def test_run_module_wrong_tag(self) -> None:
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 the data does ' \
'not exist in the database.'
assert pipeline.validate_pipeline_module('test') is None
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_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")
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")
def test_bad_pixel_map_out(self):
module = BadPixelSigmaFilterModule(name_in='sigma2',
image_in_tag='images',
image_out_tag='sigma2',
map_out_tag='bpmap',
box=9,
sigma=5,
iterate=0)
self.pipeline.add_module(module)
self.pipeline.run_module('sigma2')
data = self.pipeline.get_data('sigma2')
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)
data = self.pipeline.get_data('bpmap')
assert np.allclose(data[0, 0, 0], 1.0, rtol=limit, atol=0.)
assert np.allclose(np.sum(data), 399994.0, rtol=limit, atol=0.)
assert data.shape == (40, 100, 100)