#!/usr/bin/env python3

# -*- coding: utf-8 -*-

"""

Created on Wed Oct 9 05:22:35 2019

@author: altsai

"""

import os

import sys

import shutil

import numpy as np

import csv

import time

import math

import pandas as pd

from astropy import units as u

from astropy.coordinates import SkyCoord # High-level coordinates

#from astropy.coordinates import ICRS, Galactic, FK4, FK5 # Low-level frames

#from astropy.coordinates import Angle, Latitude, Longitude # Angles

#from astropy.coordinates import match_coordinates_sky

from astropy.table import Table

from photutils import CircularAperture

from photutils import SkyCircularAperture

from photutils import aperture_photometry

from photutils import CircularAnnulus

from photutils import SkyCircularAnnulus

# https://photutils.readthedocs.io/en/stable/aperture.html

#from phot import aperphot

# http://www.mit.edu/~iancross/python/phot.html

import matplotlib.pyplot as plt

import matplotlib.axes as ax

from astropy.io import fits

from astropy.wcs import WCS

#from photutils import DAOStarFinder

#from astropy.stats import mad_std

# https://photutils.readthedocs.io/en/stable/getting_started.html

from numpy.polynomial.polynomial import polyfit

from astropy.stats import sigma_clipped_stats

from photutils.psf import IterativelySubtractedPSFPhotometry

from statistics import mode

from astropy.visualization import simple_norm

from photutils.utils import calc_total_error

from astropy.stats import mad_std

import matplotlib.gridspec as gridspec

import julian

import datetime

'''

# 3C345-20190714@135841-R_Astrodon_2018_calib.fits

#fits_root=input('Please input the file name of the fitsinstmage: ').split('.',-1)[0].split('_calib',-1)[0]

fits_root='3C345-20190822@130653-R_Astrodon_2018'

fits_calib=fits_root+'_calib.fits'

fits_ori=fits_root+'.fts'

#print(fits_root)

#print(fits_calib)

#print(fits_ori)

date=fits_root.split('@',-1)[0].split('-',-1)[-1]

print(date)

print(type(date))

yearmonth=date[0:6]

'''

#file_info='gasp_target_fitsheader_info.txt'

file_info='gasp_target_fitsheader_info_exclude_baddata_from201904.txt'

print('... will read '+file_info+' ...')

df_info=pd.read_csv(file_info,delimiter='|')

print(df_info)

#file_iau='iau_name.txt'

#print('... will read '+file_iau+' ...')

#df_iau=pd.read_csv(file_iau,delimiter='|')

#print(df_iau)

#obj_name='3C66A'

#obj_name='3C345'

#obj_name='3C279'

#obj_name='ES2344+514'

#obj_name='L-Lacertae'

#obj_name='4C38-41'

#obj_name='4C71-07'

#obj_name='4C29-45'

#obj_name='Mkn421'

#obj_name='AO0235+16'

#obj_name='DA406'

obj_name=sys.argv[1]

#iau_name=df_iau[df_iau['obj_name']==obj_name]

#print('iau_name',iau_name)

dir_obj='Rmag_InstMag/annu_w1/'+obj_name+'/'

print('... will generate files in: ./'+dir_obj)

if os.path.exists(dir_obj):

shutil.rmtree(dir_obj)

os.makedirs(dir_obj,exist_ok=True)

dir_refstar='RefStar/'

#file_refstar='gasp_refStar_radec_annu_test.txt'

file_refstar='gasp_refStar_radec_annu.txt'

df_refstar=pd.read_csv(file_refstar,sep='|')

#print(df_refstar)

idx_refstar=df_refstar[df_refstar['ObjectName']==obj_name].index.tolist()

#print(idx_refstar)

iau_name=df_refstar.loc[df_refstar['ObjectName']==obj_name].iloc[0]['IAU_Name']

n_refstar=len(idx_refstar)

refstarID=['']*n_refstar

#print('number of reference stars : ',n_refstar)

ra_deg=np.array([0.]*n_refstar)

dec_deg=np.array([0.]*n_refstar)

#ra_pix=np.array([0.]*n_refstar)

#dec_pix=np.array([0.]*n_refstar)

radec_deg=np.array([[0.,0.]]*n_refstar)

#radec_pix=np.array([[0.,0.]]*n_refstar)

ra_hhmmss=['']*n_refstar

dec_ddmmss=['']*n_refstar

rmag=np.array([0.]*n_refstar)

rmag_err=np.array([0.]*n_refstar)

rmag_uplims=np.array([0.]*n_refstar,dtype=bool)

#mag_instrument=np.array([0.]*n_refstar)

#mag_err=np.array([0.]*n_refstar)

#snr=np.array([0.]*n_refstar)

r_circle=np.array([0.]*n_refstar)

r_inner=np.array([0.]*n_refstar)

r_outer=np.array([0.]*n_refstar)

#positions=['']*n_refstar

aperture=['']*n_refstar

aper_annu=['']*n_refstar

aperture_pix=['']*n_refstar

aper_annu_pix=['']*n_refstar

font_small=8

font_middle=10

font_large=12

colors=['red','orange','green','blue','purple','brown','olive','pink']

markers=['o','v','^','s','D','<','>','p']

print('-----------------------')

# here is for test

#ID_selected=np.array([1276,1277,1371,1372]) # 3C345

#ID_selected=np.array([810,811,1334,1335]) # ES2344+514

#idx_fitsheader=np.array([809,810,1333,1334,1575,1576]) # ES2344+514

#ID_selected=np.array([814,815,1336,1337]) # L-Lacertae

#ID_selected=np.array([1330,1331,1476,1477,1478,1479]) # 3C66A

#ID_selected=np.array([810,811,1040,1041]) # ES2344+514

#ID_selected=np.array([774,775,776,777]) # 4C38-41

#ID_selected=np.array([1036,1037]) # ES2344+514

#ID_selected=np.array([1037,1038]) # ES2344+514

#ID_selected=np.array([1436,1437,1438,1439]) # ES2344+514

#ID_selected=np.array([988,989]) # 4C29-45

#ID_selected=np.array([963,964,991,992]) # 3C279

#ID_selected=np.array([687,688,995,996]) # 4C71-07

#ID_selected=np.array([689,690,997,998]) # Mkn421

#ID_selected=np.array([1527,1528,1533,1534]) #AO0235+16

#idx_fitsheader=ID_selected-1

idx_fitsheader=df_info[df_info['Object']==obj_name].index

print(idx_fitsheader)

#obj_name=df_info['Object'][idx_fitsheader]

fits_ori=df_info['Filename'][idx_fitsheader]

print(fits_ori)

#sys.exit(0)

#=======================

df_baddata_note=pd.read_csv('bad_data_note.txt',sep='\t')

#print(df_baddata_note)

df_cannotfit=df_baddata_note.loc[(df_baddata_note['NoteIdx']==3)].reset_index(drop=True)

n_cannotfit=len(df_cannotfit)

print('... there are',n_cannotfit,'fits can not be fitted ...')

list_cannotfit=df_cannotfit['filename'].tolist()

print(list_cannotfit)

#idx_fitsheader

#del idx_fitsheader[idx_cannotfit]

n_idx=len(idx_fitsheader)

idx_cannotfit=[]

print('before drop bad fits: idx_fitsheader =',idx_fitsheader)

for i in range(n_idx):

j=idx_fitsheader[i]

fitsname=fits_ori[j]

# print(j,fitsname)

if fitsname in list_cannotfit:

idx_cannotfit.append(i)

# print(idx_cannotfit)

#ignore=ignore+1

print(i,j,fitsname,'... bad fits')

# print('skip',j,fitsname,'... bad fits ...')

print()

else:

print(i,j,fitsname)

idx_fitsheader_canfit=np.delete(idx_fitsheader,idx_cannotfit)

print(idx_fitsheader_canfit)

ID_canfit=idx_fitsheader_canfit+1

print(ID_canfit)

idx_fitsheader_cannotfit=idx_fitsheader[idx_cannotfit]

ID_cannotfit=idx_fitsheader_cannotfit+1

print(ID_cannotfit)

n_idx_canfit=len(idx_fitsheader_canfit)

n_cannotfit=len(idx_cannotfit)

print()

#sys.exit(0)

n_idx=n_idx_canfit

idx_fitsheader=idx_fitsheader_canfit

#=======================

#n_idx=len(idx_fitsheader)

#refstarRA_deg=np.array([0.]*n_idx)

#refstarDEC_deg=np.array([0.]*n_idx)

#refstar_position=np.array([0.]*n_idx)

label_source=[['']*n_refstar]*n_idx

#print(label_source)

Rmag_targets=np.array([0.]*n_idx)

Rmag_err_targets=np.array([0.]*n_idx)

SNR_targets=np.array([0.]*n_idx)

#fwhm=np.array([0.]*n_idx)

#d_rmag_fitting=np.zeros((n_idx,n_refstar-1))

#radec_pix=np.array([[0.,0.]]*n_refstar)

bkg_err=np.array([0.]*n_idx)

bkg_err_ratio=np.array([0.]*n_idx)

R_square_rmag=np.array([0.]*n_idx)

err_all=np.array([0.]*n_idx)

#err_fitting_ratio=np.array([0.]*n_idx)

#mag_instrument_sum_err=np.array([0.]*n_idx)

err_count_per_img=np.array([0.]*n_idx)

err_mag_fitting_per_img=np.array([0.]*n_idx)

err_mag_instrument_per_img=np.array([0.]*n_idx)

err_mag_total_per_img=np.array([0.]*n_idx)

#sys.exit(0)

aper_sum0=np.zeros((n_idx,n_refstar))

aper_sum1=np.zeros((n_idx,n_refstar))

aper_sum_err0=np.zeros((n_idx,n_refstar))

aper_sum_err1=np.zeros((n_idx,n_refstar))

bg_subtracted_sum=np.zeros((n_idx,n_refstar))

bg_subtracted_err=np.zeros((n_idx,n_refstar))

bg_subtracted_sum_err=np.zeros((n_idx,n_refstar))

#bg_subtracted_sum_err_p=np.zeros((n_idx,n_refstar))

#bg_subtracted_sum_err_m=np.zeros((n_idx,n_refstar))

rmag_fitting=np.zeros((n_idx,n_refstar))

mag_instrument=np.zeros((n_idx,n_refstar))

mag_instrument_sum_err=np.zeros((n_idx,n_refstar))

#mag_instrument_sum_err_p=np.zeros((n_idx,n_refstar))

#mag_instrument_sum_err_m=np.zeros((n_idx,n_refstar))

mag_instrument_err=np.zeros((n_idx,n_refstar))

#mag_instrument_err_p=np.zeros((n_idx,n_refstar))

#mag_instrument_err_m=np.zeros((n_idx,n_refstar))

calendar_date=['']*n_idx

JD=df_info['JD'][idx_fitsheader]

ID=df_info['ID'][idx_fitsheader]

#sys.exit(0)

#=======================

j1=0

for j2 in idx_refstar:

# print('j1,j2',j1,j2)

refstarID[j1]=df_refstar['RefStarID'][j2]

ra_deg[j1]=df_refstar['RefStarRA_deg'][j2]

dec_deg[j1]=df_refstar['RefStarDEC_deg'][j2]

# print(ra_deg[j1],dec_deg[j1])

radec_deg[j1]=[ra_deg[j1],dec_deg[j1]]

# print(j1,j2,radec_deg[j1])

ra_hhmmss[j1]=df_refstar['RefStarRA_hhmmss'][j2]

dec_ddmmss[j1]=df_refstar['RefStarDEC_ddmmss'][j2]

# print(i,j1,radec_deg[j1],ra_hhmmss[j1],dec_ddmmss[j1])

rmag[j1]=df_refstar['Rmag'][j2]

rmag_err[j1]=df_refstar['Rmag_err'][j2]

r_circle[j1]=df_refstar['R_circle_as'][j2]

r_inner[j1]=df_refstar['R_inner_as'][j2]

r_outer[j1]=df_refstar['R_outer_as'][j2]

# position= SkyCoord(ra_deg[j1],dec_deg[j1],unit=(u.hourangle,u.deg),frame='icrs')

position= SkyCoord(ra_deg[j1],dec_deg[j1],unit=(u.deg),frame='icrs')

# print(position)

r_circle_as=r_circle[j1]*u.arcsec

# print(r_circle_as)

aperture[j1]=SkyCircularAperture(position, r=r_circle_as)

# print(aperture[j1])

r_inner_as=r_inner[j1]*u.arcsec

r_outer_as=r_outer[j1]*u.arcsec

aper_annu[j1]=SkyCircularAnnulus(position,r_inner_as,r_outer_as)

# print(aper_annu[j1])

# print(aper_annu[j1].r_in)

# print(aper_annu[j1].r_out)

# refstarID[j1]=df_refstar['RefStarID'][j2]

# refstarRA_deg[j1]=df_refstar['RefStarRA_deg'][j2]

# refstarDEC_deg[j1]=df_refstar['RefStarDEC_deg'][j2]

# print(refstarID[j1])

# print(refstarRA_deg[j1]

# print(refstarDEC_deg[j1])

j1=j1+1

dx=500

dy=dx

#=======================

k=0

for i in idx_fitsheader_canfit:

print('=================================')

print('idx',i, ') ID =',ID[i],', #', k+1,'/',n_idx,'image of',obj_name)

fits_root=fits_ori[i].split('.',-1)[0].split('_calib',-1)[0]

fits_calib=fits_root+'_calib.fits'

print('... filename :',fits_calib)

#print(fits_root)

#print(fits_calib)

#print(fits_ori)

# sys.exit(0)

# print(radec_deg)

# print(rmag)

date=fits_root.split('@',-1)[0].split('-',-1)[-1]

year=date[0:4]

month=date[4:6]

day=date[6:8]

yearmonth=date[0:6]

# sys.exit(0)

dir_file=yearmonth+'/slt'+date+'_calib_sci/'

# dir_reg=yearmonth+'/slt'+date+'_reg/'

hdu=fits.open(dir_file+fits_calib)[0]

imhead=hdu.header

imdata=hdu.data

wcs = WCS(imhead)

# print(wcs)

calendar_date[k]=julian.from_jd(JD[i],fmt='jd')

print('calendar_date',calendar_date[k])

# radec_pix=wcs.all_world2pix(ra_deg,dec_deg,1)

ra_pix,dec_pix=wcs.all_world2pix(ra_deg,dec_deg,1)

ra_pix=ra_pix.tolist()

dec_pix=dec_pix.tolist()

# print(ra_pix,dec_pix)

# print()

# mask=np.array

# background level and error

# using FWHM

# sigma_fwhm=fwhm[k]/2.35

# print(k,fwhm[k],sigma_fwhm)

# using the median absolute deviation to estimate the background noise level gives a value

# bkg_noise=mad_std(imdata)

# print(bkg_noise)

print()

# This method provides a better estimate of the background and background noise levels:

bkg_mean,bkg_median,bkg_std=sigma_clipped_stats(imdata,sigma=3.)

print('... bkg_mean,bkg_median,bkg_std')

print('...','%.4f' %bkg_mean,'%.4f' %bkg_median,'%.4f' %bkg_std)

# bkg_std = sqrt((bkg-bkg_mean)^2/n) = background noise

imdata[imdata<bkg_median*0.9]=bkg_median

bkg_err_ratio[k]=bkg_std/bkg_median

print('... bkg_err_ratio = bkg_std/bkg_median =','%.4f' %bkg_err_ratio[k])

# bkg_err[k]=-2.5*np.log10(bkg_std/bkg_median)

# print('bkg_err (mag)',bkg_err[k])

# 1176.6646745343921 1176.0827349796416 39.1334108277639

# np.argwhere(np.isnan(imdata))

# time.sleep(1)

# print(WCS.world_axis_physical_types)

err_imdata=bkg_err_ratio[k]*imdata

print()

for j1 in range(n_refstar):

print('idx',i, '-',j1+1,'/',n_refstar,', Ref.Star:',refstarID[j1],') #', k+1,'/',n_idx,'image of',obj_name )

# aper_annu_pix[j1]=CircularAnnulus(ra_pix[j1],dec_pix[j1],r_inner_as,r_outer_as)

aperture_pix[j1]=aperture[j1].to_pixel(wcs)

# phot_table = aperture_photometry(imdata, aperture_pix[i],error=err_imdata)

aper_annu_pix[j1]=aper_annu[j1].to_pixel(wcs)

# print(aper_annu_pix[j1])

r_pix=aperture_pix[j1].r

r_in_pix=aper_annu_pix[j1].r_in

r_out_pix=aper_annu_pix[j1].r_out

# print(r_in_pix,r_out_pix)

# position_pix=(ra_pix[j1],dec_pix[j1])

# position_pix=np.transpose(positions_pix)

# r_pix=aperture_pix[i].r

# print('r_pix =',r_pix)

apper=[aperture_pix[j1],aper_annu_pix[j1]]

# phot_annu_table = aperture_photometry(imdata, apper)

phot_annu_table = aperture_photometry(imdata, apper,error=err_imdata)

# phot_annu_table = aperture_photometry(imdata, aperture_pix[i],error=err_imdata)

aper_annu_sum0=phot_annu_table['aperture_sum_0']

print('... aper_annu_sum0 =','%.2f' %aper_annu_sum0)

aper_annu_sum1=phot_annu_table['aperture_sum_1']

print('... aper_annu_sum1 =','%.2f' %aper_annu_sum1)

aper_sum0[k][j1]=aper_annu_sum0

aper_sum1[k][j1]=aper_annu_sum1

aper_annu_sum_err0=phot_annu_table['aperture_sum_err_0']

print('... aper_annu_sum_err0 =','%.2f' %aper_annu_sum_err0)

aper_annu_sum_err1=phot_annu_table['aperture_sum_err_1']

print('... aper_annu_sum_err1 =','%.2f' %aper_annu_sum_err1)

aper_sum_err0[k][j1]=aper_annu_sum_err0

aper_sum_err1[k][j1]=aper_annu_sum_err1

area_sum0=aperture_pix[j1].area

print('... area of sum0 =','%.2f' %area_sum0)

area_sum1=aper_annu_pix[j1].area

print('... area of sum1 =','%.2f' %area_sum1)

# area_annu=aper_annu_pix[j1].area

# print('area_annu',area_annu)

# bkg_mean = phot_annu_table['aperture_sum_1'] / area_annu

# print('bkg_mean',bkg_mean)

# bkg_sum = bkg_mean * aperture_pix[j1].area

annulus_mask = aper_annu_pix[j1].to_mask(method='center')

# plt.imshow(annulus_mask)

# plt.colorbar()

# bkg_median = []

# for mask in annulus_masks:

annulus_data = annulus_mask.multiply(imdata)

mask = annulus_mask.data

annulus_data_1d = annulus_data[mask > 0]

_, median_sigclip, _ = sigma_clipped_stats(annulus_data_1d)

print('... median_sigclip (annual mask per pix) =','%.2f' %median_sigclip)

print('... bkg_mean (imdata statistic per pix) =','%.2f' %bkg_mean)

print('... bkg_median (imdata statistic per pix) =','%.2f' %bkg_median)

bkg_sum=median_sigclip*area_sum0

print('... bkg_sum (median_sigclip*area_sum0) =','%.2f' %bkg_sum)

# bkg_median.append(median_sigclip)

# bkg_median = np.array(bkg_median)

bkg_sum=aper_annu_sum1/area_sum1*area_sum0

print('... bkg_sum (aper_annu_sum1/area_sum1*area_sum0) =','%.2f' %bkg_sum)

# print()

# phot_annu_table['bkg_sum']=bkg_sum

bg_subtracted_sum[k][j1]=aper_annu_sum0-bkg_sum

print('... bg_subtracted_sum =','%.2f' %bg_subtracted_sum[k][j1])

bg_subtracted_err[k][j1]=np.sqrt(aper_annu_sum_err0**2+aper_annu_sum_err1**2)

print('... bg_subtracted_err =','%.2f' %bg_subtracted_err[k][j1])

# print(phot_annu_table.colnames)

phot_annu_table['bg_subtracted_sum'] = bg_subtracted_sum[k][j1]

phot_annu_table['bg_subtracted_err'] = bg_subtracted_err[k][j1]

# print()

# phot_annu_table['bg_subtracted_sum[k][j1]_err'] = bg_subtracted_sum[k][j1]

# print(phot_annu_table)

mag_instrument[k][j1]=-2.5*np.log10(bg_subtracted_sum[k][j1])

# if bg_subtracted_sum[k][j1]>0:

# mag_instrument[k][j1]=-2.5*np.log10(bg_subtracted_sum[k][j1])

# else:

# rmag_uplims[j1]=True

# mag_instrument[k][j1]=-2.5*np.log10(bkg_sum)

print('... mag_instrument (sum) =','%.4f' %mag_instrument[k][j1])

bg_subtracted_sum_err[k][j1]=bg_subtracted_sum[k][j1]+bg_subtracted_err[k][j1]

mag_instrument_sum_err[k][j1]=-2.5*np.log10(bg_subtracted_sum_err[k][j1])

print('... mag_instrument (sum+err) =','%.4f' %mag_instrument_sum_err[k][j1])

mag_instrument_err[k][j1]=abs(mag_instrument_sum_err[k][j1]-mag_instrument[k][j1])

print('... mag_instrument (err) =','%.4f' %mag_instrument_err[k][j1])

# bg_subtracted_sum_err_p[k][j1]=bg_subtracted_sum[k][j1]+bg_subtracted_err[k][j1]

# mag_instrument_sum_err_p[k][j1]=-2.5*np.log10(bg_subtracted_sum_err_p[k][j1])

# print('... mag_instrument_sum+err =','%.4f' %mag_instrument_sum_err_p[k][j1])

# mag_instrument_err_p[k][j1]=abs(mag_instrument_sum_err_p[k][j1]-mag_instrument[k][j1])

# print('... mag_instrument+err =','%.4f' %mag_instrument_err_p[k][j1])

# bg_subtracted_sum_err_m[k][j1]=bg_subtracted_sum[k][j1]-bg_subtracted_err[k][j1]

# mag_instrument_sum_err_m[k][j1]=-2.5*np.log10(bg_subtracted_sum_err_m[k][j1])

# print('... mag_instrument_sum-err =','%.4f' %mag_instrument_sum_err_m[k][j1])

# mag_instrument_err_m[k][j1]=abs(mag_instrument_sum_err_m[k][j1]-mag_instrument[k][j1])

# print('... mag_instrument-err =','%.4f' %mag_instrument_err_p[k][j1])

# aper_sum_err0[k][j1]=phot_annu_table['aperture_sum_err_0']

# aper_sum_err1[k][j1]=phot_annu_table['aperture_sum_err_1']

print()

for col in phot_annu_table.colnames:

phot_annu_table[col].info.format = '%.8g' # for consistent table output

# phot_annu_table[col].info.format = '%.2f' # for consistent table output

print(phot_annu_table)

print()

# print(phot_annu_table.colnames)

print('=================================')

# bg_subtracted_sum_mean,bg_subtracted_sum_median,bg_subtracted_sum_std=sigma_clipped_stats(bg_subtracted_sum,sigma=3.)

# print('bg_subtracted_sum_mean,bg_subtracted_sum_median,bg_subtracted_sum_std')

# print(bg_subtracted_sum_mean,bg_subtracted_sum_median,bg_subtracted_sum_std)

# print('bg_subtracted_err[k]')

# print(bg_subtracted_err[k])

err_count_per_img[k]=np.sqrt(sum(bg_subtracted_err[k]**2)/n_refstar)

print('... measurement error after background subtraction (counts):','%.4f' %err_count_per_img[k])

err_mag_instrument_per_img[k]=np.sqrt(sum(mag_instrument_err[k]**2)/n_refstar)

print('... magnitude error after background subtraction (mag):','%.4f' %err_mag_instrument_per_img[k])

# print('aperture sum',aper_sum0[k])

# print('aperture sum error',aper_sum_err0[k])

# print('annulus sum',aper_sum1[k])

# print('annulus sum error',aper_sum_err1[k])

# mag_instrument[k][1:]=mag_instrument[k][1:]

# print(mag_instrument[k][1:])

# print(rmag[1:])

# mag_instrument_source=mag_instrument

# rmag_source=rmag

# no values

# mag_instrument_bkg=mag_instrument[-1]

# rmag_bkg=rmag[-1]

'''

# aperture_pix[i]=aperture.to_pixel(wcs)

# print(aperture_pix[i])

# positions_pix=aperture_pix[i].positions

# r_pix=aperture_pix[i].r

# print('r_pix =',r_pix)

# positions_pix=(ra_pix,dec_pix)

# positions_pix=np.transpose(positions_pix)

# aperture_pix[i]=CircularAperture(positions_pix, r_pix)

# mask_circle=aperture_pix[i].to_mask(method='center')

# mask_data=mask_circle[0].multiply(imdata)

err_imdata=bkg_err_ratio[k]*imdata

# phot_table = aperture_photometry(imdata, aperture,wcs=wcs)

phot_table = aperture_photometry(imdata, aperture_pix[i],error=err_imdata)

'''

'''

# aper_annu_pix[i]=aper_annu.to_pixel(wcs)

# print(aper_annu_pix[i])

# r_in_annu_pix=aper_annu_pix[i].r_in

# r_out_annu_pix=aper_annu_pix[i].r_out

# print(r_in_annu_pix,r_out_annu_pix)

'''

'''

annulus_masks = aper_annu_pix[i].to_mask(method='center')

bkg_median = []

for mask in annulus_masks:

annulus_data = mask.multiply(imdata)

annulus_data_1d = annulus_data[mask.data > 0]

_, median_sigclip, _ = sigma_clipped_stats(annulus_data_1d)

bkg_median.append(median_sigclip)

bkg_median = np.array(bkg_median)

'''

# bkg_sum = bkg_median * aperture_pix[i].area

# bkg_sum = bkg_mean * aperture_pix[i].area

# print(bkg_sum)

# phot_table['bkg_sum']=bkg_sum

# phot_table['bkg_sum'].info.format = '%.8g' # for consistent table output

# final_sum = phot_annu_table['aperture_sum_0'] - bkg_sum

# final_sum=aper_sum-bkg_sum

# print(final_sum)

# phot_annu_table['residual_aperture_sum'] = final_sum

# phot_table['bg_subtracted_sum'] = final_sum

# phot_annu_table['residual_aperture_sum'].info.format = '%.8g' # for consistent table output

# print(phot_annu_table['residual_aperture_sum'])

# print(phot_annu_table)

# phot_table['bg_subtracted_sum'].info.format = '%.8g' # for consistent table output

# print(phot_table)

# sys.exit(0)

'''

j=0

rmag[0]=-9999.

rmag_fitting[0]=rmag[0]

print()

print('j final_sum mag_instrument Rmag')

for j in range(n_refstar):

mag_instrument[j]=-2.5*np.log10(bg_subtract_sum[j])

print(j, final_sum[j],mag_instrument[j],rmag[j])

mag_instrument[k][1:]=mag_instrument[1:]

rmag[1:]=rmag[1:]

mag_instrument_source=mag_instrument

rmag_source=rmag

'''

# no values

# mag_instrument_bkg=mag_instrument[-1]

# rmag_bkg=rmag[-1]

# print('Instrument Mag of RefStars',mag_instrument[k][1:])

# print('Rmag of RefStars',rmag[1:])

print()

# shift,slope=polyfit(mag_instrument[k][1:],rmag[1:],1)

# param,res=polyfit(mag_instrument[k][1:],rmag[1:],1,full=True)

shift,slope=polyfit(mag_instrument[k][1:],rmag[1:],1,w=1/(mag_instrument_err[k][1:]))

# shift,slope=polyfit(mag_instrument[k][1:],rmag[1:],1)

# residual=res[0].tolist()[0]

# print('shift =','%.3f' %shift)

# print('slope =','%.3f' %slope)

# print('residual =', residual)

rmag_fitting[k]=shift+slope*mag_instrument[k]

print('... rmag_fitting (Ref.Stars only):',rmag_fitting[k][1:])

print('... rmag_fitting (Target only):',rmag_fitting[k][0])

Rmag_targets[k]=rmag_fitting[k][0]

# SN=signal_mean/signal_std

# SN=bkg_mean/bkg_std ??

# ErrorRmag=2.5*log10(1+N/S)=1.086/(S/N)

# signal=final_sum

# noise=bkg_std*aperture_pix[i].area

# mag_err=1.086/snr

# Rmag_err_targets[k]=mag_err[0]

'''

# plt.figure(figsize=(8,6))

mask_circle=aperture_pix[j1].to_mask(method='center')

# plt.imshow(mask_circle[3])

# plt.colorbar()

# plt.show()

data_in_mask=mask_circle[3].multiply(imdata)

# plt.imshow(data_in_mask)

# plt.colorbar()

# plt.show()

# plt.close()

mask_median = []

for mask in mask_circle:

circle_data = mask.multiply(imdata)

circle_data_1d = circle_data[mask.data > 0]

_, median_sigclip, _ = sigma_clipped_stats(circle_data_1d)

mask_median.append(median_sigclip)

# bkg_median = np.array(bkg_median)

'''

# snr=mask_median/bkg_std

# snr=bg_subtracted_sum/aperture_pix[j1].area/bkg_std

# snr=10

# mag_err=1.086/snr

# print('snr',snr)

# print('mag_err',mag_err)

# mag_err_target=mag_err

# Rmag_err_targets[k]=mag_err

# SNR_targets[k]=snr

'''

phot = aperture_photometry(imdata, aperture_pix[i])

# phot['circle_median'] = bkg_median

# phot['bkg_median'] = bkg_median

phot['aper_bkg'] = bkg_median * aperture_pix[i].area

# phot['aper_bkg'] = bkg_sum

phot['aper_sum_bkgsub'] = phot['aperture_sum'] - phot['aper_bkg']

for col in phot.colnames:

phot[col].info.format = '%.8g' # for consistent table output

print(phot)

'''

# refstar_ra_pix,refstar_dec_pix=wcs.all_world2pix(refstarRA_deg,refstarDEC_deg,1)

# refstar_ra_pix=refstar_ra_pix.tolist()

# refstar_dec_pix=refstar_dec_pix.tolist()

figtitle='(ID='+str(ID[i])+', JD='+str('%.0f' %JD[i])+') '+fits_ori[i]

fig1=plt.figure(figsize=(8,4))

fig1.suptitle(figtitle,fontsize=font_middle)

# fig1 = plt.figure(constrained_layout=True)

# widths = [1,1]

# heights = [1]

# spec1 = fig1.add_gridspec(ncols=len(widths), nrows=len(heights), width_ratios=widths,

# height_ratios=heights)

# fig1,axs=plt.subplots(1,2)

# axs=fig1.add_subplot(1,2,1)

plt.subplot(121)

# plt.tight_layout(rect=[0,0,1,1])

# plt.figure(dpi=200)

# if change ra,dec of reference star, run 'gasp_refStar_radec.py again.

norm = simple_norm(imdata, 'sqrt', percent=99)

plt.imshow(imdata, norm=norm)

# im=axs[0].imshow(imdata,original='lower',norm=norm)

# fig1.colorbar(im)

# axs[0].plot(imdata)

for i in range(n_refstar):

aper_annu_pix[i].plot(color='black', lw=1)

if i==0:

aperture_pix[i].plot(color='red', lw=1)

plt.text(ra_pix[i]*1.02,dec_pix[i]*0.98,str(refstarID[i]),fontsize=font_middle,color='red')

else:

aperture_pix[i].plot(color='white', lw=1)

plt.text(ra_pix[i]*1.02,dec_pix[i]*0.98,str(refstarID[i]),fontsize=font_middle)

x0=ra_pix[0]

y0=dec_pix[0]

x1=x0-dx

x2=x0+dx

y1=y0-dy

y2=y0+dy

plt.xlim(x1,x2)

plt.ylim(y1,y2)

plt.xlabel('RA (J2000)',fontsize=font_small)

plt.ylabel('Dec (J2000)',fontsize=font_small)

plt.xticks(fontsize=font_small)

plt.yticks(fontsize=font_small)

# plt.title(figtitle,fontsize=font_small)

text_rmag='Rmag='+str('%.3f' %rmag_fitting[k][0])

# text_rmag_err='+/-'+str('%.3f' %mag_err_target)

# text_fwhm='fwhm='+str('%.3f' %fwhm[i])

# text_radius='r = fwhm x '+str(xfwhm)

# text_fig=text_rmag+', '+text_fwhm

# plt.text(x0*0.95,y0*0.94,obj_name,fontsize=font_small,color='red')

# plt.text(x0*0.95,y0*0.90,text_rmag,fontsize=font_small)

# for i in range(n_refstar):

# plt.text(ra_pix[i]*0.95,dec_pix[i]*0.95,str(refstarID[i]),fontsize=font_small)

# plt.text(x0*0.95,y0*0.90,'refstar',fontsize=font_small)

# plt.text(x0*0.95,y0*0.93,text_rmag+text_rmag_err,fontsize=font_small)

# plt.text(x0*0.95,y0*0.90,text_fwhm,fontsize=font_small)

# plt.text(x0*0.95,y0*0.87,text_radius,fontsize=font_small)

# plt.text(x2*0.55,y2*0.45,text_fwhm,fontsize=font_small)

# plt.show()

# plt.savefig(dir_obj+'Rmag_InstMag_aper_'+obj_name+'_'+date+'_fwhm'+str(xfwhm)+'_'+str(k)+'.png')

# plt.savefig(dir_obj+'Rmag_InstMag_aper_'+obj_name+'_annu_'+date+'_'+str(k)+'.png')

# plt.close()

plt.subplot(122,aspect=0.5)

# plt.subplots_adjust(top=0.75)

# plt.tight_layout(rect=[0,0,0.75,0.5])

# plt.figure()

# plt.figure(figsize=(8,6))

# plt.scatter(mag_instrument[k][1:],rmag[1:])

# plt.plot(mag_instrument[k][1:],rmag[1:],'o')

d_rmag_fitting=rmag[1:]-rmag_fitting[k][1:]

print('... fitting residual:',d_rmag_fitting)

# rmag=shift+slope*mag_instrument

# mag_instrument_fitting_refstar=(rmag_fitting[k][1:]-shift)/slope

# count_instrument_fitting_refstar=10**(mag_instrument_fitting_refstar/(-2.5))

# d_count_instrument_fitting=abs(count_instrument_fitting_refstar-bg_subtracted_sum[1:])

# d_mag_instrument_fitting=-2.5*np.log10(d_count_instrument_fitting)

err_mag_fitting_per_img[k]=np.sqrt(sum(d_rmag_fitting**2)/n_refstar)

print('... fitting error (mag) =','%.4f' %err_mag_fitting_per_img[k])

# print('measurement error (mag)',bkg_err[k])

# SSregression_rmag=sum((rmag_fitting[k][1:]-np.mean(rmag[1:]))**2)

SSE_rmag=sum((d_rmag_fitting)**2)

SST_rmag=sum((rmag[1:]-np.mean(rmag[1:]))**2)

R_square_rmag[k]=1-SSE_rmag/SST_rmag

print('... error of measurement (ratio of bkg_std/bkg_mediean) =','%.4f' %bkg_err_ratio[k])

err_mag_total_per_img[k]=np.sqrt((err_mag_fitting_per_img[k])**2+(err_mag_instrument_per_img[k])**2)

print('... error of (calibration + observation) [mag]:','%.4f' %err_mag_total_per_img[k])

text_fitting='Rmag='+str('%.2f' %shift)+'+'+str('%.2f' %slope)+'*(Inst.Mag), $R^2$='+str('%.4f' %R_square_rmag[k])

label_target=obj_name+', Rmag='+str('%.2f' %rmag_fitting[k][0])+'$\pm$'+str('%.2f' %err_mag_total_per_img[k])

for i in range(n_refstar):

label_source[k][i]=obj_name+', Rmag='+str('%.2f' %rmag_fitting[k][i])

print('label_source[k]',label_source[k])

# label_source[k]=obj_name+', Rmag='+str('%.2f' %rmag_fitting[k])

plt.plot(mag_instrument[k],rmag_fitting[k],'-',color='grey',label=text_fitting)

plt.errorbar(mag_instrument[k][1:],rmag[1:],yerr=mag_instrument_err[k][1:],fmt='o',label='Reference Stars')

# plt.plot(mag_instrument[k][0],rmag_fitting[k][0],'o',color='red',label=label_target)

# plt.errorbar(mag_instrument[k][0],rmag_fitting[k][0],yerr=err_mag_fitting_per_img[k],fmt='o',color='red',label=label_target)

plt.errorbar(mag_instrument[k][0],rmag_fitting[k][0],yerr=mag_instrument_err[k][0],fmt='o',color='red',label=label_target)

print('... bg_subtracted_sum =',bg_subtracted_sum[k][j1])

# if bg_subtracted_sum[k][j1]>0:

# plt.errorbar(mag_instrument[k][0],rmag_fitting[k][0],yerr=mag_instrument_err[k][0],fmt='o',color='red',label=label_target)

# else:

# plt.errorbar(mag_instrument[k][0],rmag_fitting[k][0],yerr=0.2,uplims=True,fmt='o',color='red',label=label_target)

# plt.plot(mag_instrument[k][1:],rmag[1:],'o',label='Ref.Star')

# plt.plot(mag_instrument[k][0],rmag_fitting[k][0],'o',color='red',label=label_target)

# else:

# plt.errorbar(mag_instrument[k][0],rmag_fitting[k][0],yerr=0.2,uplims=['True'],marker='o',color='red',label=label_target)

# plt.plot(mag_instrument[k][1:],rmag_fitting[k][1:],'o',color='steelblue',label=label_source[1:])

# plt.errorbar(mag_instrument[k][0],rmag_fitting[k][0],yerr=mag_instrument_err[k][0],fmt='o',color='red',label=label_target)

# plt.errorbar(mag_instrument_source,rmag_source,yerr=mag_err[:-1])

xx=mag_instrument[k]

yy=rmag_fitting[k]

xxmin=min(xx)

xxmax=max(xx)

yymin=min(yy)

yymax=max(yy)

xxwidth=abs(xxmin-xxmax)

yywidth=abs(yymin-yymax)

# xxrange=range(int(xxmin*10),int(xxmax*10),5)

print('... InstMag_width =','%.2f' %xxwidth,', Rmag_width =','%.2f' %yywidth)

for i in range(n_refstar):

if i==0:

plt.text((xx[i]-0.01*xxwidth),(yy[i]+0.05*yywidth),str(refstarID[i]),fontsize=font_small,color='red')

else:

plt.text((xx[i]-0.01*xxwidth),(rmag[i]),str(refstarID[i]),fontsize=font_small,color='steelblue')

plt.xlabel('Instrument Mag',fontsize=font_small)

plt.ylabel('Rmag',fontsize=font_small)

# plt.title(figtitle,fontsize=font_small)

# plt.xticks(np.arange(min(xx)-1,max(xx)+1,0.5),fontsize=font_small)

# plt.yticks(np.arange(min(yy)-1,max(yy)+1,0.5),fontsize=font_small)

plt.xticks(fontsize=font_small)

plt.yticks(fontsize=font_small)

plt.gca().invert_xaxis()

plt.gca().invert_yaxis()

# print(mag_instrument,Rmag_targets)

# plt.autoscale(enable=True,axis='both')

# ax=plt.gca()

# ax.relim()

# ax.autoscale()

# ax.Axes.autoscale #(enable=True,axis='both')

# set_xlim(auto=True)

# set_ylim(auto=True)

# plt.show()

# plt.legend(loc='best') #,fontsize=font_small)

plt.legend(loc='lower left',bbox_to_anchor=(0.0,1.02),fontsize=font_small)

# plt.legend(loc='upper left', bbox_to_anchor=(-0.,1.65),fontsize=font_small)

# plt.savefig(dir_obj+'Rmag_InsMag_rmag_'+obj_name+'_annu_'+date+'_'+str(k)+'.png')

plt.savefig(dir_obj+'Rmag_InsMag_'+obj_name+'_annu_'+date+'_'+str(k+1)+'.png',dpi=200)

plt.close()

# print('target new Rmag =',rmag_fitting[k][0])

# print('Instrument Mag',mag_instrument)

# print('=================================')

k=k+1

#print('=================================')

print()

print('Rmag',Rmag_targets)

print()

df_out=df_info.iloc[idx_fitsheader_canfit]

pd.options.mode.chained_assignment = None # default='warn'

df_out['JD']=df_out['JD'].map('{:.4f}'.format)

#df_out['Rmag']=pd.Series(Rmag_targets,index=df_out.index)

df_out['Rmag']=Rmag_targets

df_out['Rmag']=df_out['Rmag'].map('{:.4f}'.format)

df_out['ErrorCounts']=err_count_per_img

df_out['ErrorCounts']=df_out['ErrorCounts'].map('{:.4f}'.format)

df_out['ErrorInstMag']=err_mag_instrument_per_img

df_out['ErrorInstMag']=df_out['ErrorInstMag'].map('{:.4f}'.format)

df_out['ErrorFitting']=err_mag_fitting_per_img

df_out['ErrorFitting']=df_out['ErrorFitting'].map('{:.4f}'.format)

df_out['ErrorRmag']=err_mag_total_per_img

df_out['ErrorRmag']=df_out['ErrorRmag'].map('{:.4f}'.format)

df_out['IAU_name']=iau_name

#fmt="{:,.4f}" # 1,234

#fmt="{:.4f}" # 1234

#df_out.style.format({'RA_deg':fmt,'DEC_deg':fmt,'RA_pix':fmt,'DEC_pix':fmt,'Zmag':fmt,'FWHM':fmt,'Altitude':fmt,'Airmass':fmt,'Rmag':fmt,'ErrorCounts':fmt,'ErrorInstMag':fmt,'ErrorFitting':fmt,'ErrorMagTotal':fmt})

#df_out.style.format({'Rmag':fmt,'ErrorCounts':fmt,'ErrorInstMag':fmt,'ErrorFitting':fmt,'ErrorMagTotal':fmt})

df_out.reset_index(drop=True)

df_out=df_out.drop(['Unnamed: 0'],axis=1)

print(df_out)

file_Rmag_out_full=dir_obj+'Rmag_aperture_'+obj_name+'_annu.txt'

df_out.to_csv(file_Rmag_out_full,sep='|')

print('... write file to: ./'+file_Rmag_out_full)

# -----------------------------------

df_Rmag=df_out[['JD','Rmag','ErrorRmag']].reset_index(drop=True)

file_Rmag_out_simple=dir_obj+'Rmag_'+obj_name+'_all.txt'

df_Rmag.to_csv(file_Rmag_out_simple,sep=',')

print('... write file to: ./'+file_Rmag_out_simple)

# -----------------------------------

#=======================

#df_baddata_note=pd.read_csv('bad_data_note.txt',sep='\t')

#print(df_baddata_note)

df_baddata=df_baddata_note.loc[(df_baddata_note['NoteIdx']==2)].reset_index(drop=True)

n_baddata=len(df_baddata)

print('... there are',n_baddata,'bad fits')

list_baddata=df_baddata['filename'].tolist()

#print(list_baddata)

#sys.exit(0)

n_idx=len(idx_fitsheader_canfit)

print(n_idx)

idx_skip=[]

print('before drop bad fits: idx_fitsheader_canfit =',idx_fitsheader_canfit)

for i in range(n_idx):

j=idx_fitsheader_canfit[i]

fitsname=fits_ori[j]

# print(j,fitsname)

if fitsname in list_baddata:

idx_skip.append(i)

# print(idx_skip)

#ignore=ignore+1

print(i,j,fitsname,'... bad fits')

# print('skip',j,fitsname,'... bad fits ...')

print()

else:

print(i,j,fitsname)

#del idx_fitsheader_canfit[idx_skip]

idx_fitsheader_keep=np.delete(idx_fitsheader_canfit,idx_skip)

print(idx_fitsheader_keep)

ID_keep=idx_fitsheader_keep+1

print(ID_keep)

idx_fitsheader_skip=idx_fitsheader_canfit[idx_skip]

ID_skip=idx_fitsheader_skip+1

print(ID_skip)

n_idx_keep=len(idx_fitsheader_keep)

n_skip=len(idx_skip)

#JD_keep=JD

print()

print('... skip idx_fitsheader_keep',idx_skip,'=',idx_fitsheader_canfit[idx_skip],'... bad fits ...')

print()

print('after drop bad fits: idx_fitsheader_keep =',idx_fitsheader_keep)

print('... keep fits ...')

print(fits_ori[idx_fitsheader_keep])

#=======================

#sys.exit(0)

df_out_keep=df_out

df_out_keep=df_out_keep[~df_out_keep['ID'].isin(ID_skip)]

print(df_out_keep)

# -----------------------------------

df_Rmag_keep=df_out_keep[['JD','Rmag','ErrorRmag']].astype(float) #.reset_index(drop=True)

#df_Rmag_keep=df_out_keep[['JD','Rmag','ErrorRmag']].reset_index(drop=True)

#df_Rmag_keep['JD']=df_Rmag_keep['JD'].map('{:.4f}'.format)

df_Rmag_keep['Observatory']='LulinSLT'

print(df_Rmag_keep)

#file_Rmag_out_keep=dir_obj+'Rmag_'+obj_name+'.txt'

file_Rmag_out_keep=dir_obj+'gasp_'+iau_name+'.dat'

df_Rmag_keep.to_csv(file_Rmag_out_keep,sep=',',index=False,float_format='%.4f')

print('... write file to: ./'+file_Rmag_out_keep)

# -----------------------------------

#JD_keep=df_out_keep['JD']

#Rmag_keep=df_out_keep['Rmag']

#ErrorRmag=df_out_keep['ErrorRmag']

# -----------------------------------

#sys.exit(0)