def test_output_port_name(self) -> None:
module = FitsReadingModule(name_in='read',
image_tag='images',
input_dir=self.test_dir + 'images')
module.add_output_port('test')
with pytest.warns(UserWarning) as warning:
module.add_output_port('test')
assert len(warning) == 1
assert warning[0].message.args[0] == 'Tag \'test\' of ReadingModule \'read\' is already ' \
'used.'
module = BadPixelSigmaFilterModule(name_in='badpixel',
image_in_tag='images',
image_out_tag='im_out')
module.add_output_port('test')
with pytest.warns(UserWarning) as warning:
module.add_output_port('test')
assert len(warning) == 1
assert warning[0].message.args[0] == 'Tag \'test\' of ProcessingModule \'badpixel\' is ' \
'already used.'
def test_output_port_name(self):
read = FitsReadingModule(name_in="read",
input_dir=self.test_dir + "images",
image_tag="images")
read.add_output_port("test")
with pytest.warns(UserWarning) as warning:
read.add_output_port("test")
assert len(warning) == 1
assert warning[0].message.args[
0] == "Tag 'test' of ReadingModule 'read' is already used."
process = BadPixelSigmaFilterModule(name_in="badpixel",
image_in_tag="images")
process.add_output_port("test")
with pytest.warns(UserWarning) as warning:
process.add_output_port("test")
assert len(warning) == 1
assert warning[0].message.args[0] == "Tag 'test' of ProcessingModule 'badpixel' is " \
"already used."
self.pipeline.m_data_storage.close_connection()
process._m_data_base = self.test_dir + "database.hdf5"
process.add_output_port("new")
def test_bad_pixel_map_out(self) -> None:
module = BadPixelSigmaFilterModule(name_in='sigma2',
image_in_tag='images',
image_out_tag='sigma2',
map_out_tag='bpmap',
box=9,
sigma=5.,
iterate=1)
self.pipeline.add_module(module)
self.pipeline.run_module('sigma2')
data = self.pipeline.get_data('sigma2')
assert data[0, 0, 0] == pytest.approx(0.00032486907273264834,
rel=self.limit,
abs=0.)
assert data[0, 5, 5] == pytest.approx(9.903775276151606e-06,
rel=self.limit,
abs=0.)
assert np.sum(data) == pytest.approx(0.007314386854009355,
rel=self.limit,
abs=0.)
assert data.shape == (5, 11, 11)
data = self.pipeline.get_data('bpmap')
assert data[0, 0, 0] == pytest.approx(1., rel=self.limit, abs=0.)
assert data[0, 5, 5] == pytest.approx(0., rel=self.limit, abs=0.)
assert np.sum(data) == pytest.approx(604., rel=self.limit, abs=0.)
assert data.shape == (5, 11, 11)
def test_remove_module(self):
pipeline = Pypeline(self.test_dir, self.test_dir, self.test_dir)
read = FitsReadingModule(name_in='read')
pipeline.add_module(read)
process = BadPixelSigmaFilterModule(name_in='badpixel',
image_in_tag='im_arr1',
image_out_tag='im_out')
pipeline.add_module(process)
assert pipeline.get_module_names() == ['read', 'badpixel']
assert pipeline.remove_module('read')
assert pipeline.get_module_names() == ['badpixel']
assert pipeline.remove_module('badpixel')
with pytest.warns(UserWarning) as warning:
pipeline.remove_module('test')
assert len(warning) == 1
assert warning[0].message.args[0] == 'Module name \'test\' not found in the Pypeline ' \
'dictionary.'
os.remove(self.test_dir + 'PynPoint_database.hdf5')
def test_remove_module(self) -> None:
pipeline = Pypeline(self.test_dir, self.test_dir, self.test_dir)
module = FitsReadingModule(name_in='read')
pipeline.add_module(module)
module = BadPixelSigmaFilterModule(name_in='badpixel',
image_in_tag='im_arr1',
image_out_tag='im_out')
pipeline.add_module(module)
assert pipeline.get_module_names() == ['read', 'badpixel']
assert pipeline.remove_module('read')
assert pipeline.get_module_names() == ['badpixel']
assert pipeline.remove_module('badpixel')
with pytest.warns(UserWarning) as warning:
pipeline.remove_module('test')
assert len(warning) == 1
assert warning[0].message.args[0] == 'Pipeline module \'test\' is not found in the ' \
'Pypeline dictionary so it could not be removed. ' \
'The dictionary contains the following modules: [].' \
os.remove(self.test_dir + 'PynPoint_database.hdf5')
def test_output_port_name(self):
read = FitsReadingModule(name_in='read',
input_dir=self.test_dir + 'images',
image_tag='images')
read.add_output_port('test')
with pytest.warns(UserWarning) as warning:
read.add_output_port('test')
assert len(warning) == 1
assert warning[0].message.args[0] == 'Tag \'test\' of ReadingModule \'read\' is already ' \
'used.'
process = BadPixelSigmaFilterModule(name_in='badpixel',
image_in_tag='images',
image_out_tag='im_out')
process.add_output_port('test')
with pytest.warns(UserWarning) as warning:
process.add_output_port('test')
assert len(warning) == 1
assert warning[0].message.args[0] == 'Tag \'test\' of ProcessingModule \'badpixel\' is ' \
'already used.'
self.pipeline.m_data_storage.close_connection()
process._m_data_base = self.test_dir + 'database.hdf5'
process.add_output_port('new')
def test_add_module(self):
pipeline = Pypeline(self.test_dir, self.test_dir, self.test_dir)
read = FitsReadingModule(name_in='read1', input_dir=None, image_tag='im_arr1')
assert pipeline.add_module(read) is None
read = FitsReadingModule(name_in='read2', input_dir=self.test_dir, image_tag='im_arr2')
assert pipeline.add_module(read) is None
with pytest.warns(UserWarning) as warning:
pipeline.add_module(read)
assert len(warning) == 1
assert warning[0].message.args[0] == 'Pipeline module names need to be unique. ' \
'Overwriting module \'read2\'.'
process = BadPixelSigmaFilterModule(name_in='badpixel',
image_in_tag='im_arr1',
image_out_tag='im_out')
assert pipeline.add_module(process) is None
write = FitsWritingModule(name_in='write1', file_name='result.fits', data_tag='im_arr1')
assert pipeline.add_module(write) is None
write = FitsWritingModule(name_in='write2', file_name='result.fits', data_tag='im_arr1',
output_dir=self.test_dir)
assert pipeline.add_module(write) is None
assert pipeline.run() is None
assert pipeline.get_module_names() == ['read1', 'read2', 'badpixel', 'write1', 'write2']
os.remove(self.test_dir+'result.fits')
os.remove(self.test_dir+'PynPoint_database.hdf5')
def test_bad_pixel_sigma_filter(self):
module = BadPixelSigmaFilterModule(name_in='sigma1',
image_in_tag='images',
image_out_tag='sigma1',
map_out_tag='None',
box=9,
sigma=5,
iterate=1)
self.pipeline.add_module(module)
self.pipeline.run_module('sigma1')
data = self.pipeline.get_data('sigma1')
assert np.allclose(data[0, 0, 0],
0.00032486907273264834,
rtol=limit,
atol=0.)
assert np.allclose(data[0, 10, 10],
0.025022559679385093,
rtol=limit,
atol=0.)
assert np.allclose(data[0, 20, 20],
0.024962143884217046,
rtol=limit,
atol=0.)
assert np.allclose(np.mean(data),
6.721637736047109e-07,
rtol=limit,
atol=0.)
assert data.shape == (40, 100, 100)
def test_bad_pixel_map_out(self) -> None:
module = BadPixelSigmaFilterModule(name_in='sigma2',
image_in_tag='images',
image_out_tag='sigma2',
map_out_tag='bpmap',
box=9,
sigma=2.,
iterate=3)
self.pipeline.add_module(module)
self.pipeline.run_module('sigma2')
data = self.pipeline.get_data('sigma2')
assert data[0, 0, 0] == pytest.approx(-2.4570591355257687e-05,
rel=self.limit,
abs=0.)
assert data[0, 5, 5] == pytest.approx(9.903775276151606e-06,
rel=self.limit,
abs=0.)
assert np.sum(data) == pytest.approx(0.011777887008566097,
rel=self.limit,
abs=0.)
assert data.shape == (5, 11, 11)
data = self.pipeline.get_data('bpmap')
assert data[0, 1, 1] == pytest.approx(1., rel=self.limit, abs=0.)
assert data[0, 5, 5] == pytest.approx(0., rel=self.limit, abs=0.)
assert np.sum(data) == pytest.approx(519.0, rel=self.limit, abs=0.)
assert data.shape == (5, 11, 11)
def test_add_module(self) -> None:
pipeline = Pypeline(self.test_dir, self.test_dir, self.test_dir)
module = FitsReadingModule(name_in='read1',
input_dir=None,
image_tag='im_arr1')
assert pipeline.add_module(module) is None
module = FitsReadingModule(name_in='read2',
input_dir=self.test_dir,
image_tag='im_arr2')
assert pipeline.add_module(module) is None
with pytest.warns(UserWarning) as warning:
pipeline.add_module(module)
assert len(warning) == 1
assert warning[0].message.args[0] == 'Names of pipeline modules that are added to the ' \
'Pypeline need to be unique. The current pipeline ' \
'module, \'read2\', does already exist in the ' \
'Pypeline dictionary so the previous module with ' \
'the same name will be overwritten.'
module = BadPixelSigmaFilterModule(name_in='badpixel',
image_in_tag='im_arr1',
image_out_tag='im_out')
assert pipeline.add_module(module) is None
module = FitsWritingModule(name_in='write1',
file_name='result.fits',
data_tag='im_arr1')
assert pipeline.add_module(module) is None
module = FitsWritingModule(name_in='write2',
file_name='result.fits',
data_tag='im_arr1',
output_dir=self.test_dir)
assert pipeline.add_module(module) is None
assert pipeline.run() is None
assert pipeline.get_module_names() == [
'read1', 'read2', 'badpixel', 'write1', 'write2'
]
os.remove(self.test_dir + 'result.fits')
os.remove(self.test_dir + 'PynPoint_database.hdf5')
def test_output_port_set_connection(self) -> None:
self.pipeline.m_data_storage.open_connection()
module = BadPixelSigmaFilterModule(name_in='badpixel2',
image_in_tag='images',
image_out_tag='im_out')
self.pipeline.add_module(module)
port = module.add_output_port('test1')
self.pipeline.m_data_storage.close_connection()
def test_bad_pixel(self):
bp_cleaning = BadPixelSigmaFilterModule(name_in="sigma_filtering",
image_in_tag="bg_cleaned_arr",
image_out_tag="bp_cleaned_arr")
self.pipeline.add_module(bp_cleaning)
self.pipeline.run_module("sigma_filtering")
data = self.pipeline.get_data("bp_cleaned_arr")
assert np.allclose(data[0, 61, 39],
-0.00013095662386792948,
rtol=limit,
atol=0.)
assert data.shape == (78, 100, 100)
def test_run_module_wrong_tag(self) -> None:
pipeline = Pypeline(self.test_dir, self.test_dir, self.test_dir)
module = FitsReadingModule(name_in='read')
pipeline.add_module(module)
module = FitsWritingModule(name_in='write',
file_name='result.fits',
data_tag='im_list')
pipeline.add_module(module)
module = BadPixelSigmaFilterModule(name_in='badpixel',
image_in_tag='im_list',
image_out_tag='im_out')
pipeline.add_module(module)
with pytest.raises(AttributeError) as error:
pipeline.run_module('badpixel')
assert str(error.value) == 'Pipeline module \'badpixel\' is looking for data under a ' \
'tag which does not exist in the database.'
with pytest.raises(AttributeError) as error:
pipeline.run_module('write')
assert str(error.value) == 'Pipeline module \'write\' is looking for data under a tag ' \
'which does not exist in the database.'
with pytest.raises(AttributeError) as error:
pipeline.run()
assert str(error.value) == 'Pipeline module \'write\' is looking for data under a tag ' \
'which is not created by a previous module or the data does ' \
'not exist in the database.'
assert pipeline.validate_pipeline_module('test') == (False, 'test')
with pytest.raises(TypeError) as error:
pipeline._validate('module', 'tag')
assert str(error.value) == 'type of argument "module" must be one of (ReadingModule, ' \
'WritingModule, ProcessingModule); got str instead'
os.remove(self.test_dir + 'PynPoint_database.hdf5')
def test_bad_pixel_sigma_filter(self) -> None:
module = BadPixelSigmaFilterModule(name_in='sigma1',
image_in_tag='images',
image_out_tag='sigma1',
map_out_tag='None',
box=9,
sigma=3.,
iterate=5)
self.pipeline.add_module(module)
self.pipeline.run_module('sigma1')
data = self.pipeline.get_data('sigma1')
assert np.sum(data) == pytest.approx(0.006513475520308432,
rel=self.limit,
abs=0.)
assert data.shape == (5, 11, 11)
def test_add_module(self):
pipeline = Pypeline(self.test_dir, self.test_dir, self.test_dir)
read = FitsReadingModule(name_in="read1",
input_dir=None,
image_tag="im_arr1")
assert pipeline.add_module(read) is None
read = FitsReadingModule(name_in="read2",
input_dir=self.test_dir,
image_tag="im_arr2")
assert pipeline.add_module(read) is None
with pytest.warns(UserWarning) as warning:
pipeline.add_module(read)
assert len(warning) == 1
assert warning[0].message.args[0] == "Processing module names need to be unique. " \
"Overwriting module 'read2'."
process = BadPixelSigmaFilterModule(name_in="badpixel",
image_in_tag="im_arr1")
assert pipeline.add_module(process) is None
write = FitsWritingModule(name_in="write1",
file_name="result.fits",
data_tag="im_arr1")
assert pipeline.add_module(write) is None
write = FitsWritingModule(name_in="write2",
file_name="result.fits",
data_tag="im_arr1",
output_dir=self.test_dir)
assert pipeline.add_module(write) is None
assert pipeline.run() is None
assert pipeline.get_module_names() == [
'read1', 'read2', 'badpixel', 'write1', 'write2'
]
os.remove(self.test_dir + "result.fits")
os.remove(self.test_dir + "PynPoint_database.hdf5")
def test_run_module_wrong_tag(self):
pipeline = Pypeline(self.test_dir, self.test_dir, self.test_dir)
read = FitsReadingModule(name_in='read')
pipeline.add_module(read)
write = FitsWritingModule(name_in='write',
file_name='result.fits',
data_tag='im_list')
pipeline.add_module(write)
process = BadPixelSigmaFilterModule(name_in='badpixel',
image_in_tag='im_list',
image_out_tag='im_out')
pipeline.add_module(process)
with pytest.raises(AttributeError) as error:
pipeline.run_module('badpixel')
assert str(error.value) == 'Pipeline module \'badpixel\' is looking for data under a ' \
'tag which does not exist in the database.'
with pytest.raises(AttributeError) as error:
pipeline.run_module('write')
assert str(error.value) == 'Pipeline module \'write\' is looking for data under a tag ' \
'which does not exist in the database.'
with pytest.raises(AttributeError) as error:
pipeline.run()
assert str(error.value) == 'Pipeline module \'write\' is looking for data under a tag ' \
'which is not created by a previous module or does not exist ' \
'in the database.'
assert pipeline.validate_pipeline_module('test') is None
assert pipeline._validate('module', 'tag') == (False, None)
os.remove(self.test_dir + 'PynPoint_database.hdf5')
def test_run_module_wrong_tag(self):
pipeline = Pypeline(self.test_dir, self.test_dir, self.test_dir)
read = FitsReadingModule(name_in="read")
pipeline.add_module(read)
write = FitsWritingModule(name_in="write",
file_name="result.fits",
data_tag="im_list")
pipeline.add_module(write)
process = BadPixelSigmaFilterModule(name_in="badpixel",
image_in_tag="im_list")
pipeline.add_module(process)
with pytest.raises(AttributeError) as error:
pipeline.run_module("badpixel")
assert str(error.value) == "Pipeline module 'badpixel' is looking for data under a tag " \
"which does not exist in the database."
with pytest.raises(AttributeError) as error:
pipeline.run_module("write")
assert str(error.value) == "Pipeline module 'write' is looking for data under a tag " \
"which does not exist in the database."
with pytest.raises(AttributeError) as error:
pipeline.run()
assert str(error.value) == "Pipeline module 'write' is looking for data under a tag " \
"which is not created by a previous module or does not exist " \
"in the database."
assert pipeline.validate_pipeline_module("test") is None
assert pipeline._validate("module", "tag") == (False, None)
os.remove(self.test_dir + "PynPoint_database.hdf5")
def test_remove_module(self):
pipeline = Pypeline(self.test_dir, self.test_dir, self.test_dir)
read = FitsReadingModule(name_in="read")
pipeline.add_module(read)
process = BadPixelSigmaFilterModule(name_in="badpixel")
pipeline.add_module(process)
assert pipeline.get_module_names() == ["read", "badpixel"]
assert pipeline.remove_module("read")
assert pipeline.get_module_names() == ["badpixel"]
assert pipeline.remove_module("badpixel")
with pytest.warns(UserWarning) as warning:
pipeline.remove_module("test")
assert len(warning) == 1
assert warning[0].message.args[0] == "Module name 'test' not found in the Pypeline " \
"dictionary."
os.remove(self.test_dir + "PynPoint_database.hdf5")