Template for how the legacypipe/Tractor pipeline is setup and run on DECam data

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module use /global/common/$NERSC_HOST/contrib/desi/modulefiles
module load desiconda/20170719-1.1.9-imaging
conda create --prefix $CSCRATCH/conda-envs/20170719-1.1.9-imaging --file $DESICONDA/pkg_list.txt
source activate $CSCRATCH/conda-envs/20170719-1.1.9-imaging


    

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# SF98 dust maps
export MYDIR=$CSCRATCH/repos
mkdir -p $MYDIR/dust/maps                                                           
cd $MYDIR/dust/maps
wget -c http://portal.nersc.gov/project/cosmo/temp/dstn/travis-ci/maps/SFD_dust_4096_ngp.fits                                                    
wget -c http://portal.nersc.gov/project/cosmo/temp/dstn/travis-ci/maps/SFD_dust_4096_sgp.fits                                                    
export DUST_DIR=$MYREPO/dust
# imaging pipeline
cd $MYDIR
git clone https://github.com/legacysurvey/legacypipe.git
cd legacypipe
git checkout f4fc46ea0


    

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cd py/test
wget https://raw.githubusercontent.com/legacysurvey/obiwan/master/py/obiwan/test/end_to_end/test_decam_rex.p
cd ../
python py/test_decam_rex.py


    

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main(args=['--brick', '1102p240', '--zoom', '500', '600', '650', '750',            
           '--force-all', '--no-write', '--no-wise',                                                   
           '--survey-dir', surveydir,                                              
           '--outdir', outdir])


    

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# https://github.com/legacysurvey/legacypipe/blob/master/py/legacypipe/decam.py
# Edited to be barebones
from __future__ import print_function
import os
import numpy as np
import fitsio
from legacypipe.image import CalibMixin
from legacypipe.cpimage import CPImage
from legacypipe.survey import LegacySurveyData

'''
Code specific to images from the Dark Energy Camera (DECam).
'''

class DecamImage(CPImage, CalibMixin):
    '''
    A LegacySurveyImage subclass to handle images from the Dark Energy
    Camera, DECam, on the Blanco telescope.
    '''
    # background subtraction fitting spline to every 512 pixels, interpolating between
    splinesky_boxsize = 512

    def __init__(self, survey, t):
        super(DecamImage, self).__init__(survey, t)
        # Check that these are set properly
        #self.imgfn # image relative path starting from legacy_survey_dir/images/
        #self.dqfn # bad pixel image
        #self.wtfn # invvar image
        
        # zeropoint units in ADU/sec
        self.ccdzpt += 2.5 * np.log10(self.exptime)
        
    def __str__(self):
        return 'DECam ' + self.name

    @classmethod
    def nominal_zeropoints(self):
        # Units ADU/sec for a good night 2 years ago
        return dict(g = 25.08,
                    r = 25.29,
                    z = 24.92,)
    
    @classmethod
    def photometric_ccds(self, survey, ccds):
        """Remove exposures from survey-ccds-1.fits.gz if image quality not 
        good enough
        
        Args:
          ccds: the survey-ccds-1.fits.gz table
        """
        # Nominal zeropoints (DECam)
        z0 = self.nominal_zeropoints()
        z0 = np.array([z0[f[0]] for f in ccds.filter])
        # You can skipping removing any of them with:
        good = np.ones(len(ccds), bool)
        return np.flatnonzero(good)

    @classmethod
    def ccd_cuts(self, survey, ccds):
        return np.zeros(len(ccds), np.int32)

    def get_good_image_subregion(self):
        """Optional"""
        x0,x1,y0,y1 = None,None,None,None
        # x0,x1,y0,y1 = 100,1023,100,self.height-100
        return x0,x1,y0,y1

    def read_dq(self, header=False, **kwargs):
        """read bad pixel image and possibly its header"""
        print('Reading data quality from', self.dqfn, 'hdu', self.hdu)
        dq,hdr = self._read_fits(self.dqfn, self.hdu, header=True, **kwargs)
        if header:
            return dq,hdr
        else:
            return dq

    def read_invvar(self, clip=True, clipThresh=0.2, **kwargs):
        print('Reading inverse-variance from', self.wtfn, 'hdu', self.hdu)
        invvar = self._read_fits(self.wtfn, self.hdu, **kwargs)
        return invvar

    def run_calibs(self, psfex=True, sky=True, se=False,
                   funpack=False, fcopy=False, use_mask=True,
                   force=False, just_check=False, git_version=None,
                   splinesky=False):
        """Read psfex PSF model and splinesky model"""
        self.read_psf_model(0, 0, pixPsf=True, hybridPsf=True)
        self.read_sky_model(splinesky=splinesky)


    

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