Tibeuleu/FOC_Reduction
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add data rotation (instead of stokes rotation) and add sentinels

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Thibault Barnouin
2021-06-10 20:02:53 +02:00
parent f7b6d9dfaf
commit 1dc40f96c4
41 changed files with 178 additions and 43 deletions
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src/FOC_reduction.py
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@@ -16,20 +16,20 @@ import lib.plots as proj_plots #Functions for plotting data
def main():
##### User inputs
## Input and output locations
globals()['data_folder'] = "../data/NGC1068_x274020/"
infiles = ['x274020at.c0f.fits','x274020bt.c0f.fits','x274020ct.c0f.fits',
'x274020dt.c0f.fits','x274020et.c0f.fits','x274020ft.c0f.fits',
'x274020gt.c0f.fits','x274020ht.c0f.fits','x274020it.c0f.fits']
globals()['plots_folder'] = "../plots/NGC1068_x274020/"
# globals()['data_folder'] = "../data/NGC1068_x274020/"
# infiles = ['x274020at.c0f.fits','x274020bt.c0f.fits','x274020ct.c0f.fits',
# 'x274020dt.c0f.fits','x274020et.c0f.fits','x274020ft.c0f.fits',
# 'x274020gt.c0f.fits','x274020ht.c0f.fits','x274020it.c0f.fits']
# globals()['plots_folder'] = "../plots/NGC1068_x274020/"
# globals()['data_folder'] = "../data/NGC1068_x14w010/"
# infiles = ['x14w0101t_c0f.fits','x14w0102t_c0f.fits','x14w0103t_c0f.fits',
# 'x14w0104t_c0f.fits','x14w0105p_c0f.fits','x14w0106t_c0f.fits']
# globals()['plots_folder'] = "../plots/NGC1068_x14w010/"
# globals()['data_folder'] = "../data/3C405_x136060/"
# infiles = ['x1360601t_c0f.fits','x1360602t_c0f.fits','x1360603t_c0f.fits']
# globals()['plots_folder'] = "../plots/3C405_x136060/"
globals()['data_folder'] = "../data/3C405_x136060/"
infiles = ['x1360601t_c0f.fits','x1360602t_c0f.fits','x1360603t_c0f.fits']
globals()['plots_folder'] = "../plots/3C405_x136060/"
# globals()['data_folder'] = "../data/CygnusA_x43w0/"
# infiles = ['x43w0101r_c0f.fits', 'x43w0102r_c0f.fits', 'x43w0103r_c0f.fits',
@@ -87,25 +87,26 @@ def main():
iterations = 10
# Error estimation
error_sub_shape = (75,75)
display_error = False
display_error = True
# Data binning
rebin = True
if rebin:
pxsize = 0.10
pxsize = 0.50
px_scale = 'arcsec' #pixel or arcsec
rebin_operation = 'sum' #sum or average
# Alignement
align_center = 'image' #If None will align image to image center
display_data = False
display_data = True
# Smoothing
smoothing_function = 'combine' #gaussian_after, gaussian or combine
smoothing_FWHM = 0.20 #If None, no smoothing is done
smoothing_FWHM = None #If None, no smoothing is done
smoothing_scale = 'arcsec' #pixel or arcsec
# Rotation
rotate = True #rotation to North convention can give erroneous results
rotate_stokes = False #rotation to North convention can give erroneous results
rotate_data = False #rotation to North convention can give erroneous results
# Polarization map output
figname = 'NGC1068_FOC' #target/intrument name
figtype = '_combine_FWHM020_rot' #additionnal informations
figname = '3C405_FOC' #target/intrument name
figtype = '' #additionnal informations
SNRp_cut = 3 #P measurments with SNR>3
SNRi_cut = 30 #I measurments with SNR>30, which implies an uncertainty in P of 4.7%.
step_vec = 1 #plot all vectors in the array. if step_vec = 2, then every other vector will be plotted
@@ -114,19 +115,40 @@ def main():
## Step 1:
# Get data from fits files and translate to flux in erg/cm²/s/Angstrom.
data_array, headers = proj_fits.get_obs_data(infiles, data_folder=data_folder, compute_flux=True)
for data in data_array:
if (data < 0.).any():
print("ETAPE 1 : ", data)
# Crop data to remove outside blank margins.
data_array, error_array = proj_red.crop_array(data_array, step=5, null_val=0., inside=True)
for data in data_array:
if (data < 0.).any():
print("ETAPE 2 : ", data)
# Deconvolve data using Richardson-Lucy iterative algorithm with a gaussian PSF of given FWHM.
if deconvolve:
data_array = proj_red.deconvolve_array(data_array, headers, psf=psf, FWHM=psf_FWHM, scale=psf_scale, shape=psf_shape, iterations=iterations)
# Estimate error from data background, estimated from sub-image of desired sub_shape.
data_array, error_array = proj_red.get_error(data_array, sub_shape=error_sub_shape, display=display_error, headers=headers, savename=figname+"_errors", plots_folder=plots_folder)
for data in data_array:
if (data < 0.).any():
print("ETAPE 3 : ", data)
# Rebin data to desired pixel size.
if rebin:
data_array, error_array, headers, Dxy = proj_red.rebin_array(data_array, error_array, headers, pxsize=pxsize, scale=px_scale, operation=rebin_operation)
for data in data_array:
if (data < 0.).any():
print("ETAPE 4 : ", data)
#Align and rescale images with oversampling.
data_array, error_array = proj_red.align_data(data_array, error_array, upsample_factor=int(Dxy.min()), ref_center=align_center, return_shifts=False)
for data in data_array:
if (data < 0.).any():
print("ETAPE 5 : ", data)
# Rotate data to have North up
ref_header = copy.deepcopy(headers[0])
if rotate_data:
data_array, error_array, headers = proj_red.rotate_data(data_array, error_array, headers, -ref_header['orientat'])
for data in data_array:
if (data < 0.).any():
print("ETAPE 6 : ", data)
#Plot array for checking output
if display_data:
proj_plots.plot_obs(data_array, headers, vmin=data_array.min(), vmax=data_array.max(), savename=figname+"_center_"+align_center, plots_folder=plots_folder)
@@ -141,7 +163,7 @@ def main():
## Step 3:
# Rotate images to have North up
if rotate:
if rotate_stokes:
ref_header = copy.deepcopy(headers[0])
I_stokes, Q_stokes, U_stokes, Stokes_cov, headers = proj_red.rotate_Stokes(I_stokes, Q_stokes, U_stokes, Stokes_cov, headers, -ref_header['orientat'])
# Compute polarimetric parameters (polarization degree and angle).