Source code for higal_sedfitter.smooth

from __future__ import print_function
import warnings
import glob
import os
import re

import numpy as np
from import fits
from astropy import units as u
from astropy import convolution
import FITS_tools.header_tools as FITS_header_tools
from FITS_tools.hcongrid import hcongrid

from higal_beams import beams
import higal_beams

FWHM_TO_SIGMA = 1./np.sqrt(8*np.log(2))

__all__ = ['smooth_images_toresolution',

[docs]def smooth_images_toresolution(target_resolution, globs=["destripe*P[LMS]W*fits", "destripe*blue*fits", "destripe*red*fits"], reject_regex='smooth|smregrid', verbose=True, skip_existing=True, regrid=True, target_header=None, regrid_order=1, clobber=False, **kwargs): """ Smooth a series of images to the same resolution. The output files will be of the form ``{inputfilename}_smooth.fits`` and ``{inputfilename}_smregrid.fits`` Parameters ---------- target_resolution : `~astropy.units.quantity.Quantity` A degree-equivalent value that specifies the beam size in the output image globs : list A list of strings to pass into `~glob.glob`. All files found will be smoothed and possibly regridded. reject_regex : str A regular expression to apply to each discovered file to choose whether to reject it. For example, if you've run this function once, you'll have files named ``file.fits`` and ``file_smooth.fits`` that you don't want to re-smooth and re-regrid. verbose : bool Print messages at each step? skip_existing : bool If the output smooth file is found and this is True, skip and move on to the next regrid : bool Regrid the file? If True, ``target_header`` is also required regrid_order : int The order of the regridding operation. Regridding is performed with interpolation, so 0'th order means nearest-neighbor and 1st order means bilinear. Regridding is done with `FITS_tools.hcongrid.hcongrid` clobber : bool Overwrite files if they exist? kwargs : dict Passed to `smooth_image_toresolution` Raises ------ ValueError If ``target_header`` is not specified but ``regrid`` is Returns ------- Nothing. All output is to disk """ for fn in [x for g in globs for x in glob.glob(g) if not, x)]: if verbose: print("Reading file {0}".format(fn),) outnum = int( smoutfn = fn.replace(".fits", "_smooth{0:d}.fits".format(outnum)) if os.path.exists(smoutfn): if skip_existing: if verbose: print("Skipping {0}".format(fn)) continue smhduL = smooth_image_toresolution(fn, smoutfn, target_resolution, verbose=verbose, clobber=clobber, **kwargs) smhdu = smhduL[0] if regrid: if target_header is None: raise ValueError("Must specify a target header if regridding.") newimage = hcongrid(, smhdu.header, target_header, order=regrid_order) rgoutfn = fn.replace(".fits", "_smregrid{0:d}.fits".format(outnum)) print("Regridding {0} to {1}".format(smoutfn, rgoutfn)) newhdu = fits.PrimaryHDU(data=newimage, header=target_header) newhdu.writeto(rgoutfn, clobber=clobber)
[docs]def smooth_image_toresolution(fn, outfn, target_resolution, clobber=False, verbose=True, write=True): """ Smooth images with known beam size to a target beam size Parameters ---------- fn : str outfn : str target_resolution : `~astropy.units.quantity.Quantity` A degree-equivalent value that specifies the beam size in the output image verbose : bool Print messages at each step? clobber : bool Overwrite files if they exist? write : bool Write the file to the output filename? Returns ------- f : `` The smoothed FITS image with appropriately updated BMAJ/BMIN """ f = header = f[0].header native_beamsize = header['BMAJ']*u.deg if header['BMIN'] != header['BMAJ']: warnings.warn("Asymmetric beam not well-supported: " "the images should be smoothed to have symmetric beams " "prior to using this task") kernelsize = ((target_resolution*FWHM_TO_SIGMA)**2 - (native_beamsize*FWHM_TO_SIGMA)**2)**0.5 if kernelsize.value < 0: raise ValueError("Cannot smooth to target resolution: " "smaller than current resolution.") platescale = FITS_header_tools.header_to_platescale(f[0].header, use_units=True) kernelsize_pixels = (kernelsize/platescale).decompose() if not kernelsize_pixels.unit.is_equivalent(u.dimensionless_unscaled): raise ValueError("Kernel size not in valid units") kernel = convolution.Gaussian2DKernel(kernelsize_pixels.value) if verbose: print("Convolving with {0}-pixel kernel".format(kernelsize_pixels)) if kernelsize_pixels > 15: sm = convolution.convolve_fft(f[0].data, kernel, interpolate_nan=True) else: sm = convolution.convolve(f[0].data, kernel) f[0].data = sm comment = "Smoothed with {0:03f}\" kernel".format( f[0].header['BMAJ'] = (, comment) f[0].header['BMIN'] = (, comment) if write: f.writeto(outfn, clobber=clobber) return f
[docs]def add_beam_information_to_higal_header(fn, wavelength=None, clobber=True, name_to_um=higal_beams.name_to_um, **kwargs): """ Given a Hi-Gal FITS file name, attempt to add beam information to its header. The beams are assumed to be symmetric using the larger of the two beam axes given in `Traficante et al 2011 <>`_. This is not a valid assumption in general, but without knowing the scan position angle you can't really do better. Parameters ---------- fn : str A filename corresponding to a Hi-Gal FITS file. MUST have one of the standard HiGal strings in the name: blue, red, PSW, PMW, or PLW clobber : bool Overwrite existing file? (has to be "True" to work!) name_to_um : dict A dictionary identifying the translation between the string that will be inserted into the file template and the wavelength. There are two built in: `higal_sedfitter.higal_beams.name_to_um` and `higal_sedfitter.higal_beams.num_to_um`. """ f = if wavelength is None: wl_names = [x for x in name_to_um if x in fn] if len(wl_names) != 1: raise ValueError("Found too few or too many matches!") wl_name = wl_names[0] else: wl_name = wavelength f[0].header.append(fits.Card(keyword='BMAJ', value=beams[name_to_um[wl_name]].to(u.deg).value, comment='From Traficante 2011')) f[0].header.append(fits.Card(keyword='BMIN', value=beams[name_to_um[wl_name]].to(u.deg).value, comment='Assumed equal to BMAJ')) f[0].header.append(fits.Card(keyword='BPA', value=0)) f[0].header.append(fits.Card(keyword='BEAMNOTE', value='2011MNRAS.416.2932T', comment='Source paper for beam')) f.writeto(fn, clobber=clobber, **kwargs)