Added missing docstrings and tests; refactored mdl_prepare_radmc_command.py. (d39fa5d8) · Commits · Andrea Giannetti / swiss_army_knife_stable

etl/assets/commons/init.py

+16 −2

Original line number	Diff line number	Diff line
		@@ -35,6 +35,12 @@ def setup_logger(name: str,

		def validate_parameter(param_to_validate,
		default):
		"""
		Substitute default value if the parameter is set to None
		:param param_to_validate: input to validate
		:param default: default value
		:return: default value if parameter is set to None, else the passed value
		"""
		return param_to_validate if param_to_validate is not None else default


		@@ -57,6 +63,13 @@ def load_config_file(config_file_path: str,

		def parse_grid_overrides(par_name: str,
		config: dict) -> np.array:
		"""
		Parse the global configuration for constructing the grid, computing the parameter values for which the grid has to
		be computed.
		:param par_name: parameter to parse
		:param config: configuration dictionary to extract the grid properties
		:return: the array of values to be considered in the grid
		"""
		config_overrides = config['overrides']
		if config_overrides[f'{par_name}_grid_type'] == 'linear':
		grid_values = np.arange(float(config_overrides[f'{par_name}_limits'][0]),
		@@ -184,7 +197,8 @@ def get_grid_edges(grid_metadata: dict) -> np.array:
		indices = np.arange(grid_metadata['grid_shape'][axis_idx] + 1) - grid_metadata['grid_refpix'][axis_idx] - 0.5
		# valid for regular grid
		grid_edges.append(compute_cartesian_coordinate_grid(indices=indices,
		physical_px_size=grid_metadata['physical_px_size'][axis_idx]))
		physical_px_size=grid_metadata['physical_px_size'][
		axis_idx]))
		# Transposed for consistent flattening
		return np.array(grid_edges).T

etl/assets/constants/init.py

+10 −0

Original line number	Diff line number	Diff line
		@@ -46,3 +46,13 @@ radmc_lines_mode_mapping = {
		'lvg': 3,
		'optically_thin_non_lte': 4,
		}

		radmc_options_mapping = {
		'inclination': 'incl',
		'position_angle': 'phi',
		'imolspec': 'imolspec',
		'iline': 'iline',
		'width_kms': 'widthkms',
		'nchannels': 'linenlam',
		'npix': 'npix'
		}

etl/mdl/mdl_prepare_radmc_command.py

+32 −3

Original line number	Diff line number	Diff line
		@@ -3,6 +3,7 @@ from typing import Union
		from astropy import units as u
		from assets.commons import (load_config_file,
		convert_frequency_to_wavelength)
		from assets.constants import radmc_options_mapping


		def main(override_config: Union[dict, None] = None):
		@@ -11,11 +12,39 @@ def main(override_config: Union[dict, None] = None):
		central_frequency = convert_frequency_to_wavelength(
		frequency=float(config['radmc']['central_frequency']) * u.Unit(config['radmc']['frequency_units']),
		output_units=u.Unit("micron"))
		assert check_config(config=config)
		with open(os.path.join('mdl', 'radmc3d_postprocessing.sh'), 'w') as outfile:
		outfile.write('cd mdl/radmc_files\n')
		outfile.write(f'radmc3d image incl {config["radmc"]["inclination"]} phi {config["radmc"]["position_angle"]}'
		f' iline {config["radmc"]["iline"]} widthkms {config["radmc"]["width_kms"]} '
		f'linenlam {config["radmc"]["nchannels"]} npix {config["radmc"]["npix"]}')
		options_set = get_command_options(config)
		outfile.write(f'radmc3d image {" ".join(options_set)}')


		def check_config(config: dict) -> bool:
		"""
		Check if all mandatory keys are present in the configuration dictionary.
		:param config: the configuration dictionary
		:return: True is all keys are present, False otherwise
		"""
		mandatory_keys = {
		'inclination',
		'position_angle',
		}
		return set(mandatory_keys).difference(set(config.keys())) == set()


		def get_command_options(config: dict) -> set:
		"""
		Parse the radmc3d command options from the configuration dictionary
		:param config: the configuration dictionary
		:return: a set of string to postpone to the radmc3d image command
		"""
		options_list = []
		for key in config["radmc"]:
		try:
		options_list.append(f'{radmc_options_mapping[key]} {config["radmc"][key]}')
		except KeyError:
		pass
		return set(options_list)


		if __name__ == '__main__':

etl/tests/test_commons.py

+47 −1

Original line number	Diff line number	Diff line
		@@ -7,7 +7,11 @@ from assets.commons import (compute_power_law_radial_profile,
		get_grid_edges,
		extract_grid_metadata,
		get_physical_px_size,
		compute_cartesian_coordinate_grid, get_distance_matrix, get_centered_indices)
		compute_cartesian_coordinate_grid,
		get_distance_matrix,
		get_centered_indices,
		validate_parameter,
		parse_grid_overrides)
		from unittest import TestCase


		@@ -173,3 +177,45 @@ class Test(TestCase):
		[-1, 0, 1]]]
		indices = get_centered_indices(grid_metadata=grid_metadata)
		self.assertTrue(np.array_equal(np.array(expected_indices), indices))

		def test_validate_parameter_none(self):
		parameter = None
		default = 10
		result = validate_parameter(param_to_validate=parameter,
		default=default)
		self.assertEqual(default, result)

		def test_validate_parameter(self):
		parameter = 100
		default = 10
		result = validate_parameter(param_to_validate=parameter,
		default=default)
		self.assertEqual(parameter, result)

		def test_parse_grid_overrides_linear(self):
		config = {
		'overrides': {
		'dust_temperature_grid_type': 'linear',
		'dust_temperature_limits': [10, 30],
		'dust_temperature_step': 1,
		}
		}
		expected_results = np.arange(config['overrides']['dust_temperature_limits'][0],
		config['overrides']['dust_temperature_limits'][1],
		config['overrides']['dust_temperature_step'])
		grid_values = parse_grid_overrides(par_name='dust_temperature',
		config=config)
		self.assertTrue(np.array_equal(expected_results, grid_values))

		def test_parse_grid_overrides_log(self):
		config = {
		'overrides': {
		'dust_temperature_grid_type': 'log',
		'dust_temperature_limits': [10, 200],
		'dust_temperature_step': 2,
		}
		}
		expected_results = np.array([10, 20, 40, 80, 160])
		grid_values = parse_grid_overrides(par_name='dust_temperature',
		config=config)
		self.assertTrue(np.array_equal(expected_results, grid_values.astype(int)))

etl/tests/test_mdl_prepare_radmc_command.py

0 → 100644

+37 −0

Original line number	Diff line number	Diff line
		from mdl.mdl_prepare_radmc_command import (get_command_options,
		check_config)
		from unittest import TestCase


		class Test(TestCase):
		def test_get_command_options(self):
		config = {
		'radmc': {
		'inclination': 30,
		'position_angle': 45,
		'imolspec': 1,
		'iline': 3
		}
		}
		options_set = get_command_options(config=config)
		expected_result = {
		'incl 30',
		'phi 45',
		'imolspec 1',
		'iline 3'
		}
		self.assertSetEqual(options_set, expected_result)

		def test_check_config_pass(self):
		config = {
		'inclination': 0,
		'position_angle': 0
		}
		self.assertTrue(check_config(config))

		def test_check_config_fail(self):
		config = {
		'inclination': 0,
		'imolspec': 1
		}
		self.assertFalse(check_config(config))