def estimateSnr(time, flux, flags, period_days, epoch_bkjd, \
duration_hrs, depth_frac, nDurForClip=2):
"""Estimate the SNR of a transit.
SNR is defined as (transit depth) / (rms scatter). Transit depth
is an input parameter, snr is calculated with the Marshall method
Inputs:
-------------
time, flux, flags
(np 1d arrays) arrays of time flux and flag values. All flag
values > 0 are treated as though they indicate bad data.
period_days, epoch_bkjd, duration_hrs, depth_frac
(floats) Parameters of transit
Optional Inputs:
----------------
nDurForClip
Points within nDurForClip*duration_hrs around each transit are
excluded from the estimate of noise.
"""
dur_days = duration_hrs / 24.
idx = kplrfits.markTransitCadences(time, period_days, epoch_bkjd, \
dur_days, nDurForClip, flags=flags)
if np.all(idx):
msg = "All cadences seem to be in or near transit: "
msg += "Period %.1f Duration %.2f hrs" % (period_days, duration_hrs)
raise ValueError(msg)
#import pdb; pdb.set_trace()
idx |= flags > 0 #Remove data flagged as bad
idx |= ~np.isfinite(time) #Or otherwise NaN
idx |= ~np.isfinite(flux) #Or otherwise NaN
idx |= outliers.indexOfOutliers(flux) #Remove outliers
#No good cadences for some reason.
if np.all(idx):
raise ValueError(
"No good cadences found for noise estimate. Check transit duration"
)
assert (np.all(np.isfinite(flux[~idx])))
expTime_days = np.median(np.diff(time[~idx]))
duration_cadences = dur_days / expTime_days
#Duration must be at least 4 cadences of sgCdpp will crash
duration_cadences = max(duration_cadences, 4)
rms = noise.computeSgCdpp_ppm(flux[~idx], duration_cadences) * 1e-6
idx = kplrfits.markTransitCadences(time, period_days, epoch_bkjd, \
dur_days, 1, flags=flags)
nCadenceInTransit = np.sum(idx)
return depth_frac / rms * np.sqrt(nCadenceInTransit)
def estimateSnr(time, flux, flags, period_days, epoch_bkjd, \
duration_hrs, depth_frac, nDurForClip=2):
"""Estimate the SNR of a transit.
SNR is defined as (transit depth) / (rms scatter). Transit depth
is an input parameter, snr is calculated with the Marshall method
Inputs:
-------------
time, flux, flags
(np 1d arrays) arrays of time flux and flag values. All flag
values > 0 are treated as though they indicate bad data.
period_days, epoch_bkjd, duration_hrs, depth_frac
(floats) Parameters of transit
Optional Inputs:
----------------
nDurForClip
Points within nDurForClip*duration_hrs around each transit are
excluded from the estimate of noise.
"""
dur_days = duration_hrs / 24.
idx = kplrfits.markTransitCadences(time, period_days, epoch_bkjd, \
dur_days, nDurForClip, flags=flags)
if np.all(idx):
msg = "All cadences seem to be in or near transit: "
msg += "Period %.1f Duration %.2f hrs" %(period_days, duration_hrs)
raise ValueError(msg)
idx |= flags > 0 #Remove data flagged as bad
idx |= ~np.isfinite(time) #Or otherwise NaN
idx |= ~np.isfinite(flux) #Or otherwise NaN
idx |= outliers.indexOfOutliers(flux) #Remove outliers
#No good cadences for some reason.
if np.all(idx):
raise ValueError("No good cadences found for noise estimate. Check transit duration")
assert( np.all(np.isfinite(flux[~idx])))
expTime_days = np.median(np.diff(time[~idx]))
duration_cadences = dur_days/expTime_days
#Duration must be at least 4 cadences of sgCdpp will crash
duration_cadences = max(duration_cadences, 4)
rms = noise.computeSgCdpp_ppm(flux[~idx], duration_cadences)*1e-6
idx = kplrfits.markTransitCadences(time, period_days, epoch_bkjd, \
dur_days, 1, flags=flags)
nCadenceInTransit = np.sum(idx)
return depth_frac/rms * np.sqrt(nCadenceInTransit)
def plotWrapper(clip):
"""Wrapper function for difference image centroid diagnostic plots
Call this function from the exporter.
Inputs:
-----------
clip
A clipboard object. Should have the following keys: serve, detrend, diffImg, rollPhase, trapFit
Returns:
-----------
Two figure handles. The zeroth figure handle shows the flux and rollPhase
plot, the first shows the centroid offset plot
Outputs:
------------
Two figures are produced.
"""
time = clip['serve.time']
qFlags = clip['serve.flags']
flux = clip['detrend.flux_frac']
flags = clip['detrend.flags']
period_days = clip['trapFit.period_days']
epoch_bkjd = clip['trapFit.epoch_bkjd']
duration_hrs = clip['trapFit.duration_hrs']
epic = clip['value']
cube = clip['serve.cube']
inTransitIndices = kplrfits.markTransitCadences(time,
period_days,
epoch_bkjd,
duration_hrs / 24.,
flags=flags)
if clip['config.detrendType'] != "tess" and (clip['config.detrendType'] !=
"eleanor"):
rollPhase = clip['rollPhase.rollPhase']
centroids = clip['diffImg.centroid_timeseries']
goodCentroidIndices = centroids[centroids[:, 1] > 1,
0].asarray().astype(int)
fig1 = mp.figure(1)
mp.clf()
multiPanelPlotDiffImgCentroidsDiagnostic(time, flux, flags, rollPhase,
inTransitIndices,
goodCentroidIndices, qFlags)
fig2 = mp.figure(2)
mp.clf()
try:
titleStr = PLOT_CENTROID_OFFSETS_VBK(clip)
# titleStr = "EPIC: %i %s" %(epic, titleStr)
except ValueError, e:
titleStr = "Error: %s" % (e)
def getIngressEgressCadences(time, period_days, epoch_btjd, duration_days):
assert np.all(np.isfinite(time))
idx = kplrfits.markTransitCadences(time, period_days, epoch_btjd,
duration_days)
transits = np.array(plateau(idx, .5))
return transits
def plotWrapper(clip):
"""Wrapper function for difference image centroid diagnostic plots
Call this function from the exporter.
Inputs:
-----------
clip
A clipboard object. Should have the following keys: serve, detrend, diffImg, rollPhase, trapFit
Returns:
-----------
Two figure handles. The zeroth figure handle shows the flux and rollPhase
plot, the first shows the centroid offset plot
Outputs:
------------
Two figures are produced.
"""
time = clip['serve.time']
qFlags = clip['serve.flags']
flux = clip['detrend.flux_frac']
flags = clip['detrend.flags']
centroids = clip['diffImg.centroid_timeseries']
rollPhase = clip['rollPhase.rollPhase']
period_days = clip['trapFit.period_days']
epoch_bkjd = clip['trapFit.epoch_bkjd']
duration_hrs = clip['trapFit.duration_hrs']
epic = clip['value']
# tce = clip['eventList'][0]
# period = tce['trapFit.period_days']
# epoch = tce['trapFit.epoch_bkjd']
# duration_hrs = tce['trapFit.duration_hrs']
inTransitIndices = kplrfits.markTransitCadences(time, period_days, epoch_bkjd, \
duration_hrs/24., flags=flags)
goodCentroidIndices = centroids[ centroids[:,1]>1, 0].asarray().astype(int)
f1 = mp.figure(1)
mp.clf()
multiPanelPlotDiffImgCentroidsDiagnostic(time, flux, flags, rollPhase, \
inTransitIndices, goodCentroidIndices, qFlags)
f2 = mp.figure(2)
mp.clf()
try:
titleStr = plotCentroidOffsets(centroids)
titleStr = "EPIC: %i %s" %(epic, titleStr)
except ValueError, e:
titleStr = "Error: %s" %(e)
mp.axis([-1,1,-1,1])
def plotWrapper(clip):
"""Wrapper function for difference image centroid diagnostic plots
Call this function from the exporter.
Inputs:
-----------
clip
A clipboard object. Should have the following keys: serve, detrend, diffImg, rollPhase, trapFit
Returns:
-----------
Two figure handles. The zeroth figure handle shows the flux and rollPhase
plot, the first shows the centroid offset plot
Outputs:
------------
Two figures are produced.
"""
time = clip['serve.time']
qFlags = clip['serve.flags']
flux = clip['detrend.flux_frac']
flags = clip['detrend.flags']
centroids = clip['diffImg.centroid_timeseries']
rollPhase = clip['rollPhase.rollPhase']
period_days = clip['trapFit.period_days']
epoch_bkjd = clip['trapFit.epoch_bkjd']
duration_hrs = clip['trapFit.duration_hrs']
epic = clip['value']
# tce = clip['eventList'][0]
# period = tce['trapFit.period_days']
# epoch = tce['trapFit.epoch_bkjd']
# duration_hrs = tce['trapFit.duration_hrs']
inTransitIndices = kplrfits.markTransitCadences(time, period_days, epoch_bkjd, \
duration_hrs/24., flags=flags)
goodCentroidIndices = centroids[ centroids[:,1]>1, 0].asarray().astype(int)
f1 = mp.figure(1)
mp.clf()
multiPanelPlotDiffImgCentroidsDiagnostic(time, flux, flags, rollPhase, \
inTransitIndices, goodCentroidIndices, qFlags)
f2 = mp.figure(2)
mp.clf()
try:
titleStr = plotCentroidOffsets(centroids)
titleStr = "EPIC: %i %s" %(epic, titleStr)
except ValueError, e:
titleStr = "Error: %s" %(e)
mp.axis([-1,1,-1,1])
def getData(fn):
clip = dpc.loadClipboard(fn)
clip = pl.serveTask(clip)
out = [clip['value']]
for k in "period epoch depth duration_hrs".split():
key1 = "bls.%s" %(k)
out.extend( [clip[key1]])
#Recompute SNR
time = clip['serve.time']
flux = clip['detrend.flux_frac']
flag = clip['detrend.flags']
per = clip['bls.period']
epc = clip['bls.epoch']
depth_frac = clip['bls.depth']
dur_days = clip['bls.duration_hrs']/24.
#Try mesauring SNR assuming there is a transit and a secondary
#we want to cut out.
try:
idx = kplrfits.markTransitCadences(time, per/2., epc, \
dur_days, flags=flag)
idx = idx | flag
snr = estSnrForK2(flux[~idx], depth_frac, dur_days)
except ValueError:
#If the above results in no data points, try just excising
#the primary
try:
idx = kplrfits.markTransitCadences(time, per, epc, \
dur_days, flags=flag)
idx = idx | flag
snr = estSnrForK2(flux[~idx], depth_frac, dur_days)
except ValueError:
#Give up
snr = -1
out.append(snr)
print out[0], out[-1]
return out
def getData(fn):
clip = dpc.loadClipboard(fn)
clip = pl.serveTask(clip)
out = [clip['value']]
for k in "period epoch depth duration_hrs".split():
key1 = "bls.%s" % (k)
out.extend([clip[key1]])
#Recompute SNR
time = clip['serve.time']
flux = clip['detrend.flux_frac']
flag = clip['detrend.flags']
per = clip['bls.period']
epc = clip['bls.epoch']
depth_frac = clip['bls.depth']
dur_days = clip['bls.duration_hrs'] / 24.
#Try mesauring SNR assuming there is a transit and a secondary
#we want to cut out.
try:
idx = kplrfits.markTransitCadences(time, per/2., epc, \
dur_days, flags=flag)
idx = idx | flag
snr = estSnrForK2(flux[~idx], depth_frac, dur_days)
except ValueError:
#If the above results in no data points, try just excising
#the primary
try:
idx = kplrfits.markTransitCadences(time, per, epc, \
dur_days, flags=flag)
idx = idx | flag
snr = estSnrForK2(flux[~idx], depth_frac, dur_days)
except ValueError:
#Give up
snr = -1
out.append(snr)
print out[0], out[-1]
return out
def searchForEvent(clip):
subClip = clip.shallowCopy()
originalKeyList = subClip.keys()
taskList = clip['config.searchTaskList']
#Set the flags attribute of the new subclip
#Problem with this code is it closely tied to the behaviour
#of multiEventSearchTask
try:
tmp = clip.eventList[-1]
flags = tmp['flags']
except (IndexError, KeyError):
flags = clip['detrend.flags']
subClip['flags'] = flags
#Check that all the tasks are properly defined
for t in taskList:
f = eval(t)
#Now run them.
for t in taskList:
f = eval(t)
subClip = f(subClip)
# #@TODO List of tasks to run should be config param
# subClip = placeholderBls(subClip)
# subClip = trapezoidFitTask(subClip)
# subClip = modshiftTask(subClip)
# subClip = measureDiffImgCentroidsTask(subClip)
# subClip = dispositionTask(subClip)
newKeys = list(set(subClip.keys()) - set(originalKeyList))
out = clipboard.Clipboard(__meta__=subClip['__meta__'])
for k in newKeys:
out[k] = subClip[k]
#Mark all locations for this event as data not to be used.
time = subClip['serve.time']
period_days = subClip['trapFit.period_days']
epoch_bkjd = subClip['trapFit.epoch_bkjd']
duration_days = subClip['trapFit.duration_hrs'] / 24.
# assert(np.all(np.isfinite(time[~flags])))
# assert(np.any(flags))
idx = kplrfits.markTransitCadences(time, period_days, epoch_bkjd, \
duration_days, numberOfDurations=2, flags=flags)
out['flags'] = flags | idx
return out
def searchForEvent(clip):
subClip = clip.shallowCopy()
originalKeyList = subClip.keys()
taskList = clip['config.searchTaskList']
#Set the flags attribute of the new subclip
#Problem with this code is it closely tied to the behaviour
#of multiEventSearchTask
try:
tmp = clip.eventList[-1]
flags = tmp['flags']
except (IndexError, KeyError):
flags = clip['detrend.flags']
subClip['flags'] = flags
#Check that all the tasks are properly defined
for t in taskList:
f = eval(t)
#Now run them.
for t in taskList:
f = eval(t)
subClip = f(subClip)
# #@TODO List of tasks to run should be config param
# subClip = placeholderBls(subClip)
# subClip = trapezoidFitTask(subClip)
# subClip = modshiftTask(subClip)
# subClip = measureDiffImgCentroidsTask(subClip)
# subClip = dispositionTask(subClip)
newKeys = list(set(subClip.keys()) - set(originalKeyList))
out = clipboard.Clipboard(__meta__=subClip['__meta__'])
for k in newKeys:
out[k] = subClip[k]
#Mark all locations for this event as data not to be used.
time = subClip['serve.time']
period_days = subClip['trapFit.period_days']
epoch_bkjd = subClip['trapFit.epoch_bkjd']
duration_days = subClip['trapFit.duration_hrs'] / 24.
# assert(np.all(np.isfinite(time[~flags])))
# assert(np.any(flags))
idx = kplrfits.markTransitCadences(time, period_days, epoch_bkjd, \
duration_days, numberOfDurations=2, flags=flags)
out['flags'] = flags | idx
return out
def computeSweetMetrics(time, flux, period, epoch, duration):
"""
period, epoch and duration all in same units (e.g days)
"""
assert len(time) == len(flux)
out = []
idx = markTransitCadences(time, period, epoch, duration)
for per in [period / 2., period, 2 * period]:
phase = np.fmod(time - epoch + per, per)
amp, ampUnc = SweetFitOotFlux(phase[~idx], flux[~idx])
out.append([amp, ampUnc, amp / ampUnc])
return np.array(out)
def skyLinePlot(clipList):
"""A plot of which cadences contribute to the most transits
Based on similar plot created by Jessie Christiansen for the
SOC pipeline.
Inputs:
-----------
clipList
(list) list of filenames of clips to process
"""
epic, vals = gather.gatherFunction(clipList, getPeriodEpochDuration)
clip = dpc.loadClipboard(clipList[0])
clip = pl.serveTask(clip)
time = clip['serve.time']
flags = clip['detrend.flags']
period = np.array(map(lambda x: x[0], vals))
epoch = np.array(map(lambda x: x[1], vals))
duration_days = np.array(map(lambda x: x[2], vals)) / 24.
isCand = np.array(map(lambda x: x[3], vals))
skyLine = time * 0
candSkyLine = time * 0
for i in range(len(period)):
idx = kplrfits.markTransitCadences(time, period[i], epoch[i], \
duration_days[i], flags=flags)
skyLine[idx] += 1
if isCand[i]:
candSkyLine[idx] += 1
mp.clf()
mp.step(time[~flags], skyLine[~flags], 'b-', lw=2, \
label="All targets")
mp.step(time[~flags], candSkyLine[~flags], 'r-', lw=2, \
label="Candidates")
mp.xlabel("Time (BKJD)")
mp.ylabel("Number of Transits on Cadence")
return mp.gcf()
def getIngressEgressCadences(time, period_days, epoch_btjd, duration_days):
"""Get a list of transit start and end times in units of cadence number
Inputs
----------
Returns
----------
A 2d numpy array. zeroth column is cadence number of transit starts, first column is cadence
number of transit ends.
"""
assert np.all(np.isfinite(time))
idx = kplrfits.markTransitCadences(time, period_days, epoch_btjd,
duration_days)
transits = np.array(plateau(idx, .5))
return transits
def fblsTask(clip):
time_days = clip['extract.time']
flux_norm = clip['detrend.flux_frac']
flags = clip['detrend.flags']
minPeriod = clip['config.blsMinPeriod']
maxPeriod = clip['config.blsMaxPeriod']
# durations = np.array([ 2,4,6,8, 10, 12])/24.
durations = np.array([ 4,6,8, 10, 12])/24.
idx = flags == 0
blsObj = fbls.BlsSearch(time_days[idx], flux_norm[idx], \
[minPeriod, maxPeriod], durations)
period, epoch, depth, duration = blsObj.getEvent()
spectrum = blsObj.compute1dBls()
duration_cadences = int(np.round(duration*48)) #Correct for K2
rms = noise.computeSgCdpp_ppm(flux_norm[idx], duration_cadences)*1e-6
idx = kplrfits.markTransitCadences(time_days, period, epoch, \
duration, flags=flags)
snr = (depth/rms)*np.sqrt(np.sum(idx))
out = dict()
out['period'] = period
out['epoch'] = epoch
out['duration_hrs'] = duration * 24
out['depth'] = depth
out['snr'] = snr
out['bls_search_periods'] = spectrum[:,0]
out['convolved_bls'] = spectrum[:,1]
#out['obj'] = blsObj
# out['bls'] = bls #bls array is extremely big
clip['bls'] = out
#Enforce contract
clip['bls.period']
clip['bls.epoch']
clip['bls.duration_hrs']
return clip
def fblsTask(clip):
time_days = clip['extract.time']
flux_norm = clip['detrend.flux_frac']
flags = clip['detrend.flags']
minPeriod = clip['config.blsMinPeriod']
maxPeriod = clip['config.blsMaxPeriod']
# durations = np.array([ 2,4,6,8, 10, 12])/24.
durations = np.array([4, 6, 8, 10, 12]) / 24.
idx = flags == 0
blsObj = fbls.BlsSearch(time_days[idx], flux_norm[idx], \
[minPeriod, maxPeriod], durations)
period, epoch, depth, duration = blsObj.getEvent()
spectrum = blsObj.compute1dBls()
duration_cadences = int(np.round(duration * 48)) #Correct for K2
rms = noise.computeSgCdpp_ppm(flux_norm[idx], duration_cadences) * 1e-6
idx = kplrfits.markTransitCadences(time_days, period, epoch, \
duration, flags=flags)
snr = (depth / rms) * np.sqrt(np.sum(idx))
out = dict()
out['period'] = period
out['epoch'] = epoch
out['duration_hrs'] = duration * 24
out['depth'] = depth
out['snr'] = snr
out['bls_search_periods'] = spectrum[:, 0]
out['convolved_bls'] = spectrum[:, 1]
#out['obj'] = blsObj
# out['bls'] = bls #bls array is extremely big
clip['bls'] = out
#Enforce contract
clip['bls.period']
clip['bls.epoch']
clip['bls.duration_hrs']
return clip
def measureDiffOffset(period_days, epoch_bkjd, duration_hrs, \
time, prfObj, ccdMod, ccdOut, cube, bbox, rollPhase, flags, qFlags):
"""Measure Centroid shift between intransit and difference image
for every in-transit cadence
Inputs:
-----------
period_days, epoch_bkjd, duration_hrs
(floats) Properties of transit
time_bkjd
Array of times per cadence for the given campaign
prfObj
An object of the class prf.KeplerPrf()
ccdMod, ccdOut
(int) CCD module and output of image. Needed to
create the correct PRF model
cube
(3d np array) A data cube created from a TPF file.
See fileio.tpf.getTargetPixelArrayFromFits()
bbox
[c1, c2, r1, r2]. Define the range of columns (c1..c2)
and rows (r1..r2) defined by the image.
An exception raised if the following equality not true
img.shape = (c2-c1), (r2-r1)
rollPhase
(1d np array) An array of roll phases for each row
of cube. len(rollPhase) == len(cube). Units of this
array don't matter, so long as cadences with similar
roll angles have similar values of rollPhase. Roll phases
for bad cadences should be set to a bad value
flags
(1d array) flag values indicating bad cadences.
Currently a non-zero value of flags indicates a bad
cadence.
qFlags
(1d array) SAP Quality flags from lightcurve files
Returns:
-------------
A array with 5 columns, and as many rows as there are
in transit cadences. The columns are
0: Relative cadence number
1: In transit centroid column
2: In transit centroid row
3: Diff img centroid column
4: Diff img centroid row
If there is a statisically significant difference between the intransit
and difference image centroids then the transit is most likely not
on the target.
"""
duration_days = duration_hrs / 24.
log = []
# idx = getIndicesInTransit(period_days, epoch_bkjd, duration_hrs, time)
idx = kplrfits.markTransitCadences(time, period_days, epoch_bkjd,\
duration_days, flags=flags)
wh = np.where(idx)[0]
out = -1 * np.ones((len(wh), 5))
diagnostics = range(len(wh))
for i, w in enumerate(wh):
out[i, 0] = w
try:
out[i, 1:], dDict = measureInTransitAndDiffCentroidForOneImg(\
prfObj, ccdMod, ccdOut, cube, w, bbox, rollPhase, qFlags, \
hdr=None, plot=False)
diagnostics[i] = dDict
except ValueError, e:
log.append("Img %i: %s" % (w, e))
pass
def psfCentroids_vbk(clip):
itrCol, itrRow, itr_cov = [], [], []
ootCol, ootRow, oot_cov = [], [], []
diffCol, diffRow, diff_cov = [], [], []
time = clip['serve.time']
flux = clip['detrend.flux_frac']
flags = clip['detrend.flags']
period_days = clip['trapFit.period_days']
epoch_bkjd = clip['trapFit.epoch_bkjd']
duration_hrs = clip['trapFit.duration_hrs']
epic = clip['value']
cube = clip['serve.cube']
hdr_ = clip['serve.tpfHeader']
if clip['config.detrendType'] == "tess":
col_zero_, row_zero_ = int(hdr_['1CRV4P']), int(hdr_['2CRV4P'])
epic_Col, epic_Row = col_zero_ + int(hdr_['1CRPX4']), row_zero_ + int(hdr_['2CRPX4'])
if clip['config.detrendType'] == "eleanor":
col_zero_, row_zero_ = int(hdr_['CRPIX1']), int(hdr_['CRPIX2'])
epic_Col, epic_Row = col_zero_ + int(hdr_['TPF_H']), row_zero_ + int(hdr_['TPF_W'])
inTransitIndices = kplrfits.markTransitCadences(time, period_days, epoch_bkjd, duration_hrs/24., flags=flags)
oot_cadence_ = np.where((inTransitIndices == False) & (flags == False))
oot_cadence = np.asarray(oot_cadence_).flatten()
itr_cadence_ = np.where(inTransitIndices == True)
itr_cadence = np.asarray(itr_cadence_).flatten()
#
#
# GET IN-TRANSIT, BEFORE TRANSIT, AND AFTER TRANSIT CADENCES ONLY
#
#
transit_number_ = 1
transits_ = [itr_cadence[0]]
tmp_idx_, = np.where(oot_cadence < transits_[0])
no_transits_ = oot_cadence[tmp_idx_[-1]]
for ii in range(1,len(itr_cadence)):
if itr_cadence[ii] - itr_cadence[ii-1] > 10:
transit_number_ += 1
transits_ = np.hstack((transits_ , itr_cadence[ii-1], itr_cadence[ii]))
transits_ = np.hstack((transits_ , itr_cadence[-1]))
cube_back_ = cube
if clip['config.detrendType'] == "tess":
cut_ = 3
cube = cube[:,epic_Col-col_zero_-cut_:epic_Col-col_zero_+ cut_, epic_Row-row_zero_-cut_:epic_Row-row_zero_+ cut_]
if clip['config.detrendType'] == "eleanor":
cut_ = 5
cube = cube[:,epic_Col-col_zero_-cut_:epic_Col-col_zero_+ cut_, epic_Row-row_zero_-cut_:epic_Row-row_zero_+ cut_]
for ii in range(transit_number_):
number_of_cadences_in_transit_ = transits_[2*ii+1] - transits_[2*ii]
idx_in_transit_ = np.linspace(transits_[2*ii], transits_[2*ii+1], int(number_of_cadences_in_transit_+1))
idx_in_transit = [int(aa) for aa in idx_in_transit_]
idx_before_, = np.where(oot_cadence < transits_[2*ii])
idx_before = oot_cadence[idx_before_[-1-number_of_cadences_in_transit_:]]
idx_after_, = np.where(oot_cadence > transits_[2*ii+1])
idx_after = oot_cadence[idx_after_[0:number_of_cadences_in_transit_+1]]
itr_mean_img_by_transit_ = np.nanmean(cube[idx_in_transit,:,:], axis = 0)
before_tr_mean_img_by_transit_ = np.nanmean(cube[idx_before,:,:], axis = 0)
after_tr_mean_img_by_transit_ = np.nanmean(cube[idx_after,:,:], axis = 0)
oot_mean_img_by_transit_ = 0.5*(before_tr_mean_img_by_transit_ + after_tr_mean_img_by_transit_)
diff_mean_img_by_transit_ = oot_mean_img_by_transit_ - itr_mean_img_by_transit_
itrCol_by_transit_, itrRow_by_transit_, itr_cov_by_transit_ = intertial_axis(itr_mean_img_by_transit_)
ootCol_by_transit_, ootRow_by_transit_, oot_cov_by_transit_ = intertial_axis(oot_mean_img_by_transit_)
diffCol_by_transit_, diffRow_by_transit_, diff_cov_by_transit_ = intertial_axis(diff_mean_img_by_transit_)
itrCol, itrRow = np.hstack((itrCol, itrCol_by_transit_)), np.hstack((itrRow, itrRow_by_transit_))
ootCol, ootRow = np.hstack((ootCol, ootCol_by_transit_)), np.hstack((ootRow, ootRow_by_transit_))
diffCol, diffRow = np.hstack((diffCol, diffCol_by_transit_)), np.hstack((diffRow, diffRow_by_transit_))
return cut_+itrCol, cut_+itrRow, cut_+ootCol, cut_+ootRow, cut_+diffCol, cut_+diffRow
def generateImages(clip):
time = clip['serve.time']
flux = clip['detrend.flux_frac']
flags = clip['detrend.flags']
period_days = clip['trapFit.period_days']
epoch_bkjd = clip['trapFit.epoch_bkjd']
duration_hrs = clip['trapFit.duration_hrs']
epic = clip['value']
cube = clip['serve.cube']
hdr_ = clip['serve.tpfHeader']
inTransitIndices = kplrfits.markTransitCadences(time,
period_days,
epoch_bkjd,
duration_hrs / 24.,
flags=flags)
oot_cadence_ = np.where((inTransitIndices == False) & (flags == False))
oot_cadence = np.asarray(oot_cadence_).flatten()
itr_cadence_ = np.where(inTransitIndices == True)
itr_cadence = np.asarray(itr_cadence_).flatten()
#
#
# GET IN-TRANSIT, BEFORE TRANSIT, AND AFTER TRANSIT CADENCES ONLY
#
#
transit_number_ = 1
transits_ = [itr_cadence[0]]
tmp_idx_, = np.where(oot_cadence < transits_[0])
no_transits_ = oot_cadence[tmp_idx_[-1]]
for ii in range(1, len(itr_cadence)):
if itr_cadence[ii] - itr_cadence[ii - 1] > 10:
transit_number_ += 1
transits_ = np.hstack(
(transits_, itr_cadence[ii - 1], itr_cadence[ii]))
transits_ = np.hstack((transits_, itr_cadence[-1]))
ss_ = cube.shape
itr_mean_cube_ = np.zeros((transit_number_, ss_[1], ss_[2]))
oot_mean_cube_ = np.zeros((transit_number_, ss_[1], ss_[2]))
diff_mean_cube_ = np.zeros((transit_number_, ss_[1], ss_[2]))
for ii in range(transit_number_):
number_of_cadences_in_transit_ = transits_[2 * ii + 1] - transits_[2 *
ii]
idx_in_transit_ = np.linspace(transits_[2 * ii], transits_[2 * ii + 1],
int(number_of_cadences_in_transit_ + 1))
idx_in_transit = [int(aa) for aa in idx_in_transit_]
idx_before_, = np.where(oot_cadence < transits_[2 * ii])
idx_before = oot_cadence[idx_before_[-1 -
number_of_cadences_in_transit_:]]
idx_after_, = np.where(oot_cadence > transits_[2 * ii + 1])
idx_after = oot_cadence[idx_after_[0:number_of_cadences_in_transit_ +
1]]
itr_mean_img_by_transit_ = np.nanmean(cube[idx_in_transit, :, :],
axis=0)
before_tr_mean_img_by_transit_ = np.nanmean(cube[idx_before, :, :],
axis=0)
after_tr_mean_img_by_transit_ = np.nanmean(cube[idx_after, :, :],
axis=0)
oot_mean_img_by_transit_ = 0.5 * (before_tr_mean_img_by_transit_ +
after_tr_mean_img_by_transit_)
diff_mean_img_by_transit_ = oot_mean_img_by_transit_ - itr_mean_img_by_transit_
itr_mean_cube_[ii, :, :] = itr_mean_img_by_transit_
oot_mean_cube_[ii, :, :] = oot_mean_img_by_transit_
diff_mean_cube_[ii, :, :] = diff_mean_img_by_transit_
itr_mean_img_ = np.nanmean(itr_mean_cube_, axis=0)
oot_mean_img_ = np.nanmean(oot_mean_cube_, axis=0)
diff_mean_img_ = oot_mean_img_ - itr_mean_img_
return itr_mean_img_, oot_mean_img_, diff_mean_img_, itr_mean_cube_, oot_mean_cube_, diff_mean_cube_, transit_number_
def plot_DiffImg_and_Centroids(
clip): #cube, centroids, goodCentroidIndices, rollPhase, quality):
time = clip['serve.time']
qFlags = clip['serve.flags']
flux = clip['detrend.flux_frac']
flags = clip['detrend.flags']
centroids = clip['diffImg.centroid_timeseries']
rollPhase = clip['rollPhase.rollPhase']
period_days = clip['trapFit.period_days']
epoch_bkjd = clip['trapFit.epoch_bkjd']
duration_hrs = clip['trapFit.duration_hrs']
epic = clip['value']
cube = clip['serve.cube']
hdr_ = clip['serve.tpfHeader']
col_zero_, row_zero_ = int(hdr_['1CRV4P']), int(hdr_['2CRV4P'])
epic_Col, epic_Row = col_zero_ + int(hdr_['1CRPX4']), row_zero_ + int(
hdr_['2CRPX4'])
idx = centroids[:, 1] > 0
cin = centroids[idx, 0]
ootCol, ootRow = centroids[idx, 1], centroids[idx, 2]
diffCol, diffRow = centroids[idx, 3], centroids[idx, 4]
inTransitIndices = kplrfits.markTransitCadences(time,
period_days,
epoch_bkjd,
duration_hrs / 24.,
flags=flags)
goodCentroidIndices = centroids[centroids[:, 1] > 1,
0].asarray().astype(int)
oot_cadence_, itr_cadence_ = np.where(inTransitIndices == False), np.where(
inTransitIndices == True)
oot_mean_img_, itr_mean_img_ = np.nanmean(
cube[oot_cadence_], axis=0), np.nanmean(cube[itr_cadence_], axis=0)
diff_mean_img_ = oot_mean_img_ - itr_mean_img_
ss_ = oot_mean_img_.shape
extent_ = [col_zero_, col_zero_ + ss_[1], row_zero_, row_zero_ + ss_[0]]
disp = lambda x: mp.imshow(x,
cmap=mp.get_cmap('binary', 512),
origin="bottom",
interpolation="nearest",
extent=extent_)
n_panels_ = 5 * 4
skip_ = 3 * 15
for ii in range(n_panels_ - 1):
print ii
mp.subplot(5, 4, ii + 1)
diff_, oot_, diag = diffimg.constructK2DifferenceImage(
cube, goodCentroidIndices[skip_ + ii], rollPhase, flags)
disp(diff_)
mp.plot(ootCol[skip_ + ii], ootRow[skip_ + ii], 'c*', ms=10)
mp.plot(diffCol[skip_ + ii], diffRow[skip_ + ii], 'mo', ms=6)
mp.title(time[goodCentroidIndices[skip_ + ii]], fontsize=10)
mp.gca().axes.get_xaxis().set_visible(False)
mp.gca().axes.get_yaxis().set_visible(False)
mp.tight_layout()
mp.subplot(5, 4, n_panels_)
disp(diff_mean_img_)
mp.scatter(diffCol[skip_ + 0:skip_ + n_panels_],
diffRow[skip_ + 0:skip_ + n_panels_],
marker='o',
c=cin[skip_ + 0:skip_ + n_panels_],
s=40,
linewidths=0,
cmap=mp.cm.RdYlBu)
cb = mp.colorbar()
cb.set_label("Cadence")
def measureDiffOffset(period_days, epoch_bkjd, duration_hrs, \
time, prfObj, ccdMod, ccdOut, cube, bbox, rollPhase, flags, qFlags):
"""Measure Centroid shift between intransit and difference image
for every in-transit cadence
Inputs:
-----------
period_days, epoch_bkjd, duration_hrs
(floats) Properties of transit
time_bkjd
Array of times per cadence for the given campaign
prfObj
An object of the class prf.KeplerPrf()
ccdMod, ccdOut
(int) CCD module and output of image. Needed to
create the correct PRF model
cube
(3d np array) A data cube created from a TPF file.
See fileio.tpf.getTargetPixelArrayFromFits()
bbox
[c1, c2, r1, r2]. Define the range of columns (c1..c2)
and rows (r1..r2) defined by the image.
An exception raised if the following equality not true
img.shape = (c2-c1), (r2-r1)
rollPhase
(1d np array) An array of roll phases for each row
of cube. len(rollPhase) == len(cube). Units of this
array don't matter, so long as cadences with similar
roll angles have similar values of rollPhase. Roll phases
for bad cadences should be set to a bad value
flags
(1d array) flag values indicating bad cadences.
Currently a non-zero value of flags indicates a bad
cadence.
qFlags
(1d array) SAP Quality flags from lightcurve files
Returns:
-------------
A array with 5 columns, and as many rows as there are
in transit cadences. The columns are
0: Relative cadence number
1: In transit centroid column
2: In transit centroid row
3: Diff img centroid column
4: Diff img centroid row
If there is a statisically significant difference between the intransit
and difference image centroids then the transit is most likely not
on the target.
"""
duration_days = duration_hrs/24.
log = []
# idx = getIndicesInTransit(period_days, epoch_bkjd, duration_hrs, time)
idx = kplrfits.markTransitCadences(time, period_days, epoch_bkjd,\
duration_days, flags=flags)
wh = np.where(idx)[0]
out = -1 * np.ones((len(wh), 5))
diagnostics = range(len(wh))
for i,w in enumerate(wh):
out[i,0] = w
try:
out[i, 1:], dDict = measureInTransitAndDiffCentroidForOneImg(\
prfObj, ccdMod, ccdOut, cube, w, bbox, rollPhase, qFlags, \
hdr=None, plot=False)
diagnostics[i] = dDict
except ValueError, e:
log.append("Img %i: %s" %(w, e))
pass
def PLOT_CENTROID_OFFSETS_VBK(clip):
from astropy import coordinates, units as u, wcs
from astroquery.skyview import SkyView
from astroquery.vizier import Vizier
import astropy.units as u
import math
from scipy.ndimage import rotate
from reproject import reproject_interp, reproject_exact, reproject_to_healpix, reproject_from_healpix
from astropy.wcs import WCS
# import pywcsgrid2
time = clip['serve.time']
qFlags = clip['serve.flags']
flux = clip['detrend.flux_frac']
flags = clip['detrend.flags']
centroids = clip['diffImg.centroid_timeseries']
# rollPhase = clip['rollPhase.rollPhase']
period_days = clip['trapFit.period_days']
epoch_bkjd = clip['trapFit.epoch_bkjd']
duration_hrs = clip['trapFit.duration_hrs']
epic = clip['value']
cube = clip['serve.cube']
hdr_ = clip['serve.tpfHeader']
col_zero_, row_zero_ = int(hdr_['1CRV4P']), int(hdr_['2CRV4P'])
epic_Col, epic_Row = col_zero_ + int(hdr_['1CRPX4']), row_zero_ + int(
hdr_['2CRPX4'])
def k2_ConvertHeaderWCS(tpf_header):
funny_keywords = {
'1CTYP4': 'CTYPE1',
'2CTYP4': 'CTYPE2',
'1CRPX4': 'CRPIX1',
'2CRPX4': 'CRPIX2',
'1CRVL4': 'CRVAL1',
'2CRVL4': 'CRVAL2',
'1CUNI4': 'CUNIT1',
'2CUNI4': 'CUNIT2',
'1CDLT4': 'CDELT1',
'2CDLT4': 'CDELT2',
'11PC4': 'PC1_1',
'12PC4': 'PC1_2',
'21PC4': 'PC2_1',
'22PC4': 'PC2_2'
}
mywcs = {}
for oldkey, newkey in funny_keywords.items():
mywcs[newkey] = tpf_header[oldkey]
return wcs.WCS(mywcs)
mywcs_ = k2_ConvertHeaderWCS(hdr_)
#
#
inTransitIndices = kplrfits.markTransitCadences(time,
period_days,
epoch_bkjd,
duration_hrs / 24.,
flags=flags)
oot_cadence_ = np.where((inTransitIndices == False) & (flags == False))
oot_mean_img_ = np.nanmean(cube[oot_cadence_], axis=0)
itr_cadence_ = np.where(inTransitIndices == True)
itr_mean_img_ = np.nanmean(cube[itr_cadence_], axis=0)
diff_mean_img_ = oot_mean_img_ - itr_mean_img_
ss_ = oot_mean_img_.shape
# disp = lambda x: mp.imshow(x, cmap=mp.cm.binary, origin = "bottom", interpolation="nearest")
extent_ = [col_zero_, col_zero_ + ss_[1], row_zero_, row_zero_ + ss_[0]]
disp = lambda x: mp.imshow(x,
cmap=mp.get_cmap('binary', 512),
origin="bottom",
interpolation="nearest",
extent=extent_)
#
# GET CENTROIDS
idx = centroids[:, 1] > 0
cin = centroids[idx, 0]
ootCol = centroids[idx, 1] # - col_zero_# - 1
ootRow = centroids[idx, 2] # - row_zero_# - 1
#itr => in transit
diffCol = centroids[idx, 3] # - col_zero_# - 1
diffRow = centroids[idx, 4] # - row_zero_# - 1
diffC = (ootCol - diffCol) # + np.median(diffCol)
diffR = (ootRow - diffRow) # + np.median(diffRow)
itrCol, itrRow = diffCol, diffRow
#
xmin_ = np.min(np.hstack((ootCol, diffCol)))
xmax_ = np.max(np.hstack((ootCol, diffCol)))
ymin_ = np.min(np.hstack((ootRow, diffRow)))
ymax_ = np.max(np.hstack((ootRow, diffRow)))
# START PLOTTING
#
ax1 = mp.subplot(221)
disp(oot_mean_img_)
ax1.plot(ootCol, ootRow, 'c*', ms=8) #, mec = 'm')#, color='yellow')
ax1.plot(np.mean(ootCol), np.mean(ootRow), 'c*', ms=14,
label='AVG_OOT') #, mec = 'm')
ax1.plot(itrCol, itrRow, 'mo', ms=3) #, mec = 'c')
ax1.plot(np.mean(itrCol), np.mean(itrRow), 'mo', ms=6,
label='AVG_DIFF') #, mec = 'c')
#
covar.plotErrorEllipse(ootCol,
ootRow,
color='c',
ms=14,
marker='*',
mfc='c') #, mec = 'm')
covar.plotErrorEllipse(itrCol,
itrRow,
color='m',
ms=14,
marker='o',
mfc='m') #, mec = 'c')
ax1.plot(epic_Col, epic_Row, 'xy', mew=3, ms=10, label='EPIC')
mp.xlabel(r"$\Delta$ Column (pixels)")
mp.ylabel(r"$\Delta$ Row (pixels)")
mp.legend(loc='best', fontsize=8)
mp.subplot(222)
mp.plot(np.mean(ootCol), np.mean(ootRow), 'c*', ms=20, label='OOT')
mp.plot(np.mean(itrCol), np.mean(itrRow), 'mo', ms=20, label='DIFF')
mp.scatter(ootCol,
ootRow,
marker='*',
c=cin,
s=64,
linewidths=0,
cmap=mp.cm.RdYlBu)
mp.scatter(itrCol,
itrRow,
marker='o',
c=cin,
s=64,
linewidths=0,
cmap=mp.cm.RdYlBu)
cb = mp.colorbar()
cb.set_label("Cadence")
covar.plotErrorEllipse(ootCol,
ootRow,
color='c',
ms=20,
marker='*',
mfc='c')
covar.plotErrorEllipse(itrCol,
itrRow,
color='m',
ms=20,
marker='o',
mfc='m')
mp.xlabel(r"$\Delta$ Column (pixels)")
probOffset, chiSq = covar.computeProbabilityOfObservedOffset(diffC, diffR)
titleStr = "Prob. On Target: %.1e: $\chi^2$: %.3f" % (1 - probOffset,
chiSq)
mp.legend(loc='best')
mp.xlim(xmin_ - 0.2, xmax_ + 0.2)
mp.ylim(ymin_ - 0.2, ymax_ + 0.2)
mp.tight_layout()
try:
ax3 = mp.subplot(223, projection=mywcs_) #mywcs_)
ra_, dec_ = hdr_['RA_OBJ'], hdr_['DEC_OBJ']
center_ = coordinates.SkyCoord(ra_,
dec_,
unit=(u.deg, u.deg),
frame='icrs')
img_survey = SkyView.get_images(position=center_,
survey='2MASS-J',
radius=1 * u.arcmin)
pix_survey = img_survey[0][0].data
hdr_survey = img_survey[0][0].header
inverted_pix_survey = np.max(pix_survey) - pix_survey
inverted_pix_survey = pix_survey #inverted_pix_survey/np.max(inverted_pix_survey)
levels_ = np.linspace(np.min(inverted_pix_survey),
np.percentile(inverted_pix_survey, 99), 10)
ax3.contourf(inverted_pix_survey,
transform=ax3.get_transform(wcs.WCS(hdr_survey)),
levels=levels_,
cmap=mp.get_cmap('binary', 256))
#
#
mp.tight_layout()
except:
mp.subplot(223)
mp.subplot(224)
titleStr_ = plotCentroidOffsets(centroids)
return titleStr