inspect_flagging_dataloss.cwl

class: CommandLineTool
cwlVersion: v1.1
id: inspect_flagging_dataloss
baseCommand:
  - python3
  - script.py
inputs:
  - id: input
    type: Directory
    inputBinding:
      position: 0
      shellQuote: false
  - id: uvw_sampling
    type: int?
    default: 100
    inputBinding:
      position: 1
outputs:
  - id: output
    type: 'File'
    outputBinding:
      glob: metrics.json
  - id: flags_output
    type: 'File'
    outputBinding:
      glob: flags.h5
label: inspect_flagging_dataloss
requirements:
  - class: ShellCommandRequirement
  - class: InitialWorkDirRequirement
    listing:
     - entryname: script.py
       entry: |
         import sys
         from casacore.tables import table
         import itertools
         import json
         import h5py
         import numpy as np
         import re
         from scipy.constants import c as LIGHT_SPEED
         input_ms_path = sys.argv[1]
         sampling = int(sys.argv[2])
         main_table = table(input_ms_path, 'r')

         antennas = table(input_ms_path + '/ANTENNA', 'r')
         spec_window = table(input_ms_path + '/SPECTRAL_WINDOW', 'r')
         observation = table(input_ms_path + '/OBSERVATION', 'r')

         sas_id, sap, sb = re.search('L(\d*).*SAP(\d{3}).*SB(\d{3}).*',
                   observation.getcell('LOFAR_FILENAME', 0)).groups()
         antenna_names = antennas.getcol('NAME')
         antenna_positions = antennas.getcol('POSITION')

         ref_frequency = spec_window.getcell('REF_FREQUENCY', 0)

         TO_UVW = ref_frequency / LIGHT_SPEED  # 1 / (c/nu)

         flags = np.array(main_table.getcol('FLAG'))
         vis = np.array(main_table.getcol('DATA'))

         uvw = np.array(main_table.getcol('UVW') * TO_UVW)

         antenna1 = np.array(main_table.getcol('ANTENNA1'))
         antenna2 = np.array(main_table.getcol('ANTENNA2'))
         time = np.array(main_table.getcol('TIME'))
         n_antennas = antennas.nrows()
         n_baselines = int((n_antennas + 1) * n_antennas * .5)
         n_times = flags.shape[0] // n_baselines
         dataloss = np.array(vis == 0, dtype=np.int)