developing Polima2

astropop/pipelines/automatic/polima2.py

@@ -0,0 +1,174 @@
+from astropy.time import Time, TimezoneInfo
+from astropy.coordinates import Angle, EarthLocation
+from astropy import units
+from astropy.io import fits
+import numpy as np
+
+from .common_processing import SimpleCalibPipeline
+from .common_photometry import StackedPhotometryPipeline
+from .common_polarimetry import PolarimetryPileline
+from ...logger import logger
+from ...image_processing.ccd_processing import trim_image
+from ..polarimetry_scripts import dualbeam_polarimetry
+
+class Polima2Calib(SimpleCalibPipeline):
+    template = 'Polima2_calib'
+    _science_group_keywords = ['object', 'acqmode', 'imgrect',
+                               'subrect', 'readtime', 'emrealgn', 'preamp',
+                               'serno', 'camgain', 'filter', 'gain', 'hbin',
+                               'vbin', 'outptamp', 'telescop', 'analyzer']
+    _science_select_rules = dict(imagetyp=['OBJECT', 'object'])
+    _science_name_keywords = ['object', 'night', 'filter', 'outptamp']
+    _bias_select_keywords = ['acqmode', 'imgrect', 'night',
+                             'subrect', 'readtime', 'emrealgn', 'preamp',
+                             'serno', 'camgain', 'gain', 'hbin',
+                             'vbin', 'outptamp', 'telescop']
+    _bias_select_rules = dict(imagetyp=['ZERO', 'zero'])
+    _bias_name_keywords = ['night', 'hbin', 'vbin', 'gain', 'outptamp']
+    _flat_select_keywords = ['acqmode', 'imgrect', 'filter', 'analyzer',
+                             'subrect', 'readtime', 'emrealgn', 'preamp',
+                             'serno', 'camgain', 'gain', 'hbin',
+                             'vbin', 'outptamp', 'telescop', 'night']
+    _flat_select_rules = dict(imagetyp=['FLAT','flat'])
+    _flat_name_keywords = ['night', 'hbin', 'vbin', 'gain', 'filter', 'outptamp']
+    _dark_select_keywords = ['acqmode', 'imgrect', 'night',
+                             'subrect', 'readtime', 'emrealgn', 'preamp',
+                             'serno', 'camgain', 'gain', 'hbin',
+                             'vbin', 'outptamp', 'telescop']
+    _dark_select_rules = dict(imagetyp=['DARK', 'dark'])
+    _dark_name_keywords = ['night', 'hbin', 'vbin', 'gain', 'outptamp']
+    calib_process_params = dict(gain_key=None,
+                                gain=None,
+                                combine_method='median',
+                                combine_sigma_clip=3,
+                                remove_cosmics=True,
+                                mem_limit=1e9,
+                                exposure_key='exptime')
+    sci_process_params = dict(gain_key=None,
+                              gain=None,
+                              lacosmic=True,
+                              exposure_key='exptime',
+                              inplace=True)
+    astrometry_params = dict(ra_key='RA',
+                             dec_key='DEC',
+                             pltscl=0.45)
+    _save_subfolder = 'BC/{night}'
+    plate_scale = 0.45
+    _align_method = 'chi2'
+    _save_fits_compressed = False
+    _save_fits_ext = 0
+    _save_fits_fmt = '.fits.gz'
+
+    def __init__(self, product_dir=None, calib_dir=None,
+                 ext=0, fits_extensions=['.fits', '.fits.gz'],
+                 compression=False):
+        super(Polima2Calib, self).__init__(product_dir=product_dir,
+                                      calib_dir=calib_dir,
+                                      ext=ext,
+                                      fits_extensions=fits_extensions,
+                                      compression=compression)
+
+    def get_frame_name(self, type, filegroup):
+        """Return a convenient name for a master frame."""
+        if type == 'bias':
+            name = 'bias_'
+            l = self._bias_name_keywords
+        elif type == 'flat':
+            name = 'flat_'
+            l = self._flat_name_keywords
+        elif type == 'dark':
+            name = 'dark_'
+            l = self._dark_name_keywords
+        elif type == 'science':
+            name = ''
+            l = self._science_name_keywords
+        else:
+            raise ValueError('Type {} not supported.'.format(type))
+        for i in l:
+            v = filegroup.values(i, unique=True)[0]
+            name += '{}_'.format(v)
+        name = name.replace(' ', '-').strip('_')
+        name += self._save_fits_fmt
+        return name
+
+    def get_platescale(self, file):
+        binning = int(file.header['ccdsum'].split()[0])
+        return self.plate_scale*binning
+
+    def tune_calib_frame(self, type, file, to_calib_filegroup):
+        """Reprocess things in calib frames in order to be usable.
+
+        like trimming, binning, etc.
+        """
+        if file is not None:
+            hdu = fits.open(file)[self._save_fits_ext]
+            return hdu
+        return
+
+class Polima2Pipeline(PolarimetryPileline):
+    photometry_parameters = dict(detect_snr=5,
+                                 detect_fwhm=4,
+                                 photometry_type='aperture',
+                                 r='auto',
+                                 r_ann='auto',
+                                 solve_photometry_type='montecarlo',
+                                 montecarlo_iters=300,
+                                 montecarlo_percentage=0.2)
+    astrometry_parameters = dict(ra_key='RA',
+                                 dec_key='DEC',
+                                 identify_limit_angle='2 arcsec')
+    save_file_name = '{object}_{analyzer}_{filter}_{night}.fits'
+    save_file_dir = 'polarimetry/'
+    filter_key = 'filter'
+    lamina_key = 'polangle'
+    retarder_key = 'retarder'
+    analyzer_key = 'pol2lin'
+    standard_catalogs = {'U': 'Simbad',
+                         'B': 'UCAC4',
+                         'V': 'UCAC4',
+                         'R': 'UCAC5',
+                         'I': 'DENIS'}
+    plate_scale = np.array([0.31, 0.65])
+    _align_method = 'chi2'
+
+    def __init__(self, product_dir, image_ext=0):
+        super(Polima2Pipeline, self).__init__(product_dir, image_ext)
+
+    def get_psi(self, filegroup):
+        """Get analyzer os retarder positions in degrees."""
+        return filegroup.values(self.lamina_key)
+
+    def get_retarder(self, filegroup):
+        """The retarder identifier, used for what polarimetry will perform."""
+        return 'half'
+
+    def get_analyzer(self, filegroup):
+        """The analyzer identifier, for polarimetry function selection."""
+        return filegroup.values(self.analyzer_key, unique=True)[0]
+
+    def get_filter(self, filegroup):
+        return filegroup.values(self.filter_key, unique=True)[0]
+
+    def validate_data(self, filegroup):
+        """Validate if it's everything ok with the data."""
+        if len(filegroup.summary) < 4:
+            raise ValueError('Not enough calibed images to process.')
+        return True
+
+    def calculate_polarimetry(self, fg, analyzer, retarder, psi, catalog,
+                              sci_catalog, astrometry, **kwargs):
+        # instrument specific tasks
+        results = dualbeam_polarimetry(fg.hdus(), psi,
+                                       identify_catalog=catalog,
+                                       retarder=retarder,
+                                       analyzer=analyzer,
+                                       match_pairs_tolerance=1.0,
+                                       calculate_mode='fit',
+                                       plate_scale=self.plate_scale,
+                                       science_catalog=sci_catalog,
+
+                                       **self.astrometry_parameters,
+                                       **self.photometry_parameters,
+                                       **kwargs)
+
+        return results

install_requires

@@ -0,0 +1,14 @@
+python>3.5
+astropy>3
+sep>1.0.3
+numpy
+scipy
+scikit-image
+matplotlib
+cython
+astroquery
+fortranformat
+astroscrappy
+reproject
+astroalign
+image_registration

pip-requirements

@@ -8,3 +8,6 @@ cython
 astroquery
 fortranformat
 astroscrappy
+reproject
+astroalign
+image_registration

pip-requirements-doc

@@ -17,3 +17,6 @@ sep
 astroquery
 fortranformat
 astroscrappy
+reproject
+astroalign
+image_registration