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authorAaron LI <aly@aaronly.me>2017-12-05 11:09:52 +0800
committerAaron LI <aly@aaronly.me>2017-12-05 11:09:52 +0800
commite44ca5fe5a638bd92459e12e6f0c2a864abc813e (patch)
tree2a954d1292af0c90fd81e62a96f5e3e2ab84144b /astro/fits
parent1b7be103d847011f5c4cd810f68804f0a40ff39f (diff)
downloadatoolbox-e44ca5fe5a638bd92459e12e6f0c2a864abc813e.tar.bz2
astro/fitscube.py: Implement "calibrate" sub-command
Diffstat (limited to 'astro/fits')
-rwxr-xr-xastro/fits/fitscube.py111
1 files changed, 111 insertions, 0 deletions
diff --git a/astro/fits/fitscube.py b/astro/fits/fitscube.py
index bdaca11..c2f9948 100755
--- a/astro/fits/fitscube.py
+++ b/astro/fits/fitscube.py
@@ -190,6 +190,14 @@ class FITSCube:
cs1, cs2 = csize//2, (csize+1)//2
return self.data[i, (rc-cs1):(rc+cs2), (cc-cs1):(cc+cs2)]
+ def apply_gain(self, gain):
+ """
+ Multiply the supplied ``gain`` to each slice, to achieve slice
+ or channel response calibration or corruption.
+ """
+ gain = np.asarray(gain)
+ self.data *= gain[:, np.newaxis, np.newaxis]
+
@property
def unit(self):
"""
@@ -262,6 +270,74 @@ def cmd_create(args):
print("Created FITS cube: %s" % args.outfile)
+def cmd_calibrate(args):
+ """
+ Sub-command: "calibrate", calibrate the z-axis slice/channel responses
+ by fitting a polynomial.
+ """
+ if not args.dryrun:
+ if args.outfile is None:
+ raise ValueError("--outfile required")
+ elif not args.clobber and os.path.exists(args.outfile):
+ raise OSError("output file already exists: %s" % args.outfile)
+
+ cube = FITSCube(args.infile)
+ zvalues = cube.zvalues
+ print("Data cube unit: %s" % cube.unit)
+ print("Image/slice size: %dx%d" % (cube.width, cube.height))
+ print("Number of slices: %d" % cube.nslice)
+ mean = np.zeros(cube.nslice)
+ std = np.zeros(cube.nslice)
+ for i in range(cube.nslice):
+ image = cube.get_slice(i, csize=args.center)
+ if args.abs:
+ image = np.abs(image)
+ threshold = np.percentile(image, q=100*args.threshold)
+ data = image[image >= threshold]
+ mean[i] = np.mean(data)
+ std[i] = np.std(data)
+ print("Fitting polynomial order: %d" % args.poly_order)
+ weights = 1.0 / std
+ pfit = np.polyfit(zvalues, mean, w=weights, deg=args.poly_order)
+ mean_new = np.polyval(pfit, zvalues)
+ coef = mean_new / mean
+
+ if args.dryrun:
+ print("*** DRY RUN MODE ***")
+ else:
+ print("Applying slice/channel calibration gains ...")
+ cube.apply_gain(coef)
+ print("Saving calibrated FITS cube ...")
+ cube.write(args.outfile, clobber=args.clobber)
+ print("Calibrated FITS cube wrote to: %s" % args.outfile)
+
+ print("Slice <z> <mean.old> +/- <std.old> " +
+ "<mean.new> <gain.coef>")
+ for i, z in enumerate(zvalues):
+ print("* %12.4e: %-12.4e %-12.4e %-12.4e %.6f" %
+ (z, mean[i], std[i], mean_new[i], coef[i]))
+
+ if args.cal_out:
+ data = np.column_stack([zvalues, mean, std, mean_new, coef])
+ header = [
+ "Parameters:",
+ "+ center: %s" % args.center,
+ "+ abs: %s" % args.abs,
+ "+ threshold (percentile): %.2f" % args.threshold,
+ "+ polynomial_order: %d" % args.poly_order,
+ "",
+ "Columns:",
+ "+ z/frequency: z-axis position / frequency [%s]" % cube.zunit,
+ "+ mean.old: mean before calibration [%s]" % cube.unit,
+ "+ std.old: standard deviation before calibration",
+ "+ mean.new: mean after calibration",
+ "+ gain_coef: calibration coefficient",
+ "",
+ ]
+ np.savetxt(args.cal_out, data, header="\n".join(header))
+ print("Saved calibration data to file: %s" % args.cal_out)
+
+
def main():
parser = argparse.ArgumentParser(
description="Create FITS cube from a series of image slices.")
@@ -305,6 +381,41 @@ def main():
nargs="+", required=True,
help="input image slices (in order)")
parser_create.set_defaults(func=cmd_create)
+ # sub-command: "calibrate"
+ parser_cal = subparsers.add_parser(
+ "calibrate",
+ help="calibrate z-axis slice/channel responses by fitting " +
+ "a polynomial")
+ parser_cal.add_argument("-n", "--dry-run", dest="dryrun",
+ action="store_true",
+ help="dry run mode")
+ parser_cal.add_argument("-C", "--clobber", dest="clobber",
+ action="store_true",
+ help="overwrite existing output file")
+ parser_cal.add_argument("-c", "--center", dest="center", type=int,
+ help="crop the central box region of specified " +
+ "size to calculate the mean/std.")
+ parser_cal.add_argument("-t", "--threshold", dest="threshold",
+ type=float, default=0.0,
+ help="percentile threshold (0 -> 1) and only " +
+ "considers image pixels with values > threshold " +
+ "to determine the channel/slice responses; " +
+ "(default: 0, i.e., all pixels are accounted for)")
+ parser_cal.add_argument("-a", "--abs", dest="abs", action="store_true",
+ help="take absolute values for image pixels")
+ parser_cal.add_argument("-p", "--poly-order", dest="poly_order",
+ type=int, default=2,
+ help="order of polynomial used for fitting " +
+ "(default: 2, i.e., quadratic)")
+ parser_cal.add_argument("-i", "--infile", dest="infile", required=True,
+ help="input FITS cube filename")
+ parser_cal.add_argument("-o", "--outfile", dest="outfile",
+ help="output calibrated FITS cube (optional " +
+ "for dry-run model)")
+ parser_cal.add_argument("-O", "--cal-out", dest="cal_out",
+ help="output TXT file to save the calibration " +
+ "coefficients for each channel/slice")
+ parser_cal.set_defaults(func=cmd_calibrate)
#
args = parser.parse_args()
args.func(args)