First working version of comment_file.py

3 years ago · dc2efae39a
1 changed files with 27 additions and 22 deletions
--- a/comment_file.py
+++ b/comment_file.py
@ -12,7 +12,7 @@ import os
 import sys
 import argparse
 import subprocess
-import datetime as dt
+from datetime import datetime as dt


 __version__ = 1.0
@ -26,6 +26,7 @@ The script will ask you in the terminal about all the required inputs.

 parser = argparse.ArgumentParser(description=help_str, prog='comment_file.py')
 parser.add_argument('experiment', type=str, default=None, help='Experiment name. Note: in case of multiple passes write {exp}_number (e.g. ev100_1')
+parser.add_argument('-o', '--output', type=str, default=None, help='Output directory where the file {experiment}.comment will be saved (by default in /jop83_0/pipe/out/{experiment})')
 parser.add_argument('-v', '--version', action='version', version='%(prog)s {}'.format(__version__))


@ -34,7 +35,7 @@ args = parser.parse_args()


 def get_sources():
-    """Parse the observed sources from the pipeline input file ($IN/{exp}/{exp}.inp.txt).
+    """Parse the observed sources from the pipeline input file (/jop83_0/pipe/in/{exp}/{exp}.inp.txt).
    It searches for the bandpass=, target= and phaseref= lines.

    Returns
@ -48,7 +49,7 @@ def get_sources():
            The targets. Should have the same dimension than the phaseref (unless it is not a phase
            referencing experiment).
    """
-    with open('$IN/{}/{}.inp.txt'.format(args.experiment.lower().split('_')[0],
+    with open('/jop83_0/pipe/in/{}/{}.inp.txt'.format(args.experiment.lower().split('_')[0],
                                       args.experiment.lower()), 'r') as inpfile:
        phaseref = None
        target = None
@ -65,8 +66,8 @@ def get_sources():
                if target is None:
                    target = [i.strip() for i in inpline.split('=')[1].strip().split(',')]

-            if target is None:
-                raise ValueError('No sources found for target (neither target or sources are defined in INP file')
+        if target is None:
+            raise ValueError('No sources found for target (neither target or sources are defined in INP file')

    return refant, bpass, phaseref, target

@ -79,7 +80,7 @@ def parse_sources(bpass, phaseref, target):
        assert len(phaseref) == len(target)
        for a_phaseref, a_target in zip(phaseref, target):
            s += 'The target source {} was calibrated using the phase-reference source {}.<br>\n'.format(
-                                                                                      a_phaseref, a_target)
+                                                                                     a_target, a_phaseref)
    else:
        if len(target) > 1:
            s += 'The target sources {} were directly fringe-fitted and bandpass calibrated.<br>\n'.format(
@ -98,7 +99,7 @@ def parse_sources(bpass, phaseref, target):

 def get_setup():
    """Get the observation setup from the {exp}.SCAN file created by the Pipeline:
-    It takes the file {exp}.SCAN that should be in $OUT/{exp}/.
+    It takes the file {exp}.SCAN that should be in /jop83_0/pipe/out/{exp}/.

    Returns
        - freq : float (GHz)
@ -115,9 +116,12 @@ def get_setup():
            2 - dual pol.
            4 - ful pol.
    """
-    with open('$OUT/{}/{}.SCAN'.format(args.experiment.lower().split('_')[0],
+    with open('/jop83_0/pipe/out/{}/{}.SCAN'.format(args.experiment.lower().split('_')[0],
                                       args.experiment.lower()), 'r') as scanfile:
+        freq = None
+        lastline = None
        for scanline in scanfile.readlines():
+            lastline = scanline # It will be the last line at the end of the loop. DO NOT JUDGE ME!!!!
            # Getting the frequency and the number of polarizations
            # The line is like Freq = XXXX GHz  Ncor = X  No. vis = XXXX
            if 'Freq = ' in scanline:
@ -137,15 +141,13 @@ def get_setup():

                pols = int(temp[4]) # number of polarizations 2=  dual, 4 = full)
                assert pols in (1, 2, 4)
-            else:
-                raise IOError('The SCAN file does not contain a line with Freq = XXX')

-            # # The line with the Frequency Table summary, listing all IFs,.
-            # if 'FQID IF#' in scanline:
-            #     pass
+        if freq is None:
+            raise IOError('The SCAN file does not contain a line with Freq = XXX')
+

        # The very last line (if not empty) is the last IF with Freq, BW, ch.Sep, and Sideband
-        last_if = scanfile.readlines()[-1].split()
+        last_if = lastline.split()
        if len(last_if) == 6:
            # It contains the FQID value
            number_ifs = int(last_if[1])
@ -169,7 +171,7 @@ def parse_setup(exp, freq, datarate, number_ifs, bandwidth, pols):
    """Returns the text to place in the comment file concerning the experiment setup.
    """
    # It gets the date of the experiment from the MASTER_PROJECTS.LIS file in ccsbeta
-    date = subprocess.getoutput('ssh jops@ccsbeta grep {} /ccs/var/log2vex/MASTER_PROJECTS.LIS | cut -d " " -f 3'.format(exp.upper())
+    date = subprocess.getoutput('ssh jops@ccsbeta grep {} /ccs/var/log2vex/MASTER_PROJECTS.LIS | cut -d " " -f 3'.format(exp.upper()))
    obsdate = dt.strptime(date, '%Y%m%d')
    if freq < 0.6:
        band = 'P'
@ -198,9 +200,9 @@ def parse_setup(exp, freq, datarate, number_ifs, bandwidth, pols):

 def get_antennas():
    """Returns a list of all antennas participating in the experiment. It takes the information
-    from the {exp}.DTSUM located in $OUT/{exp}/.
+    from the {exp}.DTSUM located in /jop83_0/pipe/out/{exp}/.
    """
-    with open('$OUT/{}/{}.DTSUM'.format(args.experiment.lower().split('_')[0],
+    with open('/jop83_0/pipe/out/{}/{}.DTSUM'.format(args.experiment.lower().split('_')[0],
                                       args.experiment.lower()), 'r') as dtsumfile:
        list_antennas = []
        inside_array = False
@ -224,21 +226,24 @@ def get_antennas():
 def parse_antennas(list_antennas):
    """Returns the text to include in the comment file concerning the participating antennas
    """
+    list_antennas = [ant.capitalize() for ant in list_antennas]
    return '{} stations participated: {}.<br>\n'.format(len(list_antennas), ', '.join(list_antennas))


 with open(template_file, 'r') as template:
    full_text = template.read()
    refant, *all_sources = get_sources()
-    full_text.format(setup_header=parse_setup(args.experiment, *get_setup()),
+    full_text = full_text.format(setup_header=parse_setup(args.experiment, *get_setup()),
                     sources_info=parse_sources(*all_sources),
                     station_info=parse_antennas(get_antennas()),
                     ref_antenna=refant)
-    comment_file = open('$OUT/{}/{}.comment'.format(args.experiment.lower().split('_')[0],
-                                                    args.experiment.lower()), 'w')
+    if args.output is None:
+        outputdir = '/jop83_0/pipe/out/{}'.format(args.experiment.lower().split('_')[0])
+    else:
+        outputdir = args.output if args.output[-1] != '/' else args.output[:-1]
+    comment_file = open('{}/{}.comment'.format(outputdir, args.experiment.lower()), 'w')
    comment_file.write(full_text)
    comment_file.close()
+    print('\nFile {0}.comment created successfully in {1}/.'.format(args.experiment.lower(), outputdir))


-print('File {0}.comment created successfully in $OUT/{0}.'.format(args.experiment.lower()))
-