def applywavelengths(wavefile, applyfile, newname):
#Read in file with wavelength solution and get header info
wave = fits.open(wavefile)
n_fr = float(wave[0].header['LINDEN'])
n_fd = float(wave[0].header['CAMFUD'])
fl = float(wave[0].header['FOCLEN'])
zPnt = float(wave[0].header['ZPOINT'])
#Read in file to apply wavelength solution and update header
spec_data = fits.getdata(applyfile)
spec_header = fits.getheader(applyfile)
rt.Fix_Header(spec_header)
spec_header.append(('LINDEN', n_fr, 'Line Desity for Grating Eq.'),
useblanks=True,
bottom=True)
spec_header.append(
('CAMFUD', n_fd, 'Camera Angle Correction Factor for Grat. Eq.'),
useblanks=True,
bottom=True)
spec_header.append(('FOCLEN', fl, 'Focal Length for Grat Eq.'),
useblanks=True,
bottom=True)
spec_header.append(('ZPOINT', zPnt, 'Zero Point Pixel for Grat Eq.'),
useblanks=True,
bottom=True)
NewspecHdu = fits.PrimaryHDU(data=spec_data, header=spec_header)
#See if new file already exists
mylist = [True for f in os.listdir('.') if f == newname]
exists = bool(mylist)
clob = False
if exists:
print 'File %s already exists.' % newname
nextstep = raw_input(
'Do you want to overwrite or designate a new name (overwrite/new)? '
)
if nextstep == 'overwrite':
clob = True
exists = False
elif nextstep == 'new':
newname = raw_input('New file name: ')
exists = False
else:
exists = False
NewspecHdu.writeto(newname, output_verify='warn', clobber=clob)
def calibrate_now(lamp,
zz_specname,
fit_zpoint,
zzceti,
offset_file,
plotall=True):
# Read Lamp Data and Header #
lamp_data = fits.getdata(lamp)
lamp_header = fits.getheader(lamp)
# Check number of image slices, and select the spectra #
if lamp_header["NAXIS"] == 2:
lamp_spec = lamp_data[0]
elif lamp_header["NAXIS"] == 3:
lamp_spec = lamp_data[0][0]
else:
print("\nDont know which data to unpack.")
print("Check the array dimensions\n")
# plt.figure(1)
# plt.plot(lamp_spec)
# plt.title('Raw')
# plt.show()
# Find the pixel number offset due to trim reindexing #
trim_sec = lamp_header["CCDSEC"]
trim_offset = float(trim_sec[1:len(trim_sec) - 1].split(':')[0]) - 1
# Find Bining #
try:
bining = float(lamp_header["PARAM18"])
except:
bining = float(lamp_header["PG3_2"])
# Get Pixel Numbers #
nx = np.size(lamp_spec)
Pixels = bining * (np.arange(0, nx, 1) + trim_offset)
# Select Set of Parameters to use #
global parm
if lamp.lower().__contains__('red'):
parm = Param_930_20_40
line_list = WaveList_Fe_930_20_40
elif lamp.lower().__contains__('blue'):
parm = Param_930_12_24
line_list = WaveList_Fe_930_12_24
else:
print "Could not detect setup!"
# Calculate Initial Guess Solution # ========================================
alpha = float(lamp_header["GRT_TARG"])
theta = float(lamp_header["CAM_TARG"])
Wavelengths = DispCalc(Pixels, alpha, theta, parm[0], parm[1], parm[2],
parm[3])
# Ask for offset # ===========================================================
print offset_file
if offset_file:
print 'Using offset file: ', offset_file
offsets = np.genfromtxt(offset_file, dtype='d')
if offsets.size == 1:
offsets = np.array([offsets])
#print offsets
if 'blue' in lamp.lower():
offset = offsets[0]
elif 'red' in lamp.lower():
offset = offsets[1]
Wavelengths = [w + offset for w in Wavelengths]
else:
# Plot Dispersion #
plt.figure(1)
plt.plot(Wavelengths, lamp_spec)
plt.hold('on')
for line in line_list[1]:
if (Wavelengths[0] <= line <= Wavelengths[-1]):
plt.axvline(line, color='r', linestyle='--')
plt.title(
"Initial Dispersion Inspection Graph. \nClose to Calculate Offset")
plt.xlabel("Wavelengths")
plt.ylabel("Counts")
plt.hold('off')
plt.show()
print "\nWould You like to set Offset?"
yn = raw_input('yes/no? >>> ')
#yn= 'yes'
if yn == 'yes':
global ax, fig, coords
fig = plt.figure(1)
ax = fig.add_subplot(111)
ax.plot(Wavelengths, lamp_spec)
plt.hold('on')
for line in line_list[1]:
if (Wavelengths[0] <= line <= Wavelengths[-1]):
plt.axvline(line, color='r', linestyle='--')
plt.title(
"First click known line(red), then click coresponding peak near center\n Then close graph."
)
plt.xlabel("Wavelengths (Ang.)")
plt.ylabel("Counts")
if lamp.__contains__('blue'):
plt.xlim(4700., 4900.)
elif lamp.__contains__('red'):
plt.xlim(6920., 7170.)
plt.hold('off')
coords = []
cid = fig.canvas.mpl_connect('button_press_event', onclick)
plt.show()
k_line = find_near(
coords[0][0], line_list[1]) # Nearest line to click cordinates
k_peak = find_near(coords[1][0],
Wavelengths) # Nearest Peak to click cordinates
i_peak = Wavelengths.index(k_peak)
X = Wavelengths[i_peak - 7:i_peak + 7]
Y = lamp_spec[i_peak - 7:i_peak + 7]
amp, center, width, b = fit_Gauss(X, Y)
offset = (k_line - center)
##########
#Save the offset
print '\n Would you like to save the offset?'
save_offset = raw_input('yes/no? >>> ')
if save_offset == 'yes':
print 'Saving offset to offsets.txt'
g = open('offsets.txt', 'a')
g.write(str(offset) + '\n')
g.close()
##########
Wavelengths = [w + offset for w in Wavelengths]
plt.figure(1)
plt.plot(Wavelengths, lamp_spec)
plt.hold('on')
for line in line_list[1]:
if (Wavelengths[0] <= line <= Wavelengths[-1]):
plt.axvline(line, color='r', linestyle='--')
plt.title("Offset Applied.")
plt.xlabel("Wavelengths (Ang.)")
plt.ylabel("Counts")
plt.hold('off')
plt.show()
else:
offset = 0.
# Ask Refit # ===============================================================
yn = 'yes'
while yn == 'yes':
#print "\nWould you like to refit and recalculate dispersion?"
#yn= raw_input('yes/no? >>> ')
yn = 'yes'
if yn == 'yes':
#print "\nOffset to apply to Grating Angle?"
#alpha_offset= float( raw_input('Offset Value? >>>') )
alpha_offset = 0.
#alpha= alpha + alpha_offset
'''
#Uncomment this part if you would like to select lines to use by hand. Otherwise, all lines in the above line lists are used.
fig = plt.figure(1)
ax = fig.add_subplot(111)
ax.plot(Wavelengths, lamp_spec)
plt.hold('on')
lines_in_range= []
for line in line_list[1]:
if (Wavelengths[0] <= line <= Wavelengths[-1]):
lines_in_range.append(line)
plt.axvline(line, color= 'r', linestyle= '--')
plt.title("Click on The Peaks You Want to Use to Refit \n Then close graph.")
plt.xlim([np.min(lines_in_range)-50, np.max(lines_in_range)+50])
plt.ylim([np.min(lamp_spec)-100, np.max(lamp_spec)/2])
plt.xlabel("Wavelengths (Ang.)")
plt.ylabel("Counts")
plt.hold('off')
coords= []
cid = fig.canvas.mpl_connect('button_press_event', onclick)
plt.show()
'''
###n_pnt, n_cor= np.shape(coords)
###coord_x= [coords[i][0] for i in range(0,n_pnt)]
coord_x = line_list[
1] #Use all lines in the line lists for the refitting.
n_pnt = len(coord_x)
peak_x = []
for i in range(0, n_pnt):
x = find_near(coord_x[i], Wavelengths)
peak_x.append(x)
centers_in_wave = find_peak_centers(peak_x, Wavelengths, lamp_spec)
centers_in_wave = [w - offset for w in centers_in_wave]
centers_in_pix = PixCalc(centers_in_wave, alpha, theta, parm[0],
parm[1], parm[2], parm[3])
known_waves = []
for i in range(0, n_pnt):
x = find_near(coord_x[i], line_list[1])
known_waves.append(x)
#Create array to save data for diagnostic purposes
global savearray, n_fr, n_fd, n_zPnt
savearray = np.zeros([len(Wavelengths), 8])
#n_fr, n_fd, n_zPnt= fit_Grating_Eq(centers_in_pix, known_waves, alpha, theta, parm)
par, rmsfit = fit_Grating_Eq(centers_in_pix,
known_waves,
alpha,
theta,
parm,
plotalot=plotall)
n_fr, n_fd, n_zPnt = par
n_Wavelengths = DispCalc(Pixels, alpha - alpha_offset, theta, n_fr,
n_fd, parm[2], n_zPnt)
if plotall:
plt.figure(1)
plt.plot(n_Wavelengths, lamp_spec)
plt.hold('on')
for line in line_list[1]:
if (n_Wavelengths[0] <= line <= n_Wavelengths[-1]):
plt.axvline(line, color='r', linestyle='--')
plt.title("Refitted Solution")
plt.xlabel("Wavelengths (Ang.)")
plt.ylabel("Counts")
plt.hold('off')
savearray[0:len(n_Wavelengths), 2] = n_Wavelengths
savearray[0:len(lamp_spec), 3] = lamp_spec
savearray[0:len(np.array(line_list[1])),
4] = np.array(line_list[1])
'''
plt.figure(2)
Diff= [ (Wavelengths[i]-n_Wavelengths[i]) for i in range(0,np.size(Wavelengths)) ]
plt.plot(Diff, '.')
plt.title("Diffence between old and new solution.")
plt.xlabel("Pixel")
plt.ylabel("old-new Wavelength (Ang.)")
'''
plt.show()
if ('blue' in lamp.lower()) and (rmsfit > 1.0):
coord_list_short = line_list[0][1:]
wave_list_short = line_list[1][1:]
line_list = np.array([coord_list_short, wave_list_short])
print 'Refitting without first line.'
yn = 'yes'
else:
yn = 'no' #Don't refit again
# Save parameters in header and write file #
#print "\nWrite solution to header?"
#yn= raw_input("yes/no? >>>")
print '\n Writing solution to header'
yn = 'yes'
if yn == "yes":
newname = 'w' + lamp
mylist = [True for f in os.listdir('.') if f == newname]
exists = bool(mylist)
clob = False
if exists:
print 'File %s already exists.' % newname
nextstep = raw_input(
'Do you want to overwrite or designate a new name (overwrite/new)? '
)
if nextstep == 'overwrite':
clob = True
exists = False
elif nextstep == 'new':
newname = raw_input('New file name: ')
exists = False
else:
exists = False
rt.Fix_Header(lamp_header)
lamp_header.append(('LINDEN', n_fr, 'Line Desity for Grating Eq.'),
useblanks=True,
bottom=True)
lamp_header.append(
('CAMFUD', n_fd, 'Camera Angle Correction Factor for Grat. Eq.'),
useblanks=True,
bottom=True)
lamp_header.append(('FOCLEN', parm[2], 'Focal Length for Grat Eq.'),
useblanks=True,
bottom=True)
lamp_header.append(('ZPOINT', n_zPnt, 'Zero Point Pixel for Grat Eq.'),
useblanks=True,
bottom=True)
lamp_header.append(('RMSWAVE', rmsfit, 'RMS from Wavelength Calib.'),
useblanks=True,
bottom=True)
NewHdu = fits.PrimaryHDU(data=lamp_data, header=lamp_header)
NewHdu.writeto(newname, output_verify='warn', clobber=clob)
#Save parameters to ZZ Ceti spectrum#
#print "\nWrite solution to header of another spectrum?"
#yn= raw_input("yes/no? >>>")
if zz_specname:
#specname = raw_input("Filename: ")
#fitspectrum = raw_input('Would you like to fit a new zero point using a spectral line? (yes/no) ')
if fit_zpoint == 'yes':
newzeropoint = WaveShift(zz_specname, zzceti, plotall)
else:
newzeropoint = n_zPnt
spec_data = fits.getdata(zz_specname)
spec_header = fits.getheader(zz_specname)
rt.Fix_Header(spec_header)
spec_header.append(('LINDEN', n_fr, 'Line Desity for Grating Eq.'),
useblanks=True,
bottom=True)
spec_header.append(
('CAMFUD', n_fd, 'Camera Angle Correction Factor for Grat. Eq.'),
useblanks=True,
bottom=True)
spec_header.append(('FOCLEN', parm[2], 'Focal Length for Grat Eq.'),
useblanks=True,
bottom=True)
spec_header.append(
('ZPOINT', newzeropoint, 'Zero Point Pixel for Grat Eq.'),
useblanks=True,
bottom=True)
spec_header.append(('RMSWAVE', rmsfit, 'RMS from Wavelength Calib.'),
useblanks=True,
bottom=True)
NewspecHdu = fits.PrimaryHDU(data=spec_data, header=spec_header)
newname = 'w' + zz_specname
mylist = [True for f in os.listdir('.') if f == newname]
exists = bool(mylist)
clob = False
if exists:
print 'File %s already exists.' % newname
nextstep = raw_input(
'Do you want to overwrite or designate a new name (overwrite/new)? '
)
if nextstep == 'overwrite':
clob = True
exists = False
elif nextstep == 'new':
newname = raw_input('New file name: ')
exists = False
else:
exists = False
NewspecHdu.writeto(newname, output_verify='warn', clobber=clob)
#Save arrays for diagnostics
now = datetime.datetime.now().strftime("%Y-%m-%dT%H:%M")
endpoint = '.ms'
with open(
'wavecal_' + zz_specname[4:zz_specname.find(endpoint)] + '_' +
now + '.txt', 'a') as handle:
header = lamp + ',' + zz_specname + '\n First 2 columns: fitted wavelengths, residuals \n Next 3 columns: wavelengths, flux, lambdas fit \n Final 3 columns: wavelengths, sky flux, fit to line for recentering'
np.savetxt(handle, savearray, fmt='%f', header=header)
