Commit ba71f003 authored by Andrea Giannetti's avatar Andrea Giannetti
Browse files

added .gitignore

parent f2e502e4

etl/assets/commons/__init__.py

+37 −0
Changes for etl/assets/commons/__init__.py: 37 added lines, 0 removed lines.
Original line number Diff line number Diff line
@@ -110,6 +110,10 @@ def convert_dvelocity_to_hz(dvelocity, rest_frequencies): 
    return dvelocity / speed_of_light.to(u.km / u.s) * rest_frequencies[0].to(u.Hz)





def convert_dfreq_to_velocity(dfrequency, rest_frequencies):

    return dfrequency / rest_frequencies[0].to(u.Hz) * speed_of_light.to(u.km / u.s)





def get_cube(filename, datadir, frequency_limits=None, smooth_data=False):

    cube = pyspeckit.Cube(os.path.join(datadir, filename), format='fits')

    if smooth_data is True:
@@ -135,3 +139,36 @@ def fill_guesses(line_peak, doppler_adjusted_frequencies, shift_hz, linewidth_gu 
                    freq.to(u.Hz).value + shift_hz,

                    linewidth_guess_hz]

    return guesses





def load_velocities_and_linewidths_from_fit(species: str, source: str, velocity_indices: dict,

                                            linewidth_indices: dict, rms: float, detection_index: dict) -> Tuple[np.ndarray, np.ndarray]:

    """

    Load velocities, linewidths, and detection mask from a pickle file containing fitting results.



    Parameters

    ----------

    species : str

        The species for which the data is being loaded.

    source : str

        The source identifier for the data file.

    velocity_indices : dict

        A dictionary mapping species names to tuples of indices for velocity data.

    linewidth_indices : dict

        A dictionary mapping species names to tuples of indices for linewidth data.

    rms : float

        The rms noise level of the data.

    detection_index : dict

        A dictionary mapping species names to the index to be used to create a detection mask.



    Returns

    -------

    tuple of np.ndarray

        A tuple containing three numpy arrays: the first with the velocity data, the second

        with the linewidth data, and the last with the detection mask for the specified species and source.

    """

    with open(f"final_results_{source}_{species}.pickle", "rb") as infile:

        fit_results = pickle.load(infile)

    return (fit_results[velocity_indices[species], :, :],

            fit_results[linewidth_indices[species], :, :],

            (fit_results[detection_index[species], :, :] >= 3 * rms))

etl/config/ch3oh_regions.yml

+1 −1
Changes for etl/config/ch3oh_regions.yml: 1 added line, 1 removed line.
Original line number Diff line number Diff line
@@ -29,7 +29,7 @@ G14: { 
    'envelope_03': [288, 338, 25, 1],

    'envelope_04': [328, 318, 20, 1],

    'envelope_05': [185, 197, 25, 1],

    'core_ch3oh_01': [251, 208, 20, 3],

    'core_ch3oh_01': [251, 208, 20, 2],

    'core_ch3oh_02': [301, 224, 8, 1],

}

G332.96: {

etl/config/config_visfit.yml

+12 −4
Changes for etl/config/config_visfit.yml: 12 added lines, 4 removed lines.
Original line number Diff line number Diff line 
random_seed: 333

check_clustering: True

check_clustering: False

colourscale: 'velocity'

grid_opacity: 0.2

G332.96: {

  n_clusters: 5,

  min_velocity: -68,

  surface_point: [291, 216, -66.43255],

  plot_velocity_limits: [-70, -62],

  plot_species: ['N2H+','CH3OH'],

  plot_fwhm_limits: [0.5, 3],

#  plot_species: ['CH3OH',],

  plot_species: ['N2H+',],

  continuum_limits: [0.1, 1]

}

G28: {
@@ -13,7 +17,9 @@ G28: { 
  min_velocity: -inf,

  surface_point: [272, 278, 79.2268463],

  plot_velocity_limits: [74, 81],

  plot_species: ['N2H+', 'CH3OH'],

  plot_fwhm_limits: [0.5, 5],

  plot_species: ['CH3OH', ],

#  plot_species: ['N2H+', ],

  continuum_limits: [0.1, 3]

}

G14: {
@@ -21,6 +27,8 @@ G14: { 
  min_velocity: -inf,

  surface_point: [197, 291, 40.2304702],

  plot_velocity_limits: [37.5, 42],

  plot_species: ['N2H+', 'CH3OH'],

  plot_fwhm_limits: [0.5, 5],

#  plot_species: ['CH3OH', ],

  plot_species: ['N2H+', ],

  continuum_limits: [0.1, 10]

}

etl/config/guesses.yml

+3 −3
Changes for etl/config/guesses.yml: 3 added lines, 3 removed lines.
Original line number Diff line number Diff line
@@ -143,9 +143,9 @@ G14: { 
    [ 2.5e+5, ]

  ],

  core_ch3oh_01: [

    [ [ 0.05, 0.07, 0.03, 0.01 ], [ 0.01, 0.02, 0.01, 0.003 ], [ 0.001, 0.002, 0.001, 0.0003 ] ],

    [ 0, 10.0e+5, -15.0e+6 ],

    [ 2.5e+5, 2.0e+5, 2.0e+6 ]

    [ [ 0.05, 0.07, 0.03, 0.01 ], [ 0.01, 0.02, 0.01, 0.003 ], ],

    [ 0, 10.0e+5,  ],

    [ 2.5e+5, 2.0e+5, ]

  ],

  core_ch3oh_02: [

    [ [ 0.06, 0.08, 0.03, 0.01 ], ],

etl/mdl/mdl_compute_infall_rate.py

0 → 100644
+23 −0
Changes for etl/mdl/mdl_compute_infall_rate.py: 23 added lines, 0 removed lines.
Original line number Diff line number Diff line 
import numpy as np

from astropy import units as u

from astropy.constants import m_p





# Computation carried out for G28

velocity_gradient = 2.96 * u.km / u.s / u.pc

proj_length = 0.5 * u.pc

proj_width = 0.25 * u.pc

depth = 0.1 * u.pc



los_angle_filament = 30 * u.deg

los_angle_sheet = 45 * u.deg



mean_molecular_weight = 2.33 # Kauffmann 2008

number_density = 5e4 * u.cm**-3



volume = np.pi * proj_length / np.cos(los_angle_filament) * proj_width / np.cos(los_angle_sheet) * depth

mass = volume * mean_molecular_weight * m_p * number_density

# \tau_{acc} = \frac{W_p}{\cos \theta} \left( \frac{\cos \theta}{V_{grad}} \frac{\cos \theta}{W_p} \right)

accretion_timescale = (np.cos(los_angle_sheet) / velocity_gradient).to(u.yr)

infall_rate = (mass / accretion_timescale).to(u.Msun / u.yr) # Same accretion on both sides

# Along the filament it would be around one dex lower, as the velocity gradient is 0.2-0.3 km/s/pc
 
 No newline at end of file