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AlecThomson committed Dec 1, 2023
1 parent 74d844d commit b3938d2
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Showing 14 changed files with 11 additions and 44 deletions.
4 changes: 1 addition & 3 deletions scripts/casda_prepare.py
Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,6 @@
import tarfile
import time
from glob import glob
from typing import Dict

import astropy.units as u
import matplotlib.pyplot as plt
Expand All @@ -25,7 +24,6 @@
from dask import delayed
from dask.distributed import Client, LocalCluster
from dask_mpi import initialize
from IPython import embed
from prefect_dask import get_dask_client
from radio_beam import Beam
from spectral_cube.cube_utils import convert_bunit
Expand Down Expand Up @@ -240,7 +238,7 @@ def convert_spectra(
spectrum_table.table.add_column(new_col)

outf = os.path.join(
spec_dir, os.path.basename(spectrum).replace(".dat", f"_polspec.fits")
spec_dir, os.path.basename(spectrum).replace(".dat", "_polspec.fits")
)
logger.info(f"Saving to {outf}")
spectrum_table.write_FITS(outf, overwrite=True)
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8 changes: 1 addition & 7 deletions scripts/check_cutout.py
Original file line number Diff line number Diff line change
Expand Up @@ -5,13 +5,7 @@
import astropy.units as u
import matplotlib.pyplot as plt
from astropy.table import Table
from astropy.visualization import (
ImageNormalize,
LogStretch,
MinMaxInterval,
SqrtStretch,
ZScaleInterval,
)
from astropy.visualization import ImageNormalize, MinMaxInterval, SqrtStretch
from matplotlib.patches import Ellipse
from spectral_cube import SpectralCube

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2 changes: 1 addition & 1 deletion scripts/compare_leakage.py
Original file line number Diff line number Diff line change
Expand Up @@ -119,7 +119,7 @@ def interpolate(field, comp, beams, cutdir, septab, holofile, verbose=True):

data[bm].update({f"{s}_holo": holo_spec})
data[bm].update({f"{s}_image": im_spec})
data[bm].update({f"freq": freq})
data[bm].update({"freq": freq})

try:
outname = make_plot(data, comp, imfile)
Expand Down
9 changes: 2 additions & 7 deletions scripts/compute_leakage.py
Original file line number Diff line number Diff line change
@@ -1,20 +1,15 @@
#!/usr/bin/env python3
import json

import astropy
import astropy.units as units
import matplotlib.pyplot as plt
import numpy as np
import pymongo
from astropy.coordinates import SkyCoord
from astropy.io import fits
from astropy.wcs import WCS
from tqdm.auto import tqdm, trange

from arrakis.logger import logger, logging
from arrakis.logger import logger
from arrakis.utils.database import get_db
from arrakis.utils.fitsutils import getdata
from arrakis.utils.json import MyEncoder


def makesurf(start, stop, field, datadir, save_plots=True, data=None):
Expand Down Expand Up @@ -265,7 +260,7 @@ def cli():
import getpass

# Help string to be shown using the -h option
descStr = f"""
descStr = """
Make leakage plots for a field.
"""
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8 changes: 1 addition & 7 deletions scripts/copy_cutouts.py
Original file line number Diff line number Diff line change
@@ -1,14 +1,8 @@
import argparse
import os
import shlex
import subprocess as sb
from glob import glob
from pprint import pprint

import copy_data
import numpy as np
import spica
from astropy.table import Table

from arrakis.logger import logger, logging
from arrakis.utils.io import try_mkdir
Expand Down Expand Up @@ -49,7 +43,7 @@ def main(field, dry_run=False, ncores=10):


def cli():
descStr = f"""
descStr = """
Copy data from RACS area to SPICE area'
"""
parser = argparse.ArgumentParser(
Expand Down
8 changes: 1 addition & 7 deletions scripts/copy_cutouts_askap.py
Original file line number Diff line number Diff line change
@@ -1,14 +1,8 @@
import argparse
import os
import shlex
import subprocess as sb
from glob import glob
from pprint import pprint

import copy_data
import numpy as np
import spica
from astropy.table import Table

from arrakis.logger import logger, logging
from arrakis.utils.io import try_mkdir
Expand Down Expand Up @@ -58,7 +52,7 @@ def main(field, dry_run=False, ncores=10):


def cli():
descStr = f"""
descStr = """
Copy data from RACS area to SPICE area'
"""
parser = argparse.ArgumentParser(
Expand Down
2 changes: 1 addition & 1 deletion scripts/copy_data.py
Original file line number Diff line number Diff line change
Expand Up @@ -82,7 +82,7 @@ def main(


def cli():
descStr = f"""
descStr = """
Copy data from RACS area to SPICE area'
"""
parser = argparse.ArgumentParser(
Expand Down
1 change: 0 additions & 1 deletion scripts/find_row.py
Original file line number Diff line number Diff line change
@@ -1,6 +1,5 @@
#!/usr/bin/env python3
import argparse
import os
from pathlib import Path

from astropy.table import Table
Expand Down
3 changes: 1 addition & 2 deletions scripts/find_sbid.py
Original file line number Diff line number Diff line change
@@ -1,9 +1,8 @@
#!/usr/bin/env python3
import argparse
import os
from pathlib import Path

from astropy.table import Row, Table
from astropy.table import Table

from arrakis.logger import logger, logging

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4 changes: 1 addition & 3 deletions scripts/fix_dr1_cat.py
Original file line number Diff line number Diff line change
Expand Up @@ -7,12 +7,10 @@

import astropy.units as u
import numpy as np
import pkg_resources
from astropy.coordinates import SkyCoord
from astropy.table import Column, Table
from astropy.time import Time
from astropy.units import cds
from IPython import embed
from rmtable import RMTable
from spica import SPICA

Expand Down Expand Up @@ -198,7 +196,7 @@ def main(cat: str, survey_dir: Path, epoch: int = 0):
_, ext = os.path.splitext(cat)
outfile = cat.replace(ext, f".corrected{ext}")

outfit = cat.replace(ext, f".corrected.leakage.pkl")
outfit = cat.replace(ext, ".corrected.leakage.pkl")
with open(outfit, "wb") as f:
pickle.dump(fit, f)
logger.info(f"Wrote leakage fit to {outfit}")
Expand Down
1 change: 0 additions & 1 deletion scripts/fix_src_cat.py
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,6 @@
import numpy as np
from astropy.coordinates import SkyCoord
from astropy.table import Table
from IPython import embed
from tqdm.auto import tqdm

from arrakis.logger import logger
Expand Down
2 changes: 1 addition & 1 deletion scripts/make_links.py
Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@ def main(indir, outdir):


def cli():
descStr = f"""
descStr = """
Create symlinks to ASKAP cubes in one directory to another.
"""
# Parse the command line options
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2 changes: 0 additions & 2 deletions scripts/spica.py
Original file line number Diff line number Diff line change
Expand Up @@ -3,11 +3,9 @@
import subprocess as sb
from glob import glob
from pathlib import Path
from pprint import pprint

import copy_data
import numpy as np
import pkg_resources
from astropy.table import Table

from arrakis.logger import logger, logging
Expand Down
1 change: 0 additions & 1 deletion scripts/tar_cubelets.py
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,6 @@

import dask
from dask import delayed
from dask.distributed import Client
from tqdm.auto import tqdm

from arrakis.logger import logger
Expand Down

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