class PhosimCmpt(object):
def __init__(self, tele):
"""Initialization of PhoSim component class.
WEP: wavefront estimation pipeline.
Parameters
----------
tele : TeleFacade
Telescope instance.
"""
# Configuration directory
self.configDir = getConfigDir()
# Telescope setting file
settingFilePath = os.path.join(self.configDir,
"phosimCmptSetting.yaml")
self._phosimCmptSettingFile = ParamReader(filePath=settingFilePath)
# OPD metrology
self.metr = OpdMetrology()
# TeleFacade instance
self.tele = tele
# Output directory of data
self.outputDir = ""
# Output directory of image
self.outputImgDir = ""
# Seed number
self.seedNum = 0
# M1M3 force error
self.m1m3ForceError = 0.05
def setM1M3ForceError(self, m1m3ForceError):
"""Set the M1M3 force error.
Parameters
----------
m1m3ForceError : float
Ratio of actuator force error between 0 and 1.
"""
self.m1m3ForceError = m1m3ForceError
def getM1M3ForceError(self):
"""Get the M1M3 force error.
Returns
-------
float
Ratio of actuator force error.
"""
return self.m1m3ForceError
def getSettingFile(self):
"""Get the setting file.
Returns
-------
lsst.ts.wep.ParamReader
Setting file.
"""
return self._phosimCmptSettingFile
def getTele(self):
"""Get the telescope object.
Returns
-------
TeleFacade
Telescope object.
"""
return self.tele
def getNumOfZk(self):
"""Get the number of Zk (annular Zernike polynomial).
Returns
-------
int
Number of Zk.
"""
return int(self._phosimCmptSettingFile.getSetting("numOfZk"))
def getIntraFocalDirName(self):
"""Get the intra-focal directory name.
Returns
-------
str
Intra-focal directory name.
"""
return self._phosimCmptSettingFile.getSetting("intraDirName")
def getExtraFocalDirName(self):
"""Get the extra-focal directory name.
Returns
-------
str
Extra-focal directory name.
"""
return self._phosimCmptSettingFile.getSetting("extraDirName")
def getOpdMetr(self):
"""Get the OPD metrology object.
OPD: optical path difference.
Returns
-------
OpdMetrology
OPD metrology object.
"""
return self.metr
def setOutputDir(self, outputDir):
"""Set the output directory.
The output directory will be constructed if there is no existed one.
Parameters
----------
outputDir : str
Output directory.
"""
self._makeDir(outputDir)
self.outputDir = outputDir
def _makeDir(self, newDir, exist_ok=True):
"""Make the new directory.
Super-mkdir; create a leaf directory and all intermediate ones. Works
like mkdir, except that any intermediate path segment (not just the
rightmost) will be created if it does not exist.
Parameters
----------
newDir : str
New directory.
exist_ok : bool, optional
If the target directory already exists, raise an OSError if
exist_ok is False. Otherwise no exception is raised. (the default
is True.)
"""
os.makedirs(newDir, exist_ok=exist_ok)
def getOutputDir(self):
"""Get the output directory.
Returns
-------
str
Output directory.
"""
return self.outputDir
def setOutputImgDir(self, outputImgDir):
"""Set the output image directory.
The output image directory will be constructed if there is no existed
one.
Parameters
----------
outputImgDir : str
Output image directory
"""
self._makeDir(outputImgDir)
self.outputImgDir = outputImgDir
def getOutputImgDir(self):
"""Get the output image directory.
Returns
-------
str
Output image directory
"""
return self.outputImgDir
def setSeedNum(self, seedNum):
"""Set the seed number for the M1M3 mirror surface purturbation.
Parameters
----------
seedNum : int
Seed number.
"""
self.seedNum = int(seedNum)
def getSeedNum(self):
"""Get the seed number for the M1M3 random surface purturbation.
Returns
-------
int or None
Seed number. None means there is no random purturbation.
"""
return self.seedNum
def setSurveyParam(self,
obsId=None,
filterType=None,
boresight=None,
zAngleInDeg=None,
rotAngInDeg=None):
"""Set the survey parameters.
Parameters
----------
obsId : int, optional
Observation Id. (the default is None.)
filterType : enum 'FilterType' in lsst.ts.wep.Utility, optional
Active filter type. (the default is None.)
boresight : tuple, optional
Telescope boresight in (ra, decl). (the default is None.)
zAngleInDeg : float, optional
Zenith angle in degree. (the default is None.)
rotAngInDeg : float, optional
Camera rotation angle in degree between -90 and 90 degrees. (the
default is None.)
"""
self.tele.setSurveyParam(obsId=obsId,
filterType=filterType,
boresight=boresight,
zAngleInDeg=zAngleInDeg,
rotAngInDeg=rotAngInDeg)
def addOpdFieldXYbyDeg(self, fieldXInDegree, fieldYInDegree):
"""Add the OPD new field X, Y in degree.
OPD: optical path difference.
Parameters
----------
fieldXInDegree : float, list, or numpy.ndarray
New field X in degree.
fieldYInDegree : float, list, or numpy.ndarray
New field Y in degree.
"""
self.metr.addFieldXYbyDeg(fieldXInDegree, fieldYInDegree)
def accDofInUm(self, dofInUm):
"""Accumulate the aggregated degree of freedom (DOF) in um.
idx 0-4: M2 dz, dx, dy, rx, ry
idx 5-9: Cam dz, dx, dy, rx, ry
idx 10-29: M1M3 20 bending modes
idx 30-49: M2 20 bending modes
Parameters
----------
dofInUm : list or numpy.ndarray
DOF in um.
"""
self.tele.accDofInUm(dofInUm)
def setDofInUm(self, dofInUm):
"""Set the accumulated degree of freedom (DOF) in um.
idx 0-4: M2 dz, dx, dy, rx, ry
idx 5-9: Cam dz, dx, dy, rx, ry
idx 10-29: M1M3 20 bending modes
idx 30-49: M2 20 bending modes
Parameters
----------
dofInUm : list or numpy.ndarray
DOF in um.
"""
self.tele.setDofInUm(dofInUm)
def getDofInUm(self):
"""Get the accumulated degree of freedom (DOF) in um.
idx 0-4: M2 dz, dx, dy, rx, ry
idx 5-9: Cam dz, dx, dy, rx, ry
idx 10-29: M1M3 20 bending modes
idx 30-49: M2 20 bending modes
Returns
-------
numpy.ndarray
DOF in um.
"""
return self.tele.getDofInUm()
def saveDofInUmFileForNextIter(self,
dofInUm,
dofInUmFileName="dofPertInNextIter.mat"):
"""Save the DOF in um data to file for the next iteration.
DOF: degree of freedom.
Parameters
----------
dofInUm : list or numpy.ndarray
DOF in um.
dofInUmFileName : str, optional
File name to save the DOF in um. (the default is
"dofPertInNextIter.mat".)
"""
filePath = os.path.join(self.outputDir, dofInUmFileName)
header = "The followings are the DOF in um:"
np.savetxt(filePath, np.transpose(dofInUm), header=header)
def runPhoSim(self, argString):
"""Run the PhoSim program.
Parameters
----------
argString : str
Arguments for PhoSim.
"""
self.tele.runPhoSim(argString)
def getComCamOpdArgsAndFilesForPhoSim(
self,
cmdFileName="opd.cmd",
instFileName="opd.inst",
logFileName="opdPhoSim.log",
cmdSettingFileName="opdDefault.cmd",
instSettingFileName="opdDefault.inst"):
"""Get the OPD calculation arguments and files of ComCam for the PhoSim
calculation.
OPD: optical path difference.
ComCam: commissioning camera.
Parameters
----------
cmdFileName : str, optional
Physical command file name. (the default is "opd.cmd".)
instFileName : str, optional
OPD instance file name. (the default is "opd.inst".)
logFileName : str, optional
Log file name. (the default is "opdPhoSim.log".)
cmdSettingFileName : str, optional
Physical command setting file name. (the default is
"opdDefault.cmd".)
instSettingFileName : str, optional
Instance setting file name. (the default is "opdDefault.inst".)
Returns
-------
str
Arguments to run the PhoSim.
"""
# Set the default ComCam OPD field positions
self.metr.setDefaultComcamGQ()
argString = self._getOpdArgsAndFilesForPhoSim(cmdFileName,
instFileName,
logFileName,
cmdSettingFileName,
instSettingFileName)
return argString
def _getOpdArgsAndFilesForPhoSim(self, cmdFileName, instFileName,
logFileName, cmdSettingFileName,
instSettingFileName):
"""Get the OPD calculation arguments and files for the PhoSim
calculation.
OPD: optical path difference.
Parameters
----------
cmdFileName : str
Physical command file name.
instFileName : str
OPD instance file name.
logFileName : str
Log file name.
cmdSettingFileName : str
Physical command setting file name.
instSettingFileName : str
Instance setting file name.
Returns
-------
str
Arguments to run the PhoSim.
"""
# Write the command file
cmdFilePath = self._writePertAndCmdFiles(cmdSettingFileName,
cmdFileName)
# Write the instance file
instSettingFile = self._getInstSettingFilePath(instSettingFileName)
instFilePath = self.tele.writeOpdInstFile(
self.outputDir,
self.metr,
instSettingFile=instSettingFile,
instFileName=instFileName)
# Get the argument to run the PhoSim
argString = self._getPhoSimArgs(logFileName, instFilePath, cmdFilePath)
return argString
def _writePertAndCmdFiles(self, cmdSettingFileName, cmdFileName):
"""Write the physical perturbation and command files.
Parameters
----------
cmdSettingFileName : str
Physical command setting file name.
cmdFileName : str
Physical command file name.
Returns
-------
str
Command file path.
"""
# Write the perturbation file
pertCmdFileName = "pert.cmd"
pertCmdFilePath = os.path.join(self.outputDir, pertCmdFileName)
if (not os.path.exists(pertCmdFilePath)):
self.tele.writePertBaseOnConfigFile(
self.outputDir,
seedNum=self.seedNum,
m1m3ForceError=self.m1m3ForceError,
saveResMapFig=True,
pertCmdFileName=pertCmdFileName)
# Write the physical command file
cmdSettingFile = os.path.join(self.configDir, "cmdFile",
cmdSettingFileName)
cmdFilePath = os.path.join(self.outputDir, cmdFileName)
if (not os.path.exists(cmdFilePath)):
self.tele.writeCmdFile(self.outputDir,
cmdSettingFile=cmdSettingFile,
pertFilePath=pertCmdFilePath,
cmdFileName=cmdFileName)
return cmdFilePath
def _getInstSettingFilePath(self, instSettingFileName):
"""Get the instance setting file path.
Parameters
----------
instSettingFileName : str
Instance setting file name.
Returns
-------
str
Instance setting file path.
"""
instSettingFile = os.path.join(self.configDir, "instFile",
instSettingFileName)
return instSettingFile
def _getPhoSimArgs(self, logFileName, instFilePath, cmdFilePath):
"""Get the arguments needed to run the PhoSim.
Parameters
----------
logFileName : str
Log file name.
instFilePath: str
Instance file path.
cmdFilePath : str
Physical command file path.
Returns
-------
str
Arguments to run the PhoSim.
"""
# PhoSim parameters
numPro = int(self._phosimCmptSettingFile.getSetting("numPro"))
e2ADC = int(self._phosimCmptSettingFile.getSetting("e2ADC"))
logFilePath = os.path.join(self.outputImgDir, logFileName)
argString = self.tele.getPhoSimArgs(instFilePath,
extraCommandFile=cmdFilePath,
numPro=numPro,
outputDir=self.outputImgDir,
e2ADC=e2ADC,
logFilePath=logFilePath)
return argString
def getComCamStarArgsAndFilesForPhoSim(
self,
extraObsId,
intraObsId,
skySim,
simSeed=1000,
cmdSettingFileName="starDefault.cmd",
instSettingFileName="starSingleExp.inst"):
"""Get the star calculation arguments and files of ComCam for the
PhoSim calculation.
Parameters
----------
extraObsId : int
Extra-focal observation Id.
intraObsId : int
Intra-focal observation Id.
skySim : SkySim
Sky simulator
simSeed : int, optional
Random number seed. (the default is 1000.)
cmdSettingFileName : str, optional
Physical command setting file name. (the default is
"starDefault.cmd".)
instSettingFileName : str, optional
Instance setting file name. (the default is "starSingleExp.inst".)
Returns
-------
list[str]
List of arguments to run the PhoSim.
"""
# Set the intra- and extra-focal related information
obsIdList = {"-1": extraObsId, "1": intraObsId}
instFileNameList = {"-1": "starExtra.inst", "1": "starIntra.inst"}
logFileNameList = {
"-1": "starExtraPhoSim.log",
"1": "starIntraPhoSim.log"
}
extraFocalDirName = self.getExtraFocalDirName()
intraFocalDirName = self.getIntraFocalDirName()
outImgDirNameList = {"-1": extraFocalDirName, "1": intraFocalDirName}
# Write the instance and command files of defocal conditions
cmdFileName = "star.cmd"
onFocalDofInUm = self.getDofInUm()
onFocalOutputImgDir = self.outputImgDir
argStringList = []
for ii in (-1, 1):
# Set the observation ID
self.setSurveyParam(obsId=obsIdList[str(ii)])
# Camera piston (Change the unit from mm to um)
pistonInUm = np.zeros(len(onFocalDofInUm))
pistonInUm[5] = ii * self.tele.getDefocalDistInMm() * 1e3
# Set the new DOF that considers the piston motion
self.setDofInUm(onFocalDofInUm + pistonInUm)
# Update the output image directory
outputImgDir = os.path.join(onFocalOutputImgDir,
outImgDirNameList[str(ii)])
self.setOutputImgDir(outputImgDir)
# Get the argument to run the phosim
argString = self.getStarArgsAndFilesForPhoSim(
skySim,
cmdFileName=cmdFileName,
instFileName=instFileNameList[str(ii)],
logFileName=logFileNameList[str(ii)],
simSeed=simSeed,
cmdSettingFileName=cmdSettingFileName,
instSettingFileName=instSettingFileName)
argStringList.append(argString)
# Put the internal state back to the focal plane condition
self.setDofInUm(onFocalDofInUm)
self.setOutputImgDir(onFocalOutputImgDir)
return argStringList
def getStarArgsAndFilesForPhoSim(self,
skySim,
cmdFileName="star.cmd",
instFileName="star.inst",
logFileName="starPhoSim.log",
simSeed=1000,
cmdSettingFileName="starDefault.cmd",
instSettingFileName="starSingleExp.inst"):
"""Get the star calculation arguments and files for the PhoSim
calculation.
Parameters
----------
skySim : SkySim
Sky simulator
cmdFileName : str, optional
Physical command file name. (the default is "star.cmd".)
instFileName : str, optional
Star instance file name. (the default is "star.inst".)
logFileName : str, optional
Log file name. (the default is "starPhoSim.log".)
simSeed : int, optional
Random number seed. (the default is 1000)
cmdSettingFileName : str, optional
Physical command setting file name. (the default is
"starDefault.cmd".)
instSettingFileName : str, optional
Instance setting file name. (the default is "starSingleExp.inst".)
Returns
-------
str
Arguments to run the PhoSim.
"""
# Write the command file
cmdFilePath = self._writePertAndCmdFiles(cmdSettingFileName,
cmdFileName)
# Write the instance file
instSettingFile = self._getInstSettingFilePath(instSettingFileName)
instFilePath = self.tele.writeStarInstFile(
self.outputDir,
skySim,
simSeed=simSeed,
sedName="sed_flat.txt",
instSettingFile=instSettingFile,
instFileName=instFileName)
# Get the argument to run the PhoSim
argString = self._getPhoSimArgs(logFileName, instFilePath, cmdFilePath)
return argString
def analyzeComCamOpdData(self,
zkFileName="opd.zer",
rotOpdInDeg=0.0,
pssnFileName="PSSN.txt"):
"""Analyze the ComCam OPD data.
Rotate OPD to simulate the output by rotated camera. When anaylzing the
PSSN, the unrotated OPD is used.
ComCam: Commissioning camera.
OPD: Optical path difference.
PSSN: Normalized point source sensitivity.
Parameters
----------
zkFileName : str, optional
OPD in zk file name. (the default is "opd.zer".)
rotOpdInDeg : float, optional
Rotate OPD in degree in the counter-clockwise direction. (the
default is 0.0.)
pssnFileName : str, optional
PSSN file name. (the default is "PSSN.txt".)
"""
self._writeOpdZkFile(zkFileName, rotOpdInDeg)
self._writeOpdPssnFile(pssnFileName)
def _writeOpdZkFile(self, zkFileName, rotOpdInDeg):
"""Write the OPD in zk file.
OPD: optical path difference.
Parameters
----------
zkFileName : str
OPD in zk file name.
rotOpdInDeg : float
Rotate OPD in degree in the counter-clockwise direction.
"""
filePath = os.path.join(self.outputImgDir, zkFileName)
opdData = self._mapOpdToZk(rotOpdInDeg)
header = "The followings are OPD in rotation angle of %.2f degree in um from z4 to z22:" % (
rotOpdInDeg)
np.savetxt(filePath, opdData, header=header)
def _mapOpdToZk(self, rotOpdInDeg):
"""Map the OPD to the basis of annular Zernike polynomial (Zk).
OPD: optical path difference.
Parameters
----------
rotOpdInDeg : float
Rotate OPD in degree in the counter-clockwise direction.
Returns
-------
numpy.ndarray
Zk data from OPD. This is a 2D array. The row is the OPD index and
the column is z4 to z22 in um. The order of OPD index is based on
the file name.
"""
# Get the sorted OPD file list
opdFileList = self._getOpdFileInDir(self.outputImgDir)
# Map the OPD to the Zk basis and do the collection
numOfZk = self.getNumOfZk()
opdData = np.zeros((len(opdFileList), numOfZk))
for idx, opdFile in enumerate(opdFileList):
opd = fits.getdata(opdFile)
# Rotate OPD if needed
if (rotOpdInDeg != 0):
opdRot = ndimage.rotate(opd, rotOpdInDeg, reshape=False)
opdRot[opd == 0] = 0
else:
opdRot = opd
# z1 to z22 (22 terms)
zk = self.metr.getZkFromOpd(opdMap=opdRot)[0]
# Only need to collect z4 to z22
initIdx = 3
opdData[idx, :] = zk[initIdx:initIdx + numOfZk]
return opdData
def _getOpdFileInDir(self, opdDir):
"""Get the sorted OPD files in the directory.
OPD: Optical path difference.
Parameters
----------
opdDir : str
OPD file directory.
Returns
-------
list
List of sorted OPD files.
"""
# Get the files
opdFileList = []
fileList = self._getFileInDir(opdDir)
for file in fileList:
fileName = os.path.basename(file)
m = re.match(r"\Aopd_\d+_(\d+).fits.gz", fileName)
if (m is not None):
opdFileList.append(file)
# Do the sorting of file name
sortedOpdFileList = sortOpdFileList(opdFileList)
return sortedOpdFileList
def _getFileInDir(self, fileDir):
"""Get the files in the directory.
Parameters
----------
fileDir : str
File directory.
Returns
-------
list
List of files.
"""
fileList = []
for name in os.listdir(fileDir):
filePath = os.path.join(fileDir, name)
if os.path.isfile(filePath):
fileList.append(filePath)
return fileList
def _writeOpdPssnFile(self, pssnFileName):
"""Write the OPD PSSN in file.
OPD: Optical path difference.
PSSN: Normalized point source sensitivity.
Parameters
----------
pssnFileName : str
PSSN file name.
"""
filePath = os.path.join(self.outputImgDir, pssnFileName)
# Calculate the PSSN
pssnList, gqEffPssn = self._calcComCamOpdPssn()
# Calculate the FWHM
effFwhmList, gqEffFwhm = self._calcComCamOpdEffFwhm(pssnList)
# Append the list to write the data into file
pssnList.append(gqEffPssn)
effFwhmList.append(gqEffFwhm)
# Stack the data
data = np.vstack((pssnList, effFwhmList))
# Write to file
header = "The followings are PSSN and FWHM (in arcsec) data. The final number is the GQ value."
np.savetxt(filePath, data, header=header)
def _calcComCamOpdPssn(self):
"""Calculate the ComCam PSSN of OPD.
ComCam: Commissioning camera.
OPD: Optical path difference.
PSSN: Normalized point source sensitivity.
GQ: Gaussian quadrature.
Returns
-------
list
PSSN list.
float
GQ effective PSSN.
"""
opdFileList = self._getOpdFileInDir(self.outputImgDir)
wavelengthInUm = self.tele.getRefWaveLength() * 1e-3
pssnList = []
for opdFile in opdFileList:
pssn = self.metr.calcPSSN(wavelengthInUm, opdFitsFile=opdFile)
pssnList.append(pssn)
# Calculate the GQ effectice PSSN
self._setComCamWgtRatio()
gqEffPssn = self.metr.calcGQvalue(pssnList)
return pssnList, gqEffPssn
def _setComCamWgtRatio(self):
"""Set the ComCam weighting ratio.
ComCam: Commissioning camera.
"""
comcamWtRatio = np.ones(9)
self.metr.setWeightingRatio(comcamWtRatio)
def _calcComCamOpdEffFwhm(self, pssnList):
"""Calculate the ComCam effective FWHM of OPD.
ComCam: Commissioning camera.
FWHM: Full width and half maximum.
PSSN: Normalized point source sensitivity.
GQ: Gaussian quadrature.
Parameters
----------
pssnList : list
List of PSSN.
Returns
-------
list
Effective FWHM list.
float
GQ effective FWHM of ComCam.
"""
# Calculate the list of effective FWHM
effFwhmList = []
for pssn in pssnList:
effFwhm = self.metr.calcFWHMeff(pssn)
effFwhmList.append(effFwhm)
# Calculate the GQ effectice FWHM
self._setComCamWgtRatio()
gqEffFwhm = self.metr.calcGQvalue(effFwhmList)
return effFwhmList, gqEffFwhm
def mapOpdDataToListOfWfErr(self, opdZkFileName, refSensorNameList):
"""Map the OPD data to the list of wavefront error.
OPD: Optical path difference.
Parameters
----------
opdZkFileName : str
OPD zk file name.
refSensorNameList : list
Reference sensor name list.
Returns
-------
list [lsst.ts.wep.ctrlIntf.SensorWavefrontError]
List of SensorWavefrontError object.
"""
opdZk = self._getZkFromFile(opdZkFileName)
mapSensorNameAndId = MapSensorNameAndId()
sensorIdList = mapSensorNameAndId.mapSensorNameToId(refSensorNameList)
listOfWfErr = []
for sensorId, zk in zip(sensorIdList, opdZk):
sensorWavefrontData = SensorWavefrontError(
numOfZk=self.getNumOfZk())
sensorWavefrontData.setSensorId(sensorId)
sensorWavefrontData.setAnnularZernikePoly(zk)
listOfWfErr.append(sensorWavefrontData)
return listOfWfErr
def _getZkFromFile(self, zkFileName):
"""Get the zk (z4-z22) from file.
Parameters
----------
zkFileName : str
Zk file name.
Returns
-------
numpy.ndarray
zk matrix. The colunm is z4-z22. The raw is each data point.
"""
filePath = os.path.join(self.outputImgDir, zkFileName)
zk = np.loadtxt(filePath)
return zk
def getOpdPssnFromFile(self, pssnFileName):
"""Get the OPD PSSN from file.
OPD: Optical path difference.
PSSN: Normalized point source sensitivity.
Parameters
----------
pssnFileName : str
PSSN file name.
Returns
-------
numpy.ndarray
PSSN.
"""
data = self._getDataOfPssnFile(pssnFileName)
pssn = data[0, :-1]
return pssn
def _getDataOfPssnFile(self, pssnFileName):
"""Get the data of the PSSN file.
PSSN: Normalized point source sensitivity.
Parameters
----------
pssnFileName : str
PSSN file name.
Returns
-------
numpy.ndarray
Data of the PSSN file.
"""
filePath = os.path.join(self.outputImgDir, pssnFileName)
data = np.loadtxt(filePath)
return data
def getOpdGqEffFwhmFromFile(self, pssnFileName):
"""Get the OPD GQ effective FWHM from file.
OPD: Optical path difference.
GQ: Gaussian quadrature.
FWHM: Full width at half maximum.
PSSN: Normalized point source sensitivity.
Parameters
----------
pssnFileName : str
PSSN file name.
Returns
-------
float
OPD GQ effective FWHM.
"""
data = self._getDataOfPssnFile(pssnFileName)
gqEffFwhm = data[1, -1]
return gqEffFwhm
def getListOfFwhmSensorData(self, pssnFileName, refSensorNameList):
"""Get the list of FWHM sensor data based on the OPD PSSN file.
FWHM: Full width at half maximum.
OPD: Optical path difference.
PSSN: Normalized point source sensitivity.
Parameters
----------
pssnFileName : str
PSSN file name.
refSensorNameList : list
Reference sensor name list.
Returns
-------
list [lsst.ts.ofc.ctrlIntf.FWHMSensorData]
List of FWHMSensorData which contains the sensor Id and FWHM data.
"""
# Get the FWHM data from the PSSN file
# The first row is the PSSN and the second one is the FWHM
# The final element in each row is the GQ value
data = self._getDataOfPssnFile(pssnFileName)
fwhmData = data[1, :-1]
mapSensorNameAndId = MapSensorNameAndId()
sensorIdList = mapSensorNameAndId.mapSensorNameToId(refSensorNameList)
listOfFWHMSensorData = []
for sensorId, fwhm in zip(sensorIdList, fwhmData):
fwhmSensorData = FWHMSensorData(sensorId, np.array([fwhm]))
listOfFWHMSensorData.append(fwhmSensorData)
return listOfFWHMSensorData
def repackageComCamAmpImgFromPhoSim(self):
"""Repackage the ComCam amplifier images from PhoSim to the single 16
extension MEFs for processing.
ComCam: commissioning camera.
MEF: multi-extension frames.
"""
self._repackageComCamImages(isEimg=False)
def _repackageComCamImages(self, isEimg=False):
"""Repackage the ComCam images from PhoSim for processing.
Parameters
----------
isEimg : bool, optional
Is eimage or not. (the default is False.)
"""
# Make a temporary directory
tmpDirPath = os.path.join(self.outputImgDir, "tmp")
self._makeDir(tmpDirPath)
intraFocalDirName = self.getIntraFocalDirName()
extraFocalDirName = self.getExtraFocalDirName()
for imgType in (intraFocalDirName, extraFocalDirName):
# Repackage the images to the temporary directory
command = "phosim_repackager.py"
phosimImgDir = os.path.join(self.outputImgDir, imgType)
argstring = "%s --out_dir=%s" % (phosimImgDir, tmpDirPath)
if (isEimg):
argstring += " --eimage"
runProgram(command, argstring=argstring)
# Remove the image data in the original directory
argString = "-rf %s/*.fits*" % phosimImgDir
runProgram("rm", argstring=argString)
# Put the repackaged data into the image directory
argstring = "%s/*.fits %s" % (tmpDirPath, phosimImgDir)
runProgram("mv", argstring=argstring)
# Remove the temporary directory
shutil.rmtree(tmpDirPath)
def repackageComCamEimgFromPhoSim(self):
"""Repackage the ComCam eimages from PhoSim for processing.
ComCam: commissioning camera.
"""
self._repackageComCamImages(isEimg=True)
def reorderAndSaveWfErrFile(self,
listOfWfErr,
refSensorNameList,
zkFileName="wfs.zer"):
"""Reorder the wavefront error in the wavefront error list according to
the reference sensor name list and save to a file.
The unexisted wavefront error will be a numpy zero array. The unit is
um.
Parameters
----------
listOfWfErr : list [lsst.ts.wep.ctrlIntf.SensorWavefrontData]
List of SensorWavefrontData object.
refSensorNameList : list
Reference sensor name list.
zkFileName : str, optional
Wavefront error file name. (the default is "wfs.zer".)
"""
# Get the sensor name that in the wavefront error map
wfErrMap = self._transListOfWfErrToMap(listOfWfErr)
nameListInWfErrMap = list(wfErrMap.keys())
# Reorder the wavefront error map based on the reference sensor name
# list.
reorderedWfErrMap = dict()
for sensorName in refSensorNameList:
if sensorName in nameListInWfErrMap:
wfErr = wfErrMap[sensorName]
else:
numOfZk = self.getNumOfZk()
wfErr = np.zeros(numOfZk)
reorderedWfErrMap[sensorName] = wfErr
# Save the file
filePath = os.path.join(self.outputImgDir, zkFileName)
wfsData = self._getWfErrValuesAndStackToMatrix(reorderedWfErrMap)
header = "The followings are ZK in um from z4 to z22:"
np.savetxt(filePath, wfsData, header=header)
def _transListOfWfErrToMap(self, listOfWfErr):
"""Transform the list of wavefront error to map.
Parameters
----------
listOfWfErr : list [lsst.ts.wep.ctrlIntf.SensorWavefrontData]
List of SensorWavefrontData object.
Returns
-------
dict
Calculated wavefront error. The dictionary key [str] is the
abbreviated sensor name (e.g. R22_S11). The dictionary item
[numpy.ndarray] is the averaged wavefront error (z4-z22) in um.
"""
mapSensorNameAndId = MapSensorNameAndId()
wfErrMap = dict()
for sensorWavefrontData in listOfWfErr:
sensorId = sensorWavefrontData.getSensorId()
sensorNameList = mapSensorNameAndId.mapSensorIdToName(sensorId)[0]
sensorName = sensorNameList[0]
avgErrInUm = sensorWavefrontData.getAnnularZernikePoly()
wfErrMap[sensorName] = avgErrInUm
return wfErrMap
def _getWfErrValuesAndStackToMatrix(self, wfErrMap):
"""Get the wavefront errors and stack them to be a matrix.
Parameters
----------
wfErrMap : dict
Calculated wavefront error. The dictionary key [str] is the
abbreviated sensor name (e.g. R22_S11). The dictionary item
[numpy.ndarray] is the averaged wavefront error (z4-z22) in um.
Returns
-------
numpy.ndarray
Wavefront errors as a matrix. The column is z4-z22 in um. The row
is the individual sensor. The order is the same as the input of
wfErrMap.
"""
numOfZk = self.getNumOfZk()
valueMatrix = np.empty((0, numOfZk))
for wfErr in wfErrMap.values():
valueMatrix = np.vstack((valueMatrix, wfErr))
return valueMatrix
class TestOpdMetrology(unittest.TestCase):
""" Test the OpdMetrology class."""
def setUp(self):
self.testDataDir = os.path.join(getModulePath(), "tests", "testData",
"testOpdFunc")
self.metr = OpdMetrology()
def testSetWeightingRatio(self):
wt = [1, 2]
self.metr.setWeightingRatio(wt)
self.assertEqual(len(self.metr.wt), len(wt))
self.assertEqual(np.sum(self.metr.wt), 1)
self.assertAlmostEqual(self.metr.wt[1] / self.metr.wt[0], 2)
self.assertRaises(ValueError, self.metr.setWeightingRatio, [-1, 1])
def testSetFieldXYinDeg(self):
fieldXInDegree = 0.1
fieldYInDegree = 0.2
self.metr.setFieldXYinDeg(fieldXInDegree, fieldYInDegree)
self.assertEqual(self.metr.fieldX, fieldXInDegree)
self.assertEqual(self.metr.fieldY, fieldYInDegree)
def testAddFieldXYbyDeg(self):
fieldXInDegree = 0.1
fieldYInDegree = 0.2
self.metr.addFieldXYbyDeg(fieldXInDegree, fieldYInDegree)
self.assertEqual(len(self.metr.fieldX), 1)
self.metr.addFieldXYbyDeg(fieldXInDegree, fieldYInDegree)
self.assertEqual(len(self.metr.fieldX), 2)
def testSetDefaultLsstGQ(self):
self.metr.setDefaultLsstGQ()
self.assertEqual(len(self.metr.fieldX), 31)
def testGetDefaultLsstWfsGQ(self):
fieldWFSx, fieldWFSy = self.metr.getDefaultLsstWfsGQ()
self.assertEqual(len(fieldWFSx), 4)
def testSetDefaultComcamGQ(self):
self.metr.setDefaultComcamGQ()
self.assertEqual(len(self.metr.fieldX), 9)
def testGetZkFromOpd(self):
opdFilePath = self._getOpdFilePath()
zk = self.metr.getZkFromOpd(opdFitsFile=opdFilePath)[0]
ansOpdFileName = "sim6_iter0_opd.zer"
ansOpdFilePath = os.path.join(self.testDataDir, ansOpdFileName)
allOpdAns = np.loadtxt(ansOpdFilePath)
self.assertLess(np.sum(np.abs(zk - allOpdAns[0, :])), 1e-10)
def _getOpdFilePath(self):
opdFileName = "sim6_iter0_opd0.fits.gz"
opdFilePath = os.path.join(self.testDataDir, opdFileName)
return opdFilePath
def testRmPTTfromOPD(self):
opdFilePath = self._getOpdFilePath()
opdRmPTT, opdx, opdy = self.metr.rmPTTfromOPD(opdFitsFile=opdFilePath)
zkRmPTT = self.metr.getZkFromOpd(opdMap=opdRmPTT)[0]
self.assertLess(np.sum(np.abs(zkRmPTT[0:3])), 5e-2)
def testAddFieldXYbyCamPos(self):
sensorName = "R22_S11"
xInpixel = 4000
yInPixel = 4072
self.metr.addFieldXYbyCamPos(sensorName, xInpixel, yInPixel,
self.testDataDir)
ansFieldXinDeg = 2000 * 0.2 / 3600
ansFieldYinDeg = 2036 * 0.2 / 3600
self.assertAlmostEqual((self.metr.fieldX[-1], self.metr.fieldY[-1]),
(ansFieldXinDeg, ansFieldYinDeg))
def calcPSSN(self):
pssn = self._calcPssn()
allData = self._getMetroAllAnsData()
self.assertAlmostEqual(pssn, allData[0, 0])
def _calcPssn(self):
wavelengthInUm = 0.5
opdFilePath = self._getOpdFilePath()
pssn = self.metr.calcPSSN(wavelengthInUm, opdFitsFile=opdFilePath)
return pssn
def _getMetroAllAnsData(self):
ansAllDataFileName = "sim6_iter0_PSSN.txt"
ansAllDataFilePath = os.path.join(self.testDataDir, ansAllDataFileName)
allData = np.loadtxt(ansAllDataFilePath)
return allData
def testCalcFWHMeff(self):
pssn = self._calcPssn()
fwhm = self.metr.calcFWHMeff(pssn)
allData = self._getMetroAllAnsData()
self.assertAlmostEqual(fwhm, allData[1, 0])
def testCalcDm5(self):
pssn = self._calcPssn()
dm5 = self.metr.calcDm5(pssn)
allData = self._getMetroAllAnsData()
self.assertAlmostEqual(dm5, allData[2, 0])
def testCalcEllip(self):
wavelengthInUm = 0.5
opdFilePath = self._getOpdFilePath()
elli = self.metr.calcEllip(wavelengthInUm, opdFitsFile=opdFilePath)
ansElliFileName = "sim6_iter0_elli.txt"
ansElliFilePath = os.path.join(self.testDataDir, ansElliFileName)
allElli = np.loadtxt(ansElliFilePath)
self.assertAlmostEqual(elli, allElli[0])
def testCalcGQvalue(self):
self.metr.setDefaultLsstGQ()
allData = self._getMetroAllAnsData()
valueList = allData[0, 0:31]
GQvalue = self.metr.calcGQvalue(valueList)
self.assertAlmostEqual(GQvalue, allData[0, -1])
class WepPhosimCmpt(object):
NUM_OF_ZK = 19
PISTON_INTRA_DIR_NAME = "intra"
PISTON_EXTRA_DIR_NAME = "extra"
def __init__(self, phosimDir):
"""Initialization of WEP PhoSim component class.
WEP: wavefront estimation pipeline.
Parameters
----------
phosimDir : str
PhoSim directory.
"""
self.metr = OpdMetrology()
self.tele = TeleFacade()
self.outputDir = ""
self.outputImgDir = ""
self.seedNum = 0
self.phosimParam = {"numPro": 1, "e2ADC": 1}
self._config(phosimDir)
def _config(self, phosimDir):
"""Do the configuration of WEP PhoSim component class.
Parameters
----------
phosimDir : str
PhoSim directory.
"""
# Configurate the TeleFacade class
configDataPath = self._getConfigDataPath()
teleConfigFilePath = os.path.join(configDataPath, "telescopeConfig",
"GT.inst")
self.tele.setConfigFile(teleConfigFilePath)
camDataDir = os.path.join(configDataPath, "camera")
M1M3dataDir = os.path.join(configDataPath, "M1M3")
M2dataDir = os.path.join(configDataPath, "M2")
self.tele.setSubSysConfigDir(camDataDir=camDataDir,
M1M3dataDir=M1M3dataDir,
M2dataDir=M2dataDir,
phosimDir=phosimDir)
self.tele.setSensorOn(sciSensorOn=True,
wfSensorOn=False,
guidSensorOn=False)
# The lsst is used here because the obs_lsst only supports the lsst now
self.tele.setInstName("lsst15")
def _getConfigDataPath(self):
"""Get the configuration data path.
Returns
-------
str
Configuration data path
"""
configDataPath = os.path.join(getModulePath(), "configData")
return configDataPath
def getOpdMetr(self):
"""Get the OPD metrology object.
OPD: optical path difference.
Returns
-------
OpdMetrology
OPD metrology object.
"""
return self.metr
def setOutputDir(self, outputDir):
"""Set the output directory.
The output directory will be constructed if there is no existed one.
Parameters
----------
outputDir : str
Output directory.
"""
self._makeDir(outputDir)
self.outputDir = outputDir
def _makeDir(self, newDir, exist_ok=True):
"""Make the new directory.
Super-mkdir; create a leaf directory and all intermediate ones. Works
like mkdir, except that any intermediate path segment (not just the
rightmost) will be created if it does not exist.
Parameters
----------
newDir : str
New directory.
exist_ok : bool, optional
If the target directory already exists, raise an OSError if
exist_ok is False. Otherwise no exception is raised. (the default
is True.)
"""
os.makedirs(newDir, exist_ok=exist_ok)
def getOutputDir(self):
"""Get the output directory.
Returns
-------
str
Output directory.
"""
return self.outputDir
def setOutputImgDir(self, outputImgDir):
"""Set the output image directory.
The output image directory will be constructed if there is no existed
one.
Parameters
----------
outputImgDir : str
Output image directory
"""
self._makeDir(outputImgDir)
self.outputImgDir = outputImgDir
def getOutputImgDir(self):
"""Get the output image directory.
Returns
-------
str
Output image directory
"""
return self.outputImgDir
def setSeedNum(self, seedNum):
"""Set the seed number for the M1M3 mirror surface purturbation.
Parameters
----------
seedNum : int
Seed number.
"""
self.seedNum = int(seedNum)
def getSeedNum(self):
"""Get the seed number for the M1M3 random surface purturbation.
Returns
-------
int or None
Seed number. None means there is no random purturbation.
"""
return self.seedNum
def setPhosimParam(self, numPro=1, e2ADC=1):
"""Set the PhoSim simulation parameters.
Parameters
----------
numPro : int, optional
Number of processors. The value should be greater than 1. (the
default is 1.)
e2ADC : int, optional
Whether to generate amplifier images (1 = true, 0 = false) (the
default is 1.)
"""
if (numPro > 0):
self.phosimParam["numPro"] = int(numPro)
if e2ADC in (0, 1):
self.phosimParam["e2ADC"] = int(e2ADC)
def getPhosimParam(self):
"""Get the PhoSim simulation parameters.
Returns
-------
dict
PhoSim simulation parameters.
"""
return self.phosimParam
def setSurveyParam(self,
obsId=None,
filterType=None,
boresight=None,
zAngleInDeg=None,
rotAngInDeg=None,
mjd=None):
"""Set the survey parameters.
Parameters
----------
obsId : int, optional
Observation Id. (the default is None.)
filterType : FilterType, optional
Active filter type. (the default is None.)
boresight : tuple, optional
Telescope boresight in (ra, decl). (the default is None.)
zAngleInDeg : float, optional
Zenith angle in degree. (the default is None.)
rotAngInDeg : float, optional
Camera rotation angle in degree between -90 and 90 degrees. (the
default is None.)
mjd : float, optional
MJD of observation. (the default is None.)
"""
self.tele.setSurveyParam(obsId=obsId,
filterType=filterType,
boresight=boresight,
zAngleInDeg=zAngleInDeg,
rotAngInDeg=rotAngInDeg,
mjd=mjd)
def addOpdFieldXYbyDeg(self, fieldXInDegree, fieldYInDegree):
"""Add the OPD new field X, Y in degree.
OPD: optical path difference.
Parameters
----------
fieldXInDegree : float, list, or numpy.ndarray
New field X in degree.
fieldYInDegree : float, list, or numpy.ndarray
New field Y in degree.
"""
self.metr.addFieldXYbyDeg(fieldXInDegree, fieldYInDegree)
def accDofInUm(self, dofInUm):
"""Accumulate the aggregated degree of freedom (DOF) in um.
idx 0-4: M2 dz, dx, dy, rx, ry
idx 5-9: Cam dz, dx, dy, rx, ry
idx 10-29: M1M3 20 bending modes
idx 30-49: M2 20 bending modes
Parameters
----------
dofInUm : list or numpy.ndarray
DOF in um.
"""
self.tele.accDofInUm(dofInUm)
def setDofInUm(self, dofInUm):
"""Set the accumulated degree of freedom (DOF) in um.
idx 0-4: M2 dz, dx, dy, rx, ry
idx 5-9: Cam dz, dx, dy, rx, ry
idx 10-29: M1M3 20 bending modes
idx 30-49: M2 20 bending modes
Parameters
----------
dofInUm : list or numpy.ndarray
DOF in um.
"""
self.tele.setDofInUm(dofInUm)
def getDofInUm(self):
"""Get the accumulated degree of freedom (DOF) in um.
idx 0-4: M2 dz, dx, dy, rx, ry
idx 5-9: Cam dz, dx, dy, rx, ry
idx 10-29: M1M3 20 bending modes
idx 30-49: M2 20 bending modes
Returns
-------
numpy.ndarray
DOF in um.
"""
return self.tele.dofInUm
def saveDofInUmFileForNextIter(self,
dofInUm,
dofInUmFileName="dofPertInNextIter.mat"):
"""Save the DOF in um data to file for the next iteration.
DOF: degree of freedom.
Parameters
----------
dofInUm : list or numpy.ndarray
DOF in um.
dofInUmFileName : str, optional
File name to save the DOF in um. (the default is
"dofPertInNextIter.mat".)
"""
filePath = os.path.join(self.outputDir, dofInUmFileName)
header = "The followings are the DOF in um:"
np.savetxt(filePath, np.transpose(dofInUm), header=header)
def runPhoSim(self, argString):
"""Run the PhoSim program.
Parameters
----------
argString : str
Arguments for PhoSim.
"""
self.tele.runPhoSim(argString)
def getComCamOpdArgsAndFilesForPhoSim(
self,
cmdFileName="opd.cmd",
instFileName="opd.inst",
logFileName="opdPhoSim.log",
cmdSettingFileName="opdDefault.cmd",
instSettingFileName="opdDefault.inst"):
"""Get the OPD calculation arguments and files of ComCam for the PhoSim
calculation.
OPD: optical path difference.
ComCam: commissioning camera.
Parameters
----------
cmdFileName : str, optional
Physical command file name. (the default is "opd.cmd".)
instFileName : str, optional
OPD instance file name. (the default is "opd.inst".)
logFileName : str, optional
Log file name. (the default is "opdPhoSim.log".)
cmdSettingFileName : str, optional
Physical command setting file name. (the default is
"opdDefault.cmd".)
instSettingFileName : str, optional
Instance setting file name. (the default is "opdDefault.inst".)
Returns
-------
str
Arguments to run the PhoSim.
"""
# Set the default ComCam OPD field positions
self.metr.setDefaultComcamGQ()
argString = self._getOpdArgsAndFilesForPhoSim(
cmdFileName=cmdFileName,
instFileName=instFileName,
logFileName=logFileName,
cmdSettingFileName=cmdSettingFileName,
instSettingFileName=instSettingFileName)
return argString
def _getOpdArgsAndFilesForPhoSim(self,
cmdFileName="opd.cmd",
instFileName="opd.inst",
logFileName="opdPhoSim.log",
cmdSettingFileName="opdDefault.cmd",
instSettingFileName="opdDefault.inst"):
"""Get the OPD calculation arguments and files for the PhoSim
calculation.
OPD: optical path difference.
Parameters
----------
cmdFileName : str, optional
Physical command file name. (the default is "opd.cmd".)
instFileName : str, optional
OPD instance file name. (the default is "opd.inst".)
logFileName : str, optional
Log file name. (the default is "opdPhoSim.log".)
cmdSettingFileName : str, optional
Physical command setting file name. (the default is
"opdDefault.cmd".)
instSettingFileName : str, optional
Instance setting file name. (the default is "opdDefault.inst".)
Returns
-------
str
Arguments to run the PhoSim.
"""
# Write the command file
cmdFilePath = self._writePertAndCmdFiles(cmdSettingFileName,
cmdFileName)
# Write the instance file
instSettingFile = self._getInstSettingFilePath(instSettingFileName)
instFilePath = self.tele.writeOpdInstFile(
self.outputDir,
self.metr,
instSettingFile=instSettingFile,
instFileName=instFileName)
# Get the argument to run the PhoSim
argString = self._getPhoSimArgs(logFileName, instFilePath, cmdFilePath)
return argString
def _writePertAndCmdFiles(self, cmdSettingFileName, cmdFileName):
"""Write the physical perturbation and command files.
Parameters
----------
cmdSettingFileName : str
Physical command setting file name.
cmdFileName : str
Physical command file name.
Returns
-------
str
Command file path.
"""
# Write the perturbation file
pertCmdFileName = "pert.cmd"
pertCmdFilePath = os.path.join(self.outputDir, pertCmdFileName)
if (not os.path.exists(pertCmdFilePath)):
self.tele.writePertBaseOnConfigFile(
self.outputDir,
seedNum=self.seedNum,
saveResMapFig=True,
pertCmdFileName=pertCmdFileName)
# Write the physical command file
configDataPath = self._getConfigDataPath()
cmdSettingFile = os.path.join(configDataPath, "cmdFile",
cmdSettingFileName)
cmdFilePath = os.path.join(self.outputDir, cmdFileName)
if (not os.path.exists(cmdFilePath)):
self.tele.writeCmdFile(self.outputDir,
cmdSettingFile=cmdSettingFile,
pertFilePath=pertCmdFilePath,
cmdFileName=cmdFileName)
return cmdFilePath
def _getInstSettingFilePath(self, instSettingFileName):
"""Get the instance setting file path.
Parameters
----------
instSettingFileName : str
Instance setting file name.
Returns
-------
str
Instance setting file path.
"""
configDataPath = self._getConfigDataPath()
instSettingFile = os.path.join(configDataPath, "instFile",
instSettingFileName)
return instSettingFile
def _getPhoSimArgs(self, logFileName, instFilePath, cmdFilePath):
"""Get the arguments needed to run the PhoSim.
Parameters
----------
logFileName : str
Log file name.
instFilePath: str
Instance file path.
cmdFilePath : str
Physical command file path.
Returns
-------
str
Arguments to run the PhoSim.
"""
numPro = self.phosimParam["numPro"]
e2ADC = self.phosimParam["e2ADC"]
logFilePath = os.path.join(self.outputImgDir, logFileName)
argString = self.tele.getPhoSimArgs(instFilePath,
extraCommandFile=cmdFilePath,
numPro=numPro,
outputDir=self.outputImgDir,
e2ADC=e2ADC,
logFilePath=logFilePath)
return argString
def getComCamStarArgsAndFilesForPhoSim(
self,
extraObsId,
intraObsId,
skySim,
simSeed=1000,
cmdSettingFileName="starDefault.cmd",
instSettingFileName="starSingleExp.inst"):
"""Get the star calculation arguments and files of ComCam for the PhoSim
calculation.
Parameters
----------
extraObsId : int
Extra-focal observation Id.
intraObsId : int
Intra-focal observation Id.
skySim : SkySim
Sky simulator
simSeed : int, optional
Random number seed. (the default is 1000.)
cmdSettingFileName : str, optional
Physical command setting file name. (the default is
"starDefault.cmd".)
instSettingFileName : {str}, optional
Instance setting file name. (the default is "starSingleExp.inst".)
Returns
-------
list[str]
List of arguments to run the PhoSim.
"""
# Set the intra- and extra-focal related information
obsIdList = {"-1": extraObsId, "1": intraObsId}
instFileNameList = {"-1": "starExtra.inst", "1": "starIntra.inst"}
logFileNameList = {
"-1": "starExtraPhoSim.log",
"1": "starIntraPhoSim.log"
}
outImgDirNameList = {
"-1": self.PISTON_EXTRA_DIR_NAME,
"1": self.PISTON_INTRA_DIR_NAME
}
# Write the instance and command files of defocal conditions
cmdFileName = "star.cmd"
onFocalDofInUm = self.getDofInUm()
onFocalOutputImgDir = self.outputImgDir
argStringList = []
for ii in (-1, 1):
# Set the observation ID
self.setSurveyParam(obsId=obsIdList[str(ii)])
# Camera piston (Change the unit from mm to um)
pistonInUm = np.zeros(len(onFocalDofInUm))
pistonInUm[5] = ii * self.tele.getDefocalDisInMm() * 1e3
# Set the new DOF that considers the piston motion
self.setDofInUm(onFocalDofInUm + pistonInUm)
# Update the output image directory
outputImgDir = os.path.join(onFocalOutputImgDir,
outImgDirNameList[str(ii)])
self.setOutputImgDir(outputImgDir)
# Get the argument to run the phosim
argString = self.getStarArgsAndFilesForPhoSim(
skySim,
cmdFileName=cmdFileName,
instFileName=instFileNameList[str(ii)],
logFileName=logFileNameList[str(ii)],
simSeed=simSeed,
cmdSettingFileName=cmdSettingFileName,
instSettingFileName=instSettingFileName)
argStringList.append(argString)
# Put the internal state back to the focal plane condition
self.setDofInUm(onFocalDofInUm)
self.setOutputImgDir(onFocalOutputImgDir)
return argStringList
def getStarArgsAndFilesForPhoSim(self,
skySim,
cmdFileName="star.cmd",
instFileName="star.inst",
logFileName="starPhoSim.log",
simSeed=1000,
cmdSettingFileName="starDefault.cmd",
instSettingFileName="starSingleExp.inst"):
"""Get the star calculation arguments and files for the PhoSim
calculation.
Parameters
----------
skySim : SkySim
Sky simulator
cmdFileName : str, optional
Physical command file name. (the default is "star.cmd".)
instFileName : str, optional
Star instance file name. (the default is "star.inst".)
logFileName : str, optional
Log file name. (the default is "starPhoSim.log".)
simSeed : int, optional
Random number seed. (the default is 1000)
cmdSettingFileName : str, optional
Physical command setting file name. (the default is
"starDefault.cmd".)
instSettingFileName : str, optional
Instance setting file name. (the default is "starSingleExp.inst".)
Returns
-------
str
Arguments to run the PhoSim.
"""
# Write the command file
cmdFilePath = self._writePertAndCmdFiles(cmdSettingFileName,
cmdFileName)
# Write the instance file
instSettingFile = self._getInstSettingFilePath(instSettingFileName)
instFilePath = self.tele.writeStarInstFile(
self.outputDir,
skySim,
simSeed=simSeed,
sedName="sed_flat.txt",
instSettingFile=instSettingFile,
instFileName=instFileName)
# Get the argument to run the PhoSim
argString = self._getPhoSimArgs(logFileName, instFilePath, cmdFilePath)
return argString
def analyzeComCamOpdData(self,
zkFileName="opd.zer",
pssnFileName="PSSN.txt"):
"""Analyze the ComCam OPD data.
ComCam: Commissioning camera.
OPD: optical path difference.
PSSN: normalized point source sensitivity.
Parameters
----------
zkFileName : str, optional
OPD in zk file name. (the default is "opd.zer".)
pssnFileName : str, optional
PSSN file name. (the default is "PSSN.txt".)
"""
self._writeOpdZkFile(zkFileName)
self._writeOpdPssnFile(pssnFileName)
def _writeOpdZkFile(self, zkFileName):
"""Write the OPD in zk file.
OPD: optical path difference.
Parameters
----------
zkFileName : str
OPD in zk file name.
"""
filePath = os.path.join(self.outputImgDir, zkFileName)
opdData = self._mapOpdToZk()
header = "The followings are OPD in um from z4 to z22:"
np.savetxt(filePath, opdData, header=header)
def _mapOpdToZk(self):
"""Map the OPD to the basis of annular Zernike polynomial (Zk).
OPD: optical path difference.
Returns
-------
numpy.ndarray
Zk data from OPD. This is a 2D array. The row is the OPD index and
the column is z4 to z22 in um. The order of OPD index is based on
the file name.
"""
# Get the OPD file list
opdFileList = self._getOpdFileInDir(self.outputImgDir)
# Map the OPD to the Zk basis and do the collection
opdData = np.zeros((len(opdFileList), self.NUM_OF_ZK))
for idx, opdFile in enumerate(opdFileList):
# z1 to z22 (22 terms)
zk = self.metr.getZkFromOpd(opdFitsFile=opdFile)[0]
# Only need to collect z4 to z22
initIdx = 3
opdData[idx, :] = zk[initIdx:initIdx + self.NUM_OF_ZK]
return opdData
def _writeOpdPssnFile(self, pssnFileName):
"""Write the OPD PSSN in file.
OPD: optical path difference.
PSSN: normalized point source sensitivity.
Parameters
----------
pssnFileName : str
PSSN file name.
"""
filePath = os.path.join(self.outputImgDir, pssnFileName)
# Calculate the PSSN
pssnList, gqEffPssn = self._calcComCamOpdPssn()
# Calculate the FWHM
effFwhmList, gqEffFwhm = self._calcComCamOpdEffFwhm(pssnList)
# Append the list to write the data into file
pssnList.append(gqEffPssn)
effFwhmList.append(gqEffFwhm)
# Stack the data
data = np.vstack((pssnList, effFwhmList))
# Write to file
header = "The followings are PSSN and FWHM (in arcsec) data. The final number is the GQ value."
np.savetxt(filePath, data, header=header)
def _calcComCamOpdPssn(self):
"""Calculate the ComCam PSSN of OPD.
ComCam: commissioning camera.
OPD: optical path difference.
PSSN: normalized point source sensitivity.
GQ: gaussian quadrature.
Returns
-------
list
PSSN list.
float
GQ effective PSSN.
"""
opdFileList = self._getOpdFileInDir(self.outputImgDir)
wavelengthInUm = self.tele.WAVELENGTH_IN_NM * 1e-3
pssnList = []
for opdFile in opdFileList:
pssn = self.metr.calcPSSN(wavelengthInUm, opdFitsFile=opdFile)
pssnList.append(pssn)
# Calculate the GQ effectice PSSN
self._setComCamWgtRatio()
gqEffPssn = self.metr.calcGQvalue(pssnList)
return pssnList, gqEffPssn
def _getOpdFileInDir(self, opdDir):
"""Get the OPD files in the directory.
OPD: optical path difference.
Parameters
----------
opdDir : str
OPD file directory.
Returns
-------
list
List of OPD files.
"""
opdFileList = []
fileList = self._getFileInDir(opdDir)
for file in fileList:
fileName = os.path.basename(file)
m = re.match(r"\Aopd_\d+_(\d+).fits.gz", fileName)
if (m is not None):
opdFileList.append(file)
return opdFileList
def _getFileInDir(self, fileDir):
"""Get the files in the directory.
Parameters
----------
fileDir : str
File directory.
Returns
-------
list
List of files.
"""
fileList = []
for name in os.listdir(fileDir):
filePath = os.path.join(fileDir, name)
if os.path.isfile(filePath):
fileList.append(filePath)
return fileList
def _setComCamWgtRatio(self):
"""Set the ComCam weighting ratio.
ComCam: Commissioning camera.
"""
comcamWtRatio = np.ones(9)
self.metr.setWeightingRatio(comcamWtRatio)
def _calcComCamOpdEffFwhm(self, pssnList):
"""Calculate the ComCam effective FWHM of OPD.
ComCam: commissioning camera.
FWHM: full width and half maximum.
PSSN: normalized point source sensitivity.
GQ: Gaussian quadrature.
Parameters
----------
pssnList : list
List of PSSN.
Returns
-------
list
Effective FWHM list.
float
GQ effective FWHM of ComCam.
"""
# Calculate the list of effective FWHM
effFwhmList = []
for pssn in pssnList:
effFwhm = self.metr.calcFWHMeff(pssn)
effFwhmList.append(effFwhm)
# Calculate the GQ effectice FWHM
self._setComCamWgtRatio()
gqEffFwhm = self.metr.calcGQvalue(effFwhmList)
return effFwhmList, gqEffFwhm
def getZkFromFile(self, zkFileName):
"""Get the zk (z4-z22) from file.
Parameters
----------
zkFileName : str
Zk file name.
Returns
-------
numpy.ndarray
zk matrix. The colunm is z4-z22. The raw is each data point.
"""
filePath = os.path.join(self.outputImgDir, zkFileName)
zk = np.loadtxt(filePath)
return zk
def getOpdPssnFromFile(self, pssnFileName):
"""Get the OPD PSSN from file.
OPD: optical path difference.
PSSN: normalized point source sensitivity.
Parameters
----------
pssnFileName : str
PSSN file name.
Returns
-------
numpy.ndarray
PSSN.
"""
data = self._getDataOfPssnFile(pssnFileName)
pssn = data[0, :-1]
return pssn
def getOpdGqEffFwhmFromFile(self, pssnFileName):
"""Get the OPD GQ effective FWHM from file.
OPD: optical path difference.
GQ: Gaussian quadrature.
FWHM: full width at half maximum.
PSSN: normalized point source sensitivity.
Parameters
----------
pssnFileName : str
PSSN file name.
Returns
-------
float
OPD GQ effective FWHM.
"""
data = self._getDataOfPssnFile(pssnFileName)
gqEffFwhm = data[1, -1]
return gqEffFwhm
def _getDataOfPssnFile(self, pssnFileName):
"""Get the data of the PSSN file.
PSSN: Normalized point source sensitivity.
Parameters
----------
pssnFileName : str
PSSN file name.
Returns
-------
numpy.ndarray
Data of the PSSN file.
"""
filePath = os.path.join(self.outputImgDir, pssnFileName)
data = np.loadtxt(filePath)
return data
def repackageComCamImgFromPhoSim(self):
"""Repackage the ComCam amplifier images from PhoSim to the single 16
extension MEFs for processing.
ComCam: commissioning camera.
MEF: multi-extension frames.
"""
# Make a temp directory
tmpDirPath = os.path.join(self.outputImgDir, "tmp")
self._makeDir(tmpDirPath)
for imgType in (self.PISTON_INTRA_DIR_NAME,
self.PISTON_EXTRA_DIR_NAME):
# Repackage the images to that temp directory
command = "phosim_repackager.py"
phosimAmgImgDir = os.path.join(self.outputImgDir, imgType)
argstring = "%s --out_dir=%s" % (phosimAmgImgDir, tmpDirPath)
runProgram(command, argstring=argstring)
# Remove the image data in the original directory
argString = "-rf %s/lsst_a_*.fits.gz" % phosimAmgImgDir
runProgram("rm", argstring=argString)
# Put the repackaged data into the image directory
argstring = "%s/*.fits %s" % (tmpDirPath, phosimAmgImgDir)
runProgram("mv", argstring=argstring)
# Remove the temp directory
shutil.rmtree(tmpDirPath)
def reorderAndSaveWfErrFile(self,
wfErrMap,
refSensorNameList,
zkFileName="wfs.zer"):
"""Reorder the wavefront error in the wavefront error map according to
the reference sensor name list and save to a file.
The unexisted wavefront error will be a numpy zero array. The unit is
um.
Parameters
----------
wfErrMap : dict
Calculated wavefront error. The dictionary key [str] is the
abbreviated sensor name (e.g. R22_S11). The dictionary item
[numpy.ndarray] is the averaged wavefront error (z4-z22) in nm.
refSensorNameList : list
Reference sensor name list
zkFileName : str, optional
Wavefront error file name. (the default is "wfs.zer".)
"""
# Get the sensor name that in the wavefront error map
nameListInWfErrMap = list(wfErrMap.keys())
# Reorder the wavefront error map based on the reference sensor name
# list. The wavefront error unit will change from nm to um.
reorderedWfErrMap = dict()
for sensorName in refSensorNameList:
if sensorName in nameListInWfErrMap:
# Change the unit from nm to um
wfErr = wfErrMap[sensorName] * 1e-3
else:
wfErr = np.zeros(self.NUM_OF_ZK)
reorderedWfErrMap[sensorName] = wfErr
# Save the file
filePath = os.path.join(self.outputImgDir, zkFileName)
wfsData = self.getWfErrValuesAndStackToMatrix(reorderedWfErrMap)
header = "The followings are ZK in um from z4 to z22:"
np.savetxt(filePath, wfsData, header=header)
def getWfErrValuesAndStackToMatrix(self, wfErrMap):
"""Get the wavefront errors and stack them to be a matrix.
Parameters
----------
wfErrMap : dict
Calculated wavefront error. The dictionary key [str] is the
abbreviated sensor name (e.g. R22_S11). The dictionary item
[numpy.ndarray] is the averaged wavefront error (z4-z22) in nm.
Returns
-------
numpy.ndarray
Wavefront errors as a matrix. The column is z4-z22 in nm. The row is
the individual sensor. The order is the same as the input of
wfErrMap.
"""
valueMatrix = np.empty((0, self.NUM_OF_ZK))
for wfErr in wfErrMap.values():
valueMatrix = np.vstack((valueMatrix, wfErr))
return valueMatrix