Commit 8a7d9487 authored by Andrea Giannetti's avatar Andrea Giannetti
Browse files

Refactored grid creation, adding config file.

parent aa5f457b

etl/assets/commons/__init__.py

+32 −4
Original line number Diff line number Diff line 
import logging

import sys

import astropy.units

import yaml

import numpy as np
@@ -11,6 +13,26 @@ from assets.constants import (radmc_grid_map, 
                              leiden_url_mapping)





def setup_logger(name: str,

                 log_level: str = None) -> logging.Logger:

    """

    Configure default logger

    :param name: Logger name

    :param log_level: Logging levels, as defined by logging

    :return: the logger object

    """

    log_level = 'DEBUG' if log_level is None else log_level

    """general logger configurator"""

    logger = logging.getLogger(name)

    logger.setLevel(log_level)

    handler = logging.StreamHandler(sys.stdout)

    handler.setLevel(log_level)

    formatter = logging.Formatter("%(asctime)s - %(name)-7s - %(levelname)s - %(message)s", datefmt="%Y-%m-%d %H:%M:%S")

    handler.setFormatter(formatter)

    logger.addHandler(handler)

    return logger





def validate_parameter(param_to_validate,

                       default):

    return param_to_validate if param_to_validate is not None else default
@@ -182,16 +204,22 @@ def get_physical_px_size(grid_metadata: dict) -> List[u.Quantity]: 
    return physical_px_size





def get_moldata(species_names: list):

def get_moldata(species_names: list,

                logger: logging.Logger):

    """

    Downloads the molecular data from the Leiden molecular database; check whether the molecule in mapped in

        leiden_url_mapping

    :param species_names: the names of the species for which to download data

    :param logger: logger for output printing

    """

    for species in species_names:

        if not os.path.isfile(os.path.join('mdl', 'radmc_files', f'molecule_{species}.inp')):

            logger.info(f'Downloading file molecule_{species}.inp...')

            data = urllib.request.urlopen(leiden_url_mapping[species]).read().decode()

            with open(os.path.join('mdl', 'radmc_files', f'molecule_{species}.inp'), 'w') as outfile:

                outfile.writelines(data)

        else:

            logger.info(f'File molecule_{species}.inp found, skipping download...')





def convert_frequency_to_wavelength(frequency: astropy.units.Quantity,

etl/config/config.yml

0 → 100644
+9 −0
Original line number Diff line number Diff line 
overrides:

    dust_temperature_grid_type: 'linear'

    dust_temperature_limits: [10, 30]

    dust_temperature_step: 5

    gas_density_grid_type: 'log'

    gas_density_limits: [1e4, 1e8]

    gas_density_step: 10

    gas_density_unit: cm^-3

    lines_to_process: [87, 86]

etl/main.py

+23 −3
Original line number Diff line number Diff line 
import os

import numpy as np

from itertools import product

from assets.commons import load_config_file

from stg.stg_radmc_input_generator import main as stg_main

from mdl.mdl_prepare_radmc_command import main as create_radmc_script

from mdl.mdl_save_results_as_fits import main as save_results

from prs.prs_compute_integrated_fluxes_and_ratios import main as prs_main



config = load_config_file(os.path.join('config', 'config.yml'))





def parse_grid_overrides(par_name: str,

                         config: dict) -> np.array:

    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]),

                                float(config_overrides[f'{par_name}_limits'][1]),

                                float(config_overrides[f'{par_name}_step']))

    else:

        grid_values = 10 ** np.arange(np.log10(float(config_overrides[f'{par_name}_limits'][0])),

                                      np.log10(float(config_overrides[f'{par_name}_limits'][1])),

                                      np.log10(float(config_overrides[f'{par_name}_step'])))

    return grid_values





# grid definition

dust_temperatures = np.arange(10, 25, 5)

central_densities = np.array([1e4, 1e5, 1e6])

lines = [86, 87]

dust_temperatures = parse_grid_overrides(par_name='dust_temperature',

                                         config=config)

central_densities = parse_grid_overrides(par_name='gas_density',

                                         config=config)

lines = config['lines_to_process']



for (tdust, nH2) in product(dust_temperatures, central_densities):

    overrides = {

etl/mdl/config/config.yml

+1 −1
Original line number Diff line number Diff line
@@ -4,6 +4,6 @@ radmc: 
    iline: 2

    central_frequency: 230.538

    frequency_units: GHz

    width_kms: 15

    width_kms: 10

    nchannels: 100

    npix: 200

etl/stg/config/config.yml

+7 −7
Original line number Diff line number Diff line
@@ -4,23 +4,23 @@ grid: 
    central_density: 1e6

    density_unit: "cm^-3"

    density_powerlaw_idx: 0

#    density_value_at_reference: 1e6

#    distance_reference: 0.5

#    distance_reference_unit: 'pc'

    density_value_at_reference: 1e6

    distance_reference: 0.5

    distance_reference_unit: 'pc'

    dust_temperature: 15

    dust_temperature_unit: 'K'

    dust_temperature_powerlaw_idx: 0

    microturbulence: 5

    microturbulence: 1.5

    microturbulence_unit: 'km/s'

    dim1: {"size":0.1, "size_units": "pc", "shape": 5, "refpix": 2}

    dim1: {"size":1, "size_units": "pc", "shape": 3, "refpix": 1}

    velocity_field: 'solid'

    velocity_gradient: 0.1

    velocity_gradient: 2

    velocity_gradient_unit: "km/s/pc"



lines:

    species_to_include: ['e-ch3oh']

    molecular_abundances: {

                              "e-ch3oh": 1e-7,

                              "e-ch3oh": 1e-8,

                              "p-h2": 0.25,

    }

    lines_mode: 3