Merge pull request #94 from SharonGoliath/master

Add caom2pipe functionality to caom2tools.

.travis.yml

@@ -30,8 +30,8 @@ after_success:
     # If coveralls.io is set up for this package, uncomment the line
     # below and replace "packagename" with the name of your package.
     # The coveragerc file may be customized as needed for your package.
-    # Run coverage for all Python versions but submit only once - 3.5
-    - if [[ $TRAVIS_PYTHON_VERSION == '3.5' ]]; then coverage combine $(ls -d */.coverage) || exit 1; coveralls; fi
+    # Run coverage for all Python versions but submit only once - 3.6
+    - if [[ $TRAVIS_PYTHON_VERSION == '3.6' ]]; then coverage combine $(ls -d */.coverage) || exit 1; coveralls; fi
 
 jobs:
   include:

caom2pipe/README.md

@@ -0,0 +1,3 @@
+# caom2pipe
+Workflow construction pieces for building 'collection'2caom2 pipelines.
+

caom2pipe/caom2pipe/__init__.py

@@ -0,0 +1,3 @@
+from .execute_composable import *  # noqa
+from .manage_composable import *  # noqa
+from .astro_composable import *  # noqa

caom2pipe/caom2pipe/astro_composable.py

@@ -0,0 +1,197 @@
+# -*- coding: utf-8 -*-
+# ***********************************************************************
+# ******************  CANADIAN ASTRONOMY DATA CENTRE  *******************
+# *************  CENTRE CANADIEN DE DONNÉES ASTRONOMIQUES  **************
+#
+#  (c) 2018.                            (c) 2018.
+#  Government of Canada                 Gouvernement du Canada
+#  National Research Council            Conseil national de recherches
+#  Ottawa, Canada, K1A 0R6              Ottawa, Canada, K1A 0R6
+#  All rights reserved                  Tous droits réservés
+#
+#  NRC disclaims any warranties,        Le CNRC dénie toute garantie
+#  expressed, implied, or               énoncée, implicite ou légale,
+#  statutory, of any kind with          de quelque nature que ce
+#  respect to the software,             soit, concernant le logiciel,
+#  including without limitation         y compris sans restriction
+#  any warranty of merchantability      toute garantie de valeur
+#  or fitness for a particular          marchande ou de pertinence
+#  purpose. NRC shall not be            pour un usage particulier.
+#  liable in any event for any          Le CNRC ne pourra en aucun cas
+#  damages, whether direct or           être tenu responsable de tout
+#  indirect, special or general,        dommage, direct ou indirect,
+#  consequential or incidental,         particulier ou général,
+#  arising from the use of the          accessoire ou fortuit, résultant
+#  software.  Neither the name          de l'utilisation du logiciel. Ni
+#  of the National Research             le nom du Conseil National de
+#  Council of Canada nor the            Recherches du Canada ni les noms
+#  names of its contributors may        de ses  participants ne peuvent
+#  be used to endorse or promote        être utilisés pour approuver ou
+#  products derived from this           promouvoir les produits dérivés
+#  software without specific prior      de ce logiciel sans autorisation
+#  written permission.                  préalable et particulière
+#                                       par écrit.
+#
+#  This file is part of the             Ce fichier fait partie du projet
+#  OpenCADC project.                    OpenCADC.
+#
+#  OpenCADC is free software:           OpenCADC est un logiciel libre ;
+#  you can redistribute it and/or       vous pouvez le redistribuer ou le
+#  modify it under the terms of         modifier suivant les termes de
+#  the GNU Affero General Public        la “GNU Affero General Public
+#  License as published by the          License” telle que publiée
+#  Free Software Foundation,            par la Free Software Foundation
+#  either version 3 of the              : soit la version 3 de cette
+#  License, or (at your option)         licence, soit (à votre gré)
+#  any later version.                   toute version ultérieure.
+#
+#  OpenCADC is distributed in the       OpenCADC est distribué
+#  hope that it will be useful,         dans l’espoir qu’il vous
+#  but WITHOUT ANY WARRANTY;            sera utile, mais SANS AUCUNE
+#  without even the implied             GARANTIE : sans même la garantie
+#  warranty of MERCHANTABILITY          implicite de COMMERCIALISABILITÉ
+#  or FITNESS FOR A PARTICULAR          ni d’ADÉQUATION À UN OBJECTIF
+#  PURPOSE.  See the GNU Affero         PARTICULIER. Consultez la Licence
+#  General Public License for           Générale Publique GNU Affero
+#  more details.                        pour plus de détails.
+#
+#  You should have received             Vous devriez avoir reçu une
+#  a copy of the GNU Affero             copie de la Licence Générale
+#  General Public License along         Publique GNU Affero avec
+#  with OpenCADC.  If not, see          OpenCADC ; si ce n’est
+#  <http://www.gnu.org/licenses/>.      pas le cas, consultez :
+#                                       <http://www.gnu.org/licenses/>.
+#
+#  $Revision: 4 $
+#
+# ***********************************************************************
+#
+
+import logging
+
+from astropy.io import fits
+from astropy.coordinates import EarthLocation
+from astropy.time import Time, TimeDelta
+
+from datetime import timedelta as dt_timedelta
+from datetime import datetime as dt_datetime
+from time import strptime as dt_strptime
+
+from caom2 import Interval as caom_Interval
+from caom2 import Time as caom_Time
+from caom2 import shape as caom_shape
+
+from caom2pipe import manage_composable as mc
+
+
+__all__ = ['convert_time', 'get_datetime', 'build_plane_time', 'get_location',
+           'get_timedelta_in_s', 'make_headers_from_string']
+
+
+def find_time_bounds(headers):
+    """Given an observation date, and time exposure length, calculate the
+    mjd_start and mjd_end time for those values."""
+    logging.debug('Begin find_time_bounds.')
+    date = headers[0].get('DATE-OBS')
+    exposure = headers[0].get('TEXP')
+    return convert_time(date, exposure)
+
+
+def convert_time(start_time, exposure):
+    """Convert a start time and exposure length into an mjd_start and mjd_end
+    time."""
+    logging.debug('Begin convert_time.')
+    if start_time is not None and exposure is not None:
+        logging.debug(
+            'Use date {} and exposure {} to convert time.'.format(start_time,
+                                                                  exposure))
+        if type(start_time) is float:
+            t_start = Time(start_time, format='mjd')
+        else:
+            t_start = Time(start_time)
+        dt = TimeDelta(exposure, format='sec')
+        t_end = t_start + dt
+        t_start.format = 'mjd'
+        t_end.format = 'mjd'
+        mjd_start = t_start.value
+        mjd_end = t_end.value
+        logging.debug('End convert_time mjd start {} mjd end {} .'.format(
+            mjd_start, mjd_end))
+        return mjd_start, mjd_end
+    return None, None
+
+
+def get_datetime(from_value):
+    """
+    Ensure datetime values are in MJD. This is meant to handle any odd formats
+    that telescopes have for datetime values.
+
+    Relies on astropy, until astropy fails.
+
+    :param from_value:
+    :return: datetime instance
+    """
+    if from_value is not None:
+        try:
+            result = Time(from_value)
+            result.format = 'mjd'
+            return result
+        except ValueError:
+            try:
+                # VLASS has a format astropy fails to understand
+                # from datetime import datetime
+                result = Time(
+                    dt_datetime.strptime(from_value, '%H:%M:%S'))
+                result.format = 'mjd'
+                return result
+            except ValueError:
+                logging.error('Cannot parse datetime {}'.format(from_value))
+                return None
+    else:
+        return None
+
+
+def get_location(latitude, longitude, elevation):
+    """The CAOM model expects the telescope location to be in geocentric
+    coordinates. Rely on astropy to do the conversion."""
+    result = EarthLocation.from_geodetic(
+        longitude, latitude, elevation, 'WGS84')
+    return result.x.value, result.y.value, result.z.value
+
+
+def build_plane_time(start_date, end_date, exposure_time):
+    """Calculate the plane-level bounding box for time."""
+    start_date.format = 'mjd'
+    end_date.format = 'mjd'
+    time_bounds = caom_Interval(mc.to_float(start_date.value),
+                                mc.to_float(end_date.value),
+                                samples=[
+                                    caom_shape.SubInterval(
+                                        mc.to_float(start_date.value),
+                                        mc.to_float(end_date.value))])
+    return caom_Time(bounds=time_bounds,
+                     dimension=1,
+                     resolution=exposure_time.to('second').value,
+                     sample_size=exposure_time.to('day').value,
+                     exposure=exposure_time.to('second').value)
+
+
+def get_timedelta_in_s(from_value):
+    """
+    :param from_value: a string representing time in H:M:S
+    :return: the value as a timedelta, in seconds
+    """
+    temp = dt_strptime(from_value, '%H:%M:%S')
+    td = dt_timedelta(
+        hours=temp.tm_hour, minutes=temp.tm_min, seconds=temp.tm_sec)
+    return td.seconds
+
+
+def make_headers_from_string(fits_header):
+    """Create a list of fits.Header instances from a string.
+    ":param fits_header a string of keyword/value pairs"""
+    delim = '\nEND'
+    extensions = \
+        [e + delim for e in fits_header.split(delim) if e.strip()]
+    headers = [fits.Header.fromstring(e, sep='\n') for e in extensions]
+    return headers