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244 lines
9.6 KiB
244 lines
9.6 KiB
#!/usr/bin/env python3
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"""
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Creates a .comment file for the EVN Pipeline.
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Given a default template, customizes it to include the basic data from the given experiment.
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The script will ask you in the terminal about all the required inputs.
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Version: 1.0
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Date: April 2019
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Author: Benito Marcote (marcote@jive.eu)
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"""
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import os
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import sys
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import argparse
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import subprocess
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import datetime as dt
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__version__ = 1.0
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# The .comment file template is located in the same directory as this script. Or it should be.
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template_file = os.path.dirname(os.path.abspath(__file__)) + '/template.comment'
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help_str = """Creates a .comment file for the EVN Pipeline.
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Given a default template, customizes it to include the basic data from the given experiment.
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The script will ask you in the terminal about all the required inputs.
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"""
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parser = argparse.ArgumentParser(description=help_str, prog='comment_file.py')
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parser.add_argument('experiment', type=str, default=None, help='Experiment name. Note: in case of multiple passes write {exp}_number (e.g. ev100_1')
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parser.add_argument('-v', '--version', action='version', version='%(prog)s {}'.format(__version__))
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args = parser.parse_args()
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def get_sources():
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"""Parse the observed sources from the pipeline input file ($IN/{exp}/{exp}.inp.txt).
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It searches for the bandpass=, target= and phaseref= lines.
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Returns
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- refant : str
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The reference antenna
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- bpass : list
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The bandpass calibrators and fringe finders used in the pipeline.
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- phaseref : list
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The phase referencing calibrators used in the pipeline. None if no phase referencing experiment.
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- target : list
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The targets. Should have the same dimension than the phaseref (unless it is not a phase
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referencing experiment).
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"""
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with open('$IN/{}/{}.inp.txt'.format(args.experiment.lower().split('_')[0],
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args.experiment.lower()), 'r') as inpfile:
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phaseref = None
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target = None
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for inpline in inpfile.readlines():
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if 'refant' in inpline:
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refant = inpline.split('=')[1].strip().split(',')[0]
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if 'bpass' in inpline:
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bpass = [i.strip() for i in inpline.split('=')[1].strip().split(',')]
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if ('phaseref' in inpline) and inpline[0] != '#':
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phaseref = [i.strip() for i in inpline.split('=')[1].strip().split(',')]
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if ('target' in inpline) and inpline[0] != '#':
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target = [i.strip() for i in inpline.split('=')[1].strip().split(',')]
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if ('sources' in inpline) and inpline[0] != '#':
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if target is None:
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target = [i.strip() for i in inpline.split('=')[1].strip().split(',')]
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if target is None:
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raise ValueError('No sources found for target (neither target or sources are defined in INP file')
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return refant, bpass, phaseref, target
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def parse_sources(bpass, phaseref, target):
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"""Returns the sentences to be placed in the comment file concerning the observed sources
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"""
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s = ''
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if phaseref is not None:
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assert len(phaseref) == len(target)
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for a_phaseref, a_target in zip(phaseref, target):
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s += 'The target source {} was calibrated using the phase-reference source {}.<br>\n'.format(
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a_phaseref, a_target)
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else:
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if len(target) > 1:
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s += 'The target sources {} were directly fringe-fitted and bandpass calibrated.<br>\n'.format(
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', '.join(target))
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else:
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s += 'The target source {} was directly fringe-fitted and bandpass calibrated.<br>\n'.format(target[0])
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if len(bpass) == 1:
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keys = ('was', '')
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else:
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keys = ('were', 's')
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s += '{0} {1} also observed as calibrator{2} and fringe finder{2}.<br>\n'.format(', '.join(bpass), *keys)
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return s
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def get_setup():
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"""Get the observation setup from the {exp}.SCAN file created by the Pipeline:
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It takes the file {exp}.SCAN that should be in $OUT/{exp}/.
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Returns
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- freq : float (GHz)
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The central frequency of the observation.
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- datarate : float (Mbps)
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The datarate of the observation.
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- number_ifs : int
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Number of IFs or subbands.
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- bandwidth : float (MHz)
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The bandwidth of each IF or subband.
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- pols : int
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Number of polarizations:
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1 - single pol.
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2 - dual pol.
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4 - ful pol.
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"""
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with open('$OUT/{}/{}.SCAN'.format(args.experiment.lower().split('_')[0],
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args.experiment.lower()), 'r') as scanfile:
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for scanline in scanfile.readlines():
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# Getting the frequency and the number of polarizations
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# The line is like Freq = XXXX GHz Ncor = X No. vis = XXXX
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if 'Freq = ' in scanline:
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# freq, pols = [i for i in map([i.strip() for i in scanline.split('=')].__getitem__, ())
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temp = ' '.join(scanline.split('=')).split()
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freq = float(temp[1])
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if temp[2] == 'GHz':
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pass
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elif temp[2] == 'MHz':
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freq *= 1e-3
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elif temp[2] == 'kHz':
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freq *= 1e-6
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elif temp[2] == 'Hz':
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freq *= 1e-9
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else:
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raise ValueError('Not units found in the Freq = XXX line inside the SCAN file')
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pols = int(temp[4]) # number of polarizations 2= dual, 4 = full)
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assert pols in (1, 2, 4)
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else:
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raise IOError('The SCAN file does not contain a line with Freq = XXX')
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# # The line with the Frequency Table summary, listing all IFs,.
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# if 'FQID IF#' in scanline:
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# pass
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# The very last line (if not empty) is the last IF with Freq, BW, ch.Sep, and Sideband
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last_if = scanfile.readlines()[-1].split()
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if len(last_if) == 6:
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# It contains the FQID value
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number_ifs = int(last_if[1])
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bandwidth = int(float(last_if[3])*1e-3)
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elif len(last_if) == 5:
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# It does not contain the FQID value
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number_ifs = int(last_if[0])
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bandwidth = int(float(last_if[2])*1e-3)
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else:
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ValueError('Unexpected number of parameters at the end of the SCAN file.')
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if pols == 1:
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datarate = number_ifs*bandwidth*2*2
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else:
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datarate = number_ifs*bandwidth*2*2*2
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return freq, datarate, number_ifs, bandwidth, pols
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def parse_setup(exp, freq, datarate, number_ifs, bandwidth, pols):
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"""Returns the text to place in the comment file concerning the experiment setup.
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"""
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# It gets the date of the experiment from the MASTER_PROJECTS.LIS file in ccsbeta
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date = subprocess.getoutput('ssh jops@ccsbeta grep {} /ccs/var/log2vex/MASTER_PROJECTS.LIS | cut -d " " -f 3'.format(exp.upper())
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obsdate = dt.strptime(date, '%Y%m%d')
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if freq < 0.6:
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band = 'P'
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elif freq < 1.9:
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band = 'L'
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elif freq < 3.0:
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band = 'S'
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elif freq < 7.0:
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band = 'C'
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elif freq < 11.0:
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band = 'X'
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elif freq < 18.0:
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band = 'U'
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elif freq < 30:
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band = 'K'
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elif freq >= 30:
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band = 'Q'
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name_pols = {1: 'single', 2: 'dual', 4: 'full'}
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s = '{}. {}-band experiment observed on {}.<br>\n'.format(exp.upper(), band, obsdate.strftime('%d %B %Y'))
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s += 'Data rate was {} Mbps ({} x {} MHz subbands, {} polarization, two-bit sampling)<br>\n'.format(
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datarate, number_ifs, bandwidth, name_pols[pols])
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return s
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def get_antennas():
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"""Returns a list of all antennas participating in the experiment. It takes the information
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from the {exp}.DTSUM located in $OUT/{exp}/.
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"""
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with open('$OUT/{}/{}.DTSUM'.format(args.experiment.lower().split('_')[0],
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args.experiment.lower()), 'r') as dtsumfile:
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list_antennas = []
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inside_array = False
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for dtline in dtsumfile.readlines():
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if inside_array:
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if '(' in dtline:
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templine = dtline
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# More antennas to get
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while '(' in templine:
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list_antennas.append(templine[templine.index('(')+1:templine.index(')')].strip())
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templine = templine[templine.index(')')+1:]
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else:
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# We are done
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inside_array = False
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if 'Array name' in dtline:
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inside_array = True
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return list_antennas
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def parse_antennas(list_antennas):
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"""Returns the text to include in the comment file concerning the participating antennas
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"""
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return '{} stations participated: {}.<br>\n'.format(len(list_antennas), ', '.join(list_antennas))
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with open(template_file, 'r') as template:
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full_text = template.read()
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refant, *all_sources = get_sources()
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full_text.format(setup_header=parse_setup(args.experiment, *get_setup()),
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sources_info=parse_sources(*all_sources),
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station_info=parse_antennas(get_antennas()),
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ref_antenna=refant)
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comment_file = open('$OUT/{}/{}.comment'.format(args.experiment.lower().split('_')[0],
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args.experiment.lower()), 'w')
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comment_file.write(full_text)
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comment_file.close()
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print('File {0}.comment created successfully in $OUT/{0}.'.format(args.experiment.lower()))
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