Source code for jwst.associations.main

"""Main entry for the association generator"""
import os
import sys
import argparse
import logging

import numpy as np

from jwst.associations import (
from jwst.associations import config
from jwst.associations.lib.dms_base import DMSAttrConstraint
from jwst.associations.lib.constraint import (
from jwst.associations.lib.log_config import (log_config, DMS_config)

__all__ = ['Main']

# Configure logging
logger = log_config(name=__package__)

# Ruleset names

[docs]class Main(): """ Generate Associations from an Association Pool Parameters ---------- args : [str, ...], or None The command line arguments. Can be one of - `None`: `sys.argv` is then used. - `[str, ...]`: A list of strings which create the command line with the similar structure as `sys.argv` pool : None or AssociationPool If `None`, a pool file must be specified in the `args`. Otherwise, an `AssociationPool` Attributes ---------- pool : `AssociationPool` The pool read in, or passed in through the parameter `pool` rules : `AssociationRegistry` The rules used for association creation. associations : [`Association`, ...] The list of generated associations. Notes ----- Refer to the :ref:`Association Generator <associations>` documentation for a full description. """ def __init__(self, args=None, pool=None): if args is None: args = sys.argv[1:] if isinstance(args, str): args = args.split(' ') parser = argparse.ArgumentParser( description='Generate Assocation Data Products', usage='asn_generate pool' ) if pool is None: parser.add_argument( 'pool', type=str, help='Association Pool' ) op_group = parser.add_mutually_exclusive_group() op_group.add_argument( '-i', '--ids', nargs='+', dest='asn_candidate_ids', help='space-separated list of association candidate IDs to operate on.' ) op_group.add_argument( '--discover', action='store_true', help='Produce discovered associations' ) op_group.add_argument( '--all-candidates', action='store_true', dest='all_candidates', help='Produce all association candidate-specific associations' ) parser.add_argument( '-p', '--path', type=str, default='.', help='Folder to save the associations to. Default: "%(default)s"' ) parser.add_argument( '--save-orphans', dest='save_orphans', nargs='?', const='orphaned.csv', default=False, help='Save orphaned items into the specified table. Default: "%(default)s"' ) parser.add_argument( '--version-id', dest='version_id', nargs='?', const=True, default=None, help=( 'Version tag to add into association name and products.' ' If not specified, no version will be used.' ' If specified without a value, the current time is used.' ' Otherwise, the specified string will be used.' ) ) parser.add_argument( '-r', '--rules', action='append', help='Association Rules file.' ) parser.add_argument( '--ignore-default', action='store_true', help='Do not include default rules. -r should be used if set.' ) parser.add_argument( '--dry-run', action='store_true', dest='dry_run', help='Execute but do not save results.' ) parser.add_argument( '-d', '--delimiter', type=str, default='|', help='''Delimiter to use if pool files are comma-separated-value (csv) type files. Default: "%(default)s" ''' ) parser.add_argument( '--pool-format', type=str, default='ascii', help=( 'Format of the pool file.' ' Any format allowed by the astropy' ' Unified File I/O interface is allowed.' ' Default: "%(default)s"' ) ) parser.add_argument( '-v', '--verbose', action='store_const', dest='loglevel', const=logging.INFO, default=logging.NOTSET, help='Output progress and results.' ) parser.add_argument( '-D', '--debug', action='store_const', dest='loglevel', const=logging.DEBUG, help='Output detailed debugging information.' ) parser.add_argument( '--DMS', action='store_true', dest='DMS_enabled', help='Running under DMS workflow conditions.' ) parser.add_argument( '--format', default='json', help='Format of the association files. Default: "%(default)s"' ) parser.add_argument( '--version', action='version', version='%(prog)s {}'.format(__version__), help='Version of the generator.' ) parser.add_argument( '--merge', action='store_true', help='Merge associations into single associations with multiple products' ) parser.add_argument( '--no-merge', action=DeprecateNoMerge, help='Deprecated: Default is to not merge. See "--merge".' ) parsed = parser.parse_args(args=args) # Configure logging logging_config = None if parsed.DMS_enabled: logging_config = DMS_config logger = log_config(name=__package__, config=logging_config) logger.setLevel(parsed.loglevel) config.DEBUG = (parsed.loglevel != 0) and (parsed.loglevel <= logging.DEBUG) # Preamble'Command-line arguments: {}'.format(args)) logger.context.set('asn_candidate_ids', parsed.asn_candidate_ids) if pool is None:'Reading pool {}'.format(parsed.pool)) self.pool = parsed.pool, delimiter=parsed.delimiter, format=parsed.pool_format, ) else: self.pool = pool # DMS: Add further info to logging. try: logger.context.set('program', self.pool[0]['PROGRAM']) except KeyError: pass # Determine mode of operation. Options are # 1) Only specified candidates # 2) Only discovered assocations that do not match # candidate associations # 3) Both discovered and all candidate associations.'Reading rules.') if not and\ not parsed.all_candidates and\ parsed.asn_candidate_ids is None: = True parsed.all_candidates = True if or parsed.all_candidates: global_constraints = constrain_on_candidates( None ) elif parsed.asn_candidate_ids is not None: global_constraints = constrain_on_candidates( parsed.asn_candidate_ids ) self.rules = AssociationRegistry( parsed.rules, include_default=not parsed.ignore_default, global_constraints=global_constraints, name=CANDIDATE_RULESET ) if self.rules.update( AssociationRegistry( parsed.rules, include_default=not parsed.ignore_default, name=DISCOVER_RULESET ) )'Generating associations.') self.associations = generate( self.pool, self.rules, version_id=parsed.version_id ) if logger.debug( '# asns found before discover filtering={}'.format( len(self.associations) ) ) self.associations = filter_discovered_only( self.associations, DISCOVER_RULESET, CANDIDATE_RULESET, keep_candidates=parsed.all_candidates, ) self.rules.Utility.resequence(self.associations) # Do a grand merging. This is done particularly for # Level2 associations. if parsed.merge: try: self.associations = self.rules.Utility.merge_asns(self.associations) except AttributeError: pass if not parsed.dry_run: path=parsed.path, format=parsed.format, save_orphans=parsed.save_orphans ) @property def orphaned(self): """The pool of exposures that do not belong to any association.""" not_in_asn = np.ones((len(self.pool),), dtype=bool) for asn in self.associations: try: indexes = [item.index for item in asn.from_items] except AttributeError: continue not_in_asn[indexes] = False orphaned = self.pool[not_in_asn] return orphaned def __str__(self): result = [] result.append(( 'There where {:d} associations ' 'and {:d} orphaned items found.\n' 'Associations found are:' ).format(len(self.associations), len(self.orphaned))) for assocs in self.associations: result.append(assocs.__str__()) return '\n'.join(result)
[docs] def save(self, path='.', format='json', save_orphans=False): """Save the associations to disk. Parameters ---------- path : str The path to save the associations to. format : str The format of the associations save_orphans : bool If true, save the orphans to an astropy.table.Table """ for asn in self.associations: (fname, serialized) = asn.dump(format=format) with open(os.path.join(path, fname), 'w') as f: f.write(serialized) if save_orphans: self.orphaned.write( os.path.join(path, save_orphans), format='ascii', delimiter='|' )
# ######### # Utilities # ######### class DeprecateNoMerge(argparse.Action): """Deprecate the `--no-merge` option""" def __init__(self, option_strings, dest, nargs=None, **kwargs): super(DeprecateNoMerge, self).__init__(option_strings, dest, const=True, nargs=0, **kwargs) def __call__(self, parser, namespace, values, option_string=None): logger.warning( 'The "--no-merge" option is now the default and deprecated.' ' Use "--merge" to force merging.') setattr(namespace, self.dest, values) def constrain_on_candidates(candidates): """Create a constraint based on a list of candidates Parameters ---------- candidates : (str, ...) or None List of candidate id's. If None, then all candidates are matched. """ if candidates is not None and len(candidates): c_list = '|'.join(candidates) values = ''.join([ '.+(', c_list, ').+' ]) else: values = None constraint = DMSAttrConstraint( name='asn_candidate', sources=['asn_candidate'], value=values, force_unique=True, is_acid=True, evaluate=True, ) return constraint def filter_discovered_only( associations, discover_ruleset, candidate_ruleset, keep_candidates=True, ): """Return only those associations that have multiple candidates Parameters ---------- associations : iterable The list of associations to check. The list is that returned by the `generate` function. discover_ruleset : str The name of the ruleset that has the discover rules candidate_ruleset : str The name of the ruleset that finds just candidates keep_candidates : bool Keep explicit candidate associations in the list. Returns ------- iterable The new list of just cross candidate associations. Notes ----- This utility is only meant to run on associations that have been constructed. Associations that have been Association.dump and then Association.load will not return proper results. """ # Split the associations along discovered/not discovered lines asn_by_ruleset = { candidate_ruleset: [], discover_ruleset: [] } for asn in associations: asn_by_ruleset[].append(asn) candidate_list = asn_by_ruleset[candidate_ruleset] discover_list = asn_by_ruleset[discover_ruleset] # Filter out the non-unique discovereds. for candidate in candidate_list: if len(discover_list) == 0: break unique_list = [] for discover in discover_list: if discover != candidate: unique_list.append(discover) # Reset the discovered list to the new unique list # and try the next candidate. discover_list = unique_list if keep_candidates: discover_list.extend(candidate_list) return discover_list if __name__ == '__main__': Main()