def test_firstcal_metrics_run(self):
# get argument object
a = utils.get_metrics_ArgumentParser('firstcal_metrics')
if DATA_PATH not in sys.path:
sys.path.append(DATA_PATH)
arg0 = "--std_cut=0.5"
arg1 = "--extension=.firstcal_metrics.json"
arg2 = "--metrics_path={}".format(
os.path.join(DATA_PATH, 'test_output'))
arguments = ' '.join([arg0, arg1, arg2])
# Test runing with no files
cmd = ' '.join([arguments, ''])
args = a.parse_args(cmd.split())
history = cmd
self.assertRaises(AssertionError,
firstcal_metrics.firstcal_metrics_run, args.files,
args, history)
# Test running with file
filename = os.path.join(DATA_PATH,
'zen.2457555.50099.yy.HH.uvcA.first.calfits')
dest_file = os.path.join(
DATA_PATH, 'test_output',
'zen.2457555.50099.yy.HH.uvcA.first.calfits.' +
'firstcal_metrics.json')
if os.path.exists(dest_file):
os.remove(dest_file)
cmd = ' '.join([arguments, filename])
args = a.parse_args(cmd.split())
history = cmd
firstcal_metrics.firstcal_metrics_run(args.files, args, history)
self.assertTrue(os.path.exists(dest_file))
os.remove(dest_file)
def test_ant_metrics_run_no_metrics():
"""Test an argument is raised if no metrics are set to True."""
# get arguments
a = utils.get_metrics_ArgumentParser('ant_metrics')
if DATA_PATH not in sys.path:
sys.path.append(DATA_PATH)
arg1 = "--crossCut=5"
arg2 = "--deadCut=5"
arg3 = "--extension=.ant_metrics.hdf5"
arg4 = "--metrics_path={}".format(os.path.join(DATA_PATH, 'test_output'))
arg5 = "--vis_format=miriad"
arg6 = "--alwaysDeadCut=10"
arg7 = "--skip_mean_vij"
arg8 = "--skip_red_corr"
arg9 = "--skip_cross_pols"
arguments = ' '.join(
[arg1, arg2, arg3, arg4, arg5, arg6, arg7, arg8, arg9])
xx_file = os.path.join(DATA_PATH, 'zen.2458002.47754.xx.HH.uvA')
dest_file = os.path.join(DATA_PATH, 'test_output',
'zen.2458002.47754.HH.uvA.ant_metrics.hdf5')
if os.path.exists(dest_file):
os.remove(dest_file)
cmd = ' '.join([arguments, xx_file])
args = a.parse_args(cmd.split())
history = cmd
pols = list(args.pol.split(','))
pytest.raises(AssertionError, ant_metrics.ant_metrics_run, args.files,
pols, args.crossCut, args.deadCut, args.alwaysDeadCut,
args.metrics_path, args.extension, args.vis_format,
args.verbose, history, args.run_mean_vij, args.run_red_corr,
args.run_cross_pols)
def test_run_ant_metrics_no_files():
# get argument object
a = utils.get_metrics_ArgumentParser('ant_metrics')
if DATA_PATH not in sys.path:
sys.path.append(DATA_PATH)
arg1 = "--crossCut=5"
arg2 = "--deadCut=5"
arg3 = "--extension=.ant_metrics.hdf5"
arg4 = "--metrics_path={}".format(os.path.join(DATA_PATH, 'test_output'))
arg5 = "--vis_format=miriad"
arg6 = "--alwaysDeadCut=10"
arg7 = "--run_mean_vij"
arg8 = "--run_red_corr"
arg9 = "--run_cross_pols"
arguments = ' '.join(
[arg1, arg2, arg3, arg4, arg5, arg6, arg7, arg8, arg9])
# test running with no files
cmd = ' '.join([arguments, ''])
args = a.parse_args(cmd.split())
pols = list(args.pol.split(','))
history = cmd
pytest.raises(AssertionError, ant_metrics.ant_metrics_run, args.files,
pols, args.crossCut, args.deadCut, args.alwaysDeadCut,
args.metrics_path, args.extension, args.vis_format,
args.verbose, history, args.run_mean_vij, args.run_red_corr,
args.run_cross_pols)
def test_run_ant_metrics_one_file():
a = utils.get_metrics_ArgumentParser('ant_metrics')
if DATA_PATH not in sys.path:
sys.path.append(DATA_PATH)
arg1 = "--crossCut=5"
arg2 = "--deadCut=5"
arg3 = "--extension=.ant_metrics.hdf5"
arg4 = "--metrics_path={}".format(os.path.join(DATA_PATH, 'test_output'))
arg5 = "--vis_format=miriad"
arg6 = "--alwaysDeadCut=10"
arg7 = "--run_mean_vij"
arg8 = "--run_red_corr"
arg9 = "--run_cross_pols"
arguments = ' '.join(
[arg1, arg2, arg3, arg4, arg5, arg6, arg7, arg8, arg9])
# test running with a lone file
lone_file = os.path.join(DATA_PATH, 'zen.2457698.40355.xx.HH.uvcAA')
cmd = ' '.join([arguments, lone_file])
args = a.parse_args(cmd.split())
history = cmd
pols = list(args.pol.split(','))
# this test raises a warning, then fails...
uvtest.checkWarnings(pytest.raises, [
AssertionError, ant_metrics.ant_metrics_run, args.files, pols,
args.crossCut, args.deadCut, args.alwaysDeadCut, args.metrics_path,
args.extension, args.vis_format, args.verbose, history,
args.run_mean_vij, args.run_red_corr, args.run_cross_pols
],
nwarnings=1,
message='Could not find')
def test_get_metrics_ArgumentParser_xrfi_run():
a = utils.get_metrics_ArgumentParser('xrfi_run')
# First try defaults - test a few of them
args = a.parse_args('')
assert args.kt_size == 8
assert args.sig_init == 6.0
assert args.ex_ants is None
# try to set something
args = a.parse_args(['--sig_adj', '3.0'])
assert args.sig_adj == 3.0
def test_get_metrics_ArgumentParser_day_threshold_run():
a = utils.get_metrics_ArgumentParser('day_threshold_run')
# First try defaults - test a few of them
args = a.parse_args(['fooey'])
assert args.nsig_f_adj == 3.0
assert args.nsig_f == 7.0
assert args.data_files == ['fooey']
# try to set something
args = a.parse_args(['--nsig_t', '3.0', 'fooey'])
assert args.nsig_t == 3.0
def test_get_metrics_ArgumentParser_firstcal_metrics():
a = utils.get_metrics_ArgumentParser('firstcal_metrics')
# First try defaults - test a few of them
args = a.parse_args('')
nt.assert_equal(args.std_cut, 0.5)
nt.assert_equal(args.extension, '.firstcal_metrics.json')
nt.assert_equal(args.metrics_path, '')
# try to set something
args = a.parse_args(['--extension', 'foo'])
nt.assert_equal(args.extension, 'foo')
def test_get_metrics_ArgumentParser_firstcal_metrics():
a = utils.get_metrics_ArgumentParser('firstcal_metrics')
# First try defaults - test a few of them
args = a.parse_args('')
assert args.std_cut == 0.5
assert args.extension == '.firstcal_metrics.hdf5'
assert args.metrics_path == ''
# try to set something
args = a.parse_args(['--extension', 'foo'])
assert args.extension == 'foo'
def test_get_metrics_ArgumentParser_xrfi_apply():
a = utils.get_metrics_ArgumentParser('xrfi_apply')
# First try defaults - test a few of them
args = a.parse_args('')
nt.assert_equal(args.infile_format, 'miriad')
nt.assert_equal(args.extension, 'R')
nt.assert_equal(args.flag_file, None)
nt.assert_equal(args.output_uvflag, True)
# try to set something
args = a.parse_args(['--waterfalls', 'a,g'])
nt.assert_equal(args.waterfalls, 'a,g')
def test_get_metrics_ArgumentParser_omnical_metrics():
a = utils.get_metrics_ArgumentParser('omnical_metrics')
# First try defaults - test a few of them
args = a.parse_args('')
assert args.fc_files is None
assert args.phs_std_cut == 0.3
assert args.extension == '.omni_metrics.json'
assert args.metrics_path == ''
# try to set something
args = a.parse_args(['--extension', 'foo'])
assert args.extension, 'foo'
def test_get_metrics_ArgumentParser_omnical_metrics():
a = utils.get_metrics_ArgumentParser('omnical_metrics')
# First try defaults - test a few of them
args = a.parse_args('')
nt.assert_equal(args.fc_files, None)
nt.assert_equal(args.phs_std_cut, 0.3)
nt.assert_equal(args.extension, '.omni_metrics.json')
nt.assert_equal(args.metrics_path, '')
# try to set something
args = a.parse_args(['--extension', 'foo'])
nt.assert_equal(args.extension, 'foo')
def test_get_metrics_ArgumentParser_ant_metrics():
a = utils.get_metrics_ArgumentParser('ant_metrics')
# First try defaults - test a few of them
args = a.parse_args('')
nt.assert_equal(args.crossCut, 5.0)
nt.assert_equal(args.alwaysDeadCut, 10.0)
nt.assert_equal(args.metrics_path, '')
nt.assert_equal(args.verbose, True)
# try to set something
args = a.parse_args(['--extension', 'foo'])
nt.assert_equal(args.extension, 'foo')
def test_get_metrics_ArgumentParser_ant_metrics():
a = utils.get_metrics_ArgumentParser('ant_metrics')
# First try defaults - test a few of them
args = a.parse_args('')
assert args.crossCut == 5.0
assert args.alwaysDeadCut == 10.0
assert args.metrics_path == ''
assert args.verbose is True
# try to set something
args = a.parse_args(['--extension', 'foo'])
assert args.extension == 'foo'
def test_get_metrics_ArgumentParser_xrfi_h1c_run():
a = utils.get_metrics_ArgumentParser('xrfi_h1c_run')
# First try defaults - test a few of them
args = a.parse_args('')
assert args.infile_format == 'miriad'
assert args.summary_ext == 'flag_summary.h5'
assert args.algorithm == 'xrfi_simple'
assert args.nsig_df == 6.0
assert args.px_threshold == 0.2
# try to set something
args = a.parse_args(['--px_threshold', '4.0'])
assert args.px_threshold == 4.0
def test_get_metrics_ArgumentParser_xrfi_apply():
a = utils.get_metrics_ArgumentParser('xrfi_apply')
# First try defaults - test a few of them
args = a.parse_args('')
assert args.infile_format == 'miriad'
assert args.extension == 'R'
assert args.flag_file is None
assert args.output_uvflag is True
assert args.output_uvflag_ext == 'flags.h5'
# try to set something
args = a.parse_args(['--waterfalls', 'a,g'])
assert args.waterfalls == 'a,g'
def test_get_metrics_ArgumentParser_xrfi_run():
a = utils.get_metrics_ArgumentParser('xrfi_run')
# First try defaults - test a few of them
args = a.parse_args('')
nt.assert_equal(args.infile_format, 'miriad')
nt.assert_equal(args.summary_ext, '.flag_summary.npz')
nt.assert_equal(args.algorithm, 'xrfi_simple')
nt.assert_equal(args.nsig_df, 6.0)
nt.assert_equal(args.px_threshold, 0.2)
# try to set something
args = a.parse_args(['--px_threshold', '4.0'])
nt.assert_equal(args.px_threshold, 4.0)
def test_get_metrics_ArgumentParser_delay_xrfi_run():
a = utils.get_metrics_ArgumentParser('delay_xrfi_run')
# First try defaults - test a few of them
args = a.parse_args('')
nt.assert_equal(args.infile_format, 'miriad')
nt.assert_equal(args.algorithm, 'xrfi_simple')
nt.assert_equal(args.nsig_dt, 6.0)
nt.assert_equal(args.px_threshold, 0.2)
nt.assert_equal(args.filename, None)
nt.assert_equal(args.tol, 1e-7)
nt.assert_equal(args.waterfalls, None)
# try to set something
args = a.parse_args(['--waterfalls', 'a,g'])
nt.assert_equal(args.waterfalls, 'a,g')
def test_get_metrics_ArgumentParser_delay_xrfi_h1c_idr2_1_run():
a = utils.get_metrics_ArgumentParser('delay_xrfi_h1c_idr2_1_run')
# First try defaults - test a few of them
args = a.parse_args('')
assert args.infile_format == 'miriad'
assert args.algorithm == 'xrfi_simple'
assert args.nsig_dt == 6.0
assert args.px_threshold == 0.2
assert args.filename is None
assert args.tol == 1e-7
assert args.waterfalls is None
# try to set something
args = a.parse_args(['--waterfalls', 'a,g'])
assert args.waterfalls == 'a,g'
def test_ant_metrics_run_only_red_corr():
# get arguments
a = utils.get_metrics_ArgumentParser('ant_metrics')
if DATA_PATH not in sys.path:
sys.path.append(DATA_PATH)
arg0 = "-p xx,yy,xy,yx"
arg1 = "--crossCut=5"
arg2 = "--deadCut=5"
arg3 = "--extension=.ant_metrics.hdf5"
arg4 = "--metrics_path={}".format(os.path.join(DATA_PATH, 'test_output'))
arg5 = "--vis_format=miriad"
arg6 = "--alwaysDeadCut=10"
arg7 = "--skip_mean_vij"
arg8 = "--run_red_corr"
arg9 = "--skip_cross_pols"
arguments = ' '.join(
[arg0, arg1, arg2, arg3, arg4, arg5, arg6, arg7, arg8, arg9])
xx_file = os.path.join(DATA_PATH, 'zen.2458002.47754.xx.HH.uvA')
dest_file = os.path.join(DATA_PATH, 'test_output',
'zen.2458002.47754.HH.ant_metrics.hdf5')
if os.path.exists(dest_file):
os.remove(dest_file)
cmd = ' '.join([arguments, xx_file])
args = a.parse_args(cmd.split())
history = cmd
pols = list(args.pol.split(','))
if os.path.exists(dest_file):
os.remove(dest_file)
ant_metrics.ant_metrics_run(args.files,
pols,
args.crossCut,
args.deadCut,
args.alwaysDeadCut,
args.metrics_path,
args.extension,
args.vis_format,
args.verbose,
history=history,
run_mean_vij=args.run_mean_vij,
run_red_corr=args.run_red_corr,
run_cross_pols=args.run_cross_pols)
assert os.path.exists(dest_file)
os.remove(dest_file)
def test_firstcal_metrics_run(self):
# get arg parse
a = utils.get_metrics_ArgumentParser('omnical_metrics')
if DATA_PATH not in sys.path:
sys.path.append(DATA_PATH)
# test w/ no file
arguments = ''
cmd = ' '.join([arguments, ''])
args = a.parse_args(cmd.split())
history = cmd
self.assertRaises(AssertionError, omnical_metrics.omnical_metrics_run,
args.files, args, history)
# test w/ no fc_file
arguments = ''
cmd = ' '.join([arguments, self.oc_file])
args = a.parse_args(cmd.split())
history = cmd
outfile = self.oc_file + '.omni_metrics.json'
if os.path.isfile(outfile):
os.remove(outfile)
omnical_metrics.omnical_metrics_run(args.files, args, history)
outfile = self.oc_file + '.omni_metrics.json'
self.assertTrue(os.path.isfile(outfile))
os.remove(outfile)
# test w/ extension
arguments = '--extension=.omni.json'
cmd = ' '.join([arguments, self.oc_file])
args = a.parse_args(cmd.split())
history = cmd
outfile = self.oc_file + '.omni.json'
if os.path.isfile(outfile):
os.remove(outfile)
omnical_metrics.omnical_metrics_run(args.files, args, history)
self.assertTrue(os.path.isfile(outfile))
os.remove(outfile)
# test w/ metrics_path
arguments = '--metrics_path={}'.format(self.out_dir)
cmd = ' '.join([arguments, self.oc_file])
args = a.parse_args(cmd.split())
history = cmd
outfile = os.path.join(self.out_dir,
self.oc_basename + '.omni_metrics.json')
if os.path.isfile(outfile):
os.remove(outfile)
omnical_metrics.omnical_metrics_run(args.files, args, history)
self.assertTrue(os.path.isfile(outfile))
os.remove(outfile)
# test w/ options
arguments = '--fc_files={0} --no_bandcut --phs_std_cut=0.5 --chisq_std_zscore_cut=4.0'.format(
self.fc_file)
cmd = ' '.join([arguments, self.oc_file])
args = a.parse_args(cmd.split())
history = cmd
outfile = self.oc_file + '.omni_metrics.json'
if os.path.isfile(outfile):
os.remove(outfile)
omnical_metrics.omnical_metrics_run(args.files, args, history)
self.assertTrue(os.path.isfile(outfile))
os.remove(outfile)
# test make plots
arguments = '--fc_files={0} --make_plots'.format(self.fc_file)
cmd = ' '.join([arguments, self.oc_file])
args = a.parse_args(cmd.split())
history = cmd
omnical_metrics.omnical_metrics_run(args.files, args, history)
outfile = self.oc_file + '.omni_metrics.json'
outpng1 = self.oc_file + '.chisq_std.png'
outpng2 = self.oc_file + '.phs_std.png'
outpng3 = self.oc_file + '.phs_ft.png'
outpng4 = self.oc_file + '.phs_hist.png'
self.assertTrue(os.path.isfile(outfile))
self.assertTrue(os.path.isfile(outpng1))
self.assertTrue(os.path.isfile(outpng2))
self.assertTrue(os.path.isfile(outpng3))
self.assertTrue(os.path.isfile(outpng4))
os.remove(outfile)
os.remove(outpng1)
os.remove(outpng2)
os.remove(outpng3)
os.remove(outpng4)
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2018 the HERA Project
# Licensed under the MIT License
from hera_qm import utils
from hera_qm import ant_metrics
import sys
a = utils.get_metrics_ArgumentParser('ant_metrics')
args = a.parse_args()
history = ' '.join(sys.argv)
if args.pol == '':
args.pol = ['xx', 'yy', 'xy', 'xy']
else:
args.pol = list(args.pol.split(','))
ant_metrics.ant_metrics_run(args.files,
pols=args.pol,
crossCut=args.crossCut,
deadCut=args.deadCut,
alwaysDeadCut=args.alwaysDeadCut,
metrics_path=args.metrics_path,
extension=args.extension,
vis_format=args.vis_format,
verbose=args.verbose,
history=history,
run_mean_vij=args.run_mean_vij,
run_red_corr=args.run_red_corr,
run_cross_pols=args.run_cross_pols)
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2019 the HERA Project
# Licensed under the MIT License
from hera_qm import utils
from hera_qm import firstcal_metrics
import sys
ap = utils.get_metrics_ArgumentParser('firstcal_metrics')
args = ap.parse_args()
files = args.files
history = ' '.join(sys.argv)
firstcal_metrics.firstcal_metrics_run(files, args, history)
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2019 the HERA Project
# Licensed under the MIT License
import sys
from hera_qm import utils
from hera_qm import xrfi
ap = utils.get_metrics_ArgumentParser('xrfi_run')
args = ap.parse_args()
history = ' '.join(sys.argv)
xrfi.xrfi_run(args.ocalfits_file, args.acalfits_file, args.model_file, args.data_file,
history, xrfi_path=args.xrfi_path,
kt_size=args.kt_size, kf_size=args.kf_size, sig_init=args.sig_init,
sig_adj=args.sig_adj, ex_ants=args.ex_ants, ant_str=args.ant_str,
metrics_file=args.metrics_file, clobber=args.clobber)
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2019 the HERA Project
# Licensed under the MIT License
import sys
from hera_qm import utils
from hera_qm import xrfi
ap = utils.get_metrics_ArgumentParser('day_threshold_run')
args = ap.parse_args()
history = ' '.join(sys.argv)
if args.run_if_first is None or sorted(
args.data_files)[0] == args.run_if_first:
xrfi.day_threshold_run(args.data_files,
history,
nsig_f=args.nsig_f,
nsig_t=args.nsig_t,
nsig_f_adj=args.nsig_f_adj,
nsig_t_adj=args.nsig_t_adj,
clobber=args.clobber)
else:
print(
sorted(args.data_files)[0], 'is not', args.run_if_first,
'...skipping.')
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2018 the HERA Project
# Licensed under the MIT License
import sys
import numpy as np
from hera_qm import utils as qm_utils
from hera_qm import xrfi
from hera_cal import delay_filter
from hera_cal import io
from pyuvdata import UVData
a = qm_utils.get_metrics_ArgumentParser('delay_xrfi_run')
args = a.parse_args()
filename = args.filename
history = ' '.join(sys.argv)
# Read data, apply delay filter, update UVData object
uv = UVData()
uv.read_miriad(filename)
# apply a priori waterfall flags
if args.waterfalls is not None:
waterfalls = args.waterfalls.split(',')
if len(waterfalls) > 0:
xrfi.flag_apply(waterfalls, uv, force_pol=True)
# set kwargs
kwargs = {}
if args.window == 'tukey':
kwargs['alpha'] = args.alpha
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2019 the HERA Project
# Licensed under the MIT License
import sys
import numpy as np
from hera_qm import utils as qm_utils
from hera_qm import xrfi
from hera_cal import delay_filter
from hera_cal import io
from pyuvdata import UVData
ap = qm_utils.get_metrics_ArgumentParser('delay_xrfi_h1c_idr2_1_run')
args = ap.parse_args()
filename = args.filename
history = ' '.join(sys.argv)
# Read data, apply delay filter, update UVData object
uv = UVData()
uv.read_miriad(filename)
# apply a priori waterfall flags
if args.waterfalls is not None:
waterfalls = args.waterfalls.split(',')
if len(waterfalls) > 0:
xrfi.flag_apply(waterfalls, uv, force_pol=True)
# set kwargs
kwargs = {}
if args.window == 'tukey':
kwargs['alpha'] = args.alpha
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2018 the HERA Project
# Licensed under the MIT License
import sys
from hera_qm import utils
from hera_qm import xrfi
a = utils.get_metrics_ArgumentParser('xrfi_apply')
args = a.parse_args()
filename = args.filename
history = ' '.join(sys.argv)
xrfi.xrfi_apply(filename, history, infile_format=args.infile_format, xrfi_path=args.xrfi_path,
outfile_format=args.outfile_format, extension=args.extension,
overwrite=args.overwrite, flag_file=args.flag_file, waterfalls=args.waterfalls,
output_uvflag=args.output_uvflag, output_uvflag_ext=args.output_uvflag_ext)
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2019 the HERA Project
# Licensed under the MIT License
from hera_qm import utils
from hera_qm import omnical_metrics
import sys
ap = utils.get_metrics_ArgumentParser('omnical_metrics')
args = ap.parse_args()
files = args.files
history = ' '.join(sys.argv)
omnical_metrics.omnical_metrics_run(files, args, history)
def test_firstcal_metrics_run(omnicalrun_data):
pytest.importorskip('matplotlib.pyplot')
# get arg parse
a = utils.get_metrics_ArgumentParser('omnical_metrics')
if DATA_PATH not in sys.path:
sys.path.append(DATA_PATH)
# test w/ no file
arguments = ''
cmd = ' '.join([arguments, ''])
args = a.parse_args(cmd.split())
history = cmd
pytest.raises(AssertionError, omnical_metrics.omnical_metrics_run,
args.files, args, history)
# test w/ no fc_file
arguments = ''
cmd = ' '.join([arguments, omnicalrun_data.oc_file])
args = a.parse_args(cmd.split())
history = cmd
outfile = utils.strip_extension(
omnicalrun_data.oc_file) + '.omni_metrics.json'
if os.path.isfile(outfile):
os.remove(outfile)
omnical_metrics.omnical_metrics_run(args.files, args, history)
assert os.path.isfile(outfile)
os.remove(outfile)
# test w/ extension
arguments = '--extension=.omni.json'
cmd = ' '.join([arguments, omnicalrun_data.oc_file])
args = a.parse_args(cmd.split())
history = cmd
outfile = utils.strip_extension(omnicalrun_data.oc_file) + '.omni.json'
if os.path.isfile(outfile):
os.remove(outfile)
omnical_metrics.omnical_metrics_run(args.files, args, history)
assert os.path.isfile(outfile)
os.remove(outfile)
# test w/ metrics_path
arguments = '--metrics_path={}'.format(omnicalrun_data.out_dir)
cmd = ' '.join([arguments, omnicalrun_data.oc_file])
args = a.parse_args(cmd.split())
history = cmd
outfile = os.path.join(
omnicalrun_data.out_dir,
utils.strip_extension(omnicalrun_data.oc_basename) +
'.omni_metrics.json')
if os.path.isfile(outfile):
os.remove(outfile)
omnical_metrics.omnical_metrics_run(args.files, args, history)
assert os.path.isfile(outfile)
os.remove(outfile)
# test w/ options
arguments = '--fc_files={0} --no_bandcut --phs_std_cut=0.5 --chisq_std_zscore_cut=4.0'.format(
omnicalrun_data.fc_file)
cmd = ' '.join([arguments, omnicalrun_data.oc_file])
args = a.parse_args(cmd.split())
history = cmd
outfile = utils.strip_extension(
omnicalrun_data.oc_file) + '.omni_metrics.json'
if os.path.isfile(outfile):
os.remove(outfile)
omnical_metrics.omnical_metrics_run(args.files, args, history)
assert os.path.isfile(outfile)
os.remove(outfile)
# test make plots
arguments = '--fc_files={0} --make_plots'.format(omnicalrun_data.fc_file)
cmd = ' '.join([arguments, omnicalrun_data.oc_file])
args = a.parse_args(cmd.split())
history = cmd
omnical_metrics.omnical_metrics_run(args.files, args, history)
basename = utils.strip_extension(omnicalrun_data.oc_file)
outfile = basename + '.omni_metrics.json'
outpng1 = basename + '.chisq_std.png'
outpng2 = basename + '.phs_std.png'
outpng3 = basename + '.phs_ft.png'
outpng4 = basename + '.phs_hist.png'
assert os.path.isfile(outfile)
assert os.path.isfile(outpng1)
assert os.path.isfile(outpng2)
assert os.path.isfile(outpng3)
assert os.path.isfile(outpng4)
os.remove(outfile)
os.remove(outpng1)
os.remove(outpng2)
os.remove(outpng3)
os.remove(outpng4)
