Script to directly produce stdplots from a NME cor

nme_standplots.py

@@ -0,0 +1,144 @@
+#!/usr/bin/env python3
+
+import os
+import sys
+import configparser
+import subprocess
+import datetime
+import jplotter
+import command
+
+__version__ = 1
+__prog__ = 'nme_standardplots.py'
+usage = "%(prog)s [-h]  <experiment_name>  <scan_number>\n"
+description = """Produces auto- and cross- correlations from a .cor file produced during a NME.
+This program retrieves the .cor file expected to be located in jops@tail.sfxc that has been produced manually from a support scientist during a NME. Then it creates the associated MS file and runs jplotter to produce the plots.
+
+The program assumes that the experiment is being conducted today (at the time of the call to this script).
+Otherwise, you may need to specify the date with the '-d' or '--date' option.
+"""
+
+
+
+
+def scp(originpath, destpath):
+    """Does a scp from originpath to destpath. If the process returns an error,
+    then it raises ValueError.
+    """
+    process = subprocess.call(["scp", originpath, destpath], shell=False,
+                        stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+    if process != 0:
+        raise ValueError(f"\nError code {process} when running scp {originpath} {destpath}.")
+
+
+def get_vixfile(expname: str):
+    """Copies the .vix file from ccs to the current directory for the given expname.
+    """
+    scp(f"jops@ccs:/ccs/expr/{expname}/{expname.lower()}.vix", '.')
+    os.symlink(f"{expname.lower()}.vix", f"{expname.upper()}.vix")
+    print('Vix file copied to the current directory.')
+
+
+def copy_cor_file(expname: str, scanno: str, date: str):
+    """Copies the correlation file produced by a local correlation during an NME for the experiment
+    name 'expname' and for the scan number 'scanno' to the current directory.
+    - Inputs
+        expname : experiment name (case-insensitive)
+        scanno : str with the scan number to be processed as expected from the syntax 'scan{scanno}.cor'.
+        date : date for the given experiment in the form YYYY_month, where month is the full name of the month.
+    """
+    scp(f"jops@tail.sfxc:/home/jops/sfxc/ftp/{date}/{expname.lower()}/output/scan{scanno}.cor", ".")
+
+
+def j2ms2(expname: str, scanno: str):
+    """Runs j2ms2 in the retrieved correlation file called 'scan{scanno}.cor' and produces the
+    '{expname}-scan{scanno}.ms' file. If this MS file already exists, it will be removed.
+    expname is case insensitive.
+    """
+    msfile = f"{expname.lower()}-scan{scanno}.ms"
+    if os.path.isdir(msfile):
+        process = subprocess.call(["rm", "-rf", f"{msfile}"], shell=True, stdout=subprocess.PIPE,
+                                  stderr=subprocess.PIPE)
+
+    subprocess.call(["j2ms2", "-o", msfile, f"scan{scanno}.cor"], shell=True,
+                    stdout=subprocess.PIPE, stderr=subprocess.PIPE, bufsize=1)
+
+
+def standardplots(expname: str, scanno: str, refant: str):
+    """Runs standardplots to create auto- and cross- correlations during an NME for the specified
+    experiment (expname; case insensitive) and scan number, expecting a MS in the current directory called
+       {expname.lower()}-scan{scanno}.ms
+    """
+    def open_ms(expname, scanno):
+        yield f"ms {expname.lower()}-scan{scanno}.ms"
+        yield "indexr"
+
+    def auto_plots():
+        yield "bl auto"
+        yield "fq */p"
+        yield "pt ampchan"
+        yield "ch none"
+        yield "avc none"
+        yield "avt vector"
+        yield "ckey p['RR']=2 p['LL']=3 p['RL']=4 p['LR']=5 p[none]=1"
+        yield "sort bl sb"
+        yield "new sb false"
+        yield "multi true"
+        yield "nxy 1 4"
+        yield "y 0 1.8"
+        yield "pl"
+
+    def cross_plots():
+        yield f"bl {refant}* -auto"
+        yield "fq *"
+        yield "pt ampchan"
+        yield "ch none"
+        yield "avc none"
+        yield "avt vector"
+        yield "ckey p['RR']=2 p['LL']=3 p['RL']=4 p['LR']=5 p[none]=1"
+        yield "sort bl sb"
+        yield "new sb false"
+        yield "multi true"
+        yield "nxy 1 4"
+        yield "y local"
+        yield "pl"
+
+    todo = [open_ms(expname, scanno), auto_plots(), cross_plots()]
+    jplotter.run_plotter(command.scripted(*todo))
+
+
+
+if __name__ == '__main__':
+    # Input parameters
+    parser = argparse.ArgumentParser(description=description, prog=__prog__, usage=usage,
+                                    formatter_class=argparse.RawTextHelpFormatter)
+    parser.add_argument('expname', type=str, help='Name of the EVN experiment (case insensitive).')
+    parser.add_argument('scan_number', type=str,
+                        help='Correlated scan number (as given in the <scan{scan_number}.cor> file name).')
+    parser.add_argument('-d', '--date', type=str, default=None,
+                        help='Date of the NME, given as YYYY_month, with month the full name of the month.')
+    parser.add_argument('-r', '--refant', type=str, default='Ef',
+                        help='Reference antenna to make plots. By default it is Ef.')
+    parser.add_argument('-v', '--version', action='version',
+                        version='%(prog)s {}'.format(__version__))
+    args = parser.parse_args()
+    if args.date is None:
+        nme_date = args.date
+    else:
+        nme_date = datetime.datetime.today().strftime('%Y_%B').lower()
+
+    get_vixfile(args.expname)
+    copy_cor_file(args.expname, args.scan_number, nme_date)
+    j2ms2(args.expname, args.scan_number)
+    standardplots(args.expname, args.scan_number, args.refant)
+
+
+
+
+
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