Loading etl/stg/stg_radmc_input_generator.py +60 −15 Original line number Diff line number Diff line Loading @@ -100,7 +100,7 @@ def write_radmc_main_input_file(config_mdl: dict, config_lines: dict, path: Union[None, str] = None): """ Creates the main input file for RADMC, which is later used for execution Creates the main input file for RADMC, which can be used to reprocess the input :param config_mdl: the model configuration :param config_lines: te line configuration, from the STG layer :param path: the path where to put the input file Loading @@ -113,6 +113,11 @@ def write_radmc_main_input_file(config_mdl: dict, def get_solid_body_rotation_y(grid_metadata): """ Generate the velocity field for solid body rotation around the y-axis according to the configuration file :param grid_metadata: the grid metadata :return: a tuple with the velocity along the x- and y-axes """ distance_xz = grid_metadata['distance_matrix'][:, grid_metadata['grid_refpix'][1], :] gradient = float(grid_metadata['velocity_gradient']) * u.Unit(grid_metadata['velocity_gradient_unit']) radial_velocity = (distance_xz * u.cm * gradient).to(u.cm / u.second) Loading Loading @@ -275,6 +280,12 @@ def write_molecular_number_density_profiles(profiles: dict, def save_fits_grid_profile(quantity: np.array, filename: str, path: str = None): """ Save the model grid to a fits file :param quantity: the array to be stored in the fits file :param filename: the name of the file to be created :param path: the path where the file will be stored """ _path = validate_parameter(path, default=os.path.join('prs', 'fits', 'grids')) if not os.path.isfile(os.path.join(_path, filename)): fits.writeto(os.path.join(_path, filename), quantity) Loading Loading @@ -390,13 +401,21 @@ def populate_grid_table(config: dict, return output_filename def populate_grid_files(quantity: str, def populate_grid_files(quantity_name: str, engine: sqla_engine, zip_filename: str, filename: str, run_id: str): """ Stores into the DB the grid filename for later reference :param quantity_name: the name of the quantity to store :param engine: the SQLAlchemy engine :param zip_filename: the name of the grid archive containing the radmc3d input files :param filename: the fits filename where the grid is stored :param run_id: the ID of the run """ raw_insert_entry = {'zipped_grid_name': zip_filename, 'quantity': quantity, 'quantity': quantity_name, 'fits_grid_name': filename, 'created_on': datetime.now(), 'run_id': run_id} Loading Loading @@ -437,6 +456,13 @@ def write_stellar_input_file(stars_metadata: dict, grid_metadata: dict, path: str, wavelengths_micron: np.array): """ Create the input file to insert stars in the computation :param stars_metadata: the metadata about the stars, as specified in the configuration file :param grid_metadata: the grid metadata :param path: the path where the files will be created :param wavelengths_micron: the wavelength to consider """ star_properties = [' '.join([str(rstar), str(mstar), str(pos[0]), str(pos[1]), str(pos[2])]) for rstar, mstar, pos in zip(stars_metadata['rstars'], stars_metadata['mstars'], stars_metadata['star_positions'])] override_defaults = { Loading @@ -457,6 +483,14 @@ def write_stellar_input_file(stars_metadata: dict, def get_grid_name(method: Union[str, None] = None, zip_filename: Union[str, None] = None, quantity_name: Union[str, None] = None): """ Compute the name of the grid file :param method: method used to compute the file name; uuid generates a random unique identifier, composite_grid appends the quantity name to the zipped archive name :param zip_filename: the zipped archive name :param quantity_name: the name of the quantity that should be processed :return: the name of the file """ _method = validate_parameter(method, default='uuid') allowed_methods = ('uuid', 'composite_grid') if method == 'uuid': Loading Loading @@ -533,18 +567,6 @@ def main(run_id: str, grid_metadata=grid_metadata, run_id=run_id) grid_file_name = get_grid_name(method='composite_grid', zip_filename=zip_filename, quantity_name='gas_number_density') save_fits_grid_profile(quantity=profiles['gas_number_density'], filename=grid_file_name) populate_grid_files(quantity='gas_number_density', engine=engine, zip_filename=zip_filename, filename=grid_file_name, run_id=run_id) write_radmc_main_input_file(config_mdl=config_mdl, config_lines=config_lines, path=input_files_dir) Loading @@ -569,11 +591,34 @@ def main(run_id: str, engine.dispose() os.chdir(execution_dir) for quantity_name in ('gas_number_density', 'dust_temperature'): save_and_persist_grid(engine=engine, profiles=profiles, run_id=run_id, zip_filename=zip_filename, quantity_name=quantity_name) make_archive(output_filename=zip_filename, source_dir=input_files_dir, archive_path=os.path.join('stg', 'archive')) return zip_filename def save_and_persist_grid(engine: sqla_engine, profiles: dict, run_id: str, zip_filename: str, quantity_name: str, method: Union[str, None] = None): _method = validate_parameter(method, default='composite_grid') grid_file_name = get_grid_name(method=_method, zip_filename=zip_filename, quantity_name=quantity_name) save_fits_grid_profile(quantity=profiles[quantity_name], filename=grid_file_name) populate_grid_files(quantity_name=quantity_name, engine=engine, zip_filename=zip_filename, filename=grid_file_name, run_id=run_id) if __name__ == '__main__': main(run_id='test_run') Loading
etl/stg/stg_radmc_input_generator.py +60 −15 Original line number Diff line number Diff line Loading @@ -100,7 +100,7 @@ def write_radmc_main_input_file(config_mdl: dict, config_lines: dict, path: Union[None, str] = None): """ Creates the main input file for RADMC, which is later used for execution Creates the main input file for RADMC, which can be used to reprocess the input :param config_mdl: the model configuration :param config_lines: te line configuration, from the STG layer :param path: the path where to put the input file Loading @@ -113,6 +113,11 @@ def write_radmc_main_input_file(config_mdl: dict, def get_solid_body_rotation_y(grid_metadata): """ Generate the velocity field for solid body rotation around the y-axis according to the configuration file :param grid_metadata: the grid metadata :return: a tuple with the velocity along the x- and y-axes """ distance_xz = grid_metadata['distance_matrix'][:, grid_metadata['grid_refpix'][1], :] gradient = float(grid_metadata['velocity_gradient']) * u.Unit(grid_metadata['velocity_gradient_unit']) radial_velocity = (distance_xz * u.cm * gradient).to(u.cm / u.second) Loading Loading @@ -275,6 +280,12 @@ def write_molecular_number_density_profiles(profiles: dict, def save_fits_grid_profile(quantity: np.array, filename: str, path: str = None): """ Save the model grid to a fits file :param quantity: the array to be stored in the fits file :param filename: the name of the file to be created :param path: the path where the file will be stored """ _path = validate_parameter(path, default=os.path.join('prs', 'fits', 'grids')) if not os.path.isfile(os.path.join(_path, filename)): fits.writeto(os.path.join(_path, filename), quantity) Loading Loading @@ -390,13 +401,21 @@ def populate_grid_table(config: dict, return output_filename def populate_grid_files(quantity: str, def populate_grid_files(quantity_name: str, engine: sqla_engine, zip_filename: str, filename: str, run_id: str): """ Stores into the DB the grid filename for later reference :param quantity_name: the name of the quantity to store :param engine: the SQLAlchemy engine :param zip_filename: the name of the grid archive containing the radmc3d input files :param filename: the fits filename where the grid is stored :param run_id: the ID of the run """ raw_insert_entry = {'zipped_grid_name': zip_filename, 'quantity': quantity, 'quantity': quantity_name, 'fits_grid_name': filename, 'created_on': datetime.now(), 'run_id': run_id} Loading Loading @@ -437,6 +456,13 @@ def write_stellar_input_file(stars_metadata: dict, grid_metadata: dict, path: str, wavelengths_micron: np.array): """ Create the input file to insert stars in the computation :param stars_metadata: the metadata about the stars, as specified in the configuration file :param grid_metadata: the grid metadata :param path: the path where the files will be created :param wavelengths_micron: the wavelength to consider """ star_properties = [' '.join([str(rstar), str(mstar), str(pos[0]), str(pos[1]), str(pos[2])]) for rstar, mstar, pos in zip(stars_metadata['rstars'], stars_metadata['mstars'], stars_metadata['star_positions'])] override_defaults = { Loading @@ -457,6 +483,14 @@ def write_stellar_input_file(stars_metadata: dict, def get_grid_name(method: Union[str, None] = None, zip_filename: Union[str, None] = None, quantity_name: Union[str, None] = None): """ Compute the name of the grid file :param method: method used to compute the file name; uuid generates a random unique identifier, composite_grid appends the quantity name to the zipped archive name :param zip_filename: the zipped archive name :param quantity_name: the name of the quantity that should be processed :return: the name of the file """ _method = validate_parameter(method, default='uuid') allowed_methods = ('uuid', 'composite_grid') if method == 'uuid': Loading Loading @@ -533,18 +567,6 @@ def main(run_id: str, grid_metadata=grid_metadata, run_id=run_id) grid_file_name = get_grid_name(method='composite_grid', zip_filename=zip_filename, quantity_name='gas_number_density') save_fits_grid_profile(quantity=profiles['gas_number_density'], filename=grid_file_name) populate_grid_files(quantity='gas_number_density', engine=engine, zip_filename=zip_filename, filename=grid_file_name, run_id=run_id) write_radmc_main_input_file(config_mdl=config_mdl, config_lines=config_lines, path=input_files_dir) Loading @@ -569,11 +591,34 @@ def main(run_id: str, engine.dispose() os.chdir(execution_dir) for quantity_name in ('gas_number_density', 'dust_temperature'): save_and_persist_grid(engine=engine, profiles=profiles, run_id=run_id, zip_filename=zip_filename, quantity_name=quantity_name) make_archive(output_filename=zip_filename, source_dir=input_files_dir, archive_path=os.path.join('stg', 'archive')) return zip_filename def save_and_persist_grid(engine: sqla_engine, profiles: dict, run_id: str, zip_filename: str, quantity_name: str, method: Union[str, None] = None): _method = validate_parameter(method, default='composite_grid') grid_file_name = get_grid_name(method=_method, zip_filename=zip_filename, quantity_name=quantity_name) save_fits_grid_profile(quantity=profiles[quantity_name], filename=grid_file_name) populate_grid_files(quantity_name=quantity_name, engine=engine, zip_filename=zip_filename, filename=grid_file_name, run_id=run_id) if __name__ == '__main__': main(run_id='test_run')
