Commit 98736fe8 authored by Andrea Giannetti's avatar Andrea Giannetti
Browse files

Persisted moment zero and ratio parameters.

parent 8368c70a

etl/assets/commons/__init__.py

+6 −1
Original line number Diff line number Diff line
@@ -93,8 +93,13 @@ def load_config_file(config_file_path: str, 
    with open(config_file_path) as config_file:

        config = yaml.load(config_file, Loader=yaml.FullLoader)

    for key in _override_config:

        if key not in config.keys():

            config[key] = {}

        for subkey in _override_config[key]:

            try:

                config[key][subkey] = _override_config[key][subkey]

            except KeyError:

                config[key] = {subkey: _override_config[key][subkey]}

    return config

etl/assets/constants/__init__.py

+6 −0
Original line number Diff line number Diff line 
import numpy as np

from .physical_constants import mean_molecular_mass



polaris_grid_map = {
@@ -57,3 +58,8 @@ radmc_options_mapping = { 
    'npix': 'npix'

}



aggregation_function_mapping = {

    'mean': np.nanmean,

    'median': np.nanmedian

}

etl/main.py

+11 −9
Original line number Diff line number Diff line
@@ -26,17 +26,19 @@ def build_model_grid(): 
            }

        }

        tarfile_filename = stg_main(override_config=overrides)

        cube_fits = []

        for line in lines:

            line_overrides = {

                'radmc': {

            mdl_overrides = {

                'lines': {},

                'model': {

                    'radmc_observation': {

                        'iline': line

                    }

                }

            execute_radmc_script(grid_tarfile=tarfile_filename,

                                 override_config=line_overrides)

        prs_main(cube_fits1=f'td_{tdust}_nh2_{nh2}_line_{lines[0]}.fits',

                 cube_fits2=f'td_{tdust}_nh2_{nh2}_line_{lines[1]}.fits',

                 ratio_fits_name=f'ratio_td_{tdust}_nh2_{nh2}_lines_{lines[0]}-{lines[1]}.fits')

            }

            cube_fits.append(execute_radmc_script(grid_tarfile=tarfile_filename,

                                                  override_config=mdl_overrides))

        prs_main(cube_fits_list=cube_fits)





if __name__ == '__main__':

etl/mdl/mdl_execute_radmc_command.py

+74 −28
Original line number Diff line number Diff line
@@ -2,7 +2,10 @@ import os 
import sys

from itertools import product

from typing import Union



import sqlalchemy

from astropy import units as u

from datetime import datetime

from radmc3dPy import image

from stg.stg_build_db_structure import (LinePars,

                                        SpeciesAndPartners,
@@ -21,6 +24,12 @@ from assets.constants import (radmc_options_mapping, 
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

    :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

    """

    _path = validate_parameter(path, default='.')

    with open(os.path.join(_path, 'radmc3d.inp'), "w") as outfile:

        outfile.write(f'nphot = {config_mdl["radmc_postprocessing"]["nphotons"]}\n')
@@ -32,6 +41,11 @@ def write_radmc_main_input_file(config_mdl: dict, 


def save_cube_as_fits(cube_out_name: Union[str, None] = None,

                      cube_out_path: Union[str, None] = None):

    """

    Convert the RADMC output to fits

    :param cube_out_name: outfile name

    :param cube_out_path: outfile path

    """

    _cube_out_name = validate_parameter(cube_out_name, default='test_cube.fits')

    _cube_out_path = validate_parameter(cube_out_path, default=os.path.join('prs', 'fits', 'cubes'))

    imdata = image.readImage(fname=os.path.join('mdl', 'radmc_files', 'image.out'))
@@ -75,10 +89,12 @@ def main(grid_tarfile: str, 
    # The reason for splitting the main input file from the rest is that some parameters can be changed

    # independently of the grid for the modeling. The mdl hash should depend on all the mdl parameters, not a subset

    logger = setup_logger(name='MDL')

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

                                    override_config=override_config)['lines']

    executed_on = datetime.now()

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

                                  override_config=override_config['lines'])

    config_lines = config_stg['lines']

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

                                  override_config=override_config)

                                  override_config=override_config['model'])

    write_radmc_main_input_file(config_mdl=config_mdl,

                                config_lines=config_lines,

                                path=os.path.join('mdl', 'radmc_files'))
@@ -93,29 +109,57 @@ def main(grid_tarfile: str, 
    os.chdir(os.path.join('mdl', 'radmc_files'))

    os.system(radmc_command)

    os.chdir(os.path.join('..', '..'))

    cube_filename = f'{compute_unique_hash_filename(config=config_mdl)}.fits'

    config_full = config_mdl.copy()

    config_full.update(config_stg)

    cube_filename = f'{compute_unique_hash_filename(config=config_full)}.fits'



    save_cube_as_fits(cube_out_name=cube_filename,

                      cube_out_path=os.path.join('prs', 'fits', 'cubes'))



    line_pars_dict = {

        'zipped_grid_name': f'{grid_tarfile}',

        'lines_mode': config_lines['lines_mode']

    populate_line_table(config_lines=config_lines,

                        engine=engine,

                        executed_on=executed_on,

                        grid_tarfile=grid_tarfile)



    populate_species_and_partner_table(config_lines, engine, executed_on, grid_tarfile)



    populate_model_table(config_mdl, cube_filename, engine, executed_on)

    return cube_filename





def populate_model_table(config_mdl, cube_filename, engine, executed_on):

    model_pars_dict = {

        'fits_cube_name': cube_filename,

        'nphotons': config_mdl['radmc_postprocessing']['nphotons'],

        'scattering_mode_max': int(config_mdl['radmc_postprocessing']['scattering_mode_max']),

        'iranfreqmode': config_mdl['radmc_postprocessing']['iranfreqmode'],

        'tgas_eq_tdust': config_mdl['radmc_postprocessing']['tgas_eq_tdust'],

        'inclination': config_mdl['radmc_observation']['inclination'],

        'position_angle': config_mdl['radmc_observation']['position_angle'],

        'imolspec': get_value_if_specified(config_mdl['radmc_observation'], 'imolspec'),

        'iline': get_value_if_specified(config_mdl['radmc_observation'], 'iline'),

        'width_kms': get_value_if_specified(config_mdl['radmc_observation'], 'width_kms'),

        'nchannels': get_value_if_specified(config_mdl['radmc_observation'], 'nchannels'),

        'npix': get_value_if_specified(config_mdl['radmc_observation'], 'npix'),

        'created_on': executed_on

    }

    upsert(

        table_object=LinePars,

        row_dict=line_pars_dict,

        conflict_keys=[LinePars.zipped_grid_name],

        table_object=ModelPars,

        row_dict=model_pars_dict,

        conflict_keys=[ModelPars.fits_cube_name],

        engine=engine

    )





def populate_species_and_partner_table(config_lines, engine, executed_on, grid_tarfile):

    for (species, collision_partner) in product(config_lines['species_to_include'], config_lines['collision_partners']):

        species_partner_dict = {

            'zipped_grid_name': f'{grid_tarfile}',

            'species_to_include': species,

            'molecular_abundance': config_lines['molecular_abundances'][species],

            'collision_partner': collision_partner,

            'molecular_abundance_collision_partner': config_lines['molecular_abundances'][collision_partner]

            'molecular_abundance_collision_partner': config_lines['molecular_abundances'][collision_partner],

            'created_on': executed_on

        }

        upsert(

            table_object=SpeciesAndPartners,
@@ -126,27 +170,29 @@ def main(grid_tarfile: str, 
            engine=engine

        )



    model_pars_dict = {

        'fits_cube_name': cube_filename,

        'nphotons': config_mdl['radmc_postprocessing']['nphotons'],

        'scattering_mode_max': int(config_mdl['radmc_postprocessing']['scattering_mode_max']),

        'iranfreqmode': config_mdl['radmc_postprocessing']['iranfreqmode'],

        'tgas_eq_tdust': config_mdl['radmc_postprocessing']['tgas_eq_tdust'],

        'inclination': config_mdl['radmc_observation']['inclination'],

        'position_angle': config_mdl['radmc_observation']['position_angle'],

        'imolspec': get_value_if_specified(config_mdl['radmc_observation'], 'imolspec'),

        'iline': get_value_if_specified(config_mdl['radmc_observation'], 'iline'),

        'width_kms': get_value_if_specified(config_mdl['radmc_observation'], 'width_kms'),

        'nchannels': get_value_if_specified(config_mdl['radmc_observation'], 'nchannels'),

        'npix': get_value_if_specified(config_mdl['radmc_observation'], 'npix'),



def populate_line_table(config_lines: dict,

                        engine: sqlalchemy.engine,

                        executed_on: datetime.timestamp,

                        grid_tarfile: str):

    """

    Populate the lines table in the DB

    :param config_lines: the dictionary containing the line configuration

    :param engine: the SQLAlchemy engine to use

    :param executed_on: the timestamp of execution, to add to the record

    :param grid_tarfile: the grid tarfile name, to be used as key

    """

    line_pars_dict = {

        'zipped_grid_name': f'{grid_tarfile}',

        'lines_mode': config_lines['lines_mode'],

        'created_on': executed_on

    }

    upsert(

        table_object=ModelPars,

        row_dict=model_pars_dict,

        conflict_keys=[ModelPars.fits_cube_name],

        table_object=LinePars,

        row_dict=line_pars_dict,

        conflict_keys=[LinePars.zipped_grid_name],

        engine=engine

    )

    return cube_filename





if __name__ == '__main__':

etl/prs/config/config.yml

+2 −1
Original line number Diff line number Diff line
@@ -2,3 +2,4 @@ flux_computation: 
    central_frequency: 230.000

    central_frequency_units: "GHz"

    integration_limits: "all"

    aggregation_function: 'mean'
 
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