Tibeuleu/FOC_Reduction
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Merge branch 'test' into main

Browse Source
This commit is contained in:
sugar_jo
2024-07-16 21:39:25 +08:00
committed by GitHub
parent 62aef1b1c4 163f37d5b2
commit 3c8ca6ac1a
16 changed files with 3029 additions and 1595 deletions
Download Patch File Download Diff File Expand all files Collapse all files

66
package/FOC_reduction.py
View File

@@ -22,16 +22,17 @@ from lib.utils import sci_not, princ_angle
def main(target=None, proposal_id=None, data_dir=None, infiles=None, output_dir="./data", crop=False, interactive=False):
# Reduction parameters
# Deconvolution
deconvolve = False
if deconvolve:
# from lib.deconvolve import from_file_psf
psf = 'gaussian' # Can be user-defined as well
psf = "gaussian" # Can be user-defined as well
# psf = from_file_psf(data_folder+psf_file)
psf_FWHM = 3.1
psf_scale = 'px'
psf_scale = "px"
psf_shape = None # (151, 151)
iterations = 1
algo = "conjgrad"
@@ -40,18 +41,20 @@ def main(target=None, proposal_id=None, data_dir=None, infiles=None, output_dir=
display_crop = False
# Background estimation
error_sub_type = 'freedman-diaconis' # sqrt, sturges, rice, scott, freedman-diaconis (default) or shape (example (51, 51))
subtract_error = 0.01
error_sub_type = "freedman-diaconis" # sqrt, sturges, rice, scott, freedman-diaconis (default) or shape (example (51, 51))
subtract_error = 1.0
display_bkg = False
# Data binning
rebin = True
pxsize = 2
px_scale = 'px' # pixel, arcsec or full
rebin_operation = 'sum' # sum or average
pxscale = "px" # pixel, arcsec or full
rebin_operation = "sum" # sum or average
# Alignement
align_center = 'center' # If None will not align the images
align_center = "center" # If None will not align the images
display_align = False
display_data = False
@@ -59,20 +62,19 @@ def main(target=None, proposal_id=None, data_dir=None, infiles=None, output_dir=
transmitcorr = True
# Smoothing
smoothing_function = 'combine' # gaussian_after, weighted_gaussian_after, gaussian, weighted_gaussian or combine
smoothing_FWHM = None # If None, no smoothing is done
smoothing_scale = 'px' # pixel or arcsec
smoothing_function = "combine" # gaussian_after, weighted_gaussian_after, gaussian, weighted_gaussian or combine
smoothing_FWHM = 2.0 # If None, no smoothing is done
smoothing_scale = "px" # pixel or arcsec
# Rotation
rotate_data = False # rotation to North convention can give erroneous results
rotate_stokes = True
rotate_North = True
# Polarization map output
SNRp_cut = 3. # P measurments with SNR>3
SNRi_cut = 3. # I measurments with SNR>30, which implies an uncertainty in P of 4.7%.
flux_lim = None # lowest and highest flux displayed on plot, defaults to bkg and maximum in cut if None
vec_scale = 5
step_vec = 1 # plot all vectors in the array. if step_vec = 2, then every other vector will be plotted if step_vec = 0 then all vectors are displayed at full length
SNRp_cut = 3.0 # P measurments with SNR>3
SNRi_cut = 1.0 # I measurments with SNR>30, which implies an uncertainty in P of 4.7%.
flux_lim = None # lowest and highest flux displayed on plot, defaults to bkg and maximum in cut if None
scale_vec = 5
step_vec = 1 # plot all vectors in the array. if step_vec = 2, then every other vector will be plotted if step_vec = 0 then all vectors are displayed at full length
# Adaptive binning
# in order to perfrom optimal binning, there are several steps to follow:
@@ -85,9 +87,10 @@ def main(target=None, proposal_id=None, data_dir=None, infiles=None, output_dir=
optimize = False
# Pipeline start
# Step 1:
# Get data from fits files and translate to flux in erg/cm²/s/Angstrom.
if data_dir is None:
if infiles is not None:
prod = np.array([["/".join(filepath.split('/')[:-1]), filepath.split('/')[-1]] for filepath in infiles], dtype=str)
@@ -114,6 +117,7 @@ def main(target=None, proposal_id=None, data_dir=None, infiles=None, output_dir=
target = input("Target name:\n>")
data_array, headers = proj_fits.get_obs_data(infiles, data_folder=data_folder, compute_flux=True)
try:
plots_folder = data_folder.replace("data", "plots")
except ValueError:
@@ -123,18 +127,20 @@ def main(target=None, proposal_id=None, data_dir=None, infiles=None, output_dir=
figname = "_".join([target, "FOC"])
figtype = ""
if rebin:
if px_scale not in ['full']:
figtype = "".join(["b", "{0:.2f}".format(pxsize), px_scale]) # additionnal informations
if (pxsize is not None) and not (pxsize == 1 and pxscale.lower() in ["px", "pixel", "pixels"]):
if pxscale not in ["full"]:
figtype = "".join(["b", "{0:.2f}".format(pxsize), pxscale]) # additionnal informations
else:
figtype = "full"
if smoothing_FWHM is not None:
figtype += "_"+"".join(["".join([s[0] for s in smoothing_function.split("_")]),
"{0:.2f}".format(smoothing_FWHM), smoothing_scale]) # additionnal informations
if smoothing_FWHM is not None and smoothing_scale is not None:
smoothstr = "".join([*[s[0] for s in smoothing_function.split("_")], "{0:.2f}".format(smoothing_FWHM), smoothing_scale])
figtype = "_".join([figtype, smoothstr] if figtype != "" else [smoothstr])
if deconvolve:
figtype += "_deconv"
figtype = "_".join([figtype, "deconv"] if figtype != "" else ["deconv"])
if align_center is None:
figtype += "_not_aligned"
figtype = "_".join([figtype, "not_aligned"] if figtype != "" else ["not_aligned"])
if optimal_binning:
options = {'optimize': optimize, 'optimal_binning': True}
@@ -337,12 +343,14 @@ def main(target=None, proposal_id=None, data_dir=None, infiles=None, output_dir=
elif px_scale.lower() not in ['full', 'integrate']:
proj_plots.pol_map(Stokes_test, SNRp_cut=SNRp_cut, SNRi_cut=SNRi_cut, flux_lim=flux_lim)
return 0
return outfiles
if __name__ == "__main__":
import argparse
parser = argparse.ArgumentParser(description='Query MAST for target products')
parser.add_argument('-t', '--target', metavar='targetname', required=False, help='the name of the target', type=str, default=None)
parser.add_argument('-p', '--proposal_id', metavar='proposal_id', required=False, help='the proposal id of the data products', type=int, default=None)
@@ -355,4 +363,4 @@ if __name__ == "__main__":
args = parser.parse_args()
exitcode = main(target=args.target, proposal_id=args.proposal_id, data_dir=args.data_dir, infiles=args.files,
output_dir=args.output_dir, crop=args.crop, interactive=args.interactive)
print("Finished with ExitCode: ", exitcode)
print("Finished with ExitCode: ", exitcode)