outPath = ast.literal_eval(config['Data']['outPath']) # path to output data
beamFile = ast.literal_eval(
config['Data']['beamFile']) # path and filename to beam map file
mapFlag = ast.literal_eval(config['Data']['mapFlag'])
filePrefix = ast.literal_eval(config['Data']['filePrefix'])
b2hPath = ast.literal_eval(config['Data']['b2hPath'])
config_file = ast.literal_eval(
config['Data']['ditherStackFile']) #path and name of ditherStack file.
print('Starting conversion of ' + config_file +
' into HDF5 files, one file per dither position. ')
print('Removing ' + str(args.bufferTime[0]) +
' seconds from the beginning and end of each h5 file.')
# Read in config file
configData = readDict()
configData.read_from_file(config_file)
nPos = configData['nPos']
startTimes = configData['startTimes']
stopTimes = configData['stopTimes']
timestamp = int(startTimes[0])
value = datetime.datetime.fromtimestamp(timestamp)
print('Data collection started on ' + value.strftime('%Y-%m-%d %H:%M:%S'))
# ********* Bin2HDF config file format is
# Path
# First file number
# nFiles
# beamFile (complete path)
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}