def setup_class(self) -> None:
self.test_dir = os.path.dirname(__file__) + '/'
create_star_data(path=self.test_dir + 'prep')
create_config(self.test_dir + 'PynPoint_config.ini')
self.pipeline = Pypeline(self.test_dir, self.test_dir, self.test_dir)
def setup_class(self):
self.test_dir = os.path.dirname(__file__) + "/"
create_star_data(path=self.test_dir + "fits")
create_config(self.test_dir + "PynPoint_config.ini")
self.pipeline = Pypeline(self.test_dir, self.test_dir, self.test_dir)
def setup_class(self):
self.test_dir = os.path.dirname(__file__) + '/'
create_random(self.test_dir, ndit=1)
create_config(self.test_dir+'PynPoint_config.ini')
self.pipeline = Pypeline(self.test_dir, self.test_dir, self.test_dir)
def setup_class(self):
self.test_dir = os.path.dirname(__file__) + "/"
create_star_data(path=self.test_dir + "images", ndit=10, nframes=11)
create_config(self.test_dir + "PynPoint_config.ini")
self.pipeline = Pypeline(self.test_dir, self.test_dir, self.test_dir)
def test_run_module(self) -> None:
pipeline = Pypeline(self.test_dir, self.test_dir, self.test_dir)
read = FitsReadingModule(name_in='read', image_tag='im_arr')
assert pipeline.add_module(read) is None
assert pipeline.run_module('read') is None
os.remove(self.test_dir + 'PynPoint_database.hdf5')
def test_run_module(self):
pipeline = Pypeline(self.test_dir, self.test_dir, self.test_dir)
read = FitsReadingModule(name_in="read", image_tag="im_arr")
assert pipeline.add_module(read) is None
assert pipeline.run_module("read") is None
os.remove(self.test_dir + "PynPoint_database.hdf5")
def setup_class(self) -> None:
self.test_dir = os.path.dirname(__file__) + '/'
create_star_data(path=self.test_dir + 'images', ndit=10, nframes=11)
create_config(self.test_dir + 'PynPoint_config.ini')
self.pipeline = Pypeline(self.test_dir, self.test_dir, self.test_dir)
def test_delete_not_found(self):
pipeline = Pypeline(self.test_dir, self.test_dir, self.test_dir)
with pytest.warns(UserWarning) as warning:
pipeline.delete_data('images')
assert len(warning) == 2
assert warning[0].message.args[0] == 'Dataset \'images\' not found in the database.'
assert warning[1].message.args[0] == 'Attributes of \'images\' not found in the database.'
def setup_class(self) -> None:
self.limit = 1e-5
self.test_dir = os.path.dirname(__file__) + '/'
create_ifs_data(self.test_dir+'science')
create_config(self.test_dir+'PynPoint_config.ini')
self.pipeline = Pypeline(self.test_dir, self.test_dir, self.test_dir)
class TestFilter:
def setup_class(self) -> None:
self.test_dir = os.path.dirname(__file__) + '/'
create_star_data(self.test_dir + 'data')
create_config(self.test_dir + 'PynPoint_config.ini')
self.pipeline = Pypeline(self.test_dir, self.test_dir, self.test_dir)
def teardown_class(self) -> None:
remove_test_data(self.test_dir, folders=['data'])
def test_read_data(self) -> None:
module = FitsReadingModule(name_in='read',
image_tag='data',
input_dir=self.test_dir + 'data',
overwrite=True,
check=True)
self.pipeline.add_module(module)
self.pipeline.run_module('read')
data = self.pipeline.get_data('data')
assert np.allclose(data[0, 50, 50],
0.09798413502193704,
rtol=limit,
atol=0.)
assert np.allclose(np.mean(data),
0.00010029494781738066,
rtol=limit,
atol=0.)
assert data.shape == (40, 100, 100)
def test_gaussian_filter(self) -> None:
module = GaussianFilterModule(name_in='filter',
image_in_tag='data',
image_out_tag='filtered',
fwhm=0.1)
self.pipeline.add_module(module)
self.pipeline.run_module('filter')
data = self.pipeline.get_data('filtered')
assert np.allclose(data[0, 50, 50],
0.0388143943049942,
rtol=limit,
atol=0.)
assert np.allclose(np.mean(data),
0.00010029494781738068,
rtol=limit,
atol=0.)
assert data.shape == (40, 100, 100)
def setup_class(self) -> None:
self.limit = 1e-10
self.test_dir = os.path.dirname(__file__) + '/'
create_star_data(self.test_dir + 'images')
create_config(self.test_dir + 'PynPoint_config.ini')
self.pipeline = Pypeline(self.test_dir, self.test_dir, self.test_dir)
def test_add_wrong_module(self):
pipeline = Pypeline(self.test_dir, self.test_dir, self.test_dir)
with pytest.raises(AssertionError) as error:
pipeline.add_module(None)
assert str(error.value) == 'The added module is not a valid Pypeline module.'
os.remove(self.test_dir+'PynPoint_database.hdf5')
def test_add_wrong_module(self) -> None:
pipeline = Pypeline(self.test_dir, self.test_dir, self.test_dir)
with pytest.raises(TypeError) as error:
pipeline.add_module(None)
assert str(error.value) == 'type of argument "module" must be ' \
'pynpoint.core.processing.PypelineModule; got NoneType instead'
os.remove(self.test_dir + 'PynPoint_database.hdf5')
def test_run_module_non_existing(self):
pipeline = Pypeline(self.test_dir, self.test_dir, self.test_dir)
with pytest.warns(UserWarning) as warning:
pipeline.run_module('test')
assert len(warning) == 1
assert warning[0].message.args[0] == 'Module \'test\' not found.'
os.remove(self.test_dir + 'PynPoint_database.hdf5')
def setup_class(self):
self.test_dir = os.path.dirname(__file__) + '/'
create_fake(path=self.test_dir + 'dither',
ndit=[20, 20, 20, 20],
nframes=[20, 20, 20, 20],
exp_no=[1, 2, 3, 4],
npix=(100, 100),
fwhm=3.,
x0=[25, 75, 75, 25],
y0=[75, 75, 25, 25],
angles=[[0., 25.], [25., 50.], [50., 75.], [75., 100.]],
sep=None,
contrast=None)
create_fake(path=self.test_dir + 'star',
ndit=[10, 10, 10, 10],
nframes=[10, 10, 10, 10],
exp_no=[1, 3, 5, 7],
npix=(100, 100),
fwhm=3.,
x0=[50, 50, 50, 50],
y0=[50, 50, 50, 50],
angles=[[0., 25.], [25., 50.], [50., 75.], [75., 100.]],
sep=None,
contrast=None)
create_fake(path=self.test_dir + 'sky',
ndit=[5, 5, 5, 5],
nframes=[5, 5, 5, 5],
exp_no=[2, 4, 6, 8],
npix=(100, 100),
fwhm=None,
x0=[50, 50, 50, 50],
y0=[50, 50, 50, 50],
angles=[[0., 25.], [25., 50.], [50., 75.], [75., 100.]],
sep=None,
contrast=None)
create_fake(path=self.test_dir + 'line',
ndit=[4, 4, 4, 4],
nframes=[4, 4, 4, 4],
exp_no=[1, 3, 5, 7],
npix=(20, 20),
fwhm=3.,
x0=[10, 10, 10, 10],
y0=[10, 10, 10, 10],
angles=[[0., 25.], [25., 50.], [50., 75.], [75., 100.]],
sep=None,
contrast=None)
create_config(self.test_dir + 'PynPoint_config.ini')
self.pipeline = Pypeline(self.test_dir, self.test_dir, self.test_dir)
def test_list_attributes(self) -> None:
pipeline = Pypeline(self.test_dir, self.test_dir, self.test_dir)
attr_dict = pipeline.list_attributes('images')
assert len(attr_dict) == 11
assert attr_dict['INSTRUMENT'] == 'IMAGER'
assert attr_dict['PIXSCALE'] == 0.027
assert attr_dict['NFRAMES'] == [5]
assert attr_dict['PARANG_START'] == [10.]
def setup_class(self) -> None:
self.limit = 1e-10
self.test_dir = os.path.dirname(__file__) + '/'
create_fake_data(self.test_dir + 'adi')
create_star_data(self.test_dir + 'psf', npix=21, pos_star=10.)
create_star_data(self.test_dir + 'ref', npix=21, pos_star=10.)
create_config(self.test_dir + 'PynPoint_config.ini')
self.pipeline = Pypeline(self.test_dir, self.test_dir, self.test_dir)
def setup_class(self):
self.test_dir = os.path.dirname(__file__) + '/'
create_random(self.test_dir, ndit=10, parang=None)
create_config(self.test_dir+'PynPoint_config.ini')
np.savetxt(self.test_dir+'parang.dat', np.arange(1., 11., 1.))
np.savetxt(self.test_dir+'new.dat', np.arange(10., 21., 1.))
np.savetxt(self.test_dir+'attribute.dat', np.arange(1, 11, 1), fmt='%i')
data2d = np.random.normal(loc=0, scale=2e-4, size=(10, 10))
np.savetxt(self.test_dir+'data_2d.dat', data2d)
self.pipeline = Pypeline(self.test_dir, self.test_dir, self.test_dir)
class TestFilter:
def setup_class(self) -> None:
self.limit = 1e-10
self.test_dir = os.path.dirname(__file__) + '/'
create_star_data(self.test_dir + 'data')
create_config(self.test_dir + 'PynPoint_config.ini')
self.pipeline = Pypeline(self.test_dir, self.test_dir, self.test_dir)
def teardown_class(self) -> None:
remove_test_data(self.test_dir, folders=['data'])
def test_read_data(self) -> None:
module = FitsReadingModule(name_in='read',
image_tag='data',
input_dir=self.test_dir + 'data',
overwrite=True,
check=True)
self.pipeline.add_module(module)
self.pipeline.run_module('read')
data = self.pipeline.get_data('data')
assert np.sum(data) == pytest.approx(105.54278879805277,
rel=self.limit,
abs=0.)
assert data.shape == (10, 11, 11)
def test_gaussian_filter(self) -> None:
module = GaussianFilterModule(name_in='filter',
image_in_tag='data',
image_out_tag='filtered',
fwhm=0.1)
self.pipeline.add_module(module)
self.pipeline.run_module('filter')
data = self.pipeline.get_data('filtered')
assert np.sum(data) == pytest.approx(105.54278879805275,
rel=self.limit,
abs=0.)
assert data.shape == (10, 11, 11)
def test_create_pipeline_existing_database(self):
np.random.seed(1)
images = np.random.normal(loc=0, scale=2e-4, size=(10, 100, 100))
with h5py.File(self.test_dir+'PynPoint_database.hdf5', 'w') as hdf_file:
dset = hdf_file.create_dataset('images', data=images)
dset.attrs['PIXSCALE'] = 0.01
pipeline = Pypeline(self.test_dir, self.test_dir, self.test_dir)
data = pipeline.get_data('images')
assert np.allclose(data[0, 0, 0], 0.00032486907273264834, rtol=limit, atol=0.)
assert np.allclose(np.mean(data), 1.0506056979365338e-06, rtol=limit, atol=0.)
assert pipeline.get_attribute('images', 'PIXSCALE') == 0.01
os.remove(self.test_dir+'PynPoint_database.hdf5')
def setup_class(self):
self.test_dir = os.path.dirname(__file__) + '/'
create_star_data(path=self.test_dir+'images',
npix_x=20,
npix_y=20,
x0=[10, 10, 10, 10],
y0=[10, 10, 10, 10],
parang_start=[0., 25., 50., 75.],
parang_end=[25., 50., 75., 100.],
exp_no=[1, 2, 3, 4])
create_config(self.test_dir+'PynPoint_config.ini')
self.pipeline = Pypeline(self.test_dir, self.test_dir, self.test_dir)
def test_get_config_attribute(self) -> None:
create_config(self.test_dir + 'PynPoint_config.ini')
Pypeline(self.test_dir, self.test_dir, self.test_dir)
storage = DataStorage(self.test_dir + 'PynPoint_database.hdf5')
port = ConfigPort('config', None)
with pytest.warns(UserWarning) as warning:
attribute = port.get_attribute('CPU')
assert len(warning) == 1
assert warning[0].message.args[0] == 'ConfigPort can not load data unless a database is ' \
'connected.'
assert attribute is None
port = ConfigPort('config', storage)
attribute = port.get_attribute('CPU')
assert attribute == 1
attribute = port.get_attribute('NFRAMES')
assert attribute == 'NAXIS3'
attribute = port.get_attribute('PIXSCALE')
assert np.allclose(attribute, 0.027, rtol=limit, atol=0.)
with pytest.warns(UserWarning) as warning:
attribute = port.get_attribute('test')
assert len(warning) == 1
assert warning[0].message.args[
0] == 'The attribute \'test\' was not found.'
assert attribute is None
def test_get_config_attribute(self):
create_config(self.test_dir + "PynPoint_config.ini")
Pypeline(self.test_dir, self.test_dir, self.test_dir)
storage = DataStorage(self.test_dir + "PynPoint_database.hdf5")
port = ConfigPort("config", None)
with pytest.warns(UserWarning) as warning:
attribute = port.get_attribute("CPU")
assert len(warning) == 1
assert warning[0].message.args[0] == "ConfigPort can not load data unless a database is " \
"connected."
assert attribute is None
port = ConfigPort("config", storage)
attribute = port.get_attribute("CPU")
assert attribute == 1
attribute = port.get_attribute("NFRAMES")
assert attribute == "NAXIS3"
attribute = port.get_attribute("PIXSCALE")
assert np.allclose(attribute, 0.027, rtol=limit, atol=0.)
with pytest.warns(UserWarning) as warning:
attribute = port.get_attribute("test")
assert len(warning) == 1
assert warning[0].message.args[
0] == "No attribute found - requested: test."
assert attribute is None
def setup_class(self):
self.test_dir = os.path.dirname(__file__) + "/"
create_star_data(path=self.test_dir+"dither",
npix_x=100,
npix_y=100,
x0=[25, 75, 75, 25],
y0=[75, 75, 25, 25],
parang_start=[0., 25., 50., 75.],
parang_end=[25., 50., 75., 100.],
exp_no=[1, 2, 3, 4])
create_star_data(path=self.test_dir+"star_odd",
npix_x=101,
npix_y=101,
x0=[50],
y0=[50],
parang_start=[0.],
parang_end=[25.],
exp_no=[1],
noise=False)
create_star_data(path=self.test_dir+"star_even",
npix_x=100,
npix_y=100,
x0=[49.5],
y0=[49.5],
parang_start=[0.],
parang_end=[25.],
exp_no=[1],
noise=False)
create_waffle_data(path=self.test_dir+"waffle_odd",
npix=101,
x_waffle=[20., 20., 80., 80.],
y_waffle=[20., 80., 80., 20.])
create_waffle_data(path=self.test_dir+"waffle_even",
npix=100,
x_waffle=[20., 20., 79., 79.],
y_waffle=[20., 79., 79., 20.])
create_config(self.test_dir+"PynPoint_config.ini")
self.pipeline = Pypeline(self.test_dir, self.test_dir, self.test_dir)
def setup_class(self) -> None:
self.test_dir = os.path.dirname(__file__) + '/'
create_star_data(path=self.test_dir+'dither',
npix_x=100,
npix_y=100,
x0=[25, 75, 75, 25],
y0=[75, 75, 25, 25],
parang_start=[0., 25., 50., 75.],
parang_end=[25., 50., 75., 100.],
exp_no=[1, 2, 3, 4])
create_star_data(path=self.test_dir+'star_odd',
npix_x=101,
npix_y=101,
x0=[50],
y0=[50],
parang_start=[0.],
parang_end=[25.],
exp_no=[1],
noise=False)
create_star_data(path=self.test_dir+'star_even',
npix_x=100,
npix_y=100,
x0=[49.5],
y0=[49.5],
parang_start=[0.],
parang_end=[25.],
exp_no=[1],
noise=False)
create_waffle_data(path=self.test_dir+'waffle_odd',
npix=101,
x_spot=[20., 20., 80., 80.],
y_spot=[20., 80., 80., 20.])
create_waffle_data(path=self.test_dir+'waffle_even',
npix=100,
x_spot=[20., 20., 79., 79.],
y_spot=[20., 79., 79., 20.])
create_config(self.test_dir+'PynPoint_config.ini')
self.pipeline = Pypeline(self.test_dir, self.test_dir, self.test_dir)
def test_create_pipeline_new_database(self):
pipeline = Pypeline(self.test_dir, self.test_dir, self.test_dir)
pipeline.m_data_storage.open_connection()
pipeline.m_data_storage.close_connection()
del pipeline
os.remove(self.test_dir + 'PynPoint_database.hdf5')
def test_create_pipeline_existing_database(self) -> None:
np.random.seed(1)
images = np.random.normal(loc=0, scale=2e-4, size=(5, 11, 11))
with h5py.File(self.test_dir+'PynPoint_database.hdf5', 'w') as hdf_file:
dset = hdf_file.create_dataset('images', data=images)
dset.attrs['PIXSCALE'] = 0.01
pipeline = Pypeline(self.test_dir, self.test_dir, self.test_dir)
data = pipeline.get_data('images')
assert np.mean(data) == pytest.approx(1.1824138000882435e-05, rel=self.limit, abs=0.)
assert data.shape == (5, 11, 11)
assert pipeline.get_attribute('images', 'PIXSCALE') == 0.01
os.remove(self.test_dir+'PynPoint_database.hdf5')
def test_get_shape(self):
pipeline = Pypeline(self.test_dir, self.test_dir, self.test_dir)
read = FitsReadingModule(name_in='read', image_tag='images')
pipeline.add_module(read)
pipeline.run_module('read')
assert pipeline.get_shape('images') == (10, 100, 100)
def test_get_shape(self):
pipeline = Pypeline(self.test_dir, self.test_dir, self.test_dir)
read = FitsReadingModule(name_in="read", image_tag="images")
pipeline.add_module(read)
pipeline.run_module("read")
assert pipeline.get_shape("images") == (10, 100, 100)
def setup_class(self) -> None:
self.limit = 1e-10
self.test_dir = os.path.dirname(__file__) + '/'
create_random(self.test_dir, nimages=10)
create_config(self.test_dir + 'PynPoint_config.ini')
np.savetxt(self.test_dir + 'parang.dat', np.arange(10., 20., 1.))
np.savetxt(self.test_dir + 'new.dat', np.arange(20., 30., 1.))
np.savetxt(self.test_dir + 'attribute.dat',
np.arange(0, 10, 1),
fmt='%i')
np.savetxt(self.test_dir + 'wavelength.dat', np.arange(0., 10., 1.))
data2d = np.random.normal(loc=0, scale=2e-4, size=(10, 10))
np.savetxt(self.test_dir + 'data_2d.dat', data2d)
self.pipeline = Pypeline(self.test_dir, self.test_dir, self.test_dir)
