def makeCubeTimestream(configFileName):
configData = readDict()
configData.read_from_file(configFileName)
# Extract parameters from config file
nPos = int(configData['nPos'])
startTimes = np.array(configData['startTimes'], dtype=int)
stopTimes = np.array(configData['stopTimes'], dtype=int)
darkSpan = np.array(configData['darkSpan'], dtype=int)
flatSpan = np.array(configData['flatSpan'], dtype=int)
xPos = np.array(configData['xPos'], dtype=int)
yPos = np.array(configData['yPos'], dtype=int)
numRows = int(configData['numRows'])
numCols = int(configData['numCols'])
upSample = int(configData['upSample'])
padFraction = float(configData['padFraction'])
coldCut = int(configData['coldCut'])
fitPos = bool(configData['fitPos'])
target = str(configData['target'])
run = str(configData['run'])
date = str(configData['date'])
outputDir = str(configData['outputDir'])
useImg = bool(configData['useImg'])
doHPM = bool(configData['doHPM'])
subtractDark = bool(configData['subtractDark'])
divideFlat = bool(configData['divideFlat'])
refFile = str(configData['refFile'])
#hard coded for now to the daytime wvl cal we did with the WL data
wvlCalTS = '1491870376'
calPath = os.getenv('MKID_PROC_PATH', '/')
timeMaskPath = os.path.join(calPath,"darkHotPixMasks")
hpPath = os.path.join(timeMaskPath,date)
#################################################
# Create empty arrays to save to npz file later
timeStamps=[]
cubes = []
#################################################
#get wvl cal soln file name
cfn = FileName(run=run,date=date,tstamp=wvlCalTS).calSoln()
#loop through obs files and each second within each file to make 1-s cubes
for ts in startTimes:
#load obs file
obsFN = FileName(run=run, date=date, tstamp=str(ts)).obs()
print obsFN
obs = darkObsFile(obsFN)
totalIntTime = obs.totalIntegrationTime
#load wvlSoln file
obs.loadWvlCalFile(cfn)
for i in range(totalIntTime):
fullTS = ts+i
timeStamps.append(fullTS)
print i, fullTS
#get spectral cube for this second
cDict = obs.getSpectralCube(i,1,weighted=False,fluxWeighted=False,energyBinWidth=0.07)
cube = cDict['cube']
cubes.append(cube)
wvlBinEdges = np.array(cDict['wvlBinEdges'])
cubes = np.array(cubes)
times = np.array(timeStamps)
#################################################
# Setup npz file to save imageStack intermediate/cal files, parameter, and output
stackPath = os.path.join(calPath,"imageStacks")
npzPath = os.path.join(stackPath,date)
#if configFileName.split('/')[0] is not 'Params':
# print "Config file not in Params! Output stack will have wrong filename!"
# print configFileName.split('/')[0]
# npzBaseName = target
#else:
npzBaseName = configFileName.split('/')[1].split('.')[0]
npzFileName = npzPath+'/%s.npz'%npzBaseName
print npzFileName
np.savez(npzFileName, times=times, cubes=cubes, wvlBinEdges = wvlBinEdges)
return {'cubes':cubes,'times':times,'wvlBinEdges':wvlBinEdges}
from Utils.FileName import FileName
from arrayPopup import plotArray
import numpy as np
import lightCurves as lc
import matplotlib.pylab as plt
plt.rc('font', family='serif')
import pdfs
from scipy import stats
from scipy.signal import periodogram
from statsmodels.tsa.stattools import acovf,acf,ccf
import HotPix.darkHotPixMask as dhpm
### WL and PiHer data used for WL vs. on-sky correlation comparisons
#load obs file for wl
wlobs = darkObsFile(FileName(run='PAL2017a',date='20170410',tstamp='1491869200').obs())
#load up timed packet images
#this WL obs file has a move at 18 seconds. Just cut it out, stationary after.
#wlTPI = wlobs.getTimedPacketImage(firstSec=18, integrationTime=118)
#Concatenate photon time stamp lists together for 3 selected pixels
wlA = wlTPI['timestamps'][24][76]
wlB = wlTPI['timestamps'][24][77]
wlD = wlTPI['timestamps'][25][76]
wlTS = wlA
wlTS = np.append(wlTS,wlB)
wlTS = np.append(wlTS,wlD)
# make 5ms light curves
wlLC = lc.lightCurve(wlTS,shortExposure=.01)
import lightCurves as lc
import matplotlib.pylab as plt
plt.rc('font', family='serif')
import pdfs
from scipy import stats
from scipy.signal import periodogram
from statsmodels.tsa.stattools import acovf, acf, ccf
import HotPix.darkHotPixMask as dhpm
#import skimage for in-painting interp
from skimage import restoration
#load bad pix mask for pi Her
bpm = dhpm.loadMask(
'/mnt/data0/CalibrationFiles/darkHotPixMasks/20170409/1491826154.npz')
#load obs file for Pi Her
phobs = darkObsFile(
FileName(run='PAL2017a', date='20170409', tstamp='1491827562').obs())
phTPI = phobs.getTimedPacketImage(firstSec=0, integrationTime=118)
shortT = 0.01
show = False
totalT = 1.000
nFrames = int(totalT / shortT)
stack = []
for n in range(nFrames):
im = np.empty((80, 40), dtype=float)
im.fill(np.nan)
for i in np.arange(20, 60): #80
for j in np.arange(40, 120): #125
from Utils.FileName import FileName
from arrayPopup import plotArray
import numpy as np
import lightCurves as lc
import matplotlib.pylab as plt
plt.rc('font', family='serif')
import pdfs
from scipy import stats
from scipy.signal import periodogram
from statsmodels.tsa.stattools import acovf,acf,ccf
import HotPix.darkHotPixMask as dhpm
### WL and PiHer data used for WL vs. on-sky correlation comparisons
#load obs file for wl
wlobs = darkObsFile(FileName(run='PAL2017a',date='20170410',tstamp='1491869200').obs())
#load up timed packet images
#this WL obs file has a move at 18 seconds. Just cut it out, stationary after.
#wlTPI = wlobs.getTimedPacketImage(firstSec=18, integrationTime=118)
#Concatenate photon time stamp lists together for 3 selected pixels
wlA = wlTPI['timestamps'][24][76]
wlB = wlTPI['timestamps'][24][77]
wlD = wlTPI['timestamps'][25][76]
wlTS = wlA
wlTS = np.append(wlTS,wlB)
wlTS = np.append(wlTS,wlD)
# 69 her companion location timestamps
saoA = saoTPI['timestamps'][46][98]
from scipy.signal import periodogram
from statsmodels.tsa.stattools import acovf, acf, ccf
import HotPix.darkHotPixMask as dhpm
object = '69h'
totalInt = 80 #for 69 Her data. Seems to be a move around 80s in.
#totalInt = 118 #for piHer data. Dither move shortly after.
### WL and PiHer data used for WL vs. on-sky correlation comparisons
#load up timed packet images
#this WL obs file has a move at 18 seconds. Just cut it out, stationary after.
if object == 'wl':
#WL timed packet image
target = r'WL'
#load obs file for wl
obs = darkObsFile(
FileName(run='PAL2017a', date='20170410', tstamp='1491869200').obs())
wlTPI = obs.getTimedPacketImage(firstSec=18, integrationTime=118)
bpm = dhpm.loadMask(
'/mnt/data0/CalibrationFiles/darkHotPixMasks/20170410/1491870115.npz')
basePath = '/mnt/data0/ProcessedData/seth/speckleAnalysis/WL_stats/allPlots_20170817/10ms/'
TPI = wlTPI
elif object == 'ph':
#pi Her timed packet image
target = r'$\pi$ Her'
#load obs file for Pi Her
obs = darkObsFile(
FileName(run='PAL2017a', date='20170409', tstamp='1491827562').obs())
phTPI = obs.getTimedPacketImage(firstSec=0, integrationTime=totalInt)
bpm = dhpm.loadMask(
'/mnt/data0/CalibrationFiles/darkHotPixMasks/20170409/1491826154.npz')
import matplotlib.pylab as plt
plt.rc('font', family='serif')
import pdfs
from scipy import stats
from scipy.signal import periodogram
from statsmodels.tsa.stattools import acovf,acf,ccf
import HotPix.darkHotPixMask as dhpm
#import skimage for in-painting interp
from skimage import restoration
#load bad pix mask for pi Her
bpm = dhpm.loadMask('/mnt/data0/CalibrationFiles/darkHotPixMasks/20170409/1491826154.npz')
#load obs file for Pi Her
phobs = darkObsFile(FileName(run='PAL2017a',date='20170409',tstamp='1491827562').obs())
phTPI = phobs.getTimedPacketImage(firstSec=0, integrationTime=118)
shortT = 0.01
show=False
totalT = 1.000
nFrames = int(totalT/shortT)
stack = []
for n in range(nFrames):
im = np.empty((80,40),dtype=float)
im.fill(np.nan)
for i in np.arange(20,60): #80
def makeCubeTimestream(configFileName):
configData = readDict()
configData.read_from_file(configFileName)
# Extract parameters from config file
nPos = int(configData['nPos'])
startTimes = np.array(configData['startTimes'], dtype=int)
stopTimes = np.array(configData['stopTimes'], dtype=int)
darkSpan = np.array(configData['darkSpan'], dtype=int)
flatSpan = np.array(configData['flatSpan'], dtype=int)
xPos = np.array(configData['xPos'], dtype=int)
yPos = np.array(configData['yPos'], dtype=int)
numRows = int(configData['numRows'])
numCols = int(configData['numCols'])
upSample = int(configData['upSample'])
padFraction = float(configData['padFraction'])
coldCut = int(configData['coldCut'])
fitPos = bool(configData['fitPos'])
target = str(configData['target'])
run = str(configData['run'])
date = str(configData['date'])
outputDir = str(configData['outputDir'])
useImg = bool(configData['useImg'])
doHPM = bool(configData['doHPM'])
subtractDark = bool(configData['subtractDark'])
divideFlat = bool(configData['divideFlat'])
refFile = str(configData['refFile'])
#hard coded for now to the daytime wvl cal we did with the WL data
wvlCalTS = '1491870376'
calPath = os.getenv('MKID_PROC_PATH', '/')
timeMaskPath = os.path.join(calPath, "darkHotPixMasks")
hpPath = os.path.join(timeMaskPath, date)
#################################################
# Create empty arrays to save to npz file later
timeStamps = []
cubes = []
#################################################
#get wvl cal soln file name
cfn = FileName(run=run, date=date, tstamp=wvlCalTS).calSoln()
#loop through obs files and each second within each file to make 1-s cubes
for ts in startTimes:
#load obs file
obsFN = FileName(run=run, date=date, tstamp=str(ts)).obs()
print obsFN
obs = darkObsFile(obsFN)
totalIntTime = obs.totalIntegrationTime
#load wvlSoln file
obs.loadWvlCalFile(cfn)
for i in range(totalIntTime):
fullTS = ts + i
timeStamps.append(fullTS)
print i, fullTS
#get spectral cube for this second
cDict = obs.getSpectralCube(i,
1,
weighted=False,
fluxWeighted=False,
energyBinWidth=0.07)
cube = cDict['cube']
cubes.append(cube)
wvlBinEdges = np.array(cDict['wvlBinEdges'])
cubes = np.array(cubes)
times = np.array(timeStamps)
#################################################
# Setup npz file to save imageStack intermediate/cal files, parameter, and output
stackPath = os.path.join(calPath, "imageStacks")
npzPath = os.path.join(stackPath, date)
#if configFileName.split('/')[0] is not 'Params':
# print "Config file not in Params! Output stack will have wrong filename!"
# print configFileName.split('/')[0]
# npzBaseName = target
#else:
npzBaseName = configFileName.split('/')[1].split('.')[0]
npzFileName = npzPath + '/%s.npz' % npzBaseName
print npzFileName
np.savez(npzFileName, times=times, cubes=cubes, wvlBinEdges=wvlBinEdges)
return {'cubes': cubes, 'times': times, 'wvlBinEdges': wvlBinEdges}
from scipy.signal import periodogram
from statsmodels.tsa.stattools import acovf,acf,ccf
import HotPix.darkHotPixMask as dhpm
object = '69h'
totalInt = 80 #for 69 Her data. Seems to be a move around 80s in.
#totalInt = 118 #for piHer data. Dither move shortly after.
### WL and PiHer data used for WL vs. on-sky correlation comparisons
#load up timed packet images
#this WL obs file has a move at 18 seconds. Just cut it out, stationary after.
if object == 'wl':
#WL timed packet image
target = r'WL'
#load obs file for wl
obs = darkObsFile(FileName(run='PAL2017a',date='20170410',tstamp='1491869200').obs())
wlTPI = obs.getTimedPacketImage(firstSec=18, integrationTime=118)
bpm = dhpm.loadMask('/mnt/data0/CalibrationFiles/darkHotPixMasks/20170410/1491870115.npz')
basePath = '/mnt/data0/ProcessedData/seth/speckleAnalysis/WL_stats/allPlots_20170817/10ms/'
TPI = wlTPI
elif object == 'ph':
#pi Her timed packet image
target = r'$\pi$ Her'
#load obs file for Pi Her
obs = darkObsFile(FileName(run='PAL2017a',date='20170409',tstamp='1491827562').obs())
phTPI = obs.getTimedPacketImage(firstSec=0, integrationTime=totalInt)
bpm = dhpm.loadMask('/mnt/data0/CalibrationFiles/darkHotPixMasks/20170409/1491826154.npz')
basePath = '/mnt/data0/ProcessedData/seth/speckleAnalysis/piHer_stats/allPlots_20170817/30ms/'
TPI = phTPI