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New pipelet.py script

master
Benito Marcote 2 years ago
parent
commit
a94e253c12
3 changed files with 144 additions and 0 deletions
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      pipelet.py
  2. +43
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      template.pipelet
  3. +13
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      template.tasav.txt

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pipelet.py View File

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#!/usr/bin/env python3
"""
Creates the {exp}.pipelet.
Given the default template, customizes it to include the basic data from the given experiment.

Version: 1.0
Date: April 2019
Author: Benito Marcote (marcote@jive.eu)

"""
import os
import sys
import glob
import argparse
from datetime import datetime as dt


__version__ = 1.0
# The .comment file template is located in the same directory as this script. Or it should be.
template_pipelet_file = os.path.dirname(os.path.abspath(__file__)) + '/template.pipelet'

help_str = """Creates a .pipelet file in the current directory.

This letter is the content that must be sent to the PI after pipelining an experiment.
It contains information about the pipeline output and the credentials to access the data.
It takes the credentials from the username_password.auth file that should be placed in the current directory
(otherwise specify its file, or the username and password as parameters).

The user must provide the following information:
- The experiment name (case insensitive).
- Who are you (the Support Scientist). Type your surname.
"""

parser = argparse.ArgumentParser(description=help_str, prog='pipelet.py')
parser.add_argument('-v', '--version', action='version', version='%(prog)s {}'.format(__version__))
parser.add_argument('-o', '--output', type=str, default='.', help='Output directory where the file {experiment}.pipelet will be store (by default the current directory)')
parser.add_argument('-c', '--credentials', type=str, default=None, help='Auth file containing the username and password in its name (required if *.auth is not in current directory).')
parser.add_argument('-u', '--username', type=str, default=None, help='Username to access the data (required if no credential file exists)')
parser.add_argument('-p', '--password', type=str, default=None, help='Password to access the data (required if no credential file exists)')
parser.add_argument('experiment', type=str, default=None, help='Experiment name.')
parser.add_argument('jss', type=str, default='', help='JIVE Support Scientist doing the post-processing (your surname).')


args = parser.parse_args()


jss = {'marcote': 'Benito Marcote', 'immer': 'Katharina Immer', 'nair': 'Dhanya Nair', '': ''}



def get_credentials_from_filename(thefile):
"""Assumes that the file name is made of the form username_password[.auth]
It thus can only contain one '_' character, which separates both sides.

Returns the username, and password.
"""
assert thefile.count('_') == 1
return thefile.split('.')[0].split('_')


# One of the following conditions must be true
if args.credentials is not None:
username, password = get_credentials_from_filename(args.credentials)
elif (args.username is not None) and (args.password is not None):
username, password = args.username, args.password
elif ((args.username is not None) and (args.password is None)) or ((args.username is None) and (args.password is not None)):
raise AttributeError('Both username and password must be passed, or none of them.')
else:
credential_file = glob.glob('*.auth')
if len(credential_file) == 0:
raise AttributeError('No credential *.auth file found and not enough paramenters passed')
elif len(credential_file) > 1:
raise AttributeError('Multiple *auth files found. Please specify the one to be used.')
username, password = get_credentials_from_filename(credential_file[0])


with open(template_pipelet_file, 'r') as template:
full_text = template.read()
full_text = full_text.format(expname=args.experiment.upper(), delimiter='-'*(41+len(args.experiment)),
username=username, password=password, supsci=jss[args.jss])

pipelet_file = open('{}/{}.pipelet'.format(args.output if args.output[-1] != '/' else args.output[:-1],
args.experiment.lower()), 'w')
pipelet_file.write(full_text)
pipelet_file.close()
print('\nFile {0}.pipelet created successfully in {1}.'.format(args.experiment.lower(), args.output))



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template.pipelet View File

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Subject: Dear PI: Pipeline Analysis of {expname}
{delimiter}

Dear PI,

We have automatically pipelined your EVN/Global VLBI experiment: {expname}.

The credentials for accessing the data are:

username: {username}
password: {password}

Please visit our web pages:
www.jive.eu/select-experiment
www.jive.eu/browse-catalogue
which provide different indexing schemes to find you experiment,
in order to download:

(i) Sets of antab/flagging files used by the pipeline and resulting
calibration tables (in FITS format). These can be downloaded and
directly applied to the data on the EVN archive.

(ii) A series of plots produced by the pipeline (pdf format), which should
be useful in assessing the antenna performance and data quality.

(iii) A history file associated with the data processed by the pipeline
and a summary of what the CL/SN tables contain (text format both).

Note: The pipeline uses AIPS versions 31DEC13. The latest version
of the pipeline script is written in Python and uses ParselTongue
to access the AIPS tasks. Visit the web page above for more details.
The pipeline is under continual development and any feedback is
appreciated. Background information to the pipeline can be found at
www.evlbi.org/pipeline/user_expts.html

If you have any feedback regarding this service please direct your comments to:
Zsolt Paragi (zparagi@jive.eu).


Clear skies,

{supsci}.


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template.tasav.txt View File

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########### List of extension tables of the experiment {expname} ##############
AN1 = AN table
CL1 = CL table created when loading data
SN1 = Output of running APCAL on TY and GC tables
CL2 = The a priori amplitude calibration (CL1 * SN1) and the parallactic angle
correction.
FG1 = Flagging band edges and data acquired when the telescope was off-source
(as determined by telescope monitor data).
SN2 = The phase, delay and phase rate solutions derived from sources
identified as calibrators via FRING: {fringe_sources}
CL3 = CL2 * SN2 (the application of SN2 to CL2)
BP1 = Bandpass amplitude and phase (the application of CL2 and FG1)
Bandpass Calibrators: {bandpass_sources}

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