Ejemplo n.º 1
0
def rd_dqc(infile=None, debug=None):
  """
   read the dqc file

  """
  
  print('dqc: ', infile)
  if not os.path.exists(infile): 
    print(infile, 'does not exist')
    print('Exiting')
    sys.exit(0)

  # open catalogue file handle
  fh = pyfits.open(infile)
  data = fh[1].data
  print('Number of rows: ', len(data))
  #help(data)

  if debug: table_stats(infile)

  #data['ra']=np.degrees(data['ra'])
  #data['dec']=np.degrees(data['dec'])

  return data
Ejemplo n.º 2
0
    result.write('results1.fits', overwrite=True)

    sys.exit()


    # extract the project ID from the file
    project = []

    # table = ascii.read(infile, header_start=0, data_start=1)
    # print()
    # print(table[0])


    # table = Table.read(infile)

    table_stats('sources.fits', debug=False)
    alma.info()
    alma.info('stats')

    Image_SourceStats(alma, filename=infile, verbose=False)

    print(len(alma), 'Sources')
    SourceStats(alma, verbose=False)
    # limit to source with CUNIT3 == 'Hz' and CTYPE3 == 'FREQ'
    itest = (alma['CTYPE3'] == 'FREQ') & (alma['NAXIS3'] == 1)
    alma = alma[itest]
    print('Number of sources with CTYPE3 = FREQ:', len(alma))

    SourceStats(alma, verbose=False)
    key=raw_input("Enter any key to continue: ")
Ejemplo n.º 3
0
                logdata = "Delete lockfile %s " % lockfile
                logger(flog, logdata)
                logger(flogerr, logdata)
                os.remove(lockfile)
            continue
        else:
            logdata = "imcore_list Finished"
            logger(flog, logdata)

        hdulist = pyfits.open(outfile)
        logdata = "Number of extensions: %d " % len(hdulist)
        logger(flog, logdata)

        n_ext = len(hdulist)
        for ext in range(1, n_ext):
            table_stats(outfile, ext=ext)

        print "listdriven photometry completed"
        # key=raw_input("Enter any key to continue: ")

    print "Deleting data files used"
    if os.path.exists(imagefile):
        print "Remove the image file:" + imagefile
        cmd = "rm -v " + imagefile
        try:
            result = os.popen(cmd)
        except OSError as (errno, strerror):
            logdata = "OS error({0}): {1}".format(errno, strerror)
            logger(flogerr, logdata)
            logdata = "error removing imagefile %s " % imagefile
            logger(flogerr, logdata)
def imcore_list_run(args=None, imagefile=None,
  confmapfile=None, listfile=None, outfile=None):
  """
  runs imcore_list using subprocess

  


  """   

  # set the imcorelist parameters; maybe need to check these againsts
  # values in the header of the catalogue file
  nustep=-1
  print('args.vhs: ', args.vhs)
  print('args.cache: ', args.cache)

  if not args.vhs:
    nustep=pyfits.getval(imagefile,'NUSTEP',0)
    print('nustep = ', nustep)
  
  if args.vhs: 
    rcore = "3.0"
    nbsize = "64"
    threshold = "1.5"

  # UKIDSS values
  if (nustep==1):
    rcore = "2.5"
    nbsize = "64"
    threshold = "1.5"
  elif (nustep==4): # i.e., 2x2
    rcore = "5.0"
    nbsize = "128"
    threshold = "1.25"
  elif (nustep==9): # i.e., 3x3
    rcore = "7.5"
    nbsize = "192"
    threshold = "1.25"

  print('rcore, nbsize, threshold: ', rcore, nbsize, threshold)

  # needs the binary location to be a parameter for portability
  #command = 'time nice -n19 ' + IMCORE_LIST  \
  command = 'time nice -n19 /home/rgm/bin/imcore_list ' \
        + ' ' + imagefile \
        + ' ' + confmapfile \
        + ' ' + listfile \
        + ' ' + outfile \
        + ' ' + threshold  \
        + ' --nbsize=' + nbsize \
        + ' --rcore=' + rcore \
        + ' --cattype=6 ' 

      # + ' --verbose '

  # save stdout and stderr to a logfile
  stdoutlog = open(logpath+'Logfile_stdout', 'w+')
  stderrlog = open(logpath+'Logfile_stderr', 'w+')

  logdata=command
  logger(flog, logdata)

  # convert comamd to string list for subprocess
  command = shlex.split(command)
  print('Print command as args: ')
  print(command)

  result = subprocess.call(command, \
       stderr=stderrlog, stdout=stdoutlog)
  
  Popen=False
  if Popen:
    result = subprocess.Popen(command, shell=True, 
      stdout=subprocess.PIPE, stderr=subprocess.PIPE)
    print('Using subprocess.Popen and communicate')
    output, errors = result.communicate()
    result=subprocess.check_output(command)
    #help(result)
    print('subprocesss output: ', output)
    print('subprocess errors: ', errors)

  #logdata='subprocess error status: ' + str(result)
  #logger(flog, logdata)
  trace = traceback.extract_stack()[-1]
  print(os.path.basename(trace[0]), ' line :', str(trace[1]))
  #if result is not 0: print(len(result))
  #print(result)

  result=0
  if result is not 0:
    print(result)
    trace = traceback.extract_stack()[-1]
    print(os.path.basename(trace[0]), ' line :', str(trace[1]))
    print('Something went wrong: ', args)
    logger(flogerr, logdata)
    logdata = 'Something went wrong: ' + command
    logger(flogerr, logdata)
    logger(flogerr, line_save)
    logger(flogerr, command)
   
    while True:
      line = result.readline()
      if line == "": break
      logdata = line
      logger(flog, logdata)
      print(line,)
      if debug: key=raw_input("Enter any key to continue: ")

    # delete the outfile if created
    if os.path.exists(outfile):
      logdata = "Delete %s " % outfile
      logger(flog, logdata)
      logger(flogerr, logdata)  
      os.remove(outfile)       
    if os.path.exists(lockfile):
      logdata = "Delete lockfile %s " % lockfile
      logger(flog, logdata)
      logger(flogerr, logdata)
      os.remove(lockfile)       
    #continue
  
    usage = resource.getrusage(resource.RUSAGE_CHILD)
    for name, desc in [
        ('ru_utime', 'User time'),
        ('ru_stime', 'System time'),
        ]:
        print('%-25s (%-10s) = %s' % (desc, name, getattr(usage, name)))


  else:
    logdata='imcore_list Finished'
    logger(flog, logdata)

  print('Read back the results and check integrity: ', outfile)
  if not os.path.exists(outfile):       
    print('File does not exist: ', outfile)

  try:
    hdulist = pyfits.open(outfile)
  except:
    traceback.print_exc(file=sys.stdout)

  logdata= 'Number of extensions: %d ' % len(hdulist)
  logger(flog, logdata)

  n_ext=len(hdulist)
  for ext in range(1, n_ext):
    table_stats(outfile, ext=ext)

  print('listdriven photometry completed')
Ejemplo n.º 5
0
    debug = False
    verbose = False

    inpath = '/data/vhs/dqc/vsa/2014/VHSv20140409/'
    filename = 'vhs_vsa_dqc_tiles_fs_metadata.fits'

    dqcfile = inpath + filename

    print('Elpased time: %.2f seconds' % (time.time() - t0))

    print('Get table stats: ', dqcfile)

    dqc = libdqc.rd_dqc(infile=dqcfile)

    table_stats(dqcfile)

    print('Elpased time: %.2f seconds' % (time.time() - t0))

    #libdqc.dqc_stats(dqc=dqc)

    test = False
    if test:
        test = (data['nite'] >= '20120901') & (data['nite'] <= '20130401')
        data = data[test]

    interactive = True
    showplots = True

    t0 = time.time()
Ejemplo n.º 6
0
  debug=False
  verbose=False


  inpath= '/data/vhs/dqc/vsa/2014/VHSv20140409/'
  filename= 'vhs_vsa_dqc_tiles_fs_metadata.fits'

  dqcfile= inpath + filename

  print('Elpased time: %.2f seconds' %(time.time() - t0))

  print('Get table stats: ', dqcfile)

  dqc = libdqc.rd_dqc(infile=dqcfile)

  table_stats(dqcfile)

  print('Elpased time: %.2f seconds' %(time.time() - t0))


  #libdqc.dqc_stats(dqc=dqc)

  test=False
  if test:
    test = (data['nite'] >= '20120901') & (data['nite'] <= '20130401')
    data=data[test]


  interactive=True
  showplots=True