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# -*- coding: utf-8 -*-
"""
Created on Fri Sep 18 17:07:16 2020
@author: Suhas Somnath, Gerd Duscher
"""
from __future__ import division, print_function, unicode_literals, \
absolute_import
import unittest
import numpy as np
import dask.array as da
import string
import ase.build
import sys
from copy import deepcopy
sys.path.insert(0, "../../sidpy/")
from sidpy.sid.dimension import Dimension
from sidpy.sid.dataset import DataType, Dataset
if sys.version_info.major == 3:
unicode = str
generic_attributes = ['title', 'quantity', 'units', 'modality', 'source']
def validate_dataset_properties(self, dataset, values,
title='generic', quantity='generic', units='generic',
modality='generic', source='generic', dimension_dict=None,
data_type=DataType.UNKNOWN, variance=None,
metadata={}, original_metadata={},
):
self.assertIsInstance(self, unittest.TestCase)
self.assertIsInstance(dataset, Dataset)
# DONE: Validate that EVERY property is set correctly
values = np.array(values)
self.assertTrue(np.all([hasattr(dataset, att) for att in generic_attributes]))
expected = values.flatten()
actual = dataset.compute().flatten()
self.assertTrue(np.allclose(expected, actual, equal_nan=True, rtol=1e-05, atol=1e-08))
# self.assertTrue(np.all([x == y for x, y in zip(expected, actual)]))
this_attributes = [title, quantity, units, modality, source]
dataset_attributes = [getattr(dataset, att) for att in generic_attributes]
for expected, actual in zip(dataset_attributes, this_attributes):
self.assertTrue(np.all([x == y for x, y in zip(expected, actual)]))
if variance is None:
self.assertEqual(dataset.variance, None)
else:
self.assertTrue(isinstance(dataset.variance, da.core.Array))
expected_var = np.array(variance).flatten()
actual_var = dataset.variance.compute().flatten()
self.assertTrue(np.allclose(expected_var, actual_var, equal_nan=True, rtol=1e-05, atol=1e-08))
self.assertEqual(dataset.data_type, data_type)
self.assertEqual(dataset.metadata, metadata)
self.assertEqual(dataset.original_metadata, original_metadata)
if dimension_dict is None:
for dim in range(len(values.shape)):
self.assertEqual(getattr(dataset, string.ascii_lowercase[dim]),
getattr(dataset, 'dim_{}'.format(dim)))
else:
for dim in range(len(values.shape)):
self.assertEqual(getattr(dataset, dimension_dict[dim].name),
getattr(dataset, 'dim_{}'.format(dim)))
self.assertEqual(dataset._axes[dim], dimension_dict[dim])
# Make sure we do not have too many dimensions
self.assertFalse(hasattr(dataset, 'dim_{}'.format(len(values.shape))))
# self.assertFalse(hasattr(dataset, string.ascii_lowercase[len(values.shape)]))
# Following 4 methods are used in testing the methods that reduce dimensions of the dataset
def single_axis_test(self, func, **kwargs):
dset_np = np.random.rand(4, 1, 5)
dset = Dataset.from_array(dset_np, title='test')
sid_func = getattr(dset, func)
np_func = getattr(dset_np, func)
dset_1 = sid_func(axis=0, keepdims=False)
dim_dict = {0: dset._axes[1].copy(), 1: dset._axes[2].copy()}
title_prefix = kwargs.get('title_prefix')
validate_dataset_properties(self, dset_1, np_func(axis=0, keepdims=False),
title=title_prefix + dset.title,
modality=dset.modality, source=dset.modality, dimension_dict=dim_dict,
data_type=DataType.UNKNOWN,
metadata={}, original_metadata={}
)
def multiple_axes_test(self, func, **kwargs):
dset_np = np.random.rand(1, 6, 4)
dset = Dataset.from_array(dset_np, title='test')
sid_func = getattr(dset, func)
np_func = getattr(dset_np, func)
dset_1 = sid_func(axis=(0, 1), keepdims=False)
dim_dict = {0: dset._axes[2].copy()}
title_prefix = kwargs.get('title_prefix')
validate_dataset_properties(self, dset_1, np_func(axis=(0, 1), keepdims=False),
title=title_prefix + dset.title,
modality=dset.modality, source=dset.modality, dimension_dict=dim_dict,
data_type=DataType.UNKNOWN,
metadata={}, original_metadata={}
)
# The following two tests are for when keep_dims is set to True
def keepdims_test(self, func, **kwargs):
dset_np = np.random.rand(2, 1, 4)
dset = Dataset.from_array(dset_np, title='test')
sid_func = getattr(dset, func)
np_func = getattr(dset_np, func)
dset_1 = sid_func(axis=0, keepdims=True)
dim_dict = dset._axes.copy()
dim_dict[0] = Dimension(np.arange(1), name=dset._axes[0].name,
quantity=dset._axes[0].quantity, units=dset._axes[0].units,
dimension_type=dset._axes[0].dimension_type)
title_prefix = kwargs.get('title_prefix')
validate_dataset_properties(self, dset_1, np_func(axis=0, keepdims=True),
title=title_prefix + dset.title,
modality=dset.modality, source=dset.modality, dimension_dict=dim_dict,
data_type=DataType.UNKNOWN,
metadata={}, original_metadata={}
)
def keepdims_multiple_axes_test(self, func, **kwargs):
dset_np = np.random.rand(1, 5, 4)
dset = Dataset.from_array(dset_np, title='test')
sid_func = getattr(dset, func)
np_func = getattr(dset_np, func)
title_prefix = kwargs.get('title_prefix')
dset_1 = sid_func(axis=(0, 1), keepdims=True)
dim_dict = dset._axes.copy()
dim_dict[0] = Dimension(np.arange(1), name=dset._axes[0].name,
quantity=dset._axes[0].quantity, units=dset._axes[0].units,
dimension_type=dset._axes[0].dimension_type)
dim_dict[1] = Dimension(np.arange(1), name=dset._axes[1].name,
quantity=dset._axes[1].quantity, units=dset._axes[1].units,
dimension_type=dset._axes[1].dimension_type)
validate_dataset_properties(self, dset_1, np_func(axis=(0, 1), keepdims=True),
title=title_prefix + dset.title,
modality=dset.modality, source=dset.modality, dimension_dict=dim_dict,
data_type=DataType.UNKNOWN,
metadata={}, original_metadata={}
)
class TestDatasetFromArray(unittest.TestCase):
def test_std_inputs(self):
# verify generic properties, dimensions, etc.
values = np.random.random([4, 5, 6])
descriptor = Dataset.from_array(values)
validate_dataset_properties(self, descriptor, values)
def test_dset_with_variance(self):
values = np.random.random([4, 5, 6])
variance = np.random.random([4, 5, 6])
descriptor = Dataset.from_array(values, variance=variance)
validate_dataset_properties(self, descriptor, values, variance=variance)
class TestDatasetConstructor(unittest.TestCase):
def test_minimal_inputs(self):
""" test minimum input requirement of an array like object
"""
with self.assertRaises(TypeError):
Dataset.from_array()
descriptor = Dataset.from_array(np.arange(3))
validate_dataset_properties(self, descriptor, np.arange(3))
def test_all_inputs(self):
descriptor = Dataset.from_array(np.arange(3), title='test')
validate_dataset_properties(self, descriptor, np.arange(3), title='test')
def test_user_defined_parms(self):
descriptor = Dataset.from_array(np.arange(3), title='test')
for att in generic_attributes:
setattr(descriptor, att, 'test')
test_dict = {0: 'test'}
descriptor.metadata = test_dict.copy()
descriptor.original_metadata = test_dict.copy()
validate_dataset_properties(self, descriptor, np.arange(3),
title='test', quantity='test', units='test',
modality='test', source='test', dimension_dict=None,
data_type=DataType.UNKNOWN,
metadata=test_dict, original_metadata=test_dict
)
def test_invalid_main_types(self):
"""
anything that is not recognized by dask will make an empty dask array
but name has to be a string
"""
# TODO: call validate_dataset_properties instead
descriptor = Dataset.from_array(DataType.UNKNOWN)
self.assertEqual(descriptor.shape, ())
descriptor = Dataset.from_array('test')
self.assertEqual(descriptor.shape, ())
descriptor = Dataset.from_array(1)
self.assertEqual(descriptor.shape, ())
with self.assertRaises(ValueError):
Dataset.from_array(1, 1)
# TODO: Should be TypeError
def test_numpy_array_input(self):
x = np.ones([3, 4, 5])
descriptor = Dataset.from_array(x, title='test')
self.assertEqual(descriptor.shape, x.shape)
# TODO: call validate_dataset_properties instead
def test_dask_array_input(self):
x = da.zeros([3, 4], chunks='auto')
descriptor = Dataset.from_array(x, chunks='auto', title='test')
self.assertEqual(descriptor.shape, x.shape)
# TODO: call validate_dataset_properties instead
def test_list_input(self):
x = [[3, 4, 6], [5, 6, 7]]
descriptor = Dataset.from_array(x, title='test')
self.assertEqual(descriptor.shape, np.array(x).shape)
# TODO: call validate_dataset_properties instead
def test_1d_main_data(self):
values = np.ones([10])
descriptor = Dataset.from_array(values)
self.assertTrue(np.all([x == y for x, y in zip(values, descriptor)]))
# TODO: call validate_dataset_properties instead
# Move such validation to validate_dataset_properties
for dim in range(len(values.shape)):
self.assertEqual(getattr(descriptor, string.ascii_lowercase[dim]),
getattr(descriptor, 'dim_{}'.format(dim)))
self.assertFalse(hasattr(descriptor, 'dim_{}'.format(len(values.shape))))
self.assertFalse(hasattr(descriptor, string.ascii_lowercase[len(values.shape)]))
def test_2d_main_data(self):
values = np.random.random([4, 5])
descriptor = Dataset.from_array(values)
for expected, actual in zip(values, descriptor):
self.assertTrue(np.all([x == y for x, y in zip(expected, actual)]))
for dim in range(len(values.shape)):
self.assertEqual(getattr(descriptor, string.ascii_lowercase[dim]),
getattr(descriptor, 'dim_{}'.format(dim)))
self.assertFalse(hasattr(descriptor, 'dim_{}'.format(len(values.shape))))
self.assertFalse(hasattr(descriptor, string.ascii_lowercase[len(values.shape)]))
def test_3d_main_data(self):
values = np.random.random([4, 5, 6])
descriptor = Dataset.from_array(values)
for expected, actual in zip(values, descriptor):
self.assertTrue(np.all([x == y for x, y in zip(expected, actual)]))
for dim in range(len(values.shape)):
self.assertEqual(getattr(descriptor, string.ascii_lowercase[dim]),
getattr(descriptor, 'dim_{}'.format(dim)))
self.assertFalse(hasattr(descriptor, 'dim_{}'.format(len(values.shape))))
self.assertFalse(hasattr(descriptor, string.ascii_lowercase[len(values.shape)]))
def test_4d_main_data(self):
values = np.random.random([4, 5, 7, 3])
descriptor = Dataset.from_array(values)
for expected, actual in zip(values, descriptor):
self.assertTrue(np.all([x == y for x, y in zip(expected, actual)]))
for dim in range(len(values.shape)):
self.assertEqual(getattr(descriptor, string.ascii_lowercase[dim]),
getattr(descriptor, 'dim_{}'.format(dim)))
self.assertFalse(hasattr(descriptor, 'dim_{}'.format(len(values.shape))))
self.assertFalse(hasattr(descriptor, string.ascii_lowercase[len(values.shape)]))
def test_dimensions_not_matching_main(self):
pass
def test_unknown_data_type(self):
values = np.random.random([4])
descriptor = Dataset.from_array(values)
expected = "Supported data_types for plotting are only:"
with self.assertRaises(Warning) as context:
descriptor.data_type = 'quark'
self.assertTrue(expected in str(context.exception))
def test_enum_data_type(self):
values = np.random.random([4])
descriptor = Dataset.from_array(values)
for dt_type in DataType:
descriptor.data_type = dt_type
self.assertTrue(descriptor.data_type == dt_type)
def test_string_data_type(self):
values = np.random.random([4])
descriptor = Dataset.from_array(values)
for dt_type in DataType:
descriptor.data_type = str(dt_type.name)
self.assertTrue(descriptor.data_type == dt_type)
class TestDatasetRepr(unittest.TestCase):
def test_minimal_inputs(self):
values = np.arange(5)
descriptor = Dataset.from_array(values)
actual = '{}'.format(descriptor)
out = 'generic'
da_array = da.from_array(values, chunks='auto')
expected = 'sidpy.Dataset of type {} with:\n '.format(DataType.UNKNOWN.name)
expected = expected + '{}'.format(da_array)
expected = expected + '\n data contains: {} ({})'.format(out, out)
expected = expected + '\n and Dimensions: '
expected = expected + '\n{}: {} ({}) of size {}'.format('a', out, out, values.shape)
"""
for exp, act in zip(expected.split('\n'), actual.split('\n')):
print('Expected:\t' + exp)
print('Actual:\t' + act)
print(exp == act)
"""
self.assertEqual(actual, expected)
def test_fully_configured(self):
values = np.arange(5)
descriptor = Dataset.from_array(values)
for att in generic_attributes:
setattr(descriptor, att, 'test')
descriptor.metadata = {0: 'test'}
actual = '{}'.format(descriptor)
out = 'test'
da_array = da.from_array(values, chunks='auto')
expected = 'sidpy.Dataset of type {} with:\n '.format(DataType.UNKNOWN.name)
expected = expected + '{}'.format(da_array)
expected = expected + '\n data contains: {} ({})'.format(out, out)
expected = expected + '\n and Dimensions: '
expected = expected + '\n{}: {} ({}) of size {}'.format('a', 'generic', 'generic', values.shape)
expected = expected + '\n with metadata: {}'.format([0])
"""
for exp, act in zip(expected.split('\n'), actual.split('\n')):
print('Expected:\t' + exp)
print('Actual:\t' + act)
print(exp == act)
"""
self.assertEqual(actual, expected)
def test_user_defined_parameters(self):
# self.blah = 14. Will / should this get printed
pass
class TestLikeData(unittest.TestCase):
def test_minimal_inputs(self):
values = np.ones([4, 5])
source_dset = Dataset.from_array(values)
values = np.zeros([4, 5])
descriptor = source_dset.like_data(values)
self.assertTrue(descriptor.shape == values.shape)
self.assertIsInstance(descriptor, Dataset)
def test_all_customized_properties(self):
values = np.ones([4, 5])
source_dset = Dataset.from_array(values)
for att in generic_attributes:
setattr(source_dset, att, 'test')
source_dset.metadata = {0: 'test'}
values = np.zeros([4, 5])
descriptor = source_dset.like_data(values)
self.assertEqual(descriptor.title, 'test_new')
descriptor.title = 'test'
self.assertTrue(np.all([getattr(descriptor, att) == 'test' for att in generic_attributes]))
self.assertEqual(descriptor.metadata, source_dset.metadata)
self.assertEqual(descriptor.original_metadata, source_dset.original_metadata)
def test_changing_size(self):
values = np.ones([4, 5])
source_dset = Dataset.from_array(values)
source_dset.a *= 0.5
source_dset.quantity = 'test'
values = np.zeros([3, 5])
descriptor = source_dset.like_data(values)
# self.assertEqual(descriptor.a.values), np.arange(3)*.5)
expected = descriptor.a.values
actual = np.arange(3) * .5
self.assertTrue(np.all([x == y for x, y in zip(expected, actual)]))
def test_variance(self):
values = np.ones([4, 5])
var = np.random.normal(size=(4, 5))
source_dset = Dataset.from_array(values, variance=var)
descriptor = source_dset.like_data(values)
self.assertEqual(descriptor.variance, None)
descriptor = source_dset.like_data(values, variance=var)
self.assertEqual(descriptor.variance.all(), source_dset.variance.all())
class TestCopy(unittest.TestCase):
def test_minimal_inputs(self):
values = np.random.random([4, 5])
dataset = Dataset.from_array(values)
descriptor = dataset.copy()
self.assertIsInstance(descriptor, Dataset)
for expected, actual in zip(dataset, descriptor):
self.assertTrue(np.all([x == y for x, y in zip(expected, actual)]))
self.assertTrue(np.all([hasattr(descriptor, att) for att in generic_attributes]))
self.assertTrue(np.all([getattr(descriptor, att) == 'generic' for att in generic_attributes]))
self.assertEqual(descriptor.data_type, DataType.UNKNOWN)
self.assertEqual(descriptor.metadata, {})
self.assertEqual(descriptor.original_metadata, {})
for dim in range(len(values.shape)):
self.assertEqual(getattr(descriptor, string.ascii_lowercase[dim]),
getattr(descriptor, 'dim_{}'.format(dim)))
self.assertFalse(hasattr(descriptor, 'dim_{}'.format(len(dataset.shape))))
self.assertFalse(hasattr(descriptor, string.ascii_lowercase[len(dataset.shape)]))
def test_all_customized_properties(self):
values = np.random.random([4, 5])
dataset = Dataset.from_array(values)
dataset.rename_dimension(0, 'x')
dataset.quantity = 'test'
descriptor = dataset.copy()
self.assertIsInstance(descriptor, Dataset)
self.assertEqual(descriptor.quantity, dataset.quantity)
self.assertTrue(hasattr(descriptor, 'x'))
class TestRenameDimension(unittest.TestCase):
def test_valid_index_and_name(self):
values = np.zeros([4, 5])
descriptor = Dataset.from_array(values)
descriptor.rename_dimension(0, 'v')
self.assertEqual(descriptor.v, descriptor.dim_0)
def test_invalid_index_object_type(self):
values = np.zeros([4, 5])
descriptor = Dataset.from_array(values)
with self.assertRaises(TypeError):
descriptor.rename_dimension('v', 'v')
def test_index_out_of_bounds(self):
values = np.zeros([4, 5])
descriptor = Dataset.from_array(values)
with self.assertRaises(IndexError):
descriptor.rename_dimension(3, 'v')
def test_invalid_name_object_types(self):
values = np.zeros([4, 5])
descriptor = Dataset.from_array(values)
with self.assertRaises(TypeError):
descriptor.rename_dimension(0, 1)
def test_empty_name_string(self):
values = np.zeros([4, 5])
descriptor = Dataset.from_array(values)
with self.assertRaises(ValueError):
descriptor.rename_dimension(0, '')
def test_existing_name(self):
values = np.zeros([4, 5])
descriptor = Dataset.from_array(values)
with self.assertRaises(ValueError):
descriptor.rename_dimension(0, 'b')
class TestSetDimension(unittest.TestCase):
def test_valid_index_and_dim_obj(self):
values = np.zeros([4, 5])
descriptor = Dataset.from_array(values)
descriptor.set_dimension(0, Dimension(np.arange(4), 'x', quantity='test', units='test'))
self.assertIsInstance(descriptor.x, Dimension)
def test_invalid_dim_object(self):
values = np.zeros([4, 5])
descriptor = Dataset.from_array(values)
with self.assertRaises(TypeError):
descriptor.set_dimension(3, "New dimension")
with self.assertRaises(TypeError):
descriptor.set_dimension('2', {'x': np.arange(4)})
with self.assertRaises(TypeError):
descriptor.set_dimension(2, np.arange(4))
# validity of index tested in TestRenameDimension
class TestHelperFunctions(unittest.TestCase):
def test_get_image_dims(self):
values = np.zeros([4, 5])
descriptor = Dataset.from_array(values)
descriptor.set_dimension(0, Dimension(np.arange(4), 'x', quantity='test', dimension_type='spatial'))
image_dims = descriptor.get_image_dims()
self.assertEqual(len(image_dims), 1)
self.assertEqual(image_dims[0], 0)
descriptor.dim_1.dimension_type = 'spatial'
image_dims = descriptor.get_image_dims()
self.assertEqual(len(image_dims), 2)
self.assertEqual(image_dims[1], 1)
def test_get_dimensions_by_type(self):
values = np.zeros([4, 5])
descriptor = Dataset.from_array(values)
descriptor.set_dimension(0, Dimension(np.arange(4), 'x', quantity='test', dimension_type='spatial'))
image_dims = descriptor.get_dimensions_by_type('spatial')
self.assertEqual(len(image_dims), 1)
self.assertEqual(image_dims[0], 0)
descriptor.dim_1.dimension_type = 'spatial'
image_dims = descriptor.get_dimensions_by_type('spatial')
self.assertEqual(len(image_dims), 2)
self.assertEqual(image_dims[1], 1)
def test_get_spectral_dims(self):
values = np.zeros([4, 5])
descriptor = Dataset.from_array(values)
descriptor.set_dimension(0, Dimension(np.arange(4), 'x', quantity='test', dimension_type='spatial'))
spec_dims = descriptor.get_spectral_dims()
self.assertEqual(len(spec_dims), 0)
descriptor.x.dimension_type = 'spectral'
spec_dims = descriptor.get_spectral_dims()
self.assertEqual(len(spec_dims), 1)
self.assertEqual(spec_dims[0], 0)
descriptor.dim_1.dimension_type = 'spectral'
spec_dims = descriptor.get_spectral_dims()
self.assertEqual(len(spec_dims), 2)
self.assertEqual(spec_dims[1], 1)
def test_get_extent(self):
values = np.zeros([4, 5])
descriptor = Dataset.from_array(values)
descriptor.set_dimension(0, Dimension(np.arange(4), 'x', quantity='test', dimension_type='spatial'))
descriptor.dim_1.dimension_type = 'spatial'
descriptor.set_dimension(0, Dimension(np.arange(4), 'x', quantity='test', dimension_type='spatial'))
extent = descriptor.get_extent([0, 1])
self.assertEqual(extent[0], -0.5)
self.assertEqual(extent[1], 3.5)
def test_get_labels(self):
values = np.zeros([4, 5])
descriptor = Dataset.from_array(values)
labels = descriptor.labels
self.assertEqual(labels[0], 'generic (generic)')
def test_empty_structure(self):
values = np.zeros([4, 5])
descriptor = Dataset.from_array(values)
structures = descriptor.structures
self.assertEqual(len(structures), 0)
def test_add_structure(self):
values = np.zeros([4, 5])
a = 5.14 # A
atoms = ase.build.bulk('Si', 'diamond', a=a, cubic=True)
descriptor = Dataset.from_array(values)
descriptor.add_structure(atoms)
descriptor.add_structure(atoms, 'reference')
self.assertEqual(len(descriptor.structures), 2)
self.assertTrue('reference' in descriptor.structures.keys())
def test__equ__(self):
values = np.zeros([4, 5])
descriptor1 = Dataset.from_array(values)
descriptor2 = Dataset.from_array(values)
# TODO: why does direct comparison not work
self.assertTrue(descriptor1.__eq__(descriptor2))
self.assertFalse(descriptor1.__eq__(np.arange(4)))
descriptor1.set_dimension(0, Dimension(np.arange(4), 'x', quantity='test', dimension_type='spatial'))
self.assertFalse(descriptor1.__eq__(descriptor2))
descriptor2.modality = 'nix'
self.assertFalse(descriptor1.__eq__(descriptor2))
descriptor2.data_type = 'image'
self.assertFalse(descriptor1.__eq__(descriptor2))
descriptor2.source = 'image'
self.assertFalse(descriptor1.__eq__(descriptor2))
descriptor2.quantity = 'image'
self.assertFalse(descriptor1.__eq__(descriptor2))
descriptor2.units = 'image'
self.assertFalse(descriptor1.__eq__(descriptor2))
def test_h5_dataset(self):
values = np.ones([4, 5])
source_dset = Dataset.from_array(values)
class TestViewMetadata(unittest.TestCase):
def test_default_empty_metadata(self):
values = np.zeros([4, 5])
descriptor = Dataset.from_array(values)
descriptor.view_metadata()
# self.assertEqual('{}'.format(descriptor.view_metadata()),'None')
def test_entered_metadata(self):
values = np.zeros([4, 5])
descriptor = Dataset.from_array(values)
descriptor.metadata = {0: 'test'}
print('{}'.format(descriptor.view_metadata()))
# self.assertEqual(descriptor.view_metadata(), '0 : test')
class TestViewOriginalMetadata(unittest.TestCase):
def test_default_empty_metadata(self):
pass
def test_entered_metadata(self):
pass
class Testallmethod(unittest.TestCase):
def test_all_single_axis(self):
single_axis_test(self, 'all', title_prefix='all_aggregate_')
def test_all_multiple_axes(self):
multiple_axes_test(self, 'all', title_prefix='all_aggregate_')
def test_all_keepdims(self):
keepdims_test(self, 'all', title_prefix='all_aggregate_')
def test_all_keepdims_multiple_axes(self):
keepdims_multiple_axes_test(self, 'all', title_prefix='all_aggregate_')
class Testanymethod(unittest.TestCase):
def test_any_single_axis(self):
single_axis_test(self, 'any', title_prefix='any_aggregate_')
def test_any_multiple_axes(self):
multiple_axes_test(self, 'any', title_prefix='any_aggregate_')
def test_any_keepdims(self):
keepdims_test(self, 'any', title_prefix='any_aggregate_')
def test_any_keepdims_multiple_axes(self):
keepdims_multiple_axes_test(self, 'any', title_prefix='any_aggregate_')
class TestMinMethod(unittest.TestCase):
def test_min_single_axis(self):
single_axis_test(self, 'min', title_prefix='min_aggregate_')
def test_min_multiple_axes(self):
multiple_axes_test(self, 'min', title_prefix='min_aggregate_')
def test_min_keepdims(self):
keepdims_test(self, 'min', title_prefix='min_aggregate_')
def test_min_keepdims_multiple_axes(self):
keepdims_multiple_axes_test(self, 'min', title_prefix='min_aggregate_')
class TestMaxMethod(unittest.TestCase):
def test_max_single_axis(self):
single_axis_test(self, 'max', title_prefix='max_aggregate_')
def test_max_multiple_axes(self):
multiple_axes_test(self, 'max', title_prefix='max_aggregate_')
def test_max_keepdims(self):
keepdims_test(self, 'max', title_prefix='max_aggregate_')
def test_min_keepdims_multiple_axes(self):
keepdims_multiple_axes_test(self, 'max', title_prefix='max_aggregate_')
class TestSumMethod(unittest.TestCase):
def test_sum_single_axis(self):
single_axis_test(self, 'sum', title_prefix='sum_aggregate_')
def test_sum_multiple_axis(self):
multiple_axes_test(self, 'sum', title_prefix='sum_aggregate_')
def test_sum_keepdims(self):
keepdims_test(self, 'sum', title_prefix='sum_aggregate_')
def test_sum_keepdims_multiple_axis(self):
keepdims_multiple_axes_test(self, 'sum', title_prefix='sum_aggregate_')
def test_sum_dtype(self):
# Have to take care of complex datasets when asked about the sum of the entire dataset
pass
class TestMeanMethod(unittest.TestCase):
def test_mean_single_axis(self):
single_axis_test(self, 'mean', title_prefix='mean_aggregate_')
def test_mean_multiple_axis(self):
multiple_axes_test(self, 'mean', title_prefix='mean_aggregate_')
def test_mean_keepdims(self):
keepdims_test(self, 'mean', title_prefix='mean_aggregate_')
def test_mean_keepdims_multiple_axis(self):
keepdims_multiple_axes_test(self, 'mean', title_prefix='mean_aggregate_')
def test_mean_dtype(self):
# Have to take care of complex datasets when asked about the sum of the entire dataset
pass
class TestSlicing(unittest.TestCase):
np.random.seed(0)
values = np.random.rand(3, 4, 6, 5)
dset = Dataset.from_array(values, title='4D_STEM', units='nA',
quantity='Current',
modality='modality', source='source')
dset.data_type = DataType.IMAGE_4D
dset.metadata = {'info_1': np.linspace(0, 5.6, 30), 'instrument': 'opportunity rover AFM'}
x_dim = np.linspace(0, 1E-6,
dset.shape[0])
y_dim = np.linspace(0, 2E-6,
dset.shape[1])
kx_dim = np.linspace(0, 12, dset.shape[2])
ky_dim = np.linspace(0, 10, dset.shape[3])
dset.set_dimension(0, Dimension(x_dim,
name='x',
units='m', quantity='x',
dimension_type='spatial'))
dset.set_dimension(1, Dimension(y_dim,
name='y',
units='m', quantity='y',
dimension_type='spatial'))
dset.set_dimension(2, Dimension(kx_dim,
name='Intensity KX',
units='counts', quantity='Intensity',
dimension_type='spectral'))
dset.set_dimension(3, Dimension(ky_dim,
name='Intensity KY',
units='counts', quantity='Intensity',
dimension_type='spectral'))
def test_getitem_integer(self):
# Create a sample Dask array
old_dset = self.dset
sliced = self.dset[:, 2]
dim_dict = {0: old_dset._axes[0].copy(),
1: old_dset._axes[2].copy(),
2: old_dset._axes[3].copy()}
validate_dataset_properties(self, sliced, self.dset.compute()[:, 2],
title=self.dset.title, quantity=self.dset.quantity,
units=self.dset.units,
modality=self.dset.modality, source=self.dset.source,
dimension_dict=dim_dict,
data_type=self.dset.data_type,
metadata=self.dset.metadata, original_metadata=self.dset.original_metadata)
def test_getitem_NoneandEllipsis1(self):
old_dset = self.dset
sliced = self.dset[..., None, :]
dim_dict = {0: old_dset._axes[0].copy(),
1: old_dset._axes[1].copy(),
2: old_dset._axes[2].copy(),
3: Dimension(1),
4: old_dset._axes[3].copy()}
validate_dataset_properties(self, sliced, self.dset.compute()[..., None, :],
title=self.dset.title, quantity=self.dset.quantity,
units=self.dset.units,
modality=self.dset.modality, source=self.dset.source,
dimension_dict=dim_dict,
data_type=self.dset.data_type,
metadata=self.dset.metadata, original_metadata=self.dset.original_metadata)
def test_getitem_NoneandEllipsis2(self):
old_dset = self.dset
sliced = self.dset[None, ..., None]
dim_dict = {0: Dimension(1),
1: old_dset._axes[0].copy(),
2: old_dset._axes[1].copy(),
3: old_dset._axes[2].copy(),
4: old_dset._axes[3].copy(),
5: Dimension(1)}
validate_dataset_properties(self, sliced, self.dset.compute()[None, ..., None],
title=self.dset.title, quantity=self.dset.quantity,
units=self.dset.units,
modality=self.dset.modality, source=self.dset.source,
dimension_dict=dim_dict,
data_type=self.dset.data_type,
metadata=self.dset.metadata, original_metadata=self.dset.original_metadata)
def test_getitem_slice1(self):
old_dset = self.dset
sliced = self.dset[0:1]
dim_dict = {0: deepcopy(old_dset._axes[0][0:1]),
1: deepcopy(old_dset._axes[1]),
2: deepcopy(old_dset._axes[2]),
3: deepcopy(old_dset._axes[3])}
validate_dataset_properties(self, sliced, self.dset.compute()[0:1],
title=self.dset.title, quantity=self.dset.quantity,
units=self.dset.units,
modality=self.dset.modality, source=self.dset.source,
dimension_dict=dim_dict,
data_type=self.dset.data_type,
metadata=self.dset.metadata, original_metadata=self.dset.original_metadata)
def test_getitem_slice2(self):
old_dset = self.dset
sliced = self.dset[0:3]
dim_dict = {0: deepcopy(old_dset._axes[0][0:3]),
1: deepcopy(old_dset._axes[1]),
2: deepcopy(old_dset._axes[2]),
3: deepcopy(old_dset._axes[3])}
validate_dataset_properties(self, sliced, self.dset.compute()[0:3],
title=self.dset.title, quantity=self.dset.quantity,
units=self.dset.units,
modality=self.dset.modality, source=self.dset.source,
dimension_dict=dim_dict,
data_type=self.dset.data_type,
metadata=self.dset.metadata, original_metadata=self.dset.original_metadata)
def test_getitem_nparray(self):
old_dset = self.dset
inds = np.array([True, False, True, False, True, False])
sliced = old_dset[:, :, inds, :]
dim_dict = {0: deepcopy(old_dset._axes[0]),
1: deepcopy(old_dset._axes[1]),
2: deepcopy(old_dset._axes[2])[inds],
3: deepcopy(old_dset._axes[3])}
validate_dataset_properties(self, sliced, self.dset.compute()[:, :, inds, :],
title=self.dset.title, quantity=self.dset.quantity,
units=self.dset.units,
modality=self.dset.modality, source=self.dset.source,
dimension_dict=dim_dict,
data_type=self.dset.data_type,
metadata=self.dset.metadata, original_metadata=self.dset.original_metadata)
def test_getitem_daarray(self):
np.random.seed(0)
old_dset = self.dset
inds = da.array(np.array([True, False, True, False, True]))
sliced = old_dset[..., inds]
dim_dict = {0: deepcopy(old_dset._axes[0]),
1: deepcopy(old_dset._axes[1]),
2: deepcopy(old_dset._axes[2]),
3: deepcopy(old_dset._axes[3])[np.array(inds)]}
validate_dataset_properties(self, sliced, self.dset.compute()[..., inds],
title=self.dset.title, quantity=self.dset.quantity,
units=self.dset.units,
modality=self.dset.modality, source=self.dset.source,
dimension_dict=dim_dict,
data_type=self.dset.data_type,
metadata=self.dset.metadata, original_metadata=self.dset.original_metadata)
if __name__ == '__main__':
unittest.main()
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