Commit 2c4a7e2c authored by Andrea Giannetti's avatar Andrea Giannetti
Browse files

Removed grids from the figures, as requested

parent 5035a841

etl/mdl/mdl_extract_ch3oh_spectra.py

+8 −7
Changes for etl/mdl/mdl_extract_ch3oh_spectra.py: 8 added lines, 7 removed lines.
Original line number Diff line number Diff line
@@ -457,9 +457,9 @@ def run_and_plot_specfit(apspec, tied, line_guesses, limits, limited, 
    # plot fit components

    apspec.plotter(title=f"{source} {_region}")

    apspec.specfit.plot_fit(show_components=True, annotate=False)

    plt.savefig(os.path.join(

        plotdir, f"{_name_prefix}_{source}_{species}{_region}.svg"

    ), bbox_inches='tight')

    # plt.savefig(os.path.join(

    #     plotdir, f"{_name_prefix}_{source}_{species}{_region}.svg"

    # ), bbox_inches='tight')



    # return the RMS of the residuals

    return float(np.nanstd(apspec.specfit.residuals))
@@ -504,7 +504,7 @@ def overlay_region_on_map(apspec, 
    ax_map.set_xlabel("RA [J2000]")

    ax_map.set_ylabel("Dec [J2000]")

    fig_map.tight_layout()

    fig_map.savefig(plotfile, bbox_inches='tight')

    # fig_map.savefig(plotfile, bbox_inches='tight')

    plt.close(fig_map)



def setup_spectral_analysis(source, species):
@@ -709,7 +709,8 @@ def process_source(source, species, guesses, prob_threshold, samples): 
                            densities=densities,

                            moment_map=moment_map,

                            wcs=wcs)

    save_results(densities, source)

    print(source, densities)

    # save_results(densities, source)





def plot_density_vs_fwhm(densities, fwhms, source, species, regions):
@@ -720,7 +721,7 @@ def plot_density_vs_fwhm(densities, fwhms, source, species, regions): 
            color = 'blue' if region.startswith('core') else 'cyan'

            plt.scatter(densities[region]['best_fit'], fwhms[region], label=region, edgecolors=color, figure=fig)

    plt.legend()

    plt.savefig(os.path.join(plotdir, f'aperture_spectra_extraction_density_FWHM_{source}_{species}.svg'), bbox_inches='tight')

    # plt.savefig(os.path.join(plotdir, f'aperture_spectra_extraction_density_FWHM_{source}_{species}.svg'), bbox_inches='tight')

    plt.close(fig)
@@ -758,7 +759,7 @@ def overlay_regions_density(source, regions, densities, moment_map, wcs): 
    plt.xlabel('RA')

    plt.colorbar(pc, label=r'log($n($H$_2)$ [cm$^{-3}$])', shrink=0.68)

    plt.tight_layout()

    plt.savefig(os.path.join(plotdir, f'aperture_spectra_extraction_{source}_{species}.svg'), bbox_inches='tight')

    # plt.savefig(os.path.join(plotdir, f'aperture_spectra_extraction_{source}_{species}.svg'), bbox_inches='tight')

    plt.close()



if __name__ == '__main__':

etl/prs/prs_2d_kinematics.py

+3 −1
Changes for etl/prs/prs_2d_kinematics.py: 3 added lines, 1 removed line.
Original line number Diff line number Diff line
@@ -6,6 +6,8 @@ from sklearn.mixture import BayesianGaussianMixture 
from scipy.optimize import curve_fit

from mpl_toolkits.axes_grid1 import make_axes_locatable

from assets.constants import config_vis3d as config, source_properties, datadir

import matplotlib

matplotlib.use('svg')



fontsize_small = 14

fontsize_medium = 16
@@ -140,7 +142,7 @@ def plot_2d_clustered_kinematics(source, species): 
    if source == 'G332.96':

        ax.legend(loc='upper right', fontsize=fontsize_small, framealpha=0.9)



    ax.grid(alpha=0.3)

    ax.grid(False)



    plt.tight_layout()

    output_filename = f'projected_2d_kinematics_{source}_{species}.png'

etl/stg/stg_check_feather.py

+22 −1
Changes for etl/stg/stg_check_feather.py: 22 added lines, 1 removed line.
Original line number Diff line number Diff line 
import os

import glob

import numpy as np

import matplotlib



# Force headless backend to prevent the Wayland/Qt crash

matplotlib.use('Agg')

import matplotlib.pyplot as plt

from spectral_cube import SpectralCube

from regions import CircleSkyRegion
@@ -39,7 +43,6 @@ def compare_tp_feather_spectralcube(source, species, ap_radius_arcsec=40.0, data 
    subcube_f = cube_f.subcube_from_regions([aperture])

    subcube_tp = cube_tp.subcube_from_regions([aperture])



    # Enable huge ops just in case the subcube is still large

    subcube_f.allow_huge_operations = True

    subcube_tp.allow_huge_operations = True
@@ -59,6 +62,24 @@ def compare_tp_feather_spectralcube(source, species, ap_radius_arcsec=40.0, data 
    spec_tp_k_interp = np.interp(freq_f, freq_tp[sort_tp], spec_tp_k[sort_tp])

    diff_k = spec_f_k - spec_tp_k_interp



    # --- Compute Maximum Relative Residual Correctly ---

    peak_tp = np.nanmax(spec_tp_k_interp)



    # We only care about residuals in the velocity range where the line actually exists

    # So we mask out the pure noise baseline (e.g., regions > 5% of peak)

    signal_mask = spec_tp_k_interp > (0.05 * peak_tp)



    if np.any(signal_mask):

        # Calculate max absolute residual within the line profile

        max_abs_res = np.nanmax(np.abs(diff_k[signal_mask]))

        # Scale it against the peak flux to get the true percentage

        max_rel_res = (max_abs_res / peak_tp) * 100

        print(f"  [Info] Peak TP signal: {peak_tp:.3f} K")

        print(f"  [Info] Max absolute residual: {max_abs_res:.3f} K")

        print(f"  [Info] Max residual relative to peak: {max_rel_res:.1f}%")

    else:

        print("  [Info] Could not compute relative residual reliably.")



    # --- Plotting ---

    if source == 'G332.96':

        source = 'G332'