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 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_create_config_port(self) -> None:
storage = DataStorage(self.test_dir + 'PynPoint_database.hdf5')
with pytest.raises(ValueError) as error:
ConfigPort('images', storage)
assert str(error.value) == 'The tag name of the central configuration should be ' \
'\'config\'.'
port = ConfigPort('config', None)
with pytest.warns(UserWarning) as warning:
check_error = port._check_error_cases()
assert len(warning) == 1
assert warning[0].message.args[0] == 'ConfigPort can not load data unless a database is ' \
'connected.'
assert not check_error
port = ConfigPort('config', storage)
assert isinstance(port, ConfigPort)
with pytest.warns(UserWarning) as warning:
port._check_error_cases()
assert len(warning) == 1
assert warning[0].message.args[0] == 'No data under the tag which is linked by the ' \
'ConfigPort.'
def test_create_config_port(self):
storage = DataStorage(self.test_dir + "PynPoint_database.hdf5")
with pytest.raises(ValueError) as error:
ConfigPort("images", storage)
assert str(
error.value
) == "The tag name of the central configuration should be 'config'."
port = ConfigPort("config", None)
with pytest.warns(UserWarning) as warning:
check_error = port._check_error_cases()
assert len(warning) == 1
assert warning[0].message.args[0] == "ConfigPort can not load data unless a database is " \
"connected."
assert not check_error
port = ConfigPort("config", storage)
assert isinstance(port, ConfigPort)
with pytest.warns(UserWarning) as warning:
port._check_error_cases()
assert len(warning) == 1
assert warning[0].message.args[
0] == "No data under the tag which is linked by the ConfigPort."
def set_extra_attr(fits_file: str, nimages: int, config_port: ConfigPort,
image_out_port: OutputPort, first_index: int) -> int:
"""
Function which adds extra attributes to the central database.
Parameters
----------
fits_file : str
Absolute path and filename of the FITS file.
nimages : int
Number of images.
config_port : pynpoint.core.dataio.ConfigPort
Configuration port.
image_out_port : pynpoint.core.dataio.OutputPort
Output port of the images to which the attributes are stored.
first_index : int
First image index of the current subset.
Returns
-------
int
First image index for the next subset.
"""
pixscale = config_port.get_attribute('PIXSCALE')
image_index = np.arange(first_index, first_index + nimages, 1)
for item in image_index:
image_out_port.append_attribute_data('INDEX', item)
image_out_port.append_attribute_data('FILES', fits_file)
image_out_port.add_attribute('PIXSCALE', pixscale, static=True)
return first_index + nimages
def set_nonstatic_attr(header: fits.header.Header,
config_port: ConfigPort,
image_out_port: OutputPort,
check: bool = True) -> None:
"""
Function which adds the non-static attributes to the central database.
Parameters
----------
header : astropy.io.fits.header.Header
Header information from the FITS file that is read.
config_port : pynpoint.core.dataio.ConfigPort
Configuration port.
image_out_port : pynpoint.core.dataio.OutputPort
Output port of the images to which the non-static attributes are stored.
Returns
-------
NoneType
None
"""
attributes = get_attributes()
nonstatic = []
for key, value in six.iteritems(attributes):
if value['attribute'] == 'non-static':
nonstatic.append(key)
for attr in nonstatic:
if attributes[attr]['config'] == 'header':
fitskey = config_port.get_attribute(attr)
# if type(fitskey) == np.bytes_:
# fitskey = str(fitskey.decode('utf-8'))
if fitskey != 'None':
if fitskey in header:
image_out_port.append_attribute_data(attr, header[fitskey])
elif header['NAXIS'] == 2 and attr == 'NFRAMES':
image_out_port.append_attribute_data(attr, 1)
elif check:
warnings.warn(
'Non-static attribute %s (=%s) not found in the '
'FITS header.' % (attr, fitskey))
image_out_port.append_attribute_data(attr, -1)
def __init__(self,
name_in):
"""
Abstract constructor of a PypelineModule which needs a name as identifier.
:param name_in: The name of the PypelineModule.
:type name_in: str
:return: None
"""
assert (isinstance(name_in, str)), "Name of the PypelineModule needs to be a string."
self._m_name = name_in
self._m_data_base = None
self._m_config_port = ConfigPort("config")
def __init__(self, name_in: str) -> None:
"""
Abstract constructor of a :class:`~pynpoint.core.processing.PypelineModule`.
Parameters
----------
name_in : str
The name of the :class:`~pynpoint.core.processing.PypelineModule`.
Returns
-------
NoneType
None
"""
self._m_name = name_in
self._m_data_base = None
self._m_config_port = ConfigPort('config')
def __init__(self,
name_in):
"""
Abstract constructor of a PypelineModule. Needs a name as identifier.
Parameters
----------
name_in : str
The name of the PypelineModule.
Returns
-------
NoneType
None
"""
assert isinstance(name_in, str), 'Name of the PypelineModule needs to be a string.'
self._m_name = name_in
self._m_data_base = None
self._m_config_port = ConfigPort('config')
def set_static_attr(fits_file: str,
header: fits.header.Header,
config_port: ConfigPort,
image_out_port: OutputPort,
check: bool = True) -> None:
"""
Function which adds the static attributes to the central database.
Parameters
----------
fits_file : str
Name of the FITS file.
header : astropy.io.fits.header.Header
Header information from the FITS file that is read.
config_port : pynpoint.core.dataio.ConfigPort
Configuration port.
image_out_port : pynpoint.core.dataio.OutputPort
Output port of the images to which the static attributes are stored.
check : bool
Print a warning if certain attributes from the configuration file are not present in
the FITS header. If set to `False`, attributes are still written to the dataset but
there will be no warning if a keyword is not found in the FITS header.
Returns
-------
NoneType
None
"""
attributes = get_attributes()
static = []
for key, value in six.iteritems(attributes):
if value['config'] == 'header' and value['attribute'] == 'static':
static.append(key)
for attr in static:
fitskey = config_port.get_attribute(attr)
if isinstance(fitskey, np.bytes_):
fitskey = str(fitskey.decode('utf-8'))
if fitskey != 'None':
if fitskey in header:
status = image_out_port.check_static_attribute(
attr, header[fitskey])
if status == 1:
image_out_port.add_attribute(attr,
header[fitskey],
static=True)
elif status == 0:
pass
elif status == -1:
warnings.warn(
f'Static attribute {fitskey} has changed. Possibly the '
f'current file {fits_file} does not belong to the data set '
f'\'{image_out_port.tag}\'. Attribute value is updated.'
)
elif check:
warnings.warn(
f'Static attribute {attr} (={fitskey}) not found in the FITS '
'header.')
