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191 lines
7.2 KiB
191 lines
7.2 KiB
#!/usr/bin/env python3
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"""
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Given a VEX file, it creates a new VEX file that is a subset of the given one,
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dropping all the information (stations, source, PI names) that are not included
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in the provided inputs.
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Usage: split_vexfile.py [-o outputfile] <vexfile> <experiment> <PI name> <first scan> <last scan>
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Options:
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vexfile : str name of the original vex file (note that this file is not modified).
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experiment : str name of the experiment for the final (output) vex file.
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the original experiment name and all the other ones stored
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in the vex file will be removed.
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pi name :str name of the pi for this experiment. all the other names will
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be removed.
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first scan : int number of the first scan to be included in the new vex file.
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all scans previous to this one will be removed from the vex file.
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last scan : int number of the last scan to be included in the new vex file.
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all scans after this one will be removed from the vex file.
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optional parameters:
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-o outputfile : str the filename for the output vex file. if not provided, the filename will
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be <experiment>.vex
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Version: 1.0
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Date: May 2018
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Written by Benito Marcote (marcote@jive.eu)
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"""
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import sys
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import argparse
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from vex import vex
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usage = "%(prog)s [-h] [-v] [-o outputfile] <vexfile> <experiment> <PI name> <scans>"
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description="""Given a VEX file, it creates a new VEX file that is a subset of the given one,
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dropping all the information (stations, source, PI names) that are not included in the provided inputs.
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In e-EVN observations, where one VEX file contains different experiments, this script produces
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a new VEX file containing the information for only one of the experiments. And thus the MS generated
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by j2ms2 will not contain sensitive information from the other experiments.
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"""
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help_vexfile = 'Name of the original vex file to read (note that this file is not modified).'
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help_experiment = """Name of the experiment for the final (output) vex file.
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The original experiment name and all the other ones stored
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in the vex file will be removed."""
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help_piname = "Name of the PI for this experiment. all the other names will be removed."
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help_firstscan ="""Number of the first scan to be included in the new vex file.
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All scans previous to this one will be removed from the vex file."""
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help_lastscan = """Number of the last scan to be included in the new vex file.
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All scans after this one will be removed from the vex file."""
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help_scans = """Scans to be included in the vex file. You can specify ranges or individual scans.
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Ranges can be specify as: XXX~YYY to include scans XXX to YYY, both included.
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Different individual scans or ranges can be provided as comma-separated lists
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(with no spaces in between). e.g. 100~110,150,120~130 to include scans
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100 to 110, 150, and 120 to 130."""
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help_verbose = "Run in verbose mode. Prints all data to be discarded."
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help_outputfile = "Filename for the output vex file. if not provided, the filename will be <experiment>.vex"
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parser = argparse.ArgumentParser(description=description, prog='split_vexfile.py', usage=usage)
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parser.add_argument('vexfile', type=str, help=help_vexfile)
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parser.add_argument('experiment', type=str, help=help_experiment)
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parser.add_argument('piname', type=str, help=help_piname)
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# parser.add_argument('firstscan', type=int, help=help_firstscan)
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# parser.add_argument('lastscan', type=int, help=help_lastscan)
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parser.add_argument('scans', type=str, help=help_scans)
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parser.add_argument('--version', action='version', version='%(prog)s 1.0')
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parser.add_argument("-v", "--verbose", default=False, action="store_true" , help=help_verbose)
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parser.add_argument("-o", "--outputfile", type=str, default=None, help=help_outputfile)
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args = parser.parse_args()
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verbose = args.verbose
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if args.outputfile is None:
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outputfile = args.experiment.lower() + '.vex'
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else:
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outputfile = args.outputfile
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# assert args.firstscan <= args.lastscan
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# Process the scans to be imported
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scans_to_include = set()
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scan_list = args.scans.split(',')
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for a_scan_list in scan_list:
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if '~' in a_scan_list:
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# it is a range
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assert a_scan_list.count('~') == 1
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s1,s2 = [int(i) for i in a_scan_list.split('~')]
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assert s1 <= s2
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for i in range(s1, s2+1):
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scans_to_include.add(i)
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else:
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# it is an isolated scan
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scans_to_include.add(int(a_scan_list))
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vexfile = vex.Vex(args.experiment, vexfile=args.vexfile)
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if verbose:
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print(f'{args.vexfile} has been read')
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# Updating experiment name
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vexfile['GLOBAL']['EXPER'].value = args.experiment.upper()
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if verbose:
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print(f'$GLOBAL>$EXPER updated to {args.experiment.upper()}')
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oldexpname = [i for i in vexfile['EXPER'].keys() if 'comment' not in i]
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if len(oldexpname) != 1:
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raise ValueError('Many definitions found under $EXPER. Only one expected.')
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oldexpname = oldexpname[0]
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vexfile['EXPER'][oldexpname].name = args.experiment.upper()
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if verbose:
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print(f'$EXPER>def {oldexpname} updated to {args.experiment.upper()}')
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vexfile['EXPER'][oldexpname]['exper_name'].value = args.experiment.upper()
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if verbose:
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print(f'$EXPER>exper_name updated to {args.experiment.upper()}')
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descr = vexfile['EXPER'][oldexpname]['exper_description'].value
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if len(descr) > 1:
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if '"e-EVN' in descr[0]:
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descr[1] = f' {args.experiment.upper()}"'
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vexfile['EXPER'][oldexpname]['exper_description'].value = descr
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if verbose:
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print(f'$EXPER>exper_description updated to contain only {args.experiment.upper()}')
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vexfile['EXPER'][oldexpname]['PI_name'].value = f'"{args.piname}"'
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if verbose:
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print(f'EXPER>PI_name updated to {args.piname}')
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# Keep sources that should be included
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# Keep only specified scans
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allsources = set([i for i in vexfile['SOURCE'].keys() if 'comment' not in i])
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sources = set()
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allscans = [i for i in vexfile['SCHED'].keys() if 'comment' not in i]
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if len(scans_to_include) == 0:
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print('WARNING: no scans to be included')
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for a_scan in allscans:
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scannumber = int(a_scan[2:])
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# if (scannumber < args.firstscan) or (scannumber > args.lastscan):
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if scannumber not in scans_to_include:
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del vexfile['SCHED'][a_scan]
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if verbose:
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print(f'Scan {a_scan} has been removed')
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else:
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# Double checking (in case the key exists, otherwise is within the 'start' key
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if 'source' in vexfile['SCHED'][a_scan]:
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sources.add(vexfile['SCHED'][a_scan]['source'].value)
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else:
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temp = vexfile['SCHED'][a_scan]['start'].value
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# print(temp)
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# print(temp.strip())
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# print(temp.strip().split(';'))
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temp = [vex.Entry.entry_from_text(i) for i in temp.strip().split(';')[1:]]
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sources.add([i.value for i in temp if i.key == 'source'][0])
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# Remove the sources from other experiments
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for a_source in allsources.difference(sources):
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del vexfile['SOURCE'][a_source]
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if verbose:
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print(f'Source {a_source} has been removed')
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# Write the VEX info to a file
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vexfile.to_file(outputfile)
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if verbose:
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print(f'File {outputfile} has been written')
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