diff --git a/src/FOC_reduction.py b/package/FOC_reduction.py similarity index 99% rename from src/FOC_reduction.py rename to package/FOC_reduction.py index 6b586e0..565ff7a 100755 --- a/src/FOC_reduction.py +++ b/package/FOC_reduction.py @@ -35,7 +35,7 @@ def main(target=None, proposal_id=None, infiles=None, output_dir="./data", crop= # Background estimation error_sub_type = 'freedman-diaconis' # sqrt, sturges, rice, scott, freedman-diaconis (default) or shape (example (51, 51)) - subtract_error = 0.01 + subtract_error = 0.50 display_bkg = True # Data binning @@ -51,7 +51,7 @@ def main(target=None, proposal_id=None, infiles=None, output_dir="./data", crop= # Smoothing smoothing_function = 'combine' # gaussian_after, weighted_gaussian_after, gaussian, weighted_gaussian or combine - smoothing_FWHM = 0.200 # If None, no smoothing is done + smoothing_FWHM = 0.150 # If None, no smoothing is done smoothing_scale = 'arcsec' # pixel or arcsec # Rotation diff --git a/package/__init__.py b/package/__init__.py new file mode 100644 index 0000000..80d0eb7 --- /dev/null +++ b/package/__init__.py @@ -0,0 +1,2 @@ +from . import lib +from . import src diff --git a/package/lib/__init__.py b/package/lib/__init__.py new file mode 100644 index 0000000..b866f6e --- /dev/null +++ b/package/lib/__init__.py @@ -0,0 +1,9 @@ +from . import background +from . import convex_hull +from . import cross_correlation +from . import deconvolve +from . import fits +from . import plots +from . import query +from . import reduction +from . import utils diff --git a/src/lib/background.py b/package/lib/background.py similarity index 99% rename from src/lib/background.py rename to package/lib/background.py index 74f41e6..fb0ae83 100755 --- a/src/lib/background.py +++ b/package/lib/background.py @@ -17,7 +17,7 @@ import matplotlib.dates as mdates from matplotlib.colors import LogNorm from matplotlib.patches import Rectangle from datetime import datetime -from lib.plots import plot_obs +from .plots import plot_obs from scipy.optimize import curve_fit diff --git a/src/lib/convex_hull.py b/package/lib/convex_hull.py similarity index 100% rename from src/lib/convex_hull.py rename to package/lib/convex_hull.py diff --git a/src/lib/cross_correlation.py b/package/lib/cross_correlation.py similarity index 100% rename from src/lib/cross_correlation.py rename to package/lib/cross_correlation.py diff --git a/src/lib/deconvolve.py b/package/lib/deconvolve.py similarity index 100% rename from src/lib/deconvolve.py rename to package/lib/deconvolve.py diff --git a/src/lib/fits.py b/package/lib/fits.py similarity index 99% rename from src/lib/fits.py rename to package/lib/fits.py index 8f9b389..e966f43 100755 --- a/src/lib/fits.py +++ b/package/lib/fits.py @@ -13,7 +13,7 @@ import numpy as np from os.path import join as path_join from astropy.io import fits from astropy.wcs import WCS -from lib.convex_hull import clean_ROI +from .convex_hull import clean_ROI def get_obs_data(infiles, data_folder="", compute_flux=False): diff --git a/src/lib/plots.py b/package/lib/plots.py similarity index 99% rename from src/lib/plots.py rename to package/lib/plots.py index dcde2be..0ea1354 100755 --- a/src/lib/plots.py +++ b/package/lib/plots.py @@ -56,9 +56,9 @@ from astropy.io import fits from astropy.coordinates import SkyCoord from scipy.ndimage import zoom as sc_zoom try: + from .utils import rot2D, princ_angle, sci_not +except ImportError: from utils import rot2D, princ_angle, sci_not -except ModuleNotFoundError: - from lib.utils import rot2D, princ_angle, sci_not def plot_obs(data_array, headers, rectangle=None, savename=None, plots_folder="", **kwargs): @@ -975,8 +975,8 @@ class overplot_pol(align_maps): px_scale = self.other_wcs.wcs.get_cdelt()[0]/self.wcs_UV.wcs.get_cdelt()[0] self.X, self.Y = np.meshgrid(np.arange(stkI.shape[1]), np.arange(stkI.shape[0])) self.U, self.V = pol*np.cos(np.pi/2.+pang*np.pi/180.), pol*np.sin(np.pi/2.+pang*np.pi/180.) - self.Q = self.ax_overplot.quiver(self.X[::step_vec, ::step_vec], self.Y[::step_vec, ::step_vec], self.U[::step_vec, ::step_vec], self.V[::step_vec, ::step_vec], units='xy', angles='uv', scale=1./self.vec_scale, scale_units='xy', pivot='mid', - headwidth=0., headlength=0., headaxislength=0., width=0.5, linewidth=0.8, color='white', edgecolor='black', transform=self.ax_overplot.get_transform(self.wcs_UV), label="{0:s} polarisation map".format(self.map_observer)) + self.Q = self.ax_overplot.quiver(self.X[::step_vec, ::step_vec], self.Y[::step_vec, ::step_vec], self.U[::step_vec, ::step_vec], self.V[::step_vec, ::step_vec], units='xy', angles='uv', scale=px_scale/self.vec_scale, scale_units='xy', pivot='mid', + headwidth=0., headlength=0., headaxislength=0., width=2.0, linewidth=1.0, color='white', edgecolor='black', transform=self.ax_overplot.get_transform(self.wcs_UV), label="{0:s} polarisation map".format(self.map_observer)) # Display Stokes I as contours if levels is None: diff --git a/src/lib/query.py b/package/lib/query.py similarity index 100% rename from src/lib/query.py rename to package/lib/query.py diff --git a/src/lib/reduction.py b/package/lib/reduction.py similarity index 99% rename from src/lib/reduction.py rename to package/lib/reduction.py index 0e74d5a..2553f13 100755 --- a/src/lib/reduction.py +++ b/package/lib/reduction.py @@ -49,12 +49,12 @@ from scipy.signal import fftconvolve from astropy.wcs import WCS from astropy import log import warnings -from lib.deconvolve import deconvolve_im, gaussian_psf, gaussian2d, zeropad -from lib.convex_hull import image_hull, clean_ROI -from lib.background import bkg_fit, bkg_hist, bkg_mini -from lib.plots import plot_obs -from lib.utils import princ_angle -from lib.cross_correlation import phase_cross_correlation +from .deconvolve import deconvolve_im, gaussian_psf, gaussian2d, zeropad +from .convex_hull import image_hull, clean_ROI +from .background import bkg_fit, bkg_hist, bkg_mini +from .plots import plot_obs +from .utils import princ_angle +from .cross_correlation import phase_cross_correlation log.setLevel('ERROR') diff --git a/src/lib/utils.py b/package/lib/utils.py similarity index 100% rename from src/lib/utils.py rename to package/lib/utils.py diff --git a/src/overplot_IC5063.py b/package/overplot_IC5063.py similarity index 100% rename from src/overplot_IC5063.py rename to package/overplot_IC5063.py diff --git a/src/overplot_MRK463E.py b/package/overplot_MRK463E.py similarity index 100% rename from src/overplot_MRK463E.py rename to package/overplot_MRK463E.py diff --git a/package/src/__init__.py b/package/src/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/utils/analysis.py b/package/src/analysis.py similarity index 96% rename from utils/analysis.py rename to package/src/analysis.py index 6daecb8..1cb3bc9 100755 --- a/utils/analysis.py +++ b/package/src/analysis.py @@ -30,7 +30,7 @@ except get_error as err: if fits_path is not None: from astropy.io import fits - from src.lib.plots import pol_map + from lib.plots import pol_map Stokes_UV = fits.open(fits_path) p = pol_map(Stokes_UV, SNRp_cut=SNRp_cut, SNRi_cut=SNRi_cut, flux_lim=flux_lim) diff --git a/utils/comparison_Kishimoto.py b/package/src/comparison_Kishimoto.py similarity index 100% rename from utils/comparison_Kishimoto.py rename to package/src/comparison_Kishimoto.py diff --git a/utils/get_cdelt.py b/package/src/get_cdelt.py similarity index 100% rename from utils/get_cdelt.py rename to package/src/get_cdelt.py