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Update docs and change variable name #395

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7 changes: 6 additions & 1 deletion docs/_cosmic_ray_removal.rst
Original file line number Diff line number Diff line change
Expand Up @@ -46,4 +46,9 @@ methods.
Asymetric binnings have not been tested but the pipeline only takes in
consideration the dispersion axis to decide. This does not mean that the spatial
binning does not impact the performance of any of the methods, we just don't
know it yet.
know it yet.

.. note::

The prefix ``c`` is added to all the comparison lamps, despite they not being
affected by cosmic rays.
3 changes: 2 additions & 1 deletion docs/_observing.rst
Original file line number Diff line number Diff line change
Expand Up @@ -49,7 +49,8 @@ Observing for Radial Velocity

Radial velocity measurements are possible with the |goodman HTS| but you have
to be careful. A very detailed description of the procedures and what you can
expect was prepared and is available `HERE <http://www.ctio.noao.edu/soar/sites/default/files/GOODMAN/goodman_rv.pdf>`_.
expect was prepared and is available `here <https://noirlab.edu/science/sites/default/files/media/archives/documents/scidoc0489.pdf>`_
and `here <https://noirlab.edu/science/sites/default/files/media/archives/documents/scidoc0490.pdf>`_ .

Please read it carefully so you don't find any surprises when trying to reduce
your data.
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3 changes: 2 additions & 1 deletion docs/install.rst
Original file line number Diff line number Diff line change
Expand Up @@ -39,8 +39,9 @@ This installation was tested on MacOS High Sierra.

2. Download Anaconda or Miniconda

``curl https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh --output miniconda.sh``
``curl https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-arm64.sh --output miniconda.sh``

If you have a different processor like intel, you can search miniconda installer url for your system.

Common Steps
************
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6 changes: 3 additions & 3 deletions goodman_pipeline/core/core.py
Original file line number Diff line number Diff line change
Expand Up @@ -302,7 +302,7 @@ def call_cosmic_rejection(ccd,
log.info('Setting cosmic ray rejection method to:'
' {:s}'.format(method))

if ccd.header['OBSTYPE'] == 'COMP' and method != 'none':
if ccd.header['OBSTYPE'] in ['COMP', 'ARC'] and method != 'none':
log.info("Changing cosmic ray rejection method from '{:s}' to 'none'"
" for comparison lamp. Prefix 'c' will be added "
"anyway.".format(method))
Expand All @@ -317,11 +317,11 @@ def call_cosmic_rejection(ccd,
'the mask use --keep-cosmic-files')

if not os.path.isfile(os.path.join(red_path, 'dcr.par')):
_create = GenerateDcrParFile()
generate_dcr_parameters_file = GenerateDcrParFile()
_instrument = ccd.header['INSTCONF']
_binning, _ = ccd.header['CCDSUM'].split()

_create(instrument=_instrument, binning=_binning, path=red_path)
generate_dcr_parameters_file(instrument=_instrument, binning=_binning, path=red_path)

#out_prefix = prefix + out_prefix #Move line here

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16 changes: 16 additions & 0 deletions goodman_pipeline/core/tests/test_core.py
Original file line number Diff line number Diff line change
Expand Up @@ -511,6 +511,22 @@ def test_call_cosmic_rejection_comp_lamp(self):
ccd.header['GSP_FNAM'])
self.assertEqual('none', ccd.header['GSP_COSM'])

def test_call_cosmic_rejection_arc_lamp(self):
self.ccd.header.set('OBSTYPE', value='ARC')
prefix = 'new_'
ccd, out_prefix = call_cosmic_rejection(ccd=self.ccd,
image_name=self.file_name,
out_prefix=self.out_prefix,
red_path=self.red_path,
keep_files=True,
prefix=prefix,
method='dcr',
save=True)
self.assertEqual(prefix + self.out_prefix, out_prefix)
self.assertEqual(f"{prefix}{self.out_prefix}_{self.file_name}",
ccd.header['GSP_FNAM'])
self.assertEqual('none', ccd.header['GSP_COSM'])

def test_call_cosmic_rejection_not_implemented_error(self):
prefix = 'new_'
self.assertRaises(NotImplementedError,
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