CubeLineMoment.py:

Script to derive Moment0, Moment1, and Moment2 from a set of input-defined spectral lines in an image cube. Currently simply calculates moments over a defined HWZI for each line in band.

To run in ipython use:

run CubeLineMoment.py yaml_scripts/CubeLineMomentInput.yaml

YAML File Input Parameters:

• cube [string]: Input FITS cube to be processed. Spectral axis can be frequency or velocity. Example: FITS/NGC253-H2COJ32K02-Feather-line.fits

• cuberegion [string]: ds9 region file used to spatial mask for input FITS cube emission region. Example: regions_folder/NGC253BoxBand6H2COJ32K02.reg

• cutoutcube [string]: Input FITS cube which contains "tracer" transition which is strong and representative of dense gas emission region traced by other molecules/transitions in cube. Note that this cube can be any image cube, as long as the PPV range overlaps with cuberegion. Example: FITS/NGC253-H213COJ32K1-Feather-line.fits

• cutoutcuberegion [string]: ds9 region file used to spatial mask input FITS "tracer" transition (spatialmaskcube). Example: regions_folder/NGC253BoxBand6H2COJ32K02.reg

• vz [float:km/s]: Target central velocity. In order to maximize the effectiveness of the spectral lines extracted from your image cube, set vz to a value near the median radial velocity of your target. Example: 258.8

• target [string]: Target name. Example: NGC253

• brightest_line_name [string]: Brightest line name. Example: 13CO_21

• brightest_line_frequency [float:MHz]: Frequency of the bright "tracer" transition in spatialmaskcube. Example: 220.398700

• width_line_frequency [float:MHz]: Frequency of the "representative" transition in cube. Example: 218.222192

• velocity_half_range [float:km/s]: Estimated half-width at zero intensity for the entire velocity extent of the "representative" transition in cube. Note that for a galaxy this would be half of the total velocity range for the chosen transition. Example: 400

• noisemapbright_baseline [list of lists:channels]: Baseline channel segments which are considered line-free in spatialmaskcube. Used to determine RMS spectral noise in spatialmaskcube. Example: [[40,60],[100,116],[150,180]]

• noisemap_baseline [list of lists:channels]: Baseline channel segments which are considered line-free in cube. Used to determine RMS spectral noise in cube. Example: [[20,35],[60,95],[360,370]]

• my_line_list [list:MHz]: List of spectral line frequencies to be extracted from cube. Example: 217.289800, 217.299162, 217.467150, 217.517110, 217.802057, 217.88639, 217.943821, 218.15897, 218.222192, 218.324711, 218.440050, 218.475632, 218.760071, 218.85439, 218.9033555, 218.981019

• my_line_widths [list:km/s]: List of estimated half-width zero-intensities for transitions in my_line_list. Example: 50.0, 50.0, 60.0, 40.0, 40.0, 40.0, 40.0, 40.0, 40.0, 40.0, 40.0, 40.0, 40.0, 50.0, 40.0, 40.0

• my_line_names [list:string]: List of transition names in my_line_list. Example: 13CNF122, CH3OH67, 13CNF132, CH3OCHO88, CH3OCHO4847, CH3OH2020, CH3OCHO4546, CH3OCHO??, H2COJ32K0, HC3N2423v0, CH3OH43, H2COJ32K221, H2COJ32K210, HC3N2423v6, OCS1817, HNCO109

• signal_mask_limit [float]: Multiplier for noise-based signal masking. Signal less than signal_mask_limit times RMS noise is masked. Example: 3

• spatial_mask_limit [float]: Multiplier for noise-based spatial masking. Signal less than spatial_mask_limit times RMS noise is masked. Example: 3

• sample_pixel [string]: File name for ds9 regions file that contains the sample pixel positions. Regions file entries must be of type "point" (i.e. point(11.88341,-25.29118) # text={GMC1}) Example: LeroyNGC253GMCPoint.reg

Masking Used in CubeLineMoment:

• [optional] Use ds9 regions to select spatial regions to process

• Create a cutout cube cutoutcube based on a bright line.

  • [optional] Select only positive values (set by mask_negatives parameter)
  • Select a subset of the cube at +/- velocity_half_range from the central velocity vz
  • Compute peak intensity max_map, width width_map, and peak velocity peak_velocity of this cube to use in future steps

• Create a noise map noisemapbright based on the bright line cube

  • Select signal-free baseline regions using the noisemapline_baseline parameter
  • Compute the standard deviation in the spectral direction of the selected region

• Create another noise map noisemap based on the target cube (the process is the same as for the bright cube)

• Create a spatial mask based on the peak intensity of the bright line cutout cube cutoutcube: pixels in the peak map max_map of the cutout cube above signal_mask_limit * noisemapbright are included

• Using the bright line maps, make a Gaussian mask cube gauss_mask_cube for each target line

  • For each included spatial pixel, produce a Gaussian spectrum using the centroid from peak_velocity, the peak intensity from max_map, and the width from width_map
  • Compute the peak signal-to-noise in each pixel by taking max_map / noisemap
  • Determine a threshold that is 1/peak_sn
  • Create a PPV inclusion mask width_mask_cube where gauss_mask_cube > threshold

• [optional] Create a S/N mask where any PPV pixel is greater than signal_mask_limit * noisemap (this is a comparison between a cube and a spatial map)

• Create a PPV mask velocity_range_mask where the velocity is within line_width of peak_velocity

• Select the data combining the velocity_range_mask, the S/N limit, and the Gaussian-based width_mask_cube

Warning Messages

Note that several of these warning messages are due to the use of NaN values as blanking values in spectral cubes. All of these warnings are for information only and can safely be ignored.

WARNING: StokesWarning: Cube is a Stokes cube, returning spectral cube for I component [spectral_cube.io.core]

Explanation: Cube contains a fourth Stokes axis. Information only. No action required.

WARNING: PossiblySlowWarning: This function (<function BaseSpectralCube.std at 0x19e9053a0>) requires loading the entire cube into memory and may therefore be slow. [spectral_cube.utils]

Explanation: CubeLineMoment does some calculation on entire cubes. Information only. No action required.

/Users/jmangum/anaconda3/envs/python39/lib/python3.9/site-packages/numpy/lib/nanfunctions.py:1878: RuntimeWarning: Degrees of freedom <= 0 for slice.
  var = nanvar(a, axis=axis, dtype=dtype, out=out, ddof=ddof,

Explanation: There is at least one spectrum that consists of only 1 pixel, so the standard deviation can't be computed. i.e., noisemask.with_mask(mask[:,None,None]).include().sum(axis=0) will have at least one pixel with value 1. Information only. No action required.

/Users/jmangum/anaconda3/envs/python39/lib/python3.9/site-packages/spectral_cube/spectral_cube.py:441: RuntimeWarning: All-NaN slice encountered

Explanation: This warning often results from the calculation of the maximum value along the spectral axis toward each pixel in cutoutcube. Since cutoutcube can have blanked (NaN) values, there is often at least one position where all spectral values are blanked (NaN). Information only. No action required.

/Users/jmangum/Python/mangum_galaxies-master/CubeLineMoment.py:435: RuntimeWarning: divide by zero encountered in divide

Explanation: This warning results from the fact that the denominator in a divide uses a cube with NaN values. Since it is common for a cube to use NaN as a blanking value, this warning is common. Information only. No action required.

GaussfitGalaxies.py:

An implementation of gaussfit_catalog (see https://github.com/radio-astro-tools/gaussfit_catalog) using astropy models to do gaussian fits to a list of input FITS files using a list of input positions from a DS9 regions file.

If you have input regions which are off the image, the script will squawk but not crash.

The input regions are the initial guesses, but they should be very close to the peak. Note that gaussfit_catalog is catered to situations where the background was a significant confusing factor once you got more than 1-2 beam FWHM from the peak, so it is quite restrictive in how far it will wander beyond the initial position guess.

The four panels in the output png files are showing:

• Top Left: Data
• Top Right: Fit
• Bottom Left: Residual
• Bottom Right: Data with the fit contoured on top

The .ipac files are in the "ascii.ipac” format from astropy. In those files, the non-obvious columns are:

• chi2_n = chi2/n_pixels, which is close to a reduced chi2
• PA is defined as east-from-north (but double check this! angle conventions are tricky)

Two examples of a similar implementation of gaussfit_catalog are: https://github.com/keflavich/W51_ALMA_2013.1.00308.S/blob/0789ccbb2fd3bfe801cfb63818ad2696825d076f/analysis/longbaseline/gaussfit_sources.py https://github.com/keflavich/SgrB2_ALMA_3mm_Mosaic/blob/93fe253f6de499cc91779bdae4f0e22ab806c161/analysis/gaussfit_sources.py