def populateFlatCals(runPath, lookupPath=None):
if lookupPath is None:
lookupPath = os.environ['MKID_CAL_LOOKUP']
if not os.path.exists(path):
writeNewCalLookupFile(path)
lookup = CalLookupFile(path, mode='a')
for root, dirs, files in os.walk(runPath):
obsFilenames = fnmatch.filter(files, 'obs*.h5')
for obsFilename in obsFilenames:
obsPath = os.path.join(root, obsFilename)
try:
obs = ObsFile(obsPath)
fn = FileName(obsFile=obsPath)
params = {}
params['obs_run'], params['obs_date'], params[
'obs_tstamp'] = fn.getComponents()
params['flatSoln_run'] = params['obs_run']
if params['obs_date'] in [
'20140923', '20140924', '20141020', '20141021',
'20141022'
]:
params['flatSoln_date'] = params['obs_date']
else:
if params['obs_date'] == '20140925':
params['flatSoln_date'] = '20140924'
print(params)
lookup.updateObs(newParams=params)
except:
pass
def makeFileName(self, obsTstamp, keyPrefix):
entry = self.lookupObs(obsTstamp)
if entry is None:
print('entry none')
return None
run = entry[keyPrefix + '_run']
date = entry[keyPrefix + '_date']
tstamp = entry[keyPrefix + '_tstamp']
if run == '' and date == '' and tstamp == '':
return None
fn = FileName(run=run, date=date, tstamp=tstamp)
return fn
def populateWaveCals(runPath, lookupPath=None):
if lookupPath is None:
lookupPath = os.environ['MKID_CAL_LOOKUP']
if not os.path.exists(path):
writeNewCalLookupFile(path)
lookup = CalLookupFile(path, mode='a')
for root, dirs, files in os.walk(runPath):
obsFilenames = fnmatch.filter(files, 'obs*.h5')
for obsFilename in obsFilenames:
obsPath = os.path.join(root, obsFilename)
try:
obs = ObsFile(obsPath)
fn = FileName(obsFile=obsPath)
params = {}
params['obs_run'], params['obs_date'], params[
'obs_tstamp'] = fn.getComponents()
params['waveSoln_run'] = params['obs_run']
obs.loadBestWvlCalFile()
waveCalPath = obs.wvlCalFileName
waveCalFilename = os.path.basename(waveCalPath)
if waveCalFilename.startswith('master'):
params['waveSoln_isMasterCal'] = True
tstamp = waveCalFilename.split('_')[1].split('.')[0]
params['waveSoln_tstamp'] = tstamp
params['waveSoln_date'] = ''
else:
params['waveSoln_isMasterCal'] = False
tstamp = waveCalFilename.split('_')[1].split('.')[0]
params['waveSoln_tstamp'] = tstamp
dirs = os.path.dirname(
os.path.normpath(waveCalPath)).split(os.sep)
params['waveSoln_date'] = dirs[-1]
print(params)
lookup.updateObs(newParams=params)
except:
pass
def populateTimeMasks(runPath, lookupPath=None):
if lookupPath is None:
lookupPath = os.environ['MKID_CAL_LOOKUP']
if not os.path.exists(path):
writeNewCalLookupFile(path)
lookup = CalLookupFile(path, mode='a')
for root, dirs, files in os.walk(runPath):
obsFilenames = fnmatch.filter(files, 'obs*.h5')
for obsFilename in obsFilenames:
obsPath = os.path.join(root, obsFilename)
try:
obs = ObsFile(obsPath)
fn = FileName(obsFile=obsPath)
params = {}
params['obs_run'], params['obs_date'], params[
'obs_tstamp'] = fn.getComponents()
params['timeMask_run'], params['timeMask_date'], params[
'timeMask_tstamp'] = fn.getComponents()
print(params)
lookup.updateObs(newParams=params)
except:
pass
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}