def test_fil_to_fil(your_object):
# from fil
w = Writer(
your_object,
nstart=1,
nsamp=2,
outname="temp",
c_min=10,
c_max=200,
outdir="./",
flag_rfi=False,
zero_dm_subt=False,
)
# test with outname
w.to_fil()
assert os.path.isfile("temp.fil")
y = Your("temp.fil")
assert y.your_header.nspectra == 2
assert y.your_header.nchans == 190
assert (y.get_data(0, 2) -
your_object.get_data(1, 2)[:, 10:200]).sum() == 0
os.remove("temp.fil")
# test without outname
w = Writer(your_object, nstart=0, nsamp=10, outdir="./", flag_rfi=True)
w.to_fil()
assert os.path.isfile("small_converted.fil")
y = Your("small_converted.fil")
assert y.your_header.nspectra == 10
assert y.your_header.nchans == your_object.your_header.nchans
os.remove("small_converted.fil")
def test_fil_to_fits():
file = os.path.join(_install_dir, "data/small.fil")
f = Your(file)
w = Writer(
f,
outname="temp",
outdir="./",
flag_rfi=False,
zero_dm_subt=False,
nstart=1,
nsamp=2,
c_min=40,
c_max=200,
)
# test with outname
w.to_fits()
assert os.path.isfile("temp.fits")
y = Your("temp.fits")
assert y.your_header.nspectra == 2
assert y.your_header.nchans == 160
assert (y.get_data(0, 2) - f.get_data(1, 2)[:, 40:200]).sum() == 0
os.remove("temp.fits")
# test without outname
w = Writer(f, outdir="./", flag_rfi=True, zero_dm_subt=True)
w.to_fits()
assert os.path.isfile("small_converted.fits")
y = Your("small_converted.fits")
assert y.your_header.nchans == f.your_header.nchans
ns = y.your_header.nspectra
os.remove("small_converted.fits")
def test_fits_to_fil():
# from fits
file = os.path.join(_install_dir, "data/small.fits")
f = Your(file)
w = Writer(f,
nstart=0,
nsamp=1,
outname="temp",
outdir="./",
c_min=0,
c_max=200)
# test with outname
w.to_fil()
assert os.path.isfile("temp.fil")
y = Your("temp.fil")
assert y.your_header.nspectra == 1
assert y.your_header.nchans == 200
assert (y.get_data(0, 1) - f.get_data(0, 1)[:, 0:200]).sum() == 0
os.remove("temp.fil")
# test without outname
w = Writer(f, outdir="./")
w.to_fil()
assert os.path.isfile("small_converted.fil")
y = Your("small_converted.fil")
assert y.your_header.nspectra == f.your_header.nspectra
ns = y.your_header.nspectra
assert y.your_header.nchans == f.your_header.nchans
assert (y.get_data(0, ns) - f.get_data(0, ns)).sum() == 0
os.remove("small_converted.fil")
def test_fil_to_fil():
# from fil
file = os.path.join(_install_dir, 'data/small.fil')
f = Your(file)
w = Writer(f)
# test with outname
w.to_fil(nstart=0,
nsamp=2,
outname='temp.fil',
c=[0, 200],
outdir='./',
flag_rfi=True,
zero_dm_subt=True)
assert os.path.isfile('temp.fil')
y = Your('temp.fil')
assert y.your_header.nspectra == 2
assert y.your_header.nchans == 200
os.remove('temp.fil')
# test without outname
w.to_fil(nstart=0, nsamp=1, outdir='./')
assert os.path.isfile('small_converted.fil')
y = Your('small_converted.fil')
assert y.your_header.nspectra == 1
assert y.your_header.nchans == f.your_header.nchans
os.remove('small_converted.fil')
def test_your_from_fits():
fits_file = os.path.join(_install_dir, 'data/28.fits')
fits_obj = Your(fits_file)
assert fits_obj.nchans == 336
fits_file = os.path.join(_install_dir, 'data/28.fits')
fits_obj = Your([fits_file])
assert fits_obj.nchans == 336
def test_your_from_fil():
fil_file = os.path.join(_install_dir, 'data/28.fil')
fil_obj = Your(fil_file)
print(fil_obj)
assert fil_obj.nchans == 336
fil_file = os.path.join(_install_dir, 'data/28.fil')
fil_obj = Your([fil_file])
assert fil_obj.nchans == 336
def _main():
from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter
parser = ArgumentParser(description='Script description', formatter_class=ArgumentDefaultsHelpFormatter)
parser.add_argument('-v', '--verbose', dest='verbose', action='store_true', help='Be verbose')
parser.add_argument('-o', '--output',type=str, default="_cutout",help='Output File Name')
parser.add_argument('-d', '--outdir',type=str, default="./",help='Output Directory')
parser.add_argument('-f','--fch1',type=int, default=0,help='split band start (freq)')
parser.add_argument('-c','--nchan',type=int, default=336,help='number of channels')
parser.add_argument('-x','--tstart',type=int, default=0,help='split band start (time)')
parser.add_argument('-s','--samples',type=int, default=-1,help='number of samples -1 for entire length')
parser.add_argument('-m', '--mode',type=int, default=0,help='Output File Format, 0 -- filterbank ; 1 -- fits')
parser.add_argument(dest='files', nargs='+')
parser.set_defaults(verbose=False)
values = parser.parse_args()
for fil in values.files:
original_file=Your(fil)
length=original_file.your_header.nspectra
if values.samples==-1:
cut_L=length
else:
cut_L=values.samples
writer_object = Writer(
original_file,
nstart=values.tstart,
nsamp=cut_L,
c_min=values.fch1,
c_max=values.fch1+values.nchan,
outdir=values.outdir,
outname=values.output)
print(f"writing cutout from {fil} to new file")
if values.mode == 0:
writer_object.to_fil()
elif values.mode == 1:
writer_object.to_fits()
def read_header(f):
y = Your(f)
dic = vars(y.your_header)
dic['tsamp'] = y.your_header.tsamp
dic['nchans'] = y.your_header.nchans
dic['foff'] = y.your_header.foff
dic['nspectra'] = y.your_header.nspectra
nice_print(dic)
def read_header(f):
y = Your(f)
dic = vars(y.your_header)
dic["tsamp"] = y.your_header.tsamp
dic["nchans"] = y.your_header.nchans
dic["channel_bandwidth"] = y.your_header.foff
dic["nspectra"] = y.your_header.nspectra
nice_print(dic)
def test_fits_to_fits():
file = os.path.join(_install_dir, 'data/small.fits')
f = Your(file)
w = Writer(f)
# test with outname
w.to_fits(outname='temp.fits', outdir='./', nstart=0, nsamp=2)
assert os.path.isfile('temp.fits')
y = Your('temp.fits')
assert y.your_header.nspectra == 2
assert y.your_header.nchans == f.your_header.nchans
os.remove('temp.fits')
# test without outname
w.to_fits(outdir='./', c=[0, 10])
assert os.path.isfile('small_converted.fits')
y = Your('small_converted.fits')
assert y.your_header.nchans == 10
os.remove('small_converted.fits')
def test_4pol_fits_to_fits():
file = os.path.join(_install_dir, "data/test_4pol.fits")
your_obj = Your(file)
w = Writer(your_obj,
nstart=1,
nsamp=20,
gulp=20,
outname="temp_4pol",
outdir="./",
npoln=4)
w.to_fits()
y = Your("temp_4pol.fits")
assert y.your_header.nspectra == 20
assert y.your_header.nchans == your_obj.your_header.nchans
assert (y.get_data(0, 5, npoln=4) -
your_obj.get_data(1, 5, npoln=4)).sum() == 0
os.remove("temp_4pol.fits")
def test_incorrect_sigmas(fil_file):
your_object = Your(fil_file)
data = your_object.get_data(0, 1024)
with pytest.raises(ValueError):
sk_sg_filter(data, your_object, -1, 1, 1)
with pytest.raises(ValueError):
sk_sg_filter(data, your_object, 3, 15, -1)
with pytest.raises(ValueError):
sk_sg_filter(data, your_object, 0, 15, 0)
def test_save_bandpass():
fil_file = os.path.join(_install_dir, "data/28.fil")
y = Your(fil_file)
bandpass = y.bandpass()
mask = np.zeros_like(bandpass, dtype=np.bool)
mask[:10] = True
save_bandpass(y, bandpass, outname="28_bp.png")
assert os.path.isfile("28_bp.png")
os.remove("28_bp.png")
save_bandpass(y, bandpass, mask=mask)
assert os.path.isfile("28_bandpass.png")
os.remove("28_bandpass.png")
def read_header(f, no_table):
"""
Makes your header for given files, hands header off to be nicely printed
Inputs:
--
f -- files to create the your header
no_table -- bool - if true, don't use rich.table
"""
y = Your(f)
dic = vars(y.your_header)
dic["tsamp"] = y.your_header.tsamp
dic["nchans"] = y.your_header.nchans
dic["channel_bandwidth"] = y.your_header.foff
dic["nspectra"] = y.your_header.nspectra
if no_table:
nice_print(dic)
else:
table_print(dic)
def test_4pol():
file = os.path.join(_install_dir, "data/test_4pol.fits")
y = Your(file)
data = y.get_data(0, 100, npoln=1)
assert data.shape == (100, 512)
data = y.get_data(0, 100, npoln=4)
assert data.shape == (100, 4, 512)
data = y.get_data(0,
100,
npoln=4,
time_decimation_factor=2,
frequency_decimation_factor=2)
assert data.shape == (50, 4, 256)
with pytest.raises(ValueError):
y.get_data(0, 100, npoln=3)
with pytest.raises(ValueError):
y.get_data(0, 100, pol=5)
def _main():
from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter
parser = ArgumentParser(description='Script description',
formatter_class=ArgumentDefaultsHelpFormatter)
parser.add_argument('-v',
'--verbose',
dest='verbose',
action='store_true',
help='Be verbose')
parser.add_argument('-o',
'--output',
type=str,
default="test",
help='Output File Name')
# parser.add_argument('--ra',type=float, default=51436.202,help='RA')
# parser.add_argument('--dec',type=float, default=270330.24,help='Dec')
# parser.add_argument('-c','--ch1',type=int, default=0,help='starting channel')
# parser.add_argument('-n','--nchans',type=int, default=8192,help='total channels')
# parser.add_argument('-b','--bin',type=int, default=1,help='tscrunch samples per bin, must be dividend of subintegration?')
# parser.add_argument('--fbin',type=int, default=1,help='fscrunch samples per bin')
# parser.add_argument('-N','--segments',type=int, default=20,help='how many files per filterbank segment')
parser.add_argument(dest='files', nargs='+')
parser.set_defaults(verbose=False)
values = parser.parse_args()
for fil in values.files:
original_file = Your(fil)
length = original_file.your_header.nspectra
writer_object = Writer(
original_file,
nstart=0,
nsamp=length,
# c_min=0,
# c_max=100,
outdir=".",
outname=values.output)
writer_object.to_fits()
def bandpass(f, time=0, nspectra=8192, outname=None):
"""
Plots and saves the bandpass
Args:
f: File to read
time: Time in seconds to read for bandpass
nspectra: Number of spectra to read for bandpass
"""
y = Your(f)
if time > 0:
ns = time // y.your_header.native_tsamp
else:
ns = nspectra
bandpass = y.bandpass(nspectra=ns)
save_bandpass(y,
bandpass,
chan_nos=None,
mask=None,
outdir=None,
outname=outname)
def test_unsupported_file():
with pytest.raises(TypeError):
Your(os.path.join(_install_dir, "data/some.blah"))
with pytest.raises(TypeError):
Your([os.path.join(_install_dir, "data/some.blah")])
def test_paths():
with pytest.raises(ValueError):
Your(bytearray("data/28.fil", "utf-8"))
def test_your_header(fits_file):
fits_obj = Your(fits_file)
print(fits_obj.your_header)
assert True
def your_object():
file = os.path.join(_install_dir, "data/small.fil")
return Your(file)
def test_repr(fil_file):
y = Your(fil_file)
assert repr(y) == f"Using <class 'str'>:\n{fil_file}"
'--sigma',
help='Sigma for the savgol filter',
required=False,
default=[6],
type=float,
nargs='+')
parser.add_argument('-o',
'--output_dir',
help='Output dir for heimdall candidates',
type=str,
required=False,
default='.')
args = parser.parse_args()
your_object = Your(file=args.files)
if args.apply_savgol:
bandpass = your_object.bandpass(nspectra=8192)
chan_nos = np.arange(0, bandpass.shape[0], dtype=np.int)
for fw, sig in zip(args.filter_window, args.sigma):
mask = savgol_filter(bandpass,
your_object.your_header.foff,
fw=fw,
sig=sig)
basename = f'{args.output_dir}/{your_object.your_header.basename}_w{fw}_sig{sig}'
save_bandpass(your_object,
bandpass,
chan_nos=chan_nos,
mask=mask,
outdir=args.output_dir + '/',
log_filename = values.outdir + '/' + datetime.utcnow().strftime(
'writer_%Y_%m_%d_%H_%M_%S_%f.log')
if values.verbose:
logging.basicConfig(filename=log_filename,
level=logging.DEBUG,
format=logging_format)
else:
logging.basicConfig(filename=log_filename,
level=logging.INFO,
format=logging_format)
logging.info("Input Arguments:-")
for arg, value in sorted(vars(values).items()):
logging.info("Argument %s: %r", arg, value)
y = Your(values.files)
w = Writer(y)
if values.type == 'fits':
w.to_fits(c=values.chans,
nstart=values.nstart,
nsamp=values.nsamp,
outdir=values.outdir,
outname=values.out_name,
progress=values.no_progress,
flag_rfi=values.flag_rfi,
sk_sig=values.sk_sig,
sg_fw=values.sg_fw,
sg_sig=values.sg_sig,
zero_dm_subt=values.zero_dm_subt)
elif values.type == 'fil':
def test_save_bandpass():
fil_file = os.path.join(_install_dir, 'data/28.fil')
y = Your(fil_file)
save_bandpass(y, y.bandpass(), outname='28_bp.png')
assert os.path.isfile('28_bp.png')
os.remove('28_bp.png')
def test_save_bandpass():
fil_file = os.path.join(_install_dir, "data/28.fil")
y = Your(fil_file)
save_bandpass(y, y.bandpass(), outname="28_bp.png")
assert os.path.isfile("28_bp.png")
os.remove("28_bp.png")
def test_your_no_file():
try:
f = Your([])
except ValueError:
assert True
def test_your_header():
fits_file = os.path.join(_install_dir, 'data/28.fits')
fits_obj = Your(fits_file)
print(fits_obj.your_header)
assert True
level=logging.DEBUG,
format=logging_format,
handlers=[RichHandler(rich_tracebacks=True)],
)
else:
logging.basicConfig(
level=logging.INFO,
format=logging_format,
handlers=[RichHandler(rich_tracebacks=True)],
)
logging.info("Input Arguments:-")
for arg, value in sorted(vars(values).items()):
logging.info("%s: %r", arg, value)
your_object = Your(file=values.files)
max_delay = your_object.dispersion_delay(dms=np.max(values.dm))
dispersion_delay_samples = np.ceil(max_delay /
your_object.your_header.tsamp)
logging.info(f"Max Dispersion delay = {max_delay} s")
logging.info(f"Max Dispersion delay = {dispersion_delay_samples} samples")
if your_object.your_header.nspectra < 2**18:
nsamps_gulp = your_object.your_header.nspectra
else:
nsamps_gulp = int(
np.max([(2**np.ceil(np.log2(dispersion_delay_samples))), 2**18]))
if values.channel_end > 0:
c_max = values.channel_end
else:
def load_file(self,
file_name=[""],
start_samp=0,
gulp_size=1024,
chan_std=False):
"""
Loads data from a file:
Inputs:
file_name -- name or list of files to load, if none given user must use gui to give file
start_samp -- sample number where to start show the file, defaults to the beginning of the file
gulp_size -- amount of data to show at a given time
"""
self.start_samp = start_samp
self.gulp_size = gulp_size
self.chan_std = chan_std
if len(file_name) == 0:
file_name = filedialog.askopenfilename(
filetypes=(("fits/fil files", "*.fil *.fits"), ("All files",
"*.*")))
logging.info(f"Reading file {file_name}.")
self.your_obj = Your(file_name)
self.master.title(self.your_obj.your_header.basename)
logging.info(f"Printing Header parameters")
self.get_header()
if self.dm != 0:
self.dispersion_delays = calc_dispersion_delays(
self.dm, self.your_obj.chan_freqs)
max_delay = np.max(np.abs(self.dispersion_delays))
if max_delay > self.gulp_size * self.your_obj.your_header.native_tsamp:
logging.warning(
f"Maximum dispersion delay for DM ({self.dm}) = {max_delay:.2f}s is greater than "
f"the input gulp size {self.gulp_size*self.your_obj.your_header.native_tsamp}s. Pulses may not be "
f"dedispersed completely.")
logging.warning(
f"Use gulp size of {int(max_delay//self.your_obj.your_header.native_tsamp):0d} to "
f"dedisperse completely.")
self.read_data()
# create three plots, for ax1=time_series, ax2=dynamic spectra, ax4=bandpass
self.gs = gridspec.GridSpec(2,
2,
width_ratios=[4, 1],
height_ratios=[1, 4],
wspace=0.02,
hspace=0.03)
ax1 = plt.subplot(self.gs[0, 0])
ax2 = plt.subplot(self.gs[1, 0])
ax3 = plt.subplot(self.gs[0, 1])
ax4 = plt.subplot(self.gs[1, 1])
ax3.axis("off")
ax1.set_xticks([])
ax4.set_yticks([])
# get the min and max image values to that we can see the typical values well
self.vmax = min(np.max(self.data),
np.median(self.data) + 5 * np.std(self.data))
self.vmin = max(np.min(self.data),
np.median(self.data) - 5 * np.std(self.data))
self.im_ft = ax2.imshow(self.data,
aspect="auto",
vmin=self.vmin,
vmax=self.vmax)
# make bandpass
bp_std = np.std(self.data, axis=1)
bp_y = np.linspace(self.your_obj.your_header.nchans, 0,
len(self.bandpass))
(self.im_bandpass, ) = ax4.plot(self.bandpass, bp_y, label="Bandpass")
if self.chan_std:
self.im_bp_fill = ax4.fill_betweenx(
x1=self.bandpass - bp_std,
x2=self.bandpass + bp_std,
y=bp_y,
interpolate=False,
alpha=0.25,
color="r",
label="1 STD",
)
ax4.legend()
ax4.set_ylim([-1, len(self.bandpass) + 1])
ax4.set_xlabel("Avg. Arb. Flux")
# make time series
ax4.set_xlabel("Avg. Arb. Flux")
(self.im_time, ) = ax1.plot(self.time_series)
ax1.set_xlim(-1, len(self.time_series + 1))
ax1.set_ylabel("Avg. Arb. Flux")
plt.colorbar(self.im_ft, orientation="vertical", pad=0.01, aspect=30)
ax = self.im_ft.axes
ax.set_xlabel("Time [sec]")
ax.set_ylabel("Frequency [MHz]")
ax.set_yticks(np.linspace(0, self.your_obj.your_header.nchans, 8))
yticks = [
str(int(j)) for j in np.linspace(self.your_obj.chan_freqs[0],
self.your_obj.chan_freqs[-1], 8)
]
ax.set_yticklabels(yticks)
self.set_x_axis()
# a tk.DrawingArea
self.canvas = FigureCanvasTkAgg(self.im_ft.figure, master=root)
self.canvas.draw()
self.canvas.get_tk_widget().pack(side=TOP, fill=BOTH, expand=1)