Merge pull request #38 from lofar-astron/fix-add-lofar-utils

Fix add lofar utils

RMextract/LOFAR_TOOLS/createRMParmdb.py

@@ -2,6 +2,7 @@
 import lofar.parmdb as parmdb
 import pyrap.tables as tab
 import numpy as np
+import argparse
 
 
 def createRMParmdb(MS,parmdbname,create=True,patchname='',
@@ -47,3 +48,44 @@ def createRMParmdb(MS,parmdbname,create=True,patchname='',
             valuename = "RotationMeasure:%s"%(st)
         myParmdb.deleteValues(valuename)            
         myParmdb.addValues(valuename,myValue)
+
+def main():
+    descriptiontext = "Create a parmDB with the Ionospheric RM predicted from data in IONEX files.\n" + \
+                      "Default is to create a parmDB that is compatible with the \"rotationmeasure\" " + \
+                      "correction in NDPPP ApplyCal.\n"
+    parser = argparse.ArgumentParser(description=descriptiontext)
+
+    parser.add_argument('MS',help='Measurement-Set for which the parmDB is to be created.')
+    parser.add_argument('-o','--out', help='name of the parmdb',dest="parmdbName",default='RMParmdb');
+    parser.add_argument('-p','--patch',dest="patch",default="",type=str,
+                        help='If given: create parameter-names that include a patch-name as needed for BBS. '
+                        'The default is to create parameter-names without a patch-name as they are needed for '
+                        'the "rotationmeasure" correction in NDPPP ApplyCal.')
+    #parser.add_argument('-s','--sky', help='name of the skymodel, if no source/patch name is given first will be selected. If you do not set the skymodel, the phasecenter of the MS will be assumed as your direction. If option --use_phase_center is used the direction in the sky model are ignored. However, it could still be useful to automatically select a patch name, which is needed for direction dependent parmareters.',dest="sky")
+    #parser.add_argument('-f','--use_phase_center', help='force using of phase center of MS, even if skymodel is supplied',action='store_true',dest="usePhaseCenter");
+    parser.add_argument('--IONprefix', help='prefix of IONEX files, either CODG or ROBR',dest="prefix",default='codg');
+    parser.add_argument('--IONserver', help='server of IONEX files',dest="server",default='ftp://cddis.gsfc.nasa.gov/gnss/products/ionex/')
+    parser.add_argument('--IONpath', help='location of IONEX files',dest="ionexPath",default='./')
+    parser.add_argument('--all','-a', help='calculate RM per station (default calculates only for CS002LBA)',action='store_true',dest="allStations")
+    parser.add_argument('-t','--timestep', help='timestep in seconds. for values <=0 (default) the timegrid of the MS is used ',dest="timestep",type=float,default=900.)
+    parser.add_argument('-e','--smart_interpol', help='float parameter describing how much of earth rotation is taken in to account in interpolation of the IONEX files. 1.0 means time interpolation assumes ionosphere rotates in opposite direction of the Earth. 0.0 (default) means no rotation applied',dest="earth_rot",type=float,default=0)
+    parser.add_argument('-r','--overwrite',help='overwrite existing parmdb',action='store_true',dest="overwrite")
+
+    args = parser.parse_args()
+
+    stat_names=None
+    if args.allStations:
+        stat_names='all'
+    if not args.overwrite and not os.path.isdir(args.parmdbName):
+        args.overwrite=True
+
+    createRMParmdb(args.MS,
+                   parmdbname=args.parmdbName,
+                   create=args.overwrite,
+                   patchname=args.patch,
+                   server=args.server,
+                   prefix=args.prefix,
+                   ionexPath=args.ionexPath,
+                   earth_rot=args.earth_rot,
+                   timestep=args.timestep,
+                   stat_names=stat_names)

RMextract/LOFAR_TOOLS/createRMh5parm.py

@@ -1,6 +1,3 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
 """
 Extract RM values for a LOFAR observation. Fill h5parm
 
@@ -19,6 +16,7 @@
 import numpy as np
 import sys
 import logging
+import argparse
 
 
 def makesolset(MS, data, solset_name):
@@ -43,7 +41,7 @@ def makesolset(MS, data, solset_name):
     sourceTable.append([('pointing',pointing)])
 
 
-def main(MSfiles, h5parmdb, solset_name = "sol000",all_stations=True,timestepRM=300,
+def createRMh5parm(MSfiles, h5parmdb, solset_name = "sol000",all_stations=True,timestepRM=300,
                 ionex_server="ftp://ftp.aiub.unibe.ch/CODE/",
                 ionex_prefix='CODG',ionexPath="./",earth_rot=0,proxyServer=None,proxyPort=None,proxyType=None,proxyUser=None,proxyPass=None):
     '''Add rotation measure to existing h5parmdb
@@ -206,8 +204,7 @@ def main(MSfiles, h5parmdb, solset_name = "sol000",all_stations=True,timestepRM=
 
 
     ########################################################################
-if __name__ == '__main__':
-    import argparse
+def main():
     parser = argparse.ArgumentParser(description='Adds CommonRotationAngle to an H5parm from RMextract.')
 
     parser.add_argument('MSfiles', type=str, nargs='+',
@@ -250,7 +247,7 @@ def main(MSfiles, h5parmdb, solset_name = "sol000",all_stations=True,timestepRM=
     MS = args.MSfiles
     h5parmdb = args.h5parm
     logging.info("Working on: %s %s" % (MS, h5parmdb))
-    main(MS, h5parmdb, ionex_server=args.server, ionex_prefix=args.prefix, 
+    createRMh5parm(MS, h5parmdb, ionex_server=args.server, ionex_prefix=args.prefix, 
                  ionexPath=args.ionexpath, solset_name=args.solsetName,
                  all_stations=args.allStations, timestepRM=args.timestep,
                  earth_rot=args.earth_rot, proxyServer=args.proxyserver, proxyPort=args.proxyport,

RMextract/LOFAR_TOOLS/download_IONEX.py

@@ -1,27 +1,23 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
 import sys
 import RMextract.getIONEX as ionex
 from RMextract import PosTools
 import numpy as np
 import logging
 import argparse
-parser = argparse.ArgumentParser(description='Downloads relevant IONEX files for a given MS')
 
-parser.add_argument('MSfiles', type=str,
-                        help='MS for which the parmdb should be created.')
-parser.add_argument('--server', type=str, default='ftp://ftp.aiub.unibe.ch/CODE/',
-                        help='URL of the server to use. (default: ftp://ftp.aiub.unibe.ch/CODE/)')
-parser.add_argument('--prefix', type=str, default='CODG',
-                        help='Prefix of the IONEX files. (default: \"CODG\")')
-parser.add_argument('--ionexpath', '--path', type=str, default='IONEXdata/',
-                        help='Directory where to store the IONEX files. (default: \"IONEXdata/\")')
 
+def main():
+    parser = argparse.ArgumentParser(description='Downloads relevant IONEX files for a given MS')
+    parser.add_argument('MSfiles', type=str,
+                            help='MS for which the parmdb should be created.')
+    parser.add_argument('--server', type=str, default='ftp://ftp.aiub.unibe.ch/CODE/',
+                            help='URL of the server to use. (default: ftp://ftp.aiub.unibe.ch/CODE/)')
+    parser.add_argument('--prefix', type=str, default='CODG',
+                            help='Prefix of the IONEX files. (default: \"CODG\")')
+    parser.add_argument('--ionexpath', '--path', type=str, default='IONEXdata/',
+                            help='Directory where to store the IONEX files. (default: \"IONEXdata/\")')
+    args = parser.parse_args()
 
-
-
-def main(argv):
-    args = parser.parse_args(argv)
     MS=args.MSfiles
     server=args.server
     prefix=args.prefix
@@ -56,6 +52,3 @@ def main(argv):
 
     return True
 
-
-if __name__ == '__main__':
-    main(sys.argv[1:])

setup.py

@@ -1,4 +1,6 @@
 import os
+import sys
+import warnings
 from setuptools import find_packages
 import numpy
 from numpy.distutils.core import setup, Extension
@@ -13,9 +15,8 @@ def read(rel_path):
         return fp.read()
 
 
-packages = find_packages(exclude=["RMextract.LOFAR_TOOLS"])
+packages = find_packages()  # exclude=["RMextract.LOFAR_TOOLS"])
 ext_modules = []
-scripts = []
 
 ext_modules.append(
     Extension(
@@ -67,17 +68,19 @@ def read(rel_path):
     )
 )
 
-if "RMextract.LOFAR_TOOLS" in packages:
-    scripts.extend(
-        [
-            os.path.join("RMextract", "LOFAR_TOOLS", f)
-            for f in ("createRMParmdb", "createRMh5parm.py", "download_IONEX.py")
-        ]
+# For backward compatibility for those who (still) use `python setup.py` to
+# install the optional LOFAR utilities.
+if "--add-lofar-utils" in sys.argv:
+    packages.append("RMextract.LOFAR_TOOLS")
+    sys.argv.remove("--add-lofar-utils")
+    warnings.warn(
+        "Use of 'python setup.py install --add-lofar-utils' is deprecated. "
+        "Use 'pip install RMextract[lofar-utils]' instead."
     )
 
 setup(
     name="RMextract",
-    version="0.4.2",
+    version="0.4.3",
     url="https://github.com/lofar-astron/RMextract",
     project_urls={"Source": "https://github.com/lofar-astron/RMextract"},
     author="Maaijke Mevius",
@@ -100,6 +103,18 @@ def read(rel_path):
     ext_modules=ext_modules,
     packages=packages,
     install_requires=["numpy", "scipy", "astropy", "python-casacore"],
+    extras_require={
+        # Note that "lofar-utils" also depends on the python bindings to the LOFAR ParmDB.
+        # Since these have never been published on PyPI, we cannot specify this dependency.
+        "lofar-utils": ["losoto"]
+    },
+    entry_points={
+        "console_scripts": [
+            "createRMParmdb = RMextract.LOFAR_TOOLS.createRMParmdb:main [lofar-utils]",
+            "createRMh5parm.py = RMextract.LOFAR_TOOLS.createRMh5parm:main [lofar-utils]",
+            "download_IONEX.py = RMextract.LOFAR_TOOLS.download_IONEX:main [lofar-utils]",
+        ]
+    },
     package_data={
         "RMextract.EMM": ["*.COF"],
         # Add *.pyf files. These files are _not_ treated as source files by Numpy's setup(),
@@ -109,5 +124,4 @@ def read(rel_path):
         "RMextract.pyiri": ["iri.pyf", "*.dat", "*.asc"],
         "RMextract.pyiriplas": ["iriplas.pyf", "*.dat", "*.asc", "kp*", "*.ASC"],
     },
-    scripts=scripts,
 )