ism3d.xyhelper.maskmoment.maskmoment.maskmoment

ism3d.xyhelper.maskmoment.maskmoment.maskmoment(img_fits, gain_fits=None, rms_fits=None, mask_fits=None, outdir='.', outname=None, snr_hi=4, snr_lo=2, minbeam=1, snr_hi_minch=1, snr_lo_minch=1, min_tot_ch=2, nguard=[0, 0], edgech=5, fwhm=None, vsm=None, vsm_type='gauss', mom1_minch=2, mom2_minch=2, altoutput=False, output_snr_cube=False, output_snr_peak=False, output_snrsm_cube=False, output_2d_mask=False, to_kelvin=True, huge_operations=True, perpixel=False)

Produce FITS images of moment maps using a dilated masking approach.

Parameters

• img_fits (FITS file name, required) – The image cube, this should be in units of K, Jy/beam, or equivalent.

• gain_fits (FITS file name, optional) – The gain cube, e.g. pb cube from CASA. This should have a value between 0 and 1, with 0 near the edges and 1 near the center of the image, and have the same dimensions as the image cube. NOTE: The gain cube is ignored if a noise cube (rms_fits) is given.

• rms_fits (FITS file name, optional) – The noise cube, providing an estimate of the rms noise at each pixel. This should have the same dimensions and units as the image cube. NOTE: If rms_fits is not given, a noise cube is generated from the image cube, after removing any gain variation using the gain cube.

• mask_fits (FITS file name, optional) – External mask cube to use. This cube should have 1’s for valid pixels and 0’s for excluded pixels. If this is provided then the mask generation is skipped and the program goes straight to calculating the moments.

• outdir (string, optional) – Directory to write the output files. Default: Write to the directory where img_fits resides. NOTE: Currently this directory is assumed to exist.

• outname (string, optional) – Basename for output files. For instance, outname=’foo’ produces files ‘foo.mom0.fits.gz’, etc. Default: Based on root name of img_fits.

• snr_hi (float, optional) – The high significance sigma threshold from which to begin mask dilation. Default: 4

• snr_lo (float, optional) – The low significance sigma threshold at which to end mask dilation. Default: 2

• snr_hi_minch (int, optional) – High significance mask is required to span at least this many channels at all pixels. Default: 1

• snr_lo_minch (int, optional) – Low significance mask is required to span at least this many channels at all pixels. Default: 1

• min_tot_ch (int, optional) – Each contiguous mask region must span at least this many channels (but it’s not necessary that every pixel in the region span this many channels). Default: 2

• minbeam (float, optional) – Minimum velocity-integrated area of a mask region in units of the beam size. Default: 1

• nguard (tuple of two ints, optional) – Expand the final mask by nguard[0] pixels in the sky directions and nguard[1] channels in velocity. Currently these values must be equal if both are non-zero. If nguard[0] = 0 then no expansion is done in sky coordinates. If nguard[1] = 0 then no expansion is done in velocity. Default: [0,0]

• edgech (int, optional) – Number of channels at each end of vel axis to use for rms estimation. Default: 5

• fwhm (float or Quantity, optional) – Spatial resolution to smooth to before generating the dilated mask. If value is not an astropy quantity, assumed to be given in arcsec. Default: No spatial smoothing is applied.

• vsm (float or Quantity, optional) – Full width of the spectral smoothing kernel (or FWHM for gaussian). If given as astropy quantity, should be given in velocity units. If not given as astropy quantity, interpreted as number of channels. Default: No spectral smoothing is applied.

• vsm_type (string, optional) – What type of spectral smoothing to employ. Currently three options: (1) ‘boxcar’ - 1D boxcar smoothing, vsm rounded to integer # of chans. (2) ‘gauss’ - 1D gaussian smoothing, vsm is the convolving gaussian FWHM. (3) ‘gaussfinal’ - 1D gaussian smoothing, vsm is the gaussian FWHM

  after convolution, assuming FWHM before convolution is 1 channel.

  Default: ‘gauss’

• mom1_minch (int, optional) – Minimum number of unmasked channels needed to calculate moment-1. Default: 2

• mom2_minch (int, optional) – Minimum number of unmasked channels needed to calculate moment-2. Default: 2

• perpixel (boolean, optional) – Whether to calculate the rms per XY pixel instead of over whole image. Set to True if you know there is a sensitivity variation across the image but you don’t have a gain cube - requires rms_fits and gain_fits unset. Default: False

• output_snr_cube (boolean, optional) – Output the cube in SNR units in addition to the moment maps. Default: False

• output_snr_peak (boolean, optional) – Output the peak SNR image in addition to the moment maps. Default: False

• output_snrsm_cube (boolean, optional) – Output the smoothed cube in SNR units in addition to the moment maps. Default: False

• output_2d_mask (boolean, optional) – Output the projected 2-D mask as well as the newly generated mask. The projected mask at a given pixel is valid for all channels as long as the parent mask is valid for any channel. Default: False

• to_kelvin (boolean, optional) – Output the moment maps in K units if the cube is in Jy/beam units. Default: True

• altoutput (boolean, optional) – Also output moment maps from a “direct” calculation instead of the moment method in spectral_cube. Mainly used for debugging. Default: False

• huge_operations (boolean, optional) – Allow huge operations in spectral_cube. Default: True