
'''
Make a mask of the emission
'''

cube = SpectralCube.read("M33_206_b_c_HI.fits")
cube = cube.with_mask(cube != 0*u.Jy)

noise_cube = Noise(cube)

new_noise = noise_cube.scale

cube = cube.with_mask(cube > new_noise*u.Jy)

# Load in the broad clean mask used
clean_mask = fits.getdata("../../../Arecibo/M33_newmask.fits")

# Need to match the dims
clean_mask = clean_mask.squeeze()
clean_mask = clean_mask[11:195, ::-1, ::-1]
clean_mask = clean_mask[:, 595:3504, 1065:3033]

old_mask = RadioMask(old_cube)
old_mask.intersection(old_arecibo_mask)


'''
Make a mask of the emission
'''

from astropy.io import fits
from spectral_cube import SpectralCube, BooleanArrayMask
from signal_id import RadioMask, Noise
from astropy import units as u


make_mask = True
save_mask = False

cube = SpectralCube.read("M33_206_b_c_HI.fits")
cube = cube.with_mask(cube != 0*u.Jy)

if make_mask:

    # noise_cube = Noise(cube)

    # new_noise = noise_cube.scale

    new_noise = 0.0010592446454102172

    cube = cube.with_mask(cube > new_noise*u.Jy)

    # Load in the broad clean mask used
    clean_mask = fits.getdata("../../../Arecibo/M33_newmask.fits")

    # Need to match the dims
    clean_mask = clean_mask.squeeze()
    clean_mask = clean_mask[11:195, ::-1, ::-1]
    clean_mask = clean_mask[:, 595:3504, 1065:3033]

    from signal_id.utils import get_pixel_scales

    pixscale = get_pixel_scales(cube.wcs)

    beam_struct = cube.beam.as_tophat_kernel(pixscale)

    mask = RadioMask(cube)
    mask.intersection(clean_mask)
    # mask.remove_small_regions()
    # mask.open(iterations=3)
    # mask.close(iterations=3)
    # mask.dilate(iterations=6)


    if save_mask:
        mask.write('M33_206_b_c.source_mask.fits')
else:
    # Try loading the mask in

    mask_fits = fits.getdata('m33_206_b_c.source_mask.fits')

    mask = BooleanArrayMask(mask_fits.astype(bool), cube.wcs)

    cube = cube.with_mask(mask)

Choose whether to make new mask
Choose whether to make new mask

  
  '''
  Make a mask of the emission
  '''
  
+ from astropy.io import fits
+ from spectral_cube import SpectralCube, BooleanArrayMask
+ from signal_id import RadioMask, Noise
+ from astropy import units as u
+ 
+ 
+ make_mask = True
+ save_mask = False
+ 
  cube = SpectralCube.read("M33_206_b_c_HI.fits")
  cube = cube.with_mask(cube != 0*u.Jy)
  
- noise_cube = Noise(cube)
+ if make_mask:
  
- new_noise = noise_cube.scale
+     # noise_cube = Noise(cube)
  
- cube = cube.with_mask(cube > new_noise*u.Jy)
+     # new_noise = noise_cube.scale
  
+     new_noise = 0.0010592446454102172
- # Load in the broad clean mask used
- clean_mask = fits.getdata("../../../Arecibo/M33_newmask.fits")
  
+     cube = cube.with_mask(cube > new_noise*u.Jy)
- # Need to match the dims
- clean_mask = clean_mask.squeeze()
- clean_mask = clean_mask[11:195, ::-1, ::-1]
- clean_mask = clean_mask[:, 595:3504, 1065:3033]
  
- old_mask = RadioMask(old_cube)
- old_mask.intersection(old_arecibo_mask)
+     # Load in the broad clean mask used
+     clean_mask = fits.getdata("../../../Arecibo/M33_newmask.fits")
  
+     # Need to match the dims
+     clean_mask = clean_mask.squeeze()
+     clean_mask = clean_mask[11:195, ::-1, ::-1]
+     clean_mask = clean_mask[:, 595:3504, 1065:3033]
+ 
+     from signal_id.utils import get_pixel_scales
+ 
+     pixscale = get_pixel_scales(cube.wcs)
+ 
+     beam_struct = cube.beam.as_tophat_kernel(pixscale)
+ 
+     mask = RadioMask(cube)
+     mask.intersection(clean_mask)
+     # mask.remove_small_regions()
+     # mask.open(iterations=3)
+     # mask.close(iterations=3)
+     # mask.dilate(iterations=6)
+ 
+ 
+     if save_mask:
+         mask.write('M33_206_b_c.source_mask.fits')
+ else:
+     # Try loading the mask in
+ 
+     mask_fits = fits.getdata('m33_206_b_c.source_mask.fits')
+ 
+     mask = BooleanArrayMask(mask_fits.astype(bool), cube.wcs)
+ 
+     cube = cube.with_mask(mask)
+ 
Choose whether to make new mask
## Code Before:

'''
Make a mask of the emission
'''

cube = SpectralCube.read("M33_206_b_c_HI.fits")
cube = cube.with_mask(cube != 0*u.Jy)

noise_cube = Noise(cube)

new_noise = noise_cube.scale

cube = cube.with_mask(cube > new_noise*u.Jy)

# Load in the broad clean mask used
clean_mask = fits.getdata("../../../Arecibo/M33_newmask.fits")

# Need to match the dims
clean_mask = clean_mask.squeeze()
clean_mask = clean_mask[11:195, ::-1, ::-1]
clean_mask = clean_mask[:, 595:3504, 1065:3033]

old_mask = RadioMask(old_cube)
old_mask.intersection(old_arecibo_mask)

## Instruction:
Choose whether to make new mask
## Code After:

'''
Make a mask of the emission
'''

from astropy.io import fits
from spectral_cube import SpectralCube, BooleanArrayMask
from signal_id import RadioMask, Noise
from astropy import units as u


make_mask = True
save_mask = False

cube = SpectralCube.read("M33_206_b_c_HI.fits")
cube = cube.with_mask(cube != 0*u.Jy)

if make_mask:

    # noise_cube = Noise(cube)

    # new_noise = noise_cube.scale

    new_noise = 0.0010592446454102172

    cube = cube.with_mask(cube > new_noise*u.Jy)

    # Load in the broad clean mask used
    clean_mask = fits.getdata("../../../Arecibo/M33_newmask.fits")

    # Need to match the dims
    clean_mask = clean_mask.squeeze()
    clean_mask = clean_mask[11:195, ::-1, ::-1]
    clean_mask = clean_mask[:, 595:3504, 1065:3033]

    from signal_id.utils import get_pixel_scales

    pixscale = get_pixel_scales(cube.wcs)

    beam_struct = cube.beam.as_tophat_kernel(pixscale)

    mask = RadioMask(cube)
    mask.intersection(clean_mask)
    # mask.remove_small_regions()
    # mask.open(iterations=3)
    # mask.close(iterations=3)
    # mask.dilate(iterations=6)


    if save_mask:
        mask.write('M33_206_b_c.source_mask.fits')
else:
    # Try loading the mask in

    mask_fits = fits.getdata('m33_206_b_c.source_mask.fits')

    mask = BooleanArrayMask(mask_fits.astype(bool), cube.wcs)

    cube = cube.with_mask(mask)
