_slicing(self):
da = self.file.blocks[0].data_arrays[0]
dv = da.get_slice((5, 8), extents=(10, 20))
npeq = np.testing.assert_almost_equal
# when stop > length, stops at len-1
npeq(dv[:100, 1], da[5:15, 9])
npeq(dv[0, 5:2000], da[5, 13:28])
npeq(dv[9:100, 18:1000], da[14:15, 26:28])
# negative slicing
npeq(dv[-5:, 1], da[10:15, 9])
npeq(dv[-5:-2, -1], da[10:13, 27])
npeq(dv[:, -10:13], da[5:15, 18:21])
def test_data_view_write_direct(self):
da = self.file.blocks[0].data_arrays[0]
np.testing.assert_almost_equal(da[:], self.data)
dv = da.get_slice((10, 3), extents=(1, 3))
dv.write_direct([1, 2, 3])
newdata = self.data.copy()
newdata[10:11, 3:6] = [1, 2, 3]
np.testing.assert_almost_equal(da[:], newdata)
def test_data_view_write_index(self):
"""
Write through DataView to the underlying DataArray using [slice]
notation.
Update copy of underlying data with expected values and compare
directly to DataArray for assertions.
"""
da = self.file.blocks[0].data_arrays[0]
dv = da.get_slice((10, 20), extents=(20, 15))
newdata = self.data.copy()
npeq = np.testing.assert_almost_equal
# straightforward slicing
rand_data = np.random.random_sample((3, 4))
dv[0:3, 1:5] = rand_data
newdata[10:13, 21:25] = rand_data
npeq(da[:], newdata)
# slicing with steps
rand_data = np.random.random_sample((5, 3))
dv[0:20:4, 0:15:5] = rand_data
newdata[10:30:4, 20:35:5] = rand_data
npeq(da[:], newdata)
# steps only
rand_data = np.random.random_sample((5, 3))
dv[::4, ::5] = rand_data
newdata[10:30:4, 20:35:5] = rand_data
npeq(da[:], newdata)
# plain index
dv[1, 1] = 20
newdata[11, 21] = 20
npeq(da[:], newdata)
# negative index
dv[-1, -1] = 80
newdata[29, 34] = 80
npeq(da[:], newdata)
# negative slice start
rand_data = np.random.random_sample(3)
dv[-3::, 10] = rand_data
newdata[27:30, 30] = rand_data
npeq(da[:], newdata)
# negative slice stop
rand_data = np.random.random_sample(15)
dv[:-5, 2] = rand_data
newdata[10:25, 22] = rand_data
npeq(da[:], newdata)
# negative slice start and stop
rand_data = np.random.random_sample(10)
dv[10, -15:-5] = rand_data
newdata[20, 20:30] = rand_data
npeq(da[:], newdata)
def test_data_view_oob(self):
da = self.file.blocks[0].data_arrays[0]
dv = da.get_slice((41, 81), extents=(1, 1))
assert not dv.valid
assert "OutOfBounds error" in dv.debug_message
dv = da.get_slice((0, 0), extents=(100, 5))
assert not dv.valid
assert "OutOfBounds error" in dv.debug_message
with self.assertRaises(nix.exceptions.IncompatibleDimensions):
da.get_slice((0, 0, 0), extents=(5, 5, 5))
dv = da.get_slice((5, 8), extents=(10, 20))
assert dv.valid
with self.assertRaises(nix.exceptions.OutOfBounds):
_ = dv[12, :]
with self.assertRaises(nix.exceptions.OutOfBounds):
_ = dv[12, :]
with self.assertRaises(nix.exceptions.OutOfBounds):
_ = dv[10]
with self.assertRaises(nix.exceptions.OutOfBounds):
_ = dv[0, 20]
with self.assertRaises(nix.exceptions.OutOfBounds):
_ = dv[:, 25]
with self.assertRaises(nix.exceptions.OutOfBounds):
_ = dv[-11]
with self.assertRaises(nix.exceptions.OutOfBounds):
_ = dv[0, -21]
def test_data_view_ellipsis(self):
block = self.file.blocks[0]
data = np.random.random_sample((10, 11, 12, 13, 14))
da = block.create_data_array("data2", "nix.test.data", data=data)
npeq = np.testing.assert_almost_equal
dv = da.get_slice((5, 6, 7, 8, 9), (5, 5, 5, 5, 5))
npeq(dv[1, ..., 2], da[6, 6:11, 7:12, 8:13, 11])
npeq(dv[..., 0, 0], da[5:10, 6:11, 7:12, 8, 9])
npeq(dv[1:3, 0, ...], da[6:8, 6, 7:12, 8:13, 9:14])
npeq(dv[1:3, :, ...], da[6:8, 6:11, 7:12, 8:13, 9:14])
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