############################################################################################################

##### Código de nome "continuo.py", tem como objetivo ajustar o contínuo de cada objeto da amostra. #####

# Devida algumas particularidades de alguns espectros, houve a necessidade de se impor valores iniciais mais espeíficos.

# Isso possibilitou o código "achar" um ajuste de forma mais rápida e sem erro. Outras particularidades são da estética do

# gráfico plotado. Para impor limites para alguns espectros em especiais, também utilizamos de particularidades como:

# - exclusão de comprimentos de onda que havia problemas instrumentais;

# - regiões de S/N muito elevado com consequentemente com picos.

######## Instruções de como rodar o código: ########

# 'python plot.py <numero>'

# <numero> indica a linha do arquivo 'sample_list.txt' que você deseja trabalhar.

#############################################################################################################

##### bibliotecas utilizadas ####

#coding: utf-8

import math as mat

import numpy as np

import matplotlib.pyplot as plt

import lineid_plot

import statistics

import copy

import sys

import os

from lmfit import Model

from lmfit import Parameters

import seaborn as sns

pal=sns.color_palette("colorblind",20)

#####################################

#inicialização e upload de arquivos

nun=int(sys.argv[1]) # argumento do terminal

# variaveis do código que são importante ser declaradas

X, Y, x = [], [], []

l=a=q=k=cont=0

d=20

flux=[None]*d

label,wave=[],[]

continuox, continuoy = [], []

wavegx, wavegy = [], []

wgx, wgy, YMAX = [], [], []

centro, alpha = [], []

n_contx,n_conty=[],[]

#reconhecendo cabeçalho do arquivo que ira entrar

data=np.genfromtxt('sample_list.txt', delimiter='\t', dtype=None, encoding=None, names=('FILE','AGN','redshift','RA','DEC','telescope','instrument','E(B-V)g','index'))

z=data['redshift']

index=data['index']

name=data['AGN']

arquivo=data['FILE']

#os.chdir('/home/usuario/INPE/agns/trabalho/sample/entrada')

os.chdir('/home/denimara/Documentos/agns/trabalho/sample/entrada/teste')

file=np.genfromtxt(arquivo[nun])

#lendo arquivo dos dados

X=file[:,0] #X=comprimendo de onda

Y=file[:,1]#/1e-15 #Y=fluxo

#linha que desejamos identificar

line_wave = [8446,8498,9531,9999,10049,10500,10830,10938,11126,12820,14300,18750,19446,21654]#,22230,22470]

line_label1 = ['O I','Ca II','[SIII]','FeII','HI','FeII','HeI','HI','FeII','HI','[SiX]','HI','HI', 'HI']#,'H$_2$','H$_2$']

#####################################################

# Identificando linhas no espectro

#####################################################

#comprimento do arquivo em coluna y

n=len(Y)

###### Primeiro for:

#contém a subdivisão de valores 'd' partes, onde para 'd' se tira uma mediana do cálculo do fluxo. Deste modo valores abaixo da mediana são guardados, e valores acima servem para identificar as linhas 'd' regiao.

for i in range (d):

y=[]

for j in range (n//d):

y.append(Y[q])

q+=1

y1=copy.copy(y)

#fazendo uma mediana do que sera um valor de fluxo

flux[i]=statistics.median(y1)

# loop para "delimitar" o fluxo relevante para identificação das linhas, depois armazena-los

for z in range(d):

for i in range (n//d):

#guarda valor da possivel posição de x que irá conter a linha

if Y[k]> (flux[z]) and Y[k]>Y[k-1]:

x.append(X[k])

n_contx.append(X[k])

n_conty.append(Y[k])

#se for menor, identifica como possivel valor de continuo

elif Y[k]<flux[z]:

#Avaliando regiões não interessantes para contio de alguns

# espectros em particular. Por ex, se for alguma do flamingos,

# não inclua os 500A finais no continuo.

if 8400<X[k]<8600 or 9440<X[k]<9600 or 9900<X[k]<10230 or 10740<X[k]<11030:

pass

else:

if nun==13 or nun==14 or nun==62 or nun==67 or nun==68:

if X[k]< (max(X)-500):

continuox.append(X[k])

continuoy.append(Y[k])

elif nun==58:

if X[k]>9810 and X[k]< (max(X)-900):

continuox.append(X[k])

continuoy.append(Y[k])

elif nun==26:

if X[k]>7950:

continuox.append(X[k])

continuoy.append(Y[k])

elif nun==71:

if X[k]>9000:

continuox.append(X[k])

continuoy.append(Y[k])

elif nun==57:

if X[k]<7676 or X[k]>7705:

continuox.append(X[k])

continuoy.append(Y[k])

elif nun==31:

if X[k]<17000 or X[k]>18430 or X[k]>23670:

continuox.append(X[k])

continuoy.append(Y[k])

elif nun==24:

if X[k]<16100 or X[k]>17000:

continuox.append(X[k])

continuoy.append(Y[k])

else:

continuox.append(X[k])

continuoy.append(Y[k])

k+=1

#quantos valores de linhas para possíveis fluxos foram identificadas

N=len(x)

###################### Salvando regiões de linhas em um arquivo ##############

#os.chdir('/home/usuario/INPE/agns/trabalho/sample/scripts/fluxo')

#os.chdir('/home/denimara/Documentos/agns/trabalho/sample/scripts/fluxo')

#np.savetxt('linhas.txt',np.c_[n_contx,n_conty],delimiter=' ', newline='\n')

###############################################################################

####### Loop grande:

# destinado a identificar linhas dentre os fluxos previamente identificados

for j in range (N):

for l in range (len(line_wave)):

#separação fina por um delta de comprimendo de onda aceitável para 'caber' tal linha

if (line_wave[l]-6)< x[j] < (line_wave[l]+6):

cont+=1

if cont==1:

wave.append(line_wave[l])

label.append(line_label1[l])

#não estava plotando em cima da onde achou a linha e sim da catalogada, então aqui se fez um 'shift' para melhor traçar a identificação

elif wave[-1]!=line_wave[l]:

if label[-1]!=line_label1[l] and (l-1)>=0:

wave.append(x[j])

label.append(line_label1[l])

qts=l

else:

if label[-1]==line_label1[l] and x[j]-wave[-1]>20:

wave.append(x[j])

label.append(line_label1[l])

#########################################################

# Identificação de valor obrigatório de CONTINUO

# (retirado de Rifell et. all 2006)

#########################################################

for i in range (len(X)):

if 8000<=X[i]<=8100 and nun!=58 and nun !=26 and nun!=71:#continuo que eu adicionei para forçar no inicio do espectro

continuox.append(X[i])

continuoy.append(Y[i])

elif 9700<=X[i]<=9800 and nun!=58:#original

continuox.append(X[i])

continuoy.append(Y[i])

elif 12299<X[i]<12301: #original

continuox.append(X[i])

continuoy.append(Y[i])

elif 16600<=X[i]<=16700 and nun!=24: #original

continuox.append(X[i])

continuoy.append(Y[i])

elif 20900<=X[i]<=21000: #original

continuox.append(X[i])

continuoy.append(Y[i])

elif 8400<X[i]<22000 and nun!=58: #motivo estético para o plot

YMAX.append(Y[i])

elif 9810<X[i]<22000 and nun==58:

YMAX.append(Y[i])

########################### Saida com valor do contínuo ########################

#arq=np.genfromtxt(arquivo[nun])

#os.chdir('/home/usuario/INPE/agns/trabalho/sample/scripts/fluxo')

#os.chdir('/home/denimara/Documentos/agns/trabalho/sample/scripts/fluxo')

#np.savetxt(arquivo[nun],np.c_[continuox,continuoy],delimiter=' ', newline='\n')

################################

# Pré ajuste

################################

#Parametros de cada modelo a serem fitados

params = Parameters()

params.add(name='scala',value=statistics.median(Y))

params.add(name='reference',value=10000)

###############################################################################################

# valores bons para temperatura inicial, obtidos a partir de tentativa e erro

# obs: nem todos espectros precisam

###############################################################################################

if nun==22 or nun==2 or nun==64 or nun==69 or nun==3 or nun==20 or nun==36 or nun==59 or nun==37 or nun==43 or nun==65:

params.add('T',value=980,min=500,max=1500)

elif nun==10 or nun==11 or nun==13 or nun==15 or nun==42 or nun==46 or nun==48 or nun==71 or nun==70 or nun==23 or nun==66 or nun==16 or nun==29 or nun==0 or nun==4 or nun==17 or nun==21 or nun==24 or nun==25 or nun==30 or nun==40 or nun==44 or nun==52 or nun==18 or nun==27 or nun==35 or nun==54 :

params.add('T',value=1255,min=500,max=1500)

elif nun==41 or nun==16 or nun==58 :

params.add('T',value=1350,min=500,max=1500 )

elif nun==56 or nun==45 or nun==38 or nun==39 :

params.add('T',value=1499,min=500,max=1500)

else:

params.add('T',value=0,min=500,max=1500)

#######################################################################

# Funções de componentes que irão ser ajustadas

#######################################################################

#POWER LAW

def PowerLow(wavelenght,scala,reference,Index):

return (scala*((wavelenght/reference)**Index))

#BLACK BODY

def Black_Body(wavelenght,T,alfa,reference):

return alfa*(top/bot)

#FIT DO CONTINUO :pw+bb

def SOMA(wavelenght, T, alfa, reference, scala, Index):

###############################

# Início do ajuste

##############################

contador=0.001

while (contador<1.0):

if nun==71 or nun==0 or nun==58 or nun==18:

params.add(name='Index',value=index[nun],min=-3.0001,max=0.00009)

else:

params.add(name='Index',value=index[nun])

if nun==11 or nun==10 or nun==12 or nun==16 or nun==25 or nun==19 or nun==24 or nun==29 or nun==30 or nun==31 or nun==36 or nun==37 or nun==41 or nun==43 or nun==45 or nun==54 or nun==56 or nun==27 or nun==57 or nun==58 or nun==59 or nun==60 or nun==61 or nun==62 or nun==63 or nun==65 or nun==67 or nun==3:

params.add('alfa',value=contador, min=0,max=1e-10)

else:

params.add('alfa',value=contador)

try:

modeloSOMA=Model(SOMA,independent_vars=['wavelenght'],param_names=['T','alfa','reference','scala','Index'])

resultSOMA=modeloSOMA.fit(continuoy,params,wavelenght=continuox)

s1=resultSOMA.params['T'].value

s2=resultSOMA.params['alfa'].value

s3=resultSOMA.params['reference'].value

s4=resultSOMA.params['scala'].value

s5=resultSOMA.params['Index'].value

fluxo_continuo=SOMA(X,s1,s2,s3,s4,s5)

#imprimindo INFORMAÇÕES sobre o FIT

#print(resultSOMA.fit_report())

#print('\n\n')

print (s1,s2,s5)

contador=1.0

except:

contador+=0.001

###################################################################

# guardando informações (T,fluxo em 2.2microns na banda K)

###################################################################

fluxoK=[]

BB =Black_Body(X,s1,s2,s3)

K=0

for i in range(len(X)):

if X[i]==22000:

fluxoK=BB[i]

K=1

else:

if K==0:

if 21998<X[i]<22002:

fluxoK=BB[i]

K=1

elif 21997 <= X[i] <= 22003:

fluxoK=BB[i]

K=1

elif max(X)<22000:

fluxoK=0

###### Fluxo integrado #####

Fluxo_IntegradoBB = np.trapz(Black_Body(X,s1,s2,s3), x=X)

#print(Fluxo_IntegradoBB)

###### saída dos valores ######

#os.chdir('/home/denimara/Documentos/agns/trabalho/sample/scripts/continuo')

#os.chdir('/home/usuario/INPE/agns/trabalho/sample/scripts/continuo')

#arq=open('entrada_dust.txt','a')

#np.savetxt(arq,np.c_[fluxoK,s1],delimiter=' ', newline='\n')

#print(fluxoK,s1)

os.chdir('/home/denimara/Documentos/agns/trabalho/sample/scripts/continuo/saida_ajuste_continuo')

arqs=open('saida_ajuste_continuo.txt','a')

#np.savetxt(arqs,np.c_[s1,s2,s3,s4,s5,Fluxo_IntegradoBB,resultSOMA.params['T'].stderr,resultSOMA.params['Index'].stderr],delimiter=' ', newline='\n')

par=open('parametros.txt', 'a')

np.savetxt(par,np.c_[s1,s2,s5], delimiter =' ', newline= '\n')

###########################

# LABELS da figura

###########################

#YMAX=YMAX/1e-15

Y=Y/1e-15

#plt.gcf().clear()

plt.rc('font', weight='bold') #bold fonte

plt.rc('axes', linewidth=1.8) #broader eixos

fig = plt.figure(1,figsize=(16,8))

plt.tight_layout()

plt.rcParams.update({'font.size': 15})

ax2=fig.add_axes([0.085,0.1,0.901,0.7])

ax2.set_ylabel(r'Flux [x 10$^{-15}$ erg / s / cm$^{2}$ / $\mathdefault{\AA}$]',fontweight='bold',fontsize=23)

ax2.set_xlabel('Wavelength [$\mathdefault{\AA}$]',fontweight='bold',fontsize=20)

ax2.set_title(name[nun],fontweight='bold',fontsize=20,y=1.17)

#delimitando extremidades dos plots especiais

if nun==11 or nun==24 or nun==26 or nun==47 or nun==49 or nun==52 or nun==63 or nun==64 or nun==65 or nun==66 or nun==69 or nun==70:

ax2.set_xlim(8000,max(X))

elif nun==58:

ax2.set_xlim(9880,(max(X)-500))

elif nun==54:

ax2.set_xlim(9000,max(X))

elif nun==57:

ax2.set_xlim(8000,max(X))

else:

ax2.set_xlim(min(X),max(X))

#valores adicionados ou subtraidos, são para dar margem ao plot

if(min(Y)<0):

ax2.set_ylim(0,(max(YMAX)+max(YMAX)/10)/1e-15)

else:

ax2.set_ylim(0,(max(YMAX)+max(YMAX)/10)/1e-15)

if nun==64:

ax2.set_ylim(min(Y)-min(Y)/2,max(Y)/3)

elif nun==69:

ax2.set_ylim(min(Y)-min(Y)/2,max(Y/5))

ax2.plot(X,Y,'-k',linewidth=2.8)

#____________________________fits_________________________________________

line1,=ax2.plot(X,fluxo_continuo/1e-15,linestyle='-',color='blue',linewidth=3,label="continnum")

line2,=ax2.plot(X,PowerLow(X,s4,s3,s5)/1e-15,'--',color=pal[3],linewidth=3,label="power-law")

line3,=ax2.plot(X,Black_Body(X,s1,s2,s3)/1e-15,'--',color=pal[2],linewidth=3,label="blackbody")

ax2.tick_params(axis='x', which='both',direction='in', length=4,width=1.7)

ax2.tick_params(axis='y', which='both',direction='in', length=4, width=1.7)

#mostrar continuo

#ax2.plot(continuox,continuoy,".",linewidth=20,color='orange')

#ax2.patch.set_facecolor('gray')

#ax2.patch.set_alpha(0.1)

lineid_plot.plot_line_ids(X, Y, wave, label,ax=ax2,max_iter=1000)

fig.set_facecolor('w')

legend_properties = {'weight':'bold'}

plt.legend(handles=[line1,line2,line3],loc="upper right",prop=legend_properties)

#### box superior ####

ax1=fig.add_axes([0.085,0.800,0.901,0.10])

ax1.set_xticks([])

ax1.set_yticks([])

ax1.plot()

ax1.patch.set_facecolor('gray')

ax1.patch.set_alpha(0.05)

#os.chdir('/home/usuario/INPE/agns/trabalho/sample/plots')

os.chdir('/home/denimara/Documentos/agns/trabalho/sample/scripts/continuo/plots')

plt.savefig(name[nun]+'.png',facecolor=fig.get_facecolor(), edgecolor='none')

#Para exibir na tela e não salvar, 'descomente'

#plt.show(block=True)