def make_sim_spec(self):
self.outdir = self.params['outDir']
self.tract = int(self.params['tract'])
self.patch = self.params['patch']
self.visit = int(self.params['visit'])
self.fiberId = self.params['fiberId']
self.ra = self.params['ra']
self.dec = self.params['dec']
self.catId = self.params['catId']
self.objId = self.params['objId']
self.spectrograph = self.params['spectrograph']
try:
self.mag_file = '%.4e' % (float(self.params['MAG_FILE']))
except:
self.mag_file = self.params['MAG_FILE']
''' some checks '''
self.writeFits = strToBool(self.params['writeFits'])
self.writePfsArm = strToBool(self.params['writePfsArm'])
self.plotArmSet = strToBool(self.params['plotArmSet'])
self.plotObject = strToBool(self.params['plotObject'])
self.asciiTable = self.params['asciiTable']
self.pfsConfigFull = strToBool(self.params['pfsConfigFull'])
nrealize = int(self.params['nrealize'])
if not self.writeFits and not self.asciiTable:
sys.exit(
"Please specify asciiTable or omit writeFits (or say writeFits true)"
)
if not os.path.exists(self.outdir):
try:
os.makedirs(self.outdir)
except OSError as e:
sys.exit("Unable to create outDir: %s" % e)
if nrealize <= 0:
sys.exit("Please specify at least one realization")
''' check magfile '''
if os.path.exists(self.mag_file):
dat = np.loadtxt(self.mag_file)
nobj = dat.shape[1] - 1
else:
nobj = 1
if self.pfsConfigFull:
try:
if len(self.fiberId) == nobj and len(self.ra) == nobj and len(
self.dec) == nobj and len(self.catId) == nobj and len(
self.objId) == nobj:
objIds = [self.objId]
catIds = [self.catId]
else:
sys.exit("specify fiberId/ra/dec/objId/catId!")
except:
sys.exit("specify fiberId/ra/dec/objId/catId!")
else:
if nobj > 1:
if nrealize > 1:
sys.exit(
"The number of realization should be one for multiple input template"
)
else:
objIds = range(self.objId, self.objId + nobj)
#catIds = sp.zeros(nobj)
else:
objIds = range(self.objId, self.objId + nrealize)
#catIds = sp.zeros(nobj)
catIds = sp.array([self.catId])
'''
## read input file ##
# arm: 0-3 telling us which arm the data comes from (arm_name will convert to b, r, n, m)
# wav: wavelength
# nsv: per-pixel (instrumental + sky) variance (counts^2)
# trn: conversion from I_nu to counts
# smp: samplingFactor. A fiddle factor for the Poisson noise in HgCdTe devices
# skm: sky flux
'''
arm, wav, nsv, trn, smp, skm = np.loadtxt(self.params['etcFile'],
usecols=(0, 2, 5, 8, 9, 10),
unpack=True)
arm = arm.astype(int)
trn[trn < 1.0e26] = 1.0e26
''' load magnitude or filename '''
if os.path.exists(self.mag_file):
dat = np.loadtxt(self.mag_file)
nobj = dat.shape[1] - 1
_lam = dat[:, 0]
mag = np.empty((len(wav), nobj))
for i in range(nobj):
_mag = dat[:, i + 1]
mag[:, i] = np.interp(wav, _lam, _mag)
else:
nobj = 1
mag = np.empty((len(wav), nobj))
mag[:, 0].fill(self.mag_file)
wav_mtrx = np.empty((len(wav), nobj))
trn_mtrx = np.empty((len(wav), nobj))
smp_mtrx = np.empty((len(wav), nobj))
nsv_mtrx = np.empty((len(wav), nobj))
for i in range(nobj):
wav_mtrx[:, i] = wav
trn_mtrx[:, i] = trn
smp_mtrx[:, i] = smp
nsv_mtrx[:, i] = nsv
''' calculate the flux etc. in observed units '''
fnu = 10**(-0.4 * (mag + 48.6))
flam = 3.0e18 * fnu / (10 * wav_mtrx)**2 / 1e-17
counts = trn_mtrx * fnu
if (counts == 0).any():
print(
"counts == 0 detected in some pixels; setting to %g for variance"
% (float(self.params['countsMin'])),
file=sys.stderr)
countsp = np.where(
counts == 0, float(self.params['countsMin']),
counts) # version of counts with zero pixels replaced
else:
countsp = counts
snr = countsp / np.sqrt(smp_mtrx * countsp + nsv_mtrx) * np.sqrt(
int(self.params['EXP_NUM']))
sigma = flam / snr
msk = np.zeros_like(wav, dtype=np.int32)
sky = 3.0e18 * (skm / trn) / (10 * wav)**2 / 1e-17
arm = arm_name(arm)
arms = np.array(
sorted(set(arm), key=lambda x: dict(b=0, r=1, m=1.5, n=2)[x])
) # unique values of arm
'''
Create and populate the objects corresponding to the datamodel
First the parameters describing the observation, in PfsConfig
'''
objectMags = []
if nobj > 1:
for i in range(nobj):
objectMags.append([
calculateFiberMagnitude(wav, mag[:, i], b) for b in "grizy"
])
else:
for i in range(nrealize):
objectMags.append([
calculateFiberMagnitude(wav, mag[:, 0], b) for b in "grizy"
])
if self.pfsConfigFull:
pfsConfig = makePfsConfig(self.tract, self.patch, self.fiberId,
self.ra, self.dec, self.catId, objIds,
objectMags)
else:
if nobj > 1:
pfsConfig = makeFakePfsConfig(self.tract,
self.patch,
self.ra,
self.dec,
self.catId,
objIds[0],
objectMags,
nFiber=nobj)
else:
pfsConfig = makeFakePfsConfig(self.tract,
self.patch,
self.ra,
self.dec,
self.catId,
objIds[0],
objectMags,
nFiber=nrealize)
'''
Create the PfsArmSet; we'll put each realisation into a different fibre
'''
pfsConfigId = pfsConfig.pfsConfigId
pfsArmSet = PfsArmSet(self.visit,
self.spectrograph,
arms=arms,
pfsConfig=pfsConfig)
for armStr, data in pfsArmSet.data.items():
thisArm = (arm == armStr)
nPt = np.sum(thisArm)
if nobj > 1:
for i in range(nobj):
data.lam.append(wav[thisArm])
data.flux.append(flam[thisArm, i] +
np.random.normal(0.0, sigma[thisArm, i]))
data.sky.append(sky[thisArm])
data.mask.append(msk[thisArm])
covar = np.zeros(3 * nPt).reshape((3, nPt))
covar[0] = sigma[thisArm, i]**2
data.covar.append(covar)
else:
for i in range(nrealize):
data.lam.append(wav[thisArm])
data.flux.append(flam[thisArm, 0] +
np.random.normal(0.0, sigma[thisArm, 0]))
data.sky.append(sky[thisArm])
data.mask.append(msk[thisArm])
covar = np.zeros(3 * nPt).reshape((3, nPt))
covar[0] = sigma[thisArm, 0]**2
data.covar.append(covar)
if self.plotArmSet:
pfsArmSet.plot(showFlux=True,
showMask=False,
showSky=False,
showCovar=False)
'''
Time for I/O
'''
''' Fits '''
if self.writeFits:
pfsConfig.write(self.outdir) # pfsConfig file
if self.writePfsArm: # write pfsArm files
for data in pfsArmSet.data.values():
data.write(self.outdir)
''' Ascii '''
if self.asciiTable != "None":
write_ascii(pfsArmSet, self.asciiTable, self.outdir)
print("ASCII table %s was generated" % self.asciiTable)
'''
Now make the PfsObject from the PfsArmSet
'''
for catId in catIds:
for objId in objIds:
pfsObject = makePfsObject(objId, [pfsArmSet], catId=catId)
self.pfsVisitHash = pfsObject.pfsVisitHash
if self.plotObject:
pfsObject.plot()
if self.writeFits:
pfsObject.write(self.outdir) # pfsObject file
return 0
def main(pfsConfigId, tract, patch, fiberId=None, dataDir=".", objId=None,
showPfsArm=False, showPfsArmSet=False, showPfsObject=False):
pfsConfig = PfsConfig(pfsConfigId, tract, patch)
pfsConfig.read(dataDir)
if objId is None:
if fiberId is None:
fiberId = 1
else:
import numpy as np
import sys
try:
_fiberId = np.where(pfsConfig.objId == objId)[0][0]
except IndexError:
print("Unable to find objId %08x in configuration with pfsConfigId 0x%08x" % \
(objId, pfsConfigId), file=sys.stderr)
return
_fiberId += 1 # 1-indexed
if fiberId is not None and fiberId != _fiberId:
print("fiberId %d doesn't match objId %08x's fiber %d" % \
(fiberId, objId, _fiberId), file=sys.stderr)
return
fiberId = _fiberId
objId = pfsConfig.objId[fiberId - 1]
print("fiberId = %d, objId = 0x%x" % (fiberId, objId))
#-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
pfsArms = PfsArmSet(visit=1, spectrograph=1, pfsConfigId=pfsConfigId)
pfsArms.read(dataDir)
if showPfsArm:
if True:
pfsArms.data['r'].plot(fiberId=fiberId)
else:
pfsArms.data['r'].plot(fiberId=fiberId,
showFlux=True, showSky=True, showCovar=True, showMask=True)
if showPfsArmSet:
if True:
pfsArms.plot(fiberId=fiberId)
else:
pfsArms.plot(fiberId=fiberId,
showFlux=True, showSky=True, showCovar=True, showMask=True)
#-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
pfsObject = makePfsObject(objId, [pfsArms])
pfsObject.write(dataDir)
npfs = PfsObject(tract, patch, objId, visits=[1])
npfs.read(dataDir)
if showPfsObject:
if True:
npfs.plot(showFluxTbl=True)
else:
npfs.plot(showFlux=True, showSky=True, showCovar=True, showCovar2=True)
npfs.plot(showFluxTbl=True, showFluxVariance=False)
def main(pfsConfigId, tract, patch, fiberId=None, dataDir=".", objId=None,
showPfsArm=False, showPfsArmSet=False, showPfsObject=False):
pfsConfig = PfsConfig(pfsConfigId)
pfsConfig.read(dataDir)
if objId is None:
if fiberId is None:
fiberId = 1
else:
import numpy as np
import sys
try:
_fiberId = np.where(pfsConfig.objId == objId)[0][0]
except IndexError:
print >> sys.stderr, "Unable to find objId %08x in configuration with pfsConfigId 0x%08x" % \
(objId, pfsConfigId)
return
_fiberId += 1 # 1-indexed
if fiberId is not None and fiberId != _fiberId:
print >> sys.stderr, "fiberId %d doesn't match objId %08x's fiber %d" % \
(fiberId, objId, _fiberId)
return
fiberId = _fiberId
objId = pfsConfig.objId[fiberId - 1]
print "fiberId = %d, objId = 0x%x" % (fiberId, objId)
#-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
pfsArms = PfsArmSet(visit=1, spectrograph=1)
pfsArms.read(dataDir)
if showPfsArm:
if True:
pfsArms.data['r'].plot(fiberId=fiberId)
else:
pfsArms.data['r'].plot(fiberId=fiberId,
showFlux=True, showSky=True, showCovar=True, showMask=True)
if showPfsArmSet:
if True:
pfsArms.plot(fiberId=fiberId)
else:
pfsArms.plot(fiberId=fiberId,
showFlux=True, showSky=True, showCovar=True, showMask=True)
#-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
pfsObject = makePfsObject(tract, patch, objId, [pfsArms])
pfsObject.write(dataDir)
npfs = PfsObject(tract, patch, objId, visits=[1])
npfs.read(dataDir)
if showPfsObject:
if True:
npfs.plot(showFluxTbl=True)
else:
npfs.plot(showFlux=True, showSky=True, showCovar=True, showCovar2=True)
npfs.plot(showFluxTbl=True, showFluxVariance=False)
def main(
inFile,
magFile,
outDir=".",
tract=0,
patch="0,0",
visit=1,
spectrograph=1,
catId=0,
objIds=[1],
nRealize=1,
nExposure=1,
countsMin=0.1,
asciiTable=None,
writeFits=True,
writePfsArm=True,
plotArmSet=False,
plotObject=False,
):
## read input file ##
# arm: 0-3 telling us which arm the data comes from (arm_name will convert to b, r, n, m)
# wav: wavelength
# nsv: per-pixel (instrumental + sky) variance (counts^2)
# trn: conversion from I_nu to counts
# smp: samplingFactor. A fiddle factor for the Poisson noise in HgCdTe devices
# skm: sky flux
arm, wav, nsv, trn, smp, skm = np.loadtxt(inFile, usecols=(0, 2, 5, 8, 9, 10), unpack=True)
arm = arm.astype(int)
trn[trn < 1.0e26] = 1.0e26
## load magnitude or filename ##
if os.path.exists(magFile):
_lam, _mag = np.loadtxt(magFile, usecols=(0, 1), unpack=True)
mag = np.interp(wav, _lam, _mag)
else:
mag = np.empty(len(wav))
mag.fill(float(magFile))
##
# Calculate the flux etc. in observed units
##
fnu = 10 ** (-0.4 * (mag + 48.6))
flam = 3.0e18 * fnu / (10 * wav) ** 2 / 1e-17
counts = trn * fnu
if (counts == 0).any():
print >> sys.stderr, "counts == 0 detected in some pixels; setting to %g for variance" % countsMin
countsp = np.where(counts == 0, countsMin, counts) # version of counts with zero pixels replaced
else:
countsp = counts
snr = countsp / np.sqrt(smp * countsp + nsv) * np.sqrt(nExposure)
sigma = flam / snr
msk = np.zeros_like(wav, dtype=np.int32)
sky = 3.0e18 * (skm / trn) / (10 * wav) ** 2 / 1e-17
arm = arm_name(arm)
arms = np.array(sorted(set(arm), key=lambda x: dict(b=0, r=1, m=1.5, n=2)[x])) # unique values of arm
#
# Create and populate the objects corresponding to the datamodel
#
# First the parameters describing the observation, in PfsConfig
objectMags = [calculateFiberMagnitude(wav, mag, b) for b in "grizy"]
pfsConfig = makeFakePfsConfig(tract, patch, 150.0, 2.0, catId, objIds[0], objectMags, nFiber=nRealize)
#
# Create the PfsArmSet; we'll put each realisation into a different fibre
#
pfsConfigId = pfsConfig.pfsConfigId
pfsArmSet = PfsArmSet(visit, spectrograph, arms=arms, pfsConfig=pfsConfig)
for armStr, data in pfsArmSet.data.items():
thisArm = arm == armStr
nPt = np.sum(thisArm)
for i in range(nRealize):
data.lam.append(wav[thisArm])
data.flux.append(flam[thisArm] + np.random.normal(0.0, sigma[thisArm]))
data.sky.append(sky[thisArm])
data.mask.append(msk[thisArm])
covar = np.zeros(3 * nPt).reshape((3, nPt))
covar[0] = sigma[thisArm] ** 2
data.covar.append(covar)
if plotArmSet:
pfsArmSet.plot(showFlux=True, showMask=False, showSky=False, showCovar=False)
#
# Time for I/O
#
# Fits
#
if writeFits:
pfsConfig.write(outDir) # pfsConfig file
if writePfsArm: # write pfsArm files
for data in pfsArmSet.data.values():
data.write(outDir)
# Ascii
#
if asciiTable:
write_ascii(pfsArmSet, asciiTable, outDir)
print "ASCII table %s was generated" % asciiTable
#
# Now make the PfsObject from the PfsArmSet
#
for objId in objIds:
pfsObject = makePfsObject(objId, [pfsArmSet])
if plotObject:
pfsObject.plot()
if writeFits:
pfsObject.write(outDir) # pfsObject file
