Source code for srttools.read_config
"""Read the configuration file."""
import os
import glob
import warnings
import numpy as np
import astropy.units as u
# For Python 2 and 3 compatibility
try:
import configparser
except ImportError:
import ConfigParser as configparser
__all__ = ["sample_config_file", "get_config_file", "read_config"]
SRT_tools_config_file = None
SRT_tools_config = None
[docs]def sample_config_file(fname="sample_config_file.ini"):
"""Create a sample config file, to be modified by hand."""
string = """
[local]
; the directory where the analysis will be executed.
workdir : .
; the root directory of the data repository.
datadir : .
; the root directory of the data repository.
productdir : None
[analysis]
projection : ARC
interpolation : spline
prefix : test_
list_of_directories :
;;Two options: either a list of directories:
; dir1
; dir2
;; or a star symbol for all directories
; *
calibrator_directories :
; if left empty, calibrator scans are taken from list_of_directories when
; calculating light curves, and ignored when calculating images
skydip_directories :
; if left empty, calibrator scans are taken from list_of_directories when
; calculating light curves, and ignored when calculating images
noise_threshold : 5
;; For spectral rms smoothing, in percentage of then number of spectral bins.
smooth_window : 0.05
;; Coordinates have to be specified in decimal degrees. ONLY use if different
;; from target coordinates!
; reference_ra : 10.5
; reference_dec : 5.3
;; Pixel size in arcminutes
pixel_size : 1
;; Channels to save from RFI filtering. It might indicate known strong spectral
;; lines
goodchans :
[debugging]
debug_file_format : jpg
"""
with open(fname, "w") as fobj:
print(string, file=fobj)
return fname
[docs]def get_config_file():
"""Get the current config file."""
return SRT_tools_config_file
[docs]def read_config(fname=None):
"""Read a config file and return a dictionary of all entries."""
global SRT_tools_config_file, SRT_tools_config
# --- If already read, use existing config ---
if fname == SRT_tools_config_file and SRT_tools_config is not None:
return SRT_tools_config
if fname is None and SRT_tools_config is not None:
return SRT_tools_config
# ---------------------------------------------
config_output = {}
Config = configparser.ConfigParser()
if fname is None:
fname = sample_config_file()
else:
if not os.path.exists(fname):
raise FileNotFoundError("Please specify an existing config file")
SRT_tools_config_file = fname
Config.read(fname)
# ---------- Set default values --------------------------------------
config_output["projection"] = "ARC"
config_output["interpolation"] = "linear"
config_output["workdir"] = os.path.abspath(os.curdir) + "/"
config_output["datadir"] = os.path.abspath(os.curdir) + "/"
config_output["productdir"] = None
config_output["list_of_directories"] = "*"
config_output["calibrator_directories"] = []
config_output["skydip_directories"] = []
config_output["pixel_size"] = "1"
config_output["goodchans"] = None
config_output["filtering_factor"] = "0"
config_output["noise_threshold"] = "5"
config_output["smooth_window"] = "0.05"
config_output["debug_file_format"] = "jpg"
config_output["ignore_suffix"] = []
config_output["ignore_prefix"] = []
# --------------------------------------------------------------------
# Read local information
local_params = dict(Config.items("local"))
config_output.update(local_params)
if not config_output["workdir"].startswith("/"):
config_output["workdir"] = os.path.abspath(
os.path.join(os.path.split(fname)[0], config_output["workdir"])
)
if not config_output["datadir"].startswith("/"):
config_output["datadir"] = os.path.abspath(
os.path.join(os.path.split(fname)[0], config_output["datadir"])
)
if config_output["productdir"] is not None and config_output["productdir"].lower() == "none":
config_output["productdir"] = None
if config_output["productdir"] is not None and not config_output["productdir"].startswith("/"):
config_output["productdir"] = os.path.abspath(
os.path.join(os.path.split(fname)[0], config_output["productdir"])
)
try:
# Read analysis information
debugging_params = dict(Config.items("debugging"))
config_output.update(debugging_params)
except configparser.NoSectionError:
pass
# Read analysis information
analysis_params = dict(Config.items("analysis"))
config_output.update(analysis_params)
try:
config_output["list_of_directories"] = [
s for s in analysis_params["list_of_directories"].splitlines() if s.strip()
] # This last instruction eliminates blank lines
except Exception:
warnings.warn("Invalid list_of_directories in config file")
try:
config_output["calibrator_directories"] = [
s for s in analysis_params["calibrator_directories"].splitlines() if s.strip()
] # This last instruction eliminates blank lines
except Exception:
warnings.warn("Invalid calibrator_directories in config file")
try:
config_output["skydip_directories"] = [
s for s in analysis_params["skydip_directories"].splitlines() if s.strip()
] # This last instruction eliminates blank lines
except Exception:
warnings.warn("Invalid skydip_directories in config file")
for key in config_output.keys():
if isinstance(config_output[key], str) and "\n" in config_output[key]:
config_output[key] = [s for s in config_output[key].splitlines() if s.strip()]
# If the list of directories is not specified, or if a '*' symbol is used,
# use glob in the datadir to determine the list
if config_output["list_of_directories"] in ([], ["*"], "*"):
config_output["list_of_directories"] = [
os.path.split(f)[1] # return name without path
for f in glob.glob(os.path.join(config_output["datadir"], "*"))
if os.path.isdir(f)
] # only if it's a directory
config_output["pixel_size"] = float(np.radians(float(config_output["pixel_size"]) / 60)) * u.rad
if config_output["goodchans"] is not None:
config_output["goodchans"] = [int(n) for n in config_output["goodchans"]]
config_output["noise_threshold"] = float(config_output["noise_threshold"])
config_output["smooth_window"] = float(config_output["smooth_window"])
config_output["filtering_factor"] = float(config_output["filtering_factor"])
SRT_tools_config = config_output
return config_output
