def newDetrendDataTask(clip):
flux = clip['cotrend.flux_frac']
flags = clip['cotrend.flags']
nPoints = clip['config.nPointsForMedianSmooth']
#When you detrend, you must do something about the gaps and bad values.
#This is the simplest possible thing. Replace all bad/missing data with
#zeros. This is a placehold. Bad data inside a transit is replaced with
#a zero, which is not what you want.
flux[flags] = 0
#Do a simple detrend.
detrend = kplrfits.medianSubtract1d(flux, nPoints)
clip['detrend'] = dict()
clip['detrend.flux_frac'] = detrend
clip['detrend.flags'] = flags
clip['detrend.source'] = "Simple Median detrend"
rollTweakAmp = noise.computeRollTweakAmplitude(detrend[~flags])
clip['detrend.rollTweakAmp'] = rollTweakAmp
cdpp6 = noise.computeSgCdpp_ppm(detrend[~flags])
clip['detrend.cdpp6_ppm'] = cdpp6
perPointScatter = noise.estimateScatterWithMarshallMethod(detrend[~flags])
clip['detrend.perPointScatter_ppm'] = 1e6 * perPointScatter
assert (detrend is not None)
return clip
def newDetrendDataTask(clip):
flux = clip['cotrend.flux_frac']
flags = clip['cotrend.flags']
nPoints = clip['config.nPointsForMedianSmooth']
#When you detrend, you must do something about the gaps and bad values.
#This is the simplest possible thing. Replace all bad/missing data with
#zeros. This is a placehold. Bad data inside a transit is replaced with
#a zero, which is not what you want.
flux[flags] = 0
#Do a simple detrend.
detrend = kplrfits.medianSubtract1d(flux, nPoints)
clip['detrend'] = dict()
clip['detrend.flux_frac'] = detrend
clip['detrend.flags'] = flags
clip['detrend.source'] = "Simple Median detrend"
rollTweakAmp = noise.computeRollTweakAmplitude(detrend[~flags])
clip['detrend.rollTweakAmp'] = rollTweakAmp
cdpp6 = noise.computeSgCdpp_ppm(detrend[~flags])
clip['detrend.cdpp6_ppm'] = cdpp6
perPointScatter = noise.estimateScatterWithMarshallMethod(detrend[~flags])
clip['detrend.perPointScatter_ppm'] = 1e6*perPointScatter
assert(detrend is not None)
return clip
def getNoiseParams(lcv):
# sigma clip it
sigmaClip_tf = noise.sigmaClip(lcv, 5.0)
lcv = lcv[~sigmaClip_tf]
# get params
rta = noise.computeRollTweakAmplitude(lcv)
sgcdpp = noise.computeSgCdpp_ppm(lcv)
scatter = noise.estimateScatterWithMarshallMethod(lcv)
return rta, sgcdpp, scatter
def getNoiseParams(lcv):
# sigma clip it
sigmaClip_tf = noise.sigmaClip(lcv, 5.)
lcv = lcv[~sigmaClip_tf]
# get params
rta = noise.computeRollTweakAmplitude(lcv)
sgcdpp = noise.computeSgCdpp_ppm(lcv)
scatter = noise.estimateScatterWithMarshallMethod(lcv)
return rta, sgcdpp, scatter
def paramSubplot(cadenceSum, numPrinCompList, results_list):
y = cadenceSum / np.mean(cadenceSum) - 1
raw_rta = noise.computeRollTweakAmplitude(y)
raw_sgcdpp = noise.computeSgCdpp_ppm(noise.sigmaClip(y, 5.0))
raw_scatter = noise.estimateScatterWithMarshallMethod(y)
f, axarr = plt.subplots(3, sharex=True)
axarr[0].axhline(raw_rta, label="RTA for raw light curve")
axarr[1].axhline(raw_sgcdpp, label="sgcdpp for raw light curve")
axarr[2].axhline(raw_scatter, label="scatter for raw light curve")
axarr[0].plot(numPrinCompList, results_list.T[1], ".", color="green")
axarr[1].plot(numPrinCompList, results_list.T[2], ".", color="green")
axarr[2].plot(numPrinCompList, results_list.T[3], ".", color="green")
plt.xlabel("Number of Principal Components")
axarr[0].set_ylabel("Roll Tweak Amplitude")
axarr[1].set_ylabel("sgcdpp")
axarr[2].set_ylabel("scatter")
plt.show()
def paramSubplot(cadenceSum, numPrinCompList, results_list):
y = cadenceSum / np.mean(cadenceSum) - 1
raw_rta = noise.computeRollTweakAmplitude(y)
raw_sgcdpp = noise.computeSgCdpp_ppm(noise.sigmaClip(y, 5.))
raw_scatter = noise.estimateScatterWithMarshallMethod(y)
f, axarr = plt.subplots(3, sharex=True)
axarr[0].axhline(raw_rta, label="RTA for raw light curve")
axarr[1].axhline(raw_sgcdpp, label="sgcdpp for raw light curve")
axarr[2].axhline(raw_scatter, label="scatter for raw light curve")
axarr[0].plot(numPrinCompList, results_list.T[1], ".", color="green")
axarr[1].plot(numPrinCompList, results_list.T[2], ".", color="green")
axarr[2].plot(numPrinCompList, results_list.T[3], ".", color="green")
plt.xlabel("Number of Principal Components")
axarr[0].set_ylabel("Roll Tweak Amplitude")
axarr[1].set_ylabel("sgcdpp")
axarr[2].set_ylabel("scatter")
plt.show()
def varyPrinComp(epic, campaign, plotMask):
# get the data
getData_return = getData(epic, campaign)
data = getData_return[0]
inds_to_eliminate = getData_return[1].astype(bool)
# plot the image
# plotCadence(data[0], axis='relative')
# create a mask for the light curve
mask = createMask(data[0], thresh=0, title="Light Curve Mask", plotMask=plotMask)
lcvMatrix = reduceAperture(mask, data)
# create a mask for PCA
pca_mask = createMask(data[0], thresh=0, title="PCA Mask", plotMask=plotMask)
pcaMatrix = reduceAperture(pca_mask, data)
# take out data points with thruster firings
lcvMatrix = lcvMatrix[:, ~inds_to_eliminate]
pcaMatrix = pcaMatrix[:, ~inds_to_eliminate]
# get rid of nans in matrices
lcvMatrix = noMoreNaN(lcvMatrix)
assert checkNaN(lcvMatrix)
pcaMatrix = noMoreNaN(pcaMatrix)
assert checkNaN(pcaMatrix)
# make the raw light curve
cadenceSum = np.sum(lcvMatrix, axis=0)
t = np.arange(len(cadenceSum))
# plot the raw light curve
make_plot(t, cadenceSum, title="Raw Light Curve, e: %s, c: %s" % (epic, campaign))
# make a list of number of principal comps to try
numPrinCompList = np.arange(2, np.sum(mask), 2)
rta_list = []
sgcdpp_list = []
scatter_list = []
results_list = []
n = 0
offset = 0.1
# plt.figure()
for numPrinComps in numPrinCompList:
curveFit_return = curveFit(pcaMatrix, cadenceSum, numPrinComps)
fittedCurve = curveFit_return[0]
# make the mean zero
corrected = correctedCurve(cadenceSum, fittedCurve)
corrected /= np.mean(corrected)
corrected -= 1
sigmaClip_tf = noise.sigmaClip(corrected, 5.0)
corrected = corrected[~sigmaClip_tf]
rta = noise.computeRollTweakAmplitude(corrected)
sgcdpp = noise.computeSgCdpp_ppm(corrected)
scatter = noise.estimateScatterWithMarshallMethod(corrected)
rta_list.append(rta)
sgcdpp_list.append(sgcdpp)
scatter_list.append(scatter)
results_list.append([numPrinComps, rta, sgcdpp, scatter])
# plt.plot(range(len(corrected)), corrected+ n*offset, ".", markersize=4, label = "%f,%i"%(sgcdpp, int(numPrinComps)))
n += 1
# plt.legend()
# plt.show()
# plot the three params wrt the raw values
if plotMask == True:
y = cadenceSum / np.mean(cadenceSum) - 1
raw_rta = noise.computeRollTweakAmplitude(y)
raw_sgcdpp = noise.computeSgCdpp_ppm(noise.sigmaClip(y, 5.0))
raw_scatter = noise.estimateScatterWithMarshallMethod(y)
f, axarr = plt.subplots(3, sharex=True)
axarr[0].axhline(raw_rta, label="RTA for raw light curve")
axarr[1].axhline(raw_sgcdpp, label="sgcdpp for raw light curve")
axarr[2].axhline(raw_scatter, label="scatter for raw light curve")
axarr[0].plot(numPrinCompList, rta_list, ".", color="green")
axarr[1].plot(numPrinCompList, sgcdpp_list, ".", color="green")
axarr[2].plot(numPrinCompList, scatter_list, ".", color="green")
plt.xlabel("Number of Principal Components")
axarr[0].set_ylabel("Roll Tweak Amplitude")
axarr[1].set_ylabel("sgcdpp")
axarr[2].set_ylabel("scatter")
plt.show()
# plot the corrected light curve with the lowest sgcdpp
# ==============================================================================
# optimalPC = numPrinCompList[np.argmin(sgcdpp_list)]
# fittedCurve = curveFit(pcaMatrix, cadenceSum, optimalPC)[0]
# optimal_lcv = correctedCurve(cadenceSum, fittedCurve)
# make_plot(t, optimal_lcv, title="e: %s, c: %s,sgcdpp=%s PC=%s"%(epic, campaign,
# str(np.min(sgcdpp_list)),
# numPrinCompList[np.argmin(sgcdpp_list)]))
# ==============================================================================
# plot the corrected light curve with the smallest slope between sgcdpp values
smallest_slope = np.argmin(np.abs(np.diff(sgcdpp_list)))
optimalPC = numPrinCompList[smallest_slope]
fittedCurve = curveFit(pcaMatrix, cadenceSum, optimalPC)[0]
optimal_lcv = correctedCurve(cadenceSum, fittedCurve)
sigmaClip_tf = noise.sigmaClip(optimal_lcv, 5.0)
make_plot(t, optimal_lcv, show=False)
make_plot(
t[sigmaClip_tf],
optimal_lcv[sigmaClip_tf],
new=False,
title="e:%s, c:%s, smallest slope, PC=%s" % (epic, campaign, numPrinCompList[smallest_slope]),
marker="ro",
)
folded = np.fmod(t, 4.16)
make_plot(t, folded)
# ==============================================================================
# # plot the corrected light curve with the lowest rta
# plt.figure()
# plt.title("epic %s campaign %s lowest rta=%s PC=%s"%(epic, campaign,
# str(np.min(rta_list)),
# numPrinCompList[np.argmin(rta_list)]))
# optimalPC = numPrinCompList[np.argmin(rta_list)]
# fittedCurve = curveFit(pcaMatrix, cadenceSum, optimalPC)[0]
# optimal_lcv = correctedCurve(cadenceSum, fittedCurve)
# plt.plot(range(len(optimal_lcv)), optimal_lcv, ".")
# ==============================================================================
# plt.show()
return np.array(results_list).T
def varyPrinComp(epic, campaign, plotMask):
# get the data
getData_return = getData(epic, campaign)
data = getData_return[0]
inds_to_eliminate = getData_return[1].astype(bool)
# plot the image
#plotCadence(data[0], axis='relative')
# create a mask for the light curve
mask = createMask(data[0],
thresh=0,
title="Light Curve Mask",
plotMask=plotMask)
lcvMatrix = reduceAperture(mask, data)
# create a mask for PCA
pca_mask = createMask(data[0],
thresh=0,
title="PCA Mask",
plotMask=plotMask)
pcaMatrix = reduceAperture(pca_mask, data)
# take out data points with thruster firings
lcvMatrix = lcvMatrix[:, ~inds_to_eliminate]
pcaMatrix = pcaMatrix[:, ~inds_to_eliminate]
#get rid of nans in matrices
lcvMatrix = noMoreNaN(lcvMatrix)
assert checkNaN(lcvMatrix)
pcaMatrix = noMoreNaN(pcaMatrix)
assert checkNaN(pcaMatrix)
# make the raw light curve
cadenceSum = np.sum(lcvMatrix, axis=0)
t = np.arange(len(cadenceSum))
# plot the raw light curve
make_plot(t,
cadenceSum,
title="Raw Light Curve, e: %s, c: %s" % (epic, campaign))
# make a list of number of principal comps to try
numPrinCompList = np.arange(2, np.sum(mask), 2)
rta_list = []
sgcdpp_list = []
scatter_list = []
results_list = []
n = 0
offset = 0.1
#plt.figure()
for numPrinComps in numPrinCompList:
curveFit_return = curveFit(pcaMatrix, cadenceSum, numPrinComps)
fittedCurve = curveFit_return[0]
# make the mean zero
corrected = correctedCurve(cadenceSum, fittedCurve)
corrected /= np.mean(corrected)
corrected -= 1
sigmaClip_tf = noise.sigmaClip(corrected, 5.)
corrected = corrected[~sigmaClip_tf]
rta = noise.computeRollTweakAmplitude(corrected)
sgcdpp = noise.computeSgCdpp_ppm(corrected)
scatter = noise.estimateScatterWithMarshallMethod(corrected)
rta_list.append(rta)
sgcdpp_list.append(sgcdpp)
scatter_list.append(scatter)
results_list.append([numPrinComps, rta, sgcdpp, scatter])
#plt.plot(range(len(corrected)), corrected+ n*offset, ".", markersize=4, label = "%f,%i"%(sgcdpp, int(numPrinComps)))
n += 1
#plt.legend()
#plt.show()
# plot the three params wrt the raw values
if plotMask == True:
y = cadenceSum / np.mean(cadenceSum) - 1
raw_rta = noise.computeRollTweakAmplitude(y)
raw_sgcdpp = noise.computeSgCdpp_ppm(noise.sigmaClip(y, 5.))
raw_scatter = noise.estimateScatterWithMarshallMethod(y)
f, axarr = plt.subplots(3, sharex=True)
axarr[0].axhline(raw_rta, label="RTA for raw light curve")
axarr[1].axhline(raw_sgcdpp, label="sgcdpp for raw light curve")
axarr[2].axhline(raw_scatter, label="scatter for raw light curve")
axarr[0].plot(numPrinCompList, rta_list, ".", color="green")
axarr[1].plot(numPrinCompList, sgcdpp_list, ".", color="green")
axarr[2].plot(numPrinCompList, scatter_list, ".", color="green")
plt.xlabel("Number of Principal Components")
axarr[0].set_ylabel("Roll Tweak Amplitude")
axarr[1].set_ylabel("sgcdpp")
axarr[2].set_ylabel("scatter")
plt.show()
# plot the corrected light curve with the lowest sgcdpp
#==============================================================================
# optimalPC = numPrinCompList[np.argmin(sgcdpp_list)]
# fittedCurve = curveFit(pcaMatrix, cadenceSum, optimalPC)[0]
# optimal_lcv = correctedCurve(cadenceSum, fittedCurve)
# make_plot(t, optimal_lcv, title="e: %s, c: %s,sgcdpp=%s PC=%s"%(epic, campaign,
# str(np.min(sgcdpp_list)),
# numPrinCompList[np.argmin(sgcdpp_list)]))
#==============================================================================
# plot the corrected light curve with the smallest slope between sgcdpp values
smallest_slope = np.argmin(np.abs(np.diff(sgcdpp_list)))
optimalPC = numPrinCompList[smallest_slope]
fittedCurve = curveFit(pcaMatrix, cadenceSum, optimalPC)[0]
optimal_lcv = correctedCurve(cadenceSum, fittedCurve)
sigmaClip_tf = noise.sigmaClip(optimal_lcv, 5.)
make_plot(t, optimal_lcv, show=False)
make_plot(t[sigmaClip_tf],
optimal_lcv[sigmaClip_tf],
new=False,
title="e:%s, c:%s, smallest slope, PC=%s" %
(epic, campaign, numPrinCompList[smallest_slope]),
marker='ro')
folded = np.fmod(t, 4.16)
make_plot(t, folded)
#==============================================================================
# # plot the corrected light curve with the lowest rta
# plt.figure()
# plt.title("epic %s campaign %s lowest rta=%s PC=%s"%(epic, campaign,
# str(np.min(rta_list)),
# numPrinCompList[np.argmin(rta_list)]))
# optimalPC = numPrinCompList[np.argmin(rta_list)]
# fittedCurve = curveFit(pcaMatrix, cadenceSum, optimalPC)[0]
# optimal_lcv = correctedCurve(cadenceSum, fittedCurve)
# plt.plot(range(len(optimal_lcv)), optimal_lcv, ".")
#==============================================================================
#plt.show()
return np.array(results_list).T