def makePfsConfig(tract, patch, fiberIds, ras, decs, catIds, objIds,
objectMags):
"""
Make and return a PfsConfig with real information
"""
nFiber = len(fiberIds)
tmp, tracts = tract, np.empty(nFiber, dtype=np.int32)
tracts.fill(tmp)
tmp, patches = patch, np.empty(nFiber, dtype=str)
patches.fill(tmp)
patches = nFiber * [tmp]
fiberMag = np.empty((nFiber, 5))
for i in range(nFiber):
fiberMag[i] = objectMags[i]
mpsCen = np.zeros((nFiber, 2))
return PfsConfig(None,
tracts,
patches,
fiberIds,
ras,
decs,
catId=catIds,
objId=objIds,
mpsCen=mpsCen,
fiberMag=fiberMag)
def testBasic(self):
"""Test basic operation of PfsConfig"""
config = PfsConfig(self.pfsDesignId, self.visit0,
self.raBoresight.asDegrees(),
self.decBoresight.asDegrees(), self.fiberId,
self.tract, self.patch, self.ra, self.dec,
self.catId, self.objId, self.targetType,
self.fiberMag, self.filterNames, self.pfiCenter,
self.pfiNominal)
dirName = os.path.splitext(__file__)[0]
if not os.path.exists(dirName):
os.makedirs(dirName)
filename = os.path.join(dirName, config.filename)
if os.path.exists(filename):
os.unlink(filename)
try:
config.write(dirName=dirName)
other = PfsConfig.read(self.pfsDesignId,
self.visit0,
dirName=dirName)
self.assertPfsConfig(config, other)
except Exception:
raise # Leave file for manual inspection
else:
os.unlink(filename)
def makePfsConfig(pfsDesignId, visit0, tracts, patches, fiberIds, ras, decs,
catIds, objIds, objectMags):
"""
Make and return a PfsConfig with real information
"""
nFiber = len(fiberIds)
fiberMag = np.empty((nFiber, 5))
for i in range(nFiber):
fiberMag[i] = objectMags[i]
raBoresight = np.median(ras)
decBoresight = np.median(decs)
targetTypes = np.array([1 for i in range(nFiber)], dtype='i4')
fiberMags = [[mag] for mag in fiberMag[:, 0]]
filterNames = [['g'] for i in range(nFiber)]
pfiNominals = np.zeros((nFiber, 2))
pfiCenters = np.zeros((nFiber, 2))
return PfsConfig(pfsDesignId=pfsDesignId,
visit0=visit0,
raBoresight=raBoresight,
decBoresight=decBoresight,
fiberId=fiberIds,
tract=tracts,
patch=patches,
ra=ras,
dec=decs,
catId=catIds,
objId=objIds,
targetType=targetTypes,
fiberMag=fiberMags,
filterNames=filterNames,
pfiCenter=pfiCenters,
pfiNominal=pfiNominals)
def makeFakePfsConfig(tract,
patch,
ra,
dec,
catId,
startingObjId,
objectMags,
nFiber=1):
"""Make and return a PfsConfig with nFiber entries referring to the same object
Successive fibres are given object IDs that increase by one, starting with objId
"""
fiberId = np.arange(1, nFiber + 1, dtype=np.int32)
tmp, ra = ra, np.empty(nFiber)
ra.fill(tmp)
tmp, dec = dec, np.empty(nFiber)
dec.fill(tmp)
catIds = np.empty(nFiber)
catIds.fill(catId)
tmp, tract = tract, np.empty(nFiber, dtype=np.int32)
tract.fill(tmp)
tmp, patch = patch, np.empty(nFiber, dtype=str)
patch.fill(tmp)
patch = nFiber * [tmp]
objIds = startingObjId + np.arange(nFiber, dtype=np.int64)
fiberMag = np.empty((nFiber, 5))
for i in range(nFiber):
fiberMag[i] = objectMags[i]
mpsCen = np.zeros((nFiber, 2))
return PfsConfig(None,
tract,
patch,
fiberId,
ra,
dec,
catId=catIds,
objId=objIds,
mpsCen=mpsCen,
fiberMag=fiberMag)
def testFromPfsDesign(self):
"""Test PfsConfig.fromPfsDesign"""
design = PfsDesign(self.pfsDesignId, self.raBoresight.asDegrees(),
self.decBoresight.asDegrees(), self.fiberId,
self.tract, self.patch, self.ra, self.dec,
self.catId, self.objId, self.targetType,
self.fiberStatus, self.fiberMag, self.filterNames,
self.pfiNominal)
config = PfsConfig(self.pfsDesignId, self.visit0,
self.raBoresight.asDegrees(),
self.decBoresight.asDegrees(), self.fiberId,
self.tract, self.patch, self.ra, self.dec,
self.catId, self.objId, self.targetType,
self.fiberStatus, self.fiberMag, self.filterNames,
self.pfiCenter, self.pfiNominal)
self.assertPfsConfig(
PfsConfig.fromPfsDesign(design, self.visit0, self.pfiCenter),
config)
def read(self, dirName=".", pfsConfigs=None, setPfsConfig=True):
"""Read self's pfsArm file from directory dirName
If provided, pfsConfigs is a dict of pfsConfig objects, indexed by pfsConfigId
If setPfsConfig is False (default is True) set the pfsConfig field
"""
if not pyfits:
raise RuntimeError(
"I failed to import pyfits, so cannot read from disk")
fileName = PfsArm.fileNameFormat % (self.visit, self.arm,
self.spectrograph)
fd = pyfits.open(os.path.join(dirName, fileName))
for hduName in ["WAVELENGTH", "FLUX", "COVAR", "MASK", "SKY"]:
hdu = fd[hduName]
hdr, data = hdu.header, hdu.data
if False:
for k, v in hdr.items():
print "%8s %s" % (k, v)
if data.ndim == 2:
if hduName == "WAVELENGTH":
self.lam = data
elif hduName == "FLUX":
self.flux = data
elif hduName == "MASK":
self.mask = data
elif hduName == "SKY":
self.sky = data
else:
raise RuntimeError("Unexpected HDU %s reading %s" %
(hduName, fileName))
else:
if hduName != "COVAR":
raise RuntimeError("Unexpected HDU %s reading %s" %
(hduName, fileName))
self.covar = data
#print hdr["EXTNAME"], hdr["XTENSION"], data.dtype, data.shape
hdu = fd["CONFIG"]
hdr, data = hdu.header, hdu.data
assert 'pfsConfigId' in data.names
assert 'visit' in data.names
assert len(data['visit']) == 1 # only one row in the table
if data['visit'][0] != self.visit:
raise RuntimeError(
"Filename corresponds to visit %d, but config gives %d" %
self.visit, data['visit'][0])
self.pfsConfigId = data['pfsConfigId'][0]
if self.pfsConfigId < 0:
self.pfsConfigId = None
if not setPfsConfig:
self.pfsConfig = None
else: # a good idea, but only if we can find the desired pfsConfig
if pfsConfigs is None:
pfsConfigs = {} # n.b. won't be passed back to caller
if self.pfsConfigId not in pfsConfigs:
pfsConfigs[self.pfsConfigId] = PfsConfig(self.pfsConfigId)
pfsConfigs[self.pfsConfigId].read(dirName)
self.pfsConfig = pfsConfigs[self.pfsConfigId]
self.checkPfsConfig()
def testBadCtor(self):
"""Test bad constructor calls"""
def extendArray(array):
"""Double the length of the array"""
return np.concatenate((array, array))
def extendList(values):
"""Double the length of the list"""
return values + values
raBoresight = self.raBoresight.asDegrees()
decBoresight = self.decBoresight.asDegrees()
with self.assertRaises(RuntimeError):
PfsConfig(self.pfsDesignId, self.visit0, raBoresight, decBoresight,
extendArray(self.fiberId), self.tract, self.patch,
self.ra, self.dec, self.catId, self.objId,
self.targetType, self.fiberStatus, self.fiberMag,
self.filterNames, self.pfiCenter, self.pfiNominal)
with self.assertRaises(RuntimeError):
PfsConfig(self.pfsDesignId, self.visit0,
raBoresight, decBoresight, self.fiberId,
extendArray(self.tract), self.patch, self.ra, self.dec,
self.catId, self.objId, self.targetType,
self.fiberStatus, self.fiberMag, self.filterNames,
self.pfiCenter, self.pfiNominal)
with self.assertRaises(RuntimeError):
PfsConfig(self.pfsDesignId, self.visit0, raBoresight,
decBoresight, self.fiberId, self.tract, self.patch,
extendArray(self.ra), self.dec, self.catId, self.objId,
self.targetType, self.fiberStatus, self.fiberMag,
self.filterNames, self.pfiCenter, self.pfiNominal)
with self.assertRaises(RuntimeError):
PfsConfig(self.pfsDesignId, self.visit0, raBoresight, decBoresight,
self.fiberId, self.tract, self.patch, self.ra,
extendArray(self.dec), self.catId, self.objId,
self.targetType, self.fiberStatus, self.fiberMag,
self.filterNames, self.pfiCenter, self.pfiNominal)
with self.assertRaises(RuntimeError):
PfsConfig(self.pfsDesignId, self.visit0, raBoresight, decBoresight,
self.fiberId, self.tract, self.patch, self.ra, self.dec,
extendArray(self.catId), self.objId, self.targetType,
self.fiberStatus, self.fiberMag, self.filterNames,
self.pfiCenter, self.pfiNominal)
with self.assertRaises(RuntimeError):
PfsConfig(self.pfsDesignId, self.visit0, raBoresight, decBoresight,
self.fiberId, self.tract, self.patch, self.ra, self.dec,
self.catId, extendArray(self.objId), self.targetType,
self.fiberStatus, self.fiberMag, self.filterNames,
self.pfiCenter, self.pfiNominal)
with self.assertRaises(RuntimeError):
PfsConfig(self.pfsDesignId, self.visit0, raBoresight, decBoresight,
self.fiberId, self.tract, self.patch, self.ra,
self.dec, self.catId, self.objId,
extendArray(self.targetType), self.fiberStatus,
self.fiberMag, self.filterNames, self.pfiCenter,
self.pfiNominal)
with self.assertRaises(RuntimeError):
PfsConfig(self.pfsDesignId, self.visit0, raBoresight, decBoresight,
self.fiberId, self.tract, self.patch, self.ra, self.dec,
self.catId, self.objId, self.targetType,
self.fiberStatus, self.fiberMag, self.filterNames,
extendArray(self.pfiCenter), self.pfiNominal)
with self.assertRaises(RuntimeError):
PfsConfig(self.pfsDesignId, self.visit0, raBoresight, decBoresight,
self.fiberId, self.tract, self.patch, self.ra, self.dec,
self.catId, self.objId, self.targetType,
self.fiberStatus, self.fiberMag, self.filterNames,
self.pfiCenter, extendArray(self.pfiNominal))
with self.assertRaises(RuntimeError):
PfsConfig(self.pfsDesignId, self.visit0, raBoresight,
decBoresight, self.fiberId, self.tract,
extendList(self.patch), self.ra, self.dec, self.catId,
self.objId, self.targetType, self.fiberStatus,
self.fiberMag, self.filterNames, self.pfiCenter,
self.pfiNominal)
with self.assertRaises(RuntimeError):
PfsConfig(self.pfsDesignId, self.visit0, raBoresight, decBoresight,
self.fiberId, self.tract, self.patch, self.ra, self.dec,
self.catId, self.objId,
self.targetType, self.fiberStatus,
extendList(self.fiberMag), self.filterNames,
self.pfiCenter, self.pfiNominal)
with self.assertRaises(RuntimeError):
PfsConfig(self.pfsDesignId, self.visit0, raBoresight, decBoresight,
self.fiberId, self.tract, self.patch, self.ra, self.dec,
self.catId, self.objId, self.targetType,
self.fiberStatus, self.fiberMag,
extendList(self.filterNames), self.pfiCenter,
self.pfiNominal)
targetType = self.targetType.copy()
targetType[self.numFibers // 2] = -1
with self.assertRaises(ValueError):
PfsConfig(self.pfsDesignId, self.visit0, raBoresight, decBoresight,
self.fiberId, self.tract, self.patch, self.ra, self.dec,
self.catId, self.objId, targetType, self.fiberStatus,
self.fiberMag, self.filterNames, self.pfiCenter,
self.pfiNominal)
fiberStatus = self.fiberStatus.copy()
fiberStatus[self.numFibers // 2] = -1
with self.assertRaises(ValueError):
PfsConfig(self.pfsDesignId, self.visit0, raBoresight, decBoresight,
self.fiberId, self.tract, self.patch, self.ra, self.dec,
self.catId, self.objId, self.targetType, fiberStatus,
self.fiberMag, self.filterNames, self.pfiCenter,
self.pfiNominal)
fiberMag = [
extendArray(mag) if ii == self.numFibers // 2 else mag
for ii, mag in enumerate(self.fiberMag)
]
with self.assertRaises(RuntimeError):
PfsConfig(self.pfsDesignId, self.visit0, raBoresight, decBoresight,
self.fiberId, self.tract, self.patch, self.ra, self.dec,
self.catId, self.objId, self.targetType,
self.fiberStatus, fiberMag, self.filterNames,
self.pfiCenter, self.pfiNominal)
filterNames = [
extendList(ff) if ii == self.numFibers // 5 else ff
for ii, ff in enumerate(self.filterNames)
]
with self.assertRaises(RuntimeError):
PfsConfig(self.pfsDesignId, self.visit0, raBoresight, decBoresight,
self.fiberId, self.tract, self.patch, self.ra, self.dec,
self.catId, self.objId, self.targetType,
self.fiberStatus, self.fiberMag, filterNames,
self.pfiCenter, self.pfiNominal)
pfiCenter = np.concatenate((self.pfiCenter, self.pfiCenter), axis=1)
with self.assertRaises(RuntimeError):
PfsConfig(self.pfsDesignId, self.visit0, raBoresight, decBoresight,
self.fiberId, self.tract, self.patch, self.ra, self.dec,
self.catId, self.objId, self.targetType,
self.fiberStatus, self.fiberMag, self.filterNames,
pfiCenter, self.pfiNominal)
pfiNominal = np.concatenate((self.pfiNominal, self.pfiNominal), axis=1)
with self.assertRaises(RuntimeError):
PfsConfig(self.pfsDesignId, self.visit0, raBoresight, decBoresight,
self.fiberId, self.tract, self.patch, self.ra, self.dec,
self.catId, self.objId, self.targetType,
self.fiberStatus, self.fiberMag, self.filterNames,
self.pfiCenter, pfiNominal)
def read(self, dirName=".", pfsConfigs=None, setPfsConfig=True):
"""Read self's pfsArm file from directory dirName
If provided, pfsConfigs is a dict of pfsConfig objects, indexed by pfsConfigId
If setPfsConfig is False (default is True) set the pfsConfig field
"""
if not pyfits:
raise RuntimeError("I failed to import pyfits, so cannot read from disk")
fileName = PfsArm.fileNameFormat % (self.visit, self.arm, self.spectrograph)
with pyfits.open(os.path.join(dirName, fileName)) as fd:
#
# Unpack the mask bits (which start with "MP_") from the header
#
hdr = fd[0].header
try:
import lsst.daf.base as dafBase
import lsst.afw.image as afwImage
except ImportError:
pass
else:
md = dafBase.PropertySet()
for k, v in hdr.items():
md.set(k, v)
self._metadata = afwImage.Mask.parseMaskPlaneMetadata(md)
for hduName in ["WAVELENGTH", "FLUX", "COVAR", "MASK", "SKY"]:
hdu = fd[hduName]
hdr, data = hdu.header, hdu.data
if False:
for k, v in hdr.items():
print("%8s %s" % (k, v))
if data.ndim == 2:
if hduName == "WAVELENGTH":
self.lam = data
elif hduName == "FLUX":
self.flux = data
elif hduName == "MASK":
self.mask = data
elif hduName == "SKY":
self.sky = data
else:
raise RuntimeError("Unexpected HDU %s reading %s" % (hduName, fileName))
else:
if hduName != "COVAR":
raise RuntimeError("Unexpected HDU %s reading %s" % (hduName, fileName))
self.covar = data
hdu = fd["CONFIG"]
hdr, data = hdu.header, hdu.data
assert 'pfsConfigId' in data.names
assert 'visit' in data.names
assert len(data['visit']) == 1 # only one row in the table
if data['visit'][0] != self.visit:
raise RuntimeError("Filename corresponds to visit %d, but config gives %d" %
self.visit, data['visit'][0])
self.pfsConfigId = data['pfsConfigId'][0]
if self.pfsConfigId < 0:
self.pfsConfigId = None
if not setPfsConfig:
self.pfsConfig = None
else: # a good idea, but only if we can find the desired pfsConfig
if pfsConfigs is None:
pfsConfigs = {} # n.b. won't be passed back to caller
if self.pfsConfigId not in pfsConfigs:
pfsConfigs[self.pfsConfigId] = PfsConfig(self.pfsConfigId)
pfsConfigs[self.pfsConfigId].read(dirName)
self.pfsConfig = pfsConfigs[self.pfsConfigId]
self.checkPfsConfig()
def make_pfsConfig(pfsDesignId, visit0, fiberIds, tracts, patches, ras, decs,
catIds, objIds, targetTypeIds, fiberMags_g, pfiNominal_x,
pfiNominal_y, pfiCenter_x, pfiCenter_y):
'''
Description
-----------
Make pfsConfig object
Parameters
----------
pfsDesignId : `int`
visit0 : `int`
fiberIds : `numpy.ndarray` of `int`
tracts : `numpy.ndarray` of `int`
patches : `numpy.ndarray` of `str`
ras : `numpy.ndarray` of `float`
decs : `numpy.ndarray` of `float`
catIds : `numpy.ndarray` of `int`
objIds : `numpy.ndarray` of `int`
targetTypeIds : `numpy.ndarray` of `int`
fiberMags_g : `numpy.ndarray` of `float`
pfiNominal_x : `numpy.ndarray` of `float`
pfiNominal_y : `numpy.ndarray` of `float`
pfiCenter_x : `numpy.ndarray` of `float`
pfiCenter_y : `numpy.ndarray` of `float`
Returns
-------
pfsConfig : `object` of `pfsConfig`
Note
----
You need to have the latest PFS datamodel
'''
nFiber = len(fiberIds)
fiberMag = np.empty((nFiber, 5))
for i in range(nFiber):
fiberMag[i] = fiberMags_g[i]
raBoresight = np.median(ras)
decBoresight = np.median(decs)
fiberMags = [[mag] for mag in fiberMag[:, 0]]
filterNames = [['g'] for i in range(nFiber)]
pfiNominal = np.array((pfiNominal_x, pfiNominal_y)).transpose()
pfiCenter = np.array((pfiCenter_x, pfiCenter_y)).transpose()
pfsConfig = PfsConfig(pfsDesignId=pfsDesignId,
visit0=visit0,
raBoresight=raBoresight,
decBoresight=decBoresight,
fiberId=fiberIds,
tract=tracts,
patch=patches,
ra=ras,
dec=decs,
catId=catIds,
objId=objIds,
targetType=targetTypeIds,
fiberMag=fiberMags,
filterNames=filterNames,
pfiCenter=pfiCenter,
pfiNominal=pfiNominal)
pfsConfig.write('./out/fits/')
return pfsConfig
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)