def calculateCM(SynthObj, nominalWave, nominalSpectrum):
solarWl = SynthObj.solarSpectrum.wave
solarFl = SynthObj.solarSpectrum.flux
resolution = 45000.0
nLines = SynthObj.lineList.numLines
nModes = 2 * nLines + 3
nFilt = nLines
IM = numpy.zeros((nModes, len(solarWl)))
stroke = numpy.ones(nModes)
factor = numpy.ones(nModes)
stroke[-1] = 0.005 # Continuum Shift
stroke[-2] = 0.1 # WL Shift
stroke[-3] = 0.01 # Smoothing
for i in range(nLines):
SynthObj.lineList.writeLineLists(i)
wave, flux = SynthObj.run()
stroke[i] = SynthObj.lineList.getGf(i) / 5.0
stroke[i + nLines] = 0.1
"""
while ((factor[i] < 0.9) | (factor[i] > 1.1)):
stroke[i] *= factor[i]
SynthObj.lineList.perturbGf(i, stroke[i])
SynthObj.lineList.writeLineLists(i,partial=True)
wave, plus = SynthObj.run()
wave, plus = SpectralTools.resample(wave, plus, resolution)
SynthObj.lineList.perturbGf(i, -2.0*stroke[i])
SynthObj.lineList.writeLineLists(i,partial=True)
wave, minus = SynthObj.run()
wave, minus = SpectralTools.resample(wave, minus, resolution)
SynthObj.lineList.perturbGf(i, stroke[i])
factor[i] = numpy.abs(target[i]/(numpy.min(plus)-numpy.min(minus)))
print factor[i]
raw_input()
#"""
for i in range(nLines):
# log gf
SynthObj.lineList.perturbGf(i, stroke[i])
SynthObj.lineList.writeLineLists(i)
wave, plus = SynthObj.run()
newWave, plus = SpectralTools.resample(wave, plus, resolution)
SynthObj.lineList.perturbGf(i, -2.0 * stroke[i])
SynthObj.lineList.writeLineLists(i)
wave, minus = SynthObj.run()
newWave, minus = SpectralTools.resample(wave, minus, resolution)
SynthObj.lineList.perturbGf(i, stroke[i])
IM[i, :] = SpectralTools.interpolate_spectrum(newWave,
solarWl, (plus - minus) /
(2.0 * stroke[i]),
pad=0.0)
factor[i] = numpy.max(numpy.abs(IM[i, :]))
IM[i, :] /= factor[i]
# damping
SynthObj.lineList.perturbVdW(i, stroke[i + nLines])
SynthObj.lineList.writeLineLists(i)
wave, plus = SynthObj.run()
newWave, plus = SpectralTools.resample(wave, plus, resolution)
SynthObj.lineList.perturbVdW(i, -2.0 * stroke[i + nLines])
SynthObj.lineList.writeLineLists(i)
wave, minus = SynthObj.run()
newWave, minus = SpectralTools.resample(wave, minus, resolution)
SynthObj.lineList.perturbVdW(i, stroke[i + nLines])
IM[i + nLines, :] = SpectralTools.interpolate_spectrum(
newWave,
solarWl, (plus - minus) / (2.0 * stroke[i + nLines]),
pad=0.0)
factor[i + nLines] = numpy.max(numpy.abs(IM[i + nLines, :]))
IM[i + nLines, :] /= factor[i + nLines]
#Continuum Level
plus = nominalSpectrum + stroke[-1]
newWave, plus = SpectralTools.resample(nominalWave, plus, resolution)
minus = nominalSpectrum - stroke[-1]
newWave, minus = SpectralTools.resample(nominalWave, minus, resolution)
IM[-1, :] = SpectralTools.interpolate_spectrum(newWave,
solarWl, (plus - minus) /
(2.0 * stroke[-1]),
pad=0.0)
factor[-1] = numpy.max(numpy.abs(IM[-1, :]))
IM[-1, :] /= factor[-1]
#Wavelength Shift
plus = SpectralTools.interpolate_spectrum(wave,
wave - stroke[-2],
nominalSpectrum,
pad=True)
newWave, plus = SpectralTools.resample(wave, plus, resolution)
minus = SpectralTools.interpolate_spectrum(wave,
wave + stroke[-2],
nominalSpectrum,
pad=True)
newWave, minus = SpectralTools.resample(wave, minus, resolution)
IM[-2, :] = SpectralTools.interpolate_spectrum(newWave,
solarWl, (plus - minus) /
(2.0 * stroke[-2]),
pad=0.0)
factor[-2] = numpy.max(numpy.abs(IM[-2, :]))
IM[-2, :] /= factor[-2]
#"""
#Instrumental Smoothing
wavePlus, plus = SpectralTools.resample(wave, nominalSpectrum,
resolution * (1.0 + stroke[-3]))
waveMinus, minus = SpectralTools.resample(wave, nominalSpectrum,
resolution * (1.0 - stroke[-3]))
diffx, diffy = SpectralTools.diff_spectra(wavePlus,
plus,
waveMinus,
minus,
pad=True)
IM[-3, :] = SpectralTools.interpolate_spectrum(diffx,
solarWl,
diffy / (2.0 * stroke[-3]),
pad=0.0)
factor[-3] = numpy.max(numpy.abs(IM[-3, :]))
IM[-3, :] /= factor[-3]
#"""
hdu = pyfits.PrimaryHDU(IM)
hdu.writeto("InteractionMatrix.fits", clobber=True)
#nFilt = Synth.lineList.numLines-2
dims = IM.shape
U, S, V = scipy.linalg.svd(IM)
D = 1.0 / S
#D = 1.0/(S[0:-nFilt])
#S[-nFilt:] = 0.0
newS = numpy.zeros((dims[0], dims[1]))
I = [i for i in range(dims[1])]
for i in range(len(D)):
newS[i][i] = D[i]
S = newS.copy()
CM = numpy.array(scipy.matrix(V.T.dot(S.T.dot(U.T)),
dtype=numpy.float32)).T
fig = pyplot.figure(0)
ax = fig.add_axes([0.1, 0.1, 0.8, 0.8])
ax.plot(S)
hdu = pyfits.PrimaryHDU(CM)
hdu.writeto('CommandMatrix.fits', clobber=True)
hdu = pyfits.PrimaryHDU(factor)
hdu.writeto('scalingfactor.fits', clobber=True)
def calculateCM(SynthObj, nominalWave, nominalSpectrum):
solarWl = SynthObj.solarSpectrum.wave
solarFl = SynthObj.solarSpectrum.flux
resolution = 45000.0
nLines = SynthObj.lineList.numLines
nModes = 2*nLines+3
nFilt = nLines
IM = numpy.zeros((nModes, len(solarWl)))
stroke = numpy.ones(nModes)
factor = numpy.ones(nModes)
stroke[-1] = 0.005 # Continuum Shift
stroke[-2] = 0.1 # WL Shift
stroke[-3] = 0.01 # Smoothing
for i in range(nLines):
SynthObj.lineList.writeLineLists(i)
wave, flux = SynthObj.run()
stroke[i] = SynthObj.lineList.getGf(i)/5.0
stroke[i+nLines] = 0.1
"""
while ((factor[i] < 0.9) | (factor[i] > 1.1)):
stroke[i] *= factor[i]
SynthObj.lineList.perturbGf(i, stroke[i])
SynthObj.lineList.writeLineLists(i,partial=True)
wave, plus = SynthObj.run()
wave, plus = SpectralTools.resample(wave, plus, resolution)
SynthObj.lineList.perturbGf(i, -2.0*stroke[i])
SynthObj.lineList.writeLineLists(i,partial=True)
wave, minus = SynthObj.run()
wave, minus = SpectralTools.resample(wave, minus, resolution)
SynthObj.lineList.perturbGf(i, stroke[i])
factor[i] = numpy.abs(target[i]/(numpy.min(plus)-numpy.min(minus)))
print factor[i]
raw_input()
#"""
for i in range(nLines):
# log gf
SynthObj.lineList.perturbGf(i, stroke[i])
SynthObj.lineList.writeLineLists(i)
wave, plus = SynthObj.run()
newWave, plus = SpectralTools.resample(wave, plus, resolution)
SynthObj.lineList.perturbGf(i, -2.0*stroke[i])
SynthObj.lineList.writeLineLists(i)
wave, minus = SynthObj.run()
newWave, minus = SpectralTools.resample(wave, minus, resolution)
SynthObj.lineList.perturbGf(i, stroke[i])
IM[i,:] = SpectralTools.interpolate_spectrum(newWave, solarWl,
(plus - minus)/(2.0*stroke[i]), pad=0.0)
factor[i] = numpy.max(numpy.abs(IM[i,:]))
IM[i,:] /= factor[i]
# damping
SynthObj.lineList.perturbVdW(i, stroke[i+nLines])
SynthObj.lineList.writeLineLists(i)
wave, plus = SynthObj.run()
newWave, plus = SpectralTools.resample(wave, plus, resolution)
SynthObj.lineList.perturbVdW(i, -2.0*stroke[i+nLines])
SynthObj.lineList.writeLineLists(i)
wave, minus = SynthObj.run()
newWave, minus = SpectralTools.resample(wave, minus, resolution)
SynthObj.lineList.perturbVdW(i, stroke[i+nLines])
IM[i+nLines,:] = SpectralTools.interpolate_spectrum(newWave, solarWl,
(plus-minus)/(2.0*stroke[i+nLines]), pad=0.0)
factor[i+nLines] = numpy.max(numpy.abs(IM[i+nLines,:]))
IM[i+nLines,:] /= factor[i+nLines]
#Continuum Level
plus = nominalSpectrum + stroke[-1]
newWave, plus = SpectralTools.resample(nominalWave, plus, resolution)
minus = nominalSpectrum - stroke[-1]
newWave, minus = SpectralTools.resample(nominalWave, minus, resolution)
IM[-1, :] = SpectralTools.interpolate_spectrum(newWave, solarWl,
(plus-minus)/(2.0*stroke[-1]), pad=0.0)
factor[-1] = numpy.max(numpy.abs(IM[-1,:]))
IM[-1,:] /= factor[-1]
#Wavelength Shift
plus = SpectralTools.interpolate_spectrum(wave, wave-stroke[-2], nominalSpectrum,
pad=True)
newWave, plus = SpectralTools.resample(wave, plus, resolution)
minus = SpectralTools.interpolate_spectrum(wave, wave+stroke[-2], nominalSpectrum,
pad=True)
newWave, minus = SpectralTools.resample(wave, minus, resolution)
IM[-2, :] = SpectralTools.interpolate_spectrum(newWave, solarWl,
(plus-minus)/(2.0*stroke[-2]), pad=0.0)
factor[-2] = numpy.max(numpy.abs(IM[-2,:]))
IM[-2,:] /= factor[-2]
#"""
#Instrumental Smoothing
wavePlus, plus = SpectralTools.resample(wave, nominalSpectrum, resolution*(1.0+stroke[-3]))
waveMinus, minus = SpectralTools.resample(wave, nominalSpectrum, resolution*(1.0-stroke[-3]))
diffx, diffy = SpectralTools.diff_spectra(wavePlus, plus, waveMinus, minus, pad=True)
IM[-3,:] = SpectralTools.interpolate_spectrum(diffx, solarWl, diffy/(2.0*stroke[-3]), pad=0.0)
factor[-3] = numpy.max(numpy.abs(IM[-3,:]))
IM[-3,:] /= factor[-3]
#"""
hdu = pyfits.PrimaryHDU(IM)
hdu.writeto("InteractionMatrix.fits", clobber=True)
#nFilt = Synth.lineList.numLines-2
dims = IM.shape
U,S,V = scipy.linalg.svd(IM)
D = 1.0/S
#D = 1.0/(S[0:-nFilt])
#S[-nFilt:] = 0.0
newS = numpy.zeros((dims[0], dims[1]))
I = [i for i in range(dims[1])]
for i in range(len(D)):
newS[i][i] = D[i]
S = newS.copy()
CM = numpy.array(scipy.matrix(V.T.dot(S.T.dot(U.T)),dtype=numpy.float32)).T
fig = pyplot.figure(0)
ax = fig.add_axes([0.1, 0.1, 0.8, 0.8])
ax.plot(S)
hdu = pyfits.PrimaryHDU(CM)
hdu.writeto('CommandMatrix.fits', clobber=True)
hdu = pyfits.PrimaryHDU(factor)
hdu.writeto('scalingfactor.fits', clobber=True)
Wavelengths = [wave]
Gain = 0.35
f2 = pyplot.figure(1)
f2.clear()
ax2 = f2.add_axes([0.1, 0.1, 0.8, 0.8])
f3 = pyplot.figure(2)
f3.clear()
ax3 = f3.add_axes([0.1, 0.1, 0.8, 0.8])
while True:
x, difference = SpectralTools.diff_spectra(solarWave,
solarFlux,
Wavelengths[-1],
Spectra[-1],
pad=True)
difference[Spectra[-1] == 0] = 0.0
command = Gain * (CM.dot(difference)) / factor
#command[[i*2+1 for i in range(Synth.lineList.numLines)]] = 0.0
Synth.lineList.applyCorrection(command[:-2])
continuum = continuum + command[-1]
wlOffset = wlOffset + command[-2]
resolution = resolution * (1.0 + command[-3])
wave, flux = Synth.run()
#Spectra.append(wave)
wavelength, spectrum = SpectralTools.resample(wave, flux, resolution)
Spectra.append(spectrum + continuum)
Wavelengths.append(wavelength + wlOffset)
Spectra = [spectrum]
Wavelengths = [wave]
Gain = 0.35
f2 = pyplot.figure(1)
f2.clear()
ax2 = f2.add_axes([0.1, 0.1, 0.8, 0.8])
f3 = pyplot.figure(2)
f3.clear()
ax3 = f3.add_axes([0.1, 0.1, 0.8, 0.8])
while True:
x, difference = SpectralTools.diff_spectra(solarWave, solarFlux,
Wavelengths[-1], Spectra[-1], pad=True)
difference[Spectra[-1] == 0] = 0.0
command = Gain*(CM.dot(difference))/factor
#command[[i*2+1 for i in range(Synth.lineList.numLines)]] = 0.0
Synth.lineList.applyCorrection(command[:-2])
continuum = continuum+command[-1]
wlOffset = wlOffset+command[-2]
resolution = resolution*(1.0+command[-3])
wave, flux = Synth.run()
#Spectra.append(wave)
wavelength, spectrum = SpectralTools.resample(wave, flux, resolution)
Spectra.append(spectrum+continuum)
Wavelengths.append(wavelength+wlOffset)
ax2.clear()
