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+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2016-2017 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+"""Tests for array_like module"""
+
+__authors__ = ["P. Knobel"]
+__license__ = "MIT"
+__date__ = "09/01/2017"
+
+try:
+ import h5py
+except ImportError:
+ h5py = None
+
+import numpy
+import os
+import tempfile
+import unittest
+
+from ..array_like import DatasetView, ListOfImages
+from ..array_like import get_dtype, get_concatenated_dtype, get_shape,\
+ is_array, is_nested_sequence, is_list_of_arrays
+
+
+@unittest.skipIf(h5py is None,
+ "h5py is needed to test DatasetView")
+class TestTransposedDatasetView(unittest.TestCase):
+
+ def setUp(self):
+ # dataset attributes
+ self.ndim = 3
+ self.original_shape = (5, 10, 20)
+ self.size = 1
+ for dim in self.original_shape:
+ self.size *= dim
+
+ self.volume = numpy.arange(self.size).reshape(self.original_shape)
+
+ self.tempdir = tempfile.mkdtemp()
+ self.h5_fname = os.path.join(self.tempdir, "tempfile.h5")
+ with h5py.File(self.h5_fname, "w") as f:
+ f["volume"] = self.volume
+
+ self.h5f = h5py.File(self.h5_fname, "r")
+
+ self.all_permutations = [(0, 1, 2), (0, 2, 1), (1, 0, 2), (1, 2, 0),
+ (2, 0, 1), (2, 1, 0)]
+
+ def tearDown(self):
+ self.h5f.close()
+ os.unlink(self.h5_fname)
+ os.rmdir(self.tempdir)
+
+ def _testSize(self, obj):
+ """These assertions apply to all following test cases"""
+ self.assertEqual(obj.ndim, self.ndim)
+ self.assertEqual(obj.size, self.size)
+ size_from_shape = 1
+ for dim in obj.shape:
+ size_from_shape *= dim
+ self.assertEqual(size_from_shape, self.size)
+
+ for dim in self.original_shape:
+ self.assertIn(dim, obj.shape)
+
+ def testNoTransposition(self):
+ """no transposition (transposition = (0, 1, 2))"""
+ a = DatasetView(self.h5f["volume"])
+
+ self.assertEqual(a.shape, self.original_shape)
+ self._testSize(a)
+
+ # reversing the dimensions twice results in no change
+ rtrans = list(reversed(range(self.ndim)))
+ self.assertTrue(numpy.array_equal(
+ a,
+ a.transpose(rtrans).transpose(rtrans)))
+
+ for i in range(a.shape[0]):
+ for j in range(a.shape[1]):
+ for k in range(a.shape[2]):
+ self.assertEqual(self.h5f["volume"][i, j, k],
+ a[i, j, k])
+
+ def _testTransposition(self, transposition):
+ """test transposed dataset
+
+ :param tuple transposition: List of dimensions (0... n-1) sorted
+ in the desired order
+ """
+ a = DatasetView(self.h5f["volume"],
+ transposition=transposition)
+ self._testSize(a)
+
+ # sort shape of transposed object, to hopefully find the original shape
+ sorted_shape = tuple(dim_size for (_, dim_size) in
+ sorted(zip(transposition, a.shape)))
+ self.assertEqual(sorted_shape, self.original_shape)
+
+ a_as_array = numpy.array(self.h5f["volume"]).transpose(transposition)
+
+ # test the __array__ method
+ self.assertTrue(numpy.array_equal(
+ numpy.array(a),
+ a_as_array))
+
+ # test slicing
+ for selection in [(2, slice(None), slice(None)),
+ (slice(None), 1, slice(0, 8)),
+ (slice(0, 3), slice(None), 3),
+ (1, 3, slice(None)),
+ (slice(None), 2, 1),
+ (4, slice(1, 9, 2), 2)]:
+ self.assertIsInstance(a[selection], numpy.ndarray)
+ self.assertTrue(numpy.array_equal(
+ a[selection],
+ a_as_array[selection]))
+
+ # test the DatasetView.__getitem__ for single values
+ # (step adjusted to test at least 3 indices in each dimension)
+ for i in range(0, a.shape[0], a.shape[0] // 3):
+ for j in range(0, a.shape[1], a.shape[1] // 3):
+ for k in range(0, a.shape[2], a.shape[2] // 3):
+ sorted_indices = tuple(idx for (_, idx) in
+ sorted(zip(transposition, [i, j, k])))
+ viewed_value = a[i, j, k]
+ corresponding_original_value = self.h5f["volume"][sorted_indices]
+ self.assertEqual(viewed_value,
+ corresponding_original_value)
+
+ # reversing the dimensions twice results in no change
+ rtrans = list(reversed(range(self.ndim)))
+ self.assertTrue(numpy.array_equal(
+ a,
+ a.transpose(rtrans).transpose(rtrans)))
+
+ # test .T property
+ self.assertTrue(numpy.array_equal(
+ a.T,
+ a.transpose(rtrans)))
+
+ def testTransposition012(self):
+ """transposition = (0, 1, 2)
+ (should be the same as testNoTransposition)"""
+ self._testTransposition((0, 1, 2))
+
+ def testTransposition021(self):
+ """transposition = (0, 2, 1)"""
+ self._testTransposition((0, 2, 1))
+
+ def testTransposition102(self):
+ """transposition = (1, 0, 2)"""
+ self._testTransposition((1, 0, 2))
+
+ def testTransposition120(self):
+ """transposition = (1, 2, 0)"""
+ self._testTransposition((1, 2, 0))
+
+ def testTransposition201(self):
+ """transposition = (2, 0, 1)"""
+ self._testTransposition((2, 0, 1))
+
+ def testTransposition210(self):
+ """transposition = (2, 1, 0)"""
+ self._testTransposition((2, 1, 0))
+
+ def testAllDoubleTranspositions(self):
+ for trans1 in self.all_permutations:
+ for trans2 in self.all_permutations:
+ self._testDoubleTransposition(trans1, trans2)
+
+ def _testDoubleTransposition(self, transposition1, transposition2):
+ a = DatasetView(self.h5f["volume"],
+ transposition=transposition1).transpose(transposition2)
+
+ b = self.volume.transpose(transposition1).transpose(transposition2)
+
+ self.assertTrue(numpy.array_equal(a, b),
+ "failed with double transposition %s %s" % (transposition1, transposition2))
+
+ def test1DIndex(self):
+ a = DatasetView(self.h5f["volume"])
+ self.assertTrue(numpy.array_equal(self.volume[1],
+ a[1]))
+
+ b = DatasetView(self.h5f["volume"], transposition=(1, 0, 2))
+ self.assertTrue(numpy.array_equal(self.volume[:, 1, :],
+ b[1]))
+
+
+class TestTransposedListOfImages(unittest.TestCase):
+ def setUp(self):
+ # images attributes
+ self.ndim = 3
+ self.original_shape = (5, 10, 20)
+ self.size = 1
+ for dim in self.original_shape:
+ self.size *= dim
+
+ volume = numpy.arange(self.size).reshape(self.original_shape)
+
+ self.images = []
+ for i in range(self.original_shape[0]):
+ self.images.append(
+ volume[i])
+
+ self.images_as_3D_array = numpy.array(self.images)
+
+ self.all_permutations = [(0, 1, 2), (0, 2, 1), (1, 0, 2), (1, 2, 0),
+ (2, 0, 1), (2, 1, 0)]
+
+ def tearDown(self):
+ pass
+
+ def _testSize(self, obj):
+ """These assertions apply to all following test cases"""
+ self.assertEqual(obj.ndim, self.ndim)
+ self.assertEqual(obj.size, self.size)
+ size_from_shape = 1
+ for dim in obj.shape:
+ size_from_shape *= dim
+ self.assertEqual(size_from_shape, self.size)
+
+ for dim in self.original_shape:
+ self.assertIn(dim, obj.shape)
+
+ def testNoTransposition(self):
+ """no transposition (transposition = (0, 1, 2))"""
+ a = ListOfImages(self.images)
+
+ self.assertEqual(a.shape, self.original_shape)
+ self._testSize(a)
+
+ for i in range(a.shape[0]):
+ for j in range(a.shape[1]):
+ for k in range(a.shape[2]):
+ self.assertEqual(self.images[i][j, k],
+ a[i, j, k])
+
+ # reversing the dimensions twice results in no change
+ rtrans = list(reversed(range(self.ndim)))
+ self.assertTrue(numpy.array_equal(
+ a,
+ a.transpose(rtrans).transpose(rtrans)))
+
+ # test .T property
+ self.assertTrue(numpy.array_equal(
+ a.T,
+ a.transpose(rtrans)))
+
+ def _testTransposition(self, transposition):
+ """test transposed dataset
+
+ :param tuple transposition: List of dimensions (0... n-1) sorted
+ in the desired order
+ """
+ a = ListOfImages(self.images,
+ transposition=transposition)
+ self._testSize(a)
+
+ # sort shape of transposed object, to hopefully find the original shape
+ sorted_shape = tuple(dim_size for (_, dim_size) in
+ sorted(zip(transposition, a.shape)))
+ self.assertEqual(sorted_shape, self.original_shape)
+
+ a_as_array = numpy.array(self.images).transpose(transposition)
+
+ # test the DatasetView.__array__ method
+ self.assertTrue(numpy.array_equal(
+ numpy.array(a),
+ a_as_array))
+
+ # test slicing
+ for selection in [(2, slice(None), slice(None)),
+ (slice(None), 1, slice(0, 8)),
+ (slice(0, 3), slice(None), 3),
+ (1, 3, slice(None)),
+ (slice(None), 2, 1),
+ (4, slice(1, 9, 2), 2)]:
+ self.assertIsInstance(a[selection], numpy.ndarray)
+ self.assertTrue(numpy.array_equal(
+ a[selection],
+ a_as_array[selection]))
+
+ # test the DatasetView.__getitem__ for single values
+ # (step adjusted to test at least 3 indices in each dimension)
+ for i in range(0, a.shape[0], a.shape[0] // 3):
+ for j in range(0, a.shape[1], a.shape[1] // 3):
+ for k in range(0, a.shape[2], a.shape[2] // 3):
+ viewed_value = a[i, j, k]
+ sorted_indices = tuple(idx for (_, idx) in
+ sorted(zip(transposition, [i, j, k])))
+ corresponding_original_value = self.images[sorted_indices[0]][sorted_indices[1:]]
+ self.assertEqual(viewed_value,
+ corresponding_original_value)
+
+ # reversing the dimensions twice results in no change
+ rtrans = list(reversed(range(self.ndim)))
+ self.assertTrue(numpy.array_equal(
+ a,
+ a.transpose(rtrans).transpose(rtrans)))
+
+ # test .T property
+ self.assertTrue(numpy.array_equal(
+ a.T,
+ a.transpose(rtrans)))
+
+ def _testDoubleTransposition(self, transposition1, transposition2):
+ a = ListOfImages(self.images,
+ transposition=transposition1).transpose(transposition2)
+
+ b = self.images_as_3D_array.transpose(transposition1).transpose(transposition2)
+
+ self.assertTrue(numpy.array_equal(a, b),
+ "failed with double transposition %s %s" % (transposition1, transposition2))
+
+ def testTransposition012(self):
+ """transposition = (0, 1, 2)
+ (should be the same as testNoTransposition)"""
+ self._testTransposition((0, 1, 2))
+
+ def testTransposition021(self):
+ """transposition = (0, 2, 1)"""
+ self._testTransposition((0, 2, 1))
+
+ def testTransposition102(self):
+ """transposition = (1, 0, 2)"""
+ self._testTransposition((1, 0, 2))
+
+ def testTransposition120(self):
+ """transposition = (1, 2, 0)"""
+ self._testTransposition((1, 2, 0))
+
+ def testTransposition201(self):
+ """transposition = (2, 0, 1)"""
+ self._testTransposition((2, 0, 1))
+
+ def testTransposition210(self):
+ """transposition = (2, 1, 0)"""
+ self._testTransposition((2, 1, 0))
+
+ def testAllDoubleTranspositions(self):
+ for trans1 in self.all_permutations:
+ for trans2 in self.all_permutations:
+ self._testDoubleTransposition(trans1, trans2)
+
+ def test1DIndex(self):
+ a = ListOfImages(self.images)
+ self.assertTrue(numpy.array_equal(self.images[1],
+ a[1]))
+
+ b = ListOfImages(self.images, transposition=(1, 0, 2))
+ self.assertTrue(numpy.array_equal(self.images_as_3D_array[:, 1, :],
+ b[1]))
+
+
+class TestFunctions(unittest.TestCase):
+ """Test functions to guess the dtype and shape of an array_like
+ object"""
+ def testListOfLists(self):
+ l = [[0, 1, 2], [2, 3, 4]]
+ self.assertEqual(get_dtype(l),
+ numpy.dtype(int))
+ self.assertEqual(get_shape(l),
+ (2, 3))
+ self.assertTrue(is_nested_sequence(l))
+ self.assertFalse(is_array(l))
+ self.assertFalse(is_list_of_arrays(l))
+
+ l = [[0., 1.], [2., 3.]]
+ self.assertEqual(get_dtype(l),
+ numpy.dtype(float))
+ self.assertEqual(get_shape(l),
+ (2, 2))
+ self.assertTrue(is_nested_sequence(l))
+ self.assertFalse(is_array(l))
+ self.assertFalse(is_list_of_arrays(l))
+
+ # concatenated dtype of int and float
+ l = [numpy.array([[0, 1, 2], [2, 3, 4]]),
+ numpy.array([[0., 1., 2.], [2., 3., 4.]])]
+
+ self.assertEqual(get_concatenated_dtype(l),
+ numpy.array(l).dtype)
+ self.assertEqual(get_shape(l),
+ (2, 2, 3))
+ self.assertFalse(is_nested_sequence(l))
+ self.assertFalse(is_array(l))
+ self.assertTrue(is_list_of_arrays(l))
+
+ def testNumpyArray(self):
+ a = numpy.array([[0, 1], [2, 3]])
+ self.assertEqual(get_dtype(a),
+ a.dtype)
+ self.assertFalse(is_nested_sequence(a))
+ self.assertTrue(is_array(a))
+ self.assertFalse(is_list_of_arrays(a))
+
+ @unittest.skipIf(h5py is None,
+ "h5py is needed for this test")
+ def testH5pyDataset(self):
+ a = numpy.array([[0, 1], [2, 3]])
+
+ tempdir = tempfile.mkdtemp()
+ h5_fname = os.path.join(tempdir, "tempfile.h5")
+ with h5py.File(h5_fname, "w") as h5f:
+ h5f["dataset"] = a
+ d = h5f["dataset"]
+
+ self.assertEqual(get_dtype(d),
+ numpy.dtype(int))
+ self.assertFalse(is_nested_sequence(d))
+ self.assertTrue(is_array(d))
+ self.assertFalse(is_list_of_arrays(d))
+
+ os.unlink(h5_fname)
+ os.rmdir(tempdir)
+
+
+def suite():
+ test_suite = unittest.TestSuite()
+ test_suite.addTest(
+ unittest.defaultTestLoader.loadTestsFromTestCase(TestTransposedDatasetView))
+ test_suite.addTest(
+ unittest.defaultTestLoader.loadTestsFromTestCase(TestTransposedListOfImages))
+ test_suite.addTest(
+ unittest.defaultTestLoader.loadTestsFromTestCase(TestFunctions))
+ return test_suite
+
+
+if __name__ == '__main__':
+ unittest.main(defaultTest='suite')