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_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_attribute_length(self):
text = 'long_text_long_text_long_text_long_text_long_text_long_text_long_text_long_text'
self.pipeline.set_attribute('images', 'short', 'value', static=True)
self.pipeline.set_attribute('images',
'longer_than_eight1',
'value',
static=True)
self.pipeline.set_attribute('images',
'longer_than_eight2',
text,
static=True)
module = FitsWritingModule(file_name='test.fits',
name_in='write8',
output_dir=None,
data_tag='images',
data_range=None,
overwrite=True,
subset_size=None)
self.pipeline.add_module(module)
with pytest.warns(UserWarning) as warning:
self.pipeline.run_module('write8')
assert len(warning) == 1
assert warning[0].message.args[0] == 'Key \'hierarch longer_than_eight2\' with value ' \
'\'long_text_long_text_long_text_long_text_long_' \
'text_long_text_long_text_long_text\' is too ' \
'long for the FITS format. To avoid an error, ' \
'the value was truncated to \'long_text_long_text' \
'_long_text_long_text_long_tex\'.'
def test_attribute_length(self):
text = "long_text_long_text_long_text_long_text_long_text_long_text_long_text_long_text"
self.pipeline.set_attribute("images", "short", "value", static=True)
self.pipeline.set_attribute("images",
"longer_than_eight1",
"value",
static=True)
self.pipeline.set_attribute("images",
"longer_than_eight2",
text,
static=True)
write = FitsWritingModule(file_name="test.fits",
name_in="write6",
output_dir=None,
data_tag="images",
data_range=None,
overwrite=True)
self.pipeline.add_module(write)
with pytest.warns(UserWarning) as warning:
self.pipeline.run_module("write6")
assert len(warning) == 1
assert warning[0].message.args[0] == "Key 'hierarch longer_than_eight2' with value " \
"'long_text_long_text_long_text_long_text_long_" \
"text_long_text_long_text_long_text' is too " \
"long for the FITS format. To avoid an error, " \
"the value was truncated to 'long_text_long_text" \
"_long_text_long_text_long_tex'."
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_write_fits(self):
writing = FitsWritingModule(name_in="fits_writing",
file_name="test.fits",
data_tag="res_mean")
self.pipeline.add_module(writing)
self.pipeline.run_module("fits_writing")
assert os.path.exists(self.test_dir + "test.fits")
def test_filename_extension(self):
with pytest.raises(ValueError) as error:
FitsWritingModule(file_name='test.dat',
name_in='write3',
output_dir=None,
data_tag='images',
data_range=None,
overwrite=True)
assert str(error.value) == 'Output \'file_name\' requires the FITS extension.'
def test_filename_string(self):
with pytest.raises(ValueError) as error:
FitsWritingModule(file_name=0.,
name_in='write2',
output_dir=None,
data_tag='images',
data_range=None,
overwrite=True)
assert str(error.value) == 'Output \'file_name\' needs to be a string.'
def test_data_range(self):
write = FitsWritingModule(file_name="test.fits",
name_in="write4",
output_dir=None,
data_tag="images",
data_range=(0, 10),
overwrite=True)
self.pipeline.add_module(write)
self.pipeline.run_module("write4")
def test_data_range(self):
write = FitsWritingModule(file_name='test.fits',
name_in='write4',
output_dir=None,
data_tag='images',
data_range=(0, 10),
overwrite=True)
self.pipeline.add_module(write)
self.pipeline.run_module('write4')
def test_fits_writing(self):
module = FitsWritingModule(file_name='test.fits',
name_in='write1',
output_dir=None,
data_tag='images',
data_range=None,
overwrite=True)
self.pipeline.add_module(module)
self.pipeline.run_module('write1')
def test_filename_extension(self):
with pytest.raises(ValueError) as error:
FitsWritingModule(file_name="test.dat",
name_in="write3",
output_dir=None,
data_tag="images",
data_range=None,
overwrite=True)
assert str(
error.value) == "Output 'file_name' requires the FITS extension."
def test_subset_size_data_range(self):
module = FitsWritingModule(file_name='test.fits',
name_in='write7',
output_dir=None,
data_tag='images',
data_range=(8, 18),
overwrite=True,
subset_size=10)
self.pipeline.add_module(module)
self.pipeline.run_module('write7')
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_not_overwritten(self):
write = FitsWritingModule(file_name='test.fits',
name_in='write5',
output_dir=None,
data_tag='images',
data_range=None,
overwrite=False)
self.pipeline.add_module(write)
with pytest.warns(UserWarning) as warning:
self.pipeline.run_module('write5')
assert len(warning) == 1
assert warning[0].message.args[0] == 'Filename already present. Use overwrite=True ' \
'to overwrite an existing FITS file.'
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")