Voffset.py.original

import tools as tls
from astropy.io import fits
import numpy as np
import scipy.interpolate as sp
import matplotlib.pyplot as plt
from plot_format import plot_format
import os
import sys

lines = [line.rstrip('\n') for line in open('filelist')]
plot_format()
#print lines
k = 0
for j in range(len(lines)):
    path = lines[j]

    c = 299792.458 #km/s
    basename = os.path.basename(path)[:-5]
    
    timeTaken = basename[15:]
    #timeTaken = basename[7:]
    #print timeTaken

    header = fits.getheader(path)
    wl_start, wl_end = map(float,header['W_RANGE'].split(" "))
    
    Owl,Normflux = tls.NormNoPlot(path)

    ## Halpha, Hbeta, Hgamma, Hdelta, Hepsilon, H9, H10
    lineList =  np.array([6562.79, 4861.35, 4340.472, 4101.734, 3970.075, 3889.064, 3835.397])
    lineWindows = np.array([[4060.0, 4150.0], [4300.0,4375.0], [4800.0,4950.0]])
    
    lineIndex = 3

    offset = 15

    upperLine = lineList[lineIndex] + offset
    lowerLine = lineList[lineIndex] - offset

    #plt.axvline(upperLine,color='black')
    #plt.axvline(lowerLine,color="black")
    #plt.plot(Owl,Normflux)
    #plt.show()

    wherr = np.where((Owl >= lowerLine) & (Owl <= upperLine))
    flux = Normflux[wherr]
    wl = np.linspace(lowerLine,upperLine,len(flux))

    #plt.plot(wl,flux)
    #plt.show()

    vel = []
    for i in range(len(wl)):
        v = c*(lineList[lineIndex] - wl[i])/lineList[lineIndex]
        vel.append(v)


    #Plot Hbeta vertical line
    if (j < len(lines)/2):
        plt.subplot(1,2,1)
        plt.axvline(0,ls='--',color='black')
        
        plt.step(vel,flux+j*2.5,where='mid',color='black',linewidth=2)
        #plt.plot(vel,flux+j,drawstyle='steps',color='black',linewidth=2)
        #plt.plot(vel,flux+j*0.5)
        
        #plt.annotate(timeTaken, xy=(1000,j*2.5+1.5),color='blue')
        plt.annotate(timeTaken, xy=(1000,j+1),color='blue')
        plt.xlim(min(vel),max(vel))
        #plt.title("Hbeta velocity space")
        plt.xlabel("velocity [km/s]")
        plt.ylabel("Normalized flux + offset")
    else:
        plt.subplot(1,2,2)
        plt.axvline(0,ls='--',color='black')

        plt.step(vel,flux+k*2.5,where='mid',color='black',linewidth=2)
        #plt.plot(vel,flux+k,drawstyle='steps',color='black',linewidth=2)
        #plt.plot(vel,flux+j*0.5)
        
        #plt.annotate(timeTaken, xy=(1000,k*2.5+1.5),color='blue')
        plt.annotate(timeTaken, xy=(1000,k+1),color='blue')

        plt.xlim(min(vel),max(vel))
        #plt.title("Hbeta velocity space")
        plt.xlabel("velocity [km/s]")
        plt.ylabel("Normalized flux + offset")
        k+=1

if (lineIndex == 1):
    #plt.savefig("/home/seth/research/VoffsetPlots/Hbeta_offset.pdf")
    plt.savefig("vPlots/Hbeta_offset.pdf")
elif (lineIndex == 2):
    plt.savefig("vPlots/Hgamma_offset.pdf")
elif (lineIndex == 3):
    plt.savefig("vPlots/Hdelta_offset.pdf")
elif (lineIndex == 4):
    plt.savefig("vPlots/Hepsilon_offset.pdf")