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# Tests specific to the dask class
import os
from numpy.core.shape_base import block
import pytest
import numpy as np
from unittest.mock import patch
from numpy.testing import assert_allclose
from astropy.tests.helper import assert_quantity_allclose
from astropy import units as u
from astropy.utils import data
try:
from distributed.utils_test import client, loop, cluster_fixture, cleanup, loop_in_thread # noqa
# zarr & fsspec required for writing to disk w/dask
import zarr, fsspec # noqa
DISTRIBUTED_INSTALLED = True
except ImportError:
DISTRIBUTED_INSTALLED = False
from spectral_cube import DaskSpectralCube, SpectralCube, DaskVaryingResolutionSpectralCube
from .test_casafuncs import make_casa_testimage
try:
import casatools
from casatools import image
CASA_INSTALLED = True
except ImportError:
try:
from taskinit import ia as image
CASA_INSTALLED = True
except ImportError:
CASA_INSTALLED = False
DATA = os.path.join(os.path.dirname(__file__), 'data')
class Array:
args = None
kwargs = None
def compute(self, *args, **kwargs):
self.args = args
self.kwargs = kwargs
def test_scheduler(data_adv):
cube = DaskSpectralCube.read(data_adv)
fake_array = Array()
cube._compute(fake_array)
assert fake_array.kwargs == {'scheduler': 'synchronous'}
with cube.use_dask_scheduler('threads'):
cube._compute(fake_array)
assert fake_array.kwargs == {'scheduler': 'threads'}
cube._compute(fake_array)
assert fake_array.kwargs == {'scheduler': 'synchronous'}
cube.use_dask_scheduler('threads')
cube._compute(fake_array)
assert fake_array.kwargs == {'scheduler': 'threads'}
with cube.use_dask_scheduler('processes', num_workers=4):
cube._compute(fake_array)
assert fake_array.kwargs == {'scheduler': 'processes', 'num_workers': 4}
cube._compute(fake_array)
assert fake_array.kwargs == {'scheduler': 'threads'}
def test_save_to_tmp_dir(data_adv):
pytest.importorskip('zarr')
cube = DaskSpectralCube.read(data_adv)
cube_new = cube.sigma_clip_spectrally(3, save_to_tmp_dir=True)
# The following test won't necessarily always work in future since the name
# is not really guaranteed, but this is pragmatic enough for now
assert cube_new._data.name.startswith('from-zarr')
def test_rechunk(data_adv):
cube = DaskSpectralCube.read(data_adv)
assert cube._data.chunksize == (4, 3, 2)
cube_new = cube.rechunk(chunks=(1, 2, 3))
# note last element is 2 because the chunk size we asked for
# is larger than cube - this is fine and deliberate in this test
assert cube_new._data.chunksize == (1, 2, 2)
def test_statistics(data_adv):
cube = DaskSpectralCube.read(data_adv).rechunk(chunks=(1, 2, 3))
stats = cube.statistics()
assert_quantity_allclose(stats['npts'], 24)
assert_quantity_allclose(stats['mean'], 0.4941651776136591 * u.K)
assert_quantity_allclose(stats['sigma'], 0.3021908870982011 * u.K)
assert_quantity_allclose(stats['sum'], 11.85996426272782 * u.K)
assert_quantity_allclose(stats['sumsq'], 7.961125988022091 * u.K ** 2)
assert_quantity_allclose(stats['min'], 0.0363300285196364 * u.K)
assert_quantity_allclose(stats['max'], 0.9662900439556562 * u.K)
assert_quantity_allclose(stats['rms'], 0.5759458158839716 * u.K)
def test_statistics_withnans(data_adv):
cube = DaskSpectralCube.read(data_adv).rechunk(chunks=(1, 2, 3))
# shape is 4, 3, 2 for adv
cube._data[:2,:,:] = np.nan
# ensure some chunks are all nan
cube.rechunk((1,2,2))
stats = cube.statistics()
for key in ('min', 'max', 'sum'):
assert_allclose(stats[key], getattr(cube, key)())
@pytest.mark.skipif(not CASA_INSTALLED, reason='Requires CASA to be installed')
def test_statistics_consistency_casa(data_adv, tmp_path):
# Similar to test_statistics but compares to CASA directly.
cube = DaskSpectralCube.read(data_adv)
stats = cube.statistics()
make_casa_testimage(data_adv, tmp_path / 'casa.image')
ia = casatools.image()
ia.open(str(tmp_path / 'casa.image'))
stats_casa = ia.statistics()
ia.close()
for key in stats:
if isinstance(stats[key], u.Quantity):
value = stats[key].value
else:
value = stats[key]
assert_allclose(value, stats_casa[key])
def test_apply_function_parallel_spectral_noncube(data_adv):
'''
Testing returning a non-SpectralCube object with a user-defined
function for spectral operations.
'''
chunk_size = (-1, 1, 2)
cube = DaskSpectralCube.read(data_adv).rechunk(chunks=chunk_size)
def sum_blocks_spectral(data_chunk):
return data_chunk.sum(0)
# Tell dask.map_blocks that we expect the zeroth axis to be (1,)
output_chunk_size = (1, 2)
test = cube.apply_function_parallel_spectral(sum_blocks_spectral,
return_new_cube=False,
accepts_chunks=True,
drop_axis=[0], # The output will no longer contain the spectral axis
chunks=output_chunk_size)
# The total shape of test should be the (1,) + cube.shape[1:]
assert test.shape == cube.shape[1:]
# Test we get the same output as the builtin sum
assert_allclose(test.compute(), cube.sum(axis=0).unitless_filled_data[:])
def test_apply_function_parallel_spectral_noncube_withblockinfo(data_adv):
'''
Test receiving block_info information from da.map_blocks so we can place
the chunk's location in the whole cube when needed.
https://docs.dask.org/en/latest/array-api.html#dask.array.map_blocks
'''
chunk_size = (-1, 1, 2)
cube = DaskSpectralCube.read(data_adv).rechunk(chunks=chunk_size)
sum_spectral_plane = cube.sum(axis=0).unitless_filled_data[:]
# Each value should be different. This is important to check the right positions being used
# for the check in sums_block_spectral
assert np.unique(sum_spectral_plane).size == sum_spectral_plane.size
def sum_blocks_spectral(data_chunk, block_info=None, comparison_array=None):
chunk_sum = data_chunk.sum(0)
# When the block_info kwarg is defined, it should not be None
assert block_info is not None
# Check the block location compared to `comparison_array`
# Get the lower corner location in the whole cube.
loc = [block_range[0] for block_range in block_info[0]['array-location']]
# Should have 3 dimensions for the corner.
assert len(loc) == 3
# Slice comparison array to compare with this data chunk
thisslice = (slice(loc[1], loc[1] + chunk_sum.shape[0]),
slice(loc[2], loc[2] + chunk_sum.shape[1]),)
return chunk_sum == comparison_array[thisslice]
# Tell dask.map_blocks that we expect the zeroth axis to be (1,)
output_chunk_size = (1, 2)
test = cube.apply_function_parallel_spectral(sum_blocks_spectral,
return_new_cube=False,
accepts_chunks=True,
drop_axis=[0], # The output will no longer contain the spectral axis
chunks=output_chunk_size,
comparison_array=sum_spectral_plane) # Passed to `sum_blocks_spectral`
# The total shape of test should be the (1,) + cube.shape[1:]
assert test.shape == cube.shape[1:]
# Test all True
assert np.all(test.compute())
@pytest.mark.parametrize(('accepts_chunks'),
((True, False)))
def test_apply_function_parallel_shape(accepts_chunks):
# regression test for #772
def func(x, add=None):
if add is not None:
y = x + add
else:
raise ValueError("This test is supposed to have add=1")
return y
fn = data.get_pkg_data_filename('tests/data/example_cube.fits', 'spectral_cube')
cube = SpectralCube.read(fn, use_dask=True)
cube2 = SpectralCube.read(fn, use_dask=False)
# Check dask w/both threaded and unthreaded
rslt3 = cube.apply_function_parallel_spectral(func, add=1,
accepts_chunks=accepts_chunks)
with cube.use_dask_scheduler('threads', num_workers=4):
rslt = cube.apply_function_parallel_spectral(func, add=1,
accepts_chunks=accepts_chunks)
rslt2 = cube2.apply_function_parallel_spectral(func, add=1)
np.testing.assert_almost_equal(cube.filled_data[:].value,
cube2.filled_data[:].value)
np.testing.assert_almost_equal(rslt.filled_data[:].value,
rslt2.filled_data[:].value)
np.testing.assert_almost_equal(rslt.filled_data[:].value,
rslt3.filled_data[:].value)
@pytest.mark.parametrize('filename', ('data_adv', 'data_adv_beams',
'data_vda_beams', 'data_vda_beams_image'))
def test_cube_on_cube(filename, request):
if 'image' in filename and not CASA_INSTALLED:
pytest.skip('Requires CASA to be installed')
dataname = request.getfixturevalue(filename)
# regression test for #782
# the regression applies only to VaryingResolutionSpectralCubes
# since they are not SpectralCube subclasses
cube = DaskSpectralCube.read(dataname)
assert isinstance(cube, (DaskSpectralCube, DaskVaryingResolutionSpectralCube))
if 'image' in filename:
# no choice - non-dask can't read casa images
cube2 = SpectralCube.read(dataname)
else:
cube2 = SpectralCube.read(dataname, use_dask=False)
if 'image' not in filename:
# 'image' would be CASA and must be dask
assert not isinstance(cube2, (DaskSpectralCube, DaskVaryingResolutionSpectralCube))
with patch.object(cube, '_cube_on_cube_operation') as mock:
cube * cube
mock.assert_called_once()
with patch.object(cube, '_cube_on_cube_operation') as mock:
cube * cube2
mock.assert_called_once()
with patch.object(cube2, '_cube_on_cube_operation') as mock:
cube2 * cube
mock.assert_called_once()
if DISTRIBUTED_INSTALLED:
def test_dask_distributed(client, tmpdir): # noqa
# Make sure that we can use dask distributed. This is a regression test for
# a bug caused by FilledArrayHandler not being serializable.
cube = DaskSpectralCube.read(os.path.join(DATA, 'basic.image'))
cube.use_dask_scheduler(client)
cube.sigma_clip_spectrally(2, save_to_tmp_dir=tmpdir.strpath)
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