def __init__(self, imList, target="", steps={}, rawPath="./", calPath="", \
mdf="", biasIm="", flatList="", arcDir="", arcList="", sFunc="", \
logRoot=""):
self.target = target
self.steps = steps
self.rawPath = rawPath
self.calPath = calPath
self.bias = self.calPath + biasIm
self.mdf = mdf
self.imList = imList
self.arcDir = arcDir
self.arcList = arcList
if len(flatList) > 0:
self.flats = utils.getImPaths(flatList)
self.sFunc = self.calPath + sFunc
self.logRoot = logRoot
return
def checkMDF(self, rawMDF, flatList, **kwargs):
# copy raw MDF to local directory
mdf = rawMDF
if not os.path.exists(mdf):
print "\nFETCHING RAW MDF"
mdfPath = "/Users/roedigerj/anaconda/envs/astroconda/iraf_extern/gemini/gmos/data/"
rawMDF = mdfPath + rawMDF
shutil.copy(rawMDF, "./")
# TODO: check that flatList is not empty
# grab the name of a single flat to reduce
im = utils.getImPaths(flatList)[0]
print "\nCHECKING MDF WITH " + im
# repeat the following steps until the MDF deemed correct
while True:
# do basic reduction of selected exposure
_ = self.reduceIm(im, fl_inter="no", fl_gscrrej="no", \
fl_extract="no", fl_wavtran="no", fl_skysub="no", \
fl_fluxcal="no", mdffile=mdf, mdfdir="./", verbose="no", \
**kwargs)
# extract spectrum to check match between MDF and IFU flat
logFile = ""
if "logfile" in kwargs.keys():
logFile = kwargs["logfile"]
iraf.delete("database/aperg" + im[:im.find(".")] + "*",
verify="yes")
self.extractSpec("rg" + im, fl_inter="yes", logfile=logFile, \
verbose="no")
# TODO: remove any extracted files
# call tcalc to fix MDF (if necessary)
fixMDF = bool(input("\nDoes MDF need fixing? (True/False): "))
if fixMDF:
fiber = input("Fiber to fix: ")
flag = input("Flag value: ")
iraf.tcalc(
mdf, "BEAM", "if NO == " + str(fiber) + "then " +
str(flag) + " else BEAM")
else:
break
return
def stackCubes(self, cubeList, **kwargs):
outCube = self.target + "_finalCube.fits"
# extract filenames of individual data cubes
cubePaths = utils.getImPaths(cubeList)
cubes = ", ".join(cubePaths)
print "\nCOMBINING DATA CUBES: " + cubes
# make work directory and copy images there
cmd = "mkdir -v scratch/"
os.system(cmd)
for i, cube in enumerate(cubePaths):
cmd = "cp -v " + cube + " scratch/"
os.system(cmd)
cubePaths[i] = "scratch/" + cube
# update the WCS header cards of the cubes to their centroids
# TODO: allow for lower pixel limit?
# TODO: put calls to pyfalign and pyfmosaic into iterative loop?
pyfu.pyfalign(cubePaths, method="centroid", llimit=0)
# resample and align the cubes without stacking them
# TODO: add line below to view alignment
iraf.imdelete("scratch/separatedCubes.fits")
pyfu.pyfmosaic(cubePaths,
"scratch/separatedCubes.fits",
separate="yes")
# stack the aligned cubes and view the result
# (both as white-light image and slow-paced movie)
iraf.imdelete(outCube)
pyfu.pyfmosaic(cubePaths, outCube, propvar="yes")
self.viewWhiteIm(outCube)
time.sleep(30)
self.viewCubeMov(outCube)
# remove work directory and its contents
cmd = "rm scratch/*.fits"
os.system(cmd)
cmd = "rmdir scratch/"
os.system(cmd)
return
def run(self):
imPaths = utils.getImPaths(self.imList)
for i, im in enumerate(imPaths):
# attach MDF, subtract the bias+overscan, and trim the overscan
if self.steps["reduceIm"]:
logFile = self.logRoot + "_reduceIm.log"
# TODO: remove hard-coding of slits and mdfdir parms
self.reduceIm(im, rawpath=self.rawPath, slits="both", \
fl_over="yes", fl_trim="yes", fl_gscrrej="no", \
fl_wavtran="no", fl_skysub="no", fl_extract="no", \
fl_fluxcal="no", fl_inter="no", fl_vardq="yes", \
bias=self.bias, mdffile=self.mdf, mdfdir="./", \
logfile=logFile, verbose="no")
# model and subtract the scattered light
if self.steps["subScatLgt"]:
self.subScatLgt("rg" + im, self.calPath + "blkMask_" + \
self.flats[i], prefix = "b", fl_inter="yes", cross="yes")
# clean the cosmic rays
if self.steps["cleanCosRays"]:
logFile = self.logRoot + "_cleanCosRays.log"
self.cleanCosRays("brg" + im, fl_vardq="yes", xorder=9, \
yorder=-1, sigclip=4.5, sigfrac=0.5, objlim=1.0, niter=4, \
key_ron="RDNOISE", key_gain="GAIN", logfile=logFile, \
verbose="no")
# correct for QE changes
if self.steps["correctQE"]:
logFile = self.logRoot + "_correctQE.log"
# retrieve arc of matching central wavelength
arc = utils.matchCentWave(im, self.rawPath, self.arcList,
"arc/")
refIm = "erg" + arc
os.system("mv " + self.calPath + refIm + " ./")
self.correctQE("xbrg" + im, refimages=refIm, fl_correct="yes", \
fl_vardq="yes", logfile=logFile, verbose="no")
# return arc from whence it came
os.system("mv " + refIm + " " + self.calPath)
# extract the spectra
if self.steps["extractSpec"]:
logFile = self.logRoot + "_extractSpec.log"
# retrieve flat of matching central wavelength
# TODO: set flat through call to matchCentWave?
flat = self.flats[i]
refIm = "eqbrg" + flat
os.system("mv " + self.calPath + refIm + " ./")
respIm = self.calPath + flat[:flat.find(".")] + "_resp.fits"
self.extractSpec("qxbrg" + im, reference=refIm, \
response=respIm, fl_inter="no", fl_vardq="yes", \
recenter="no", trace="no", weights="none", logfile=logFile, \
verbose="no")
# return flat from whence it came
os.system("mv " + refIm + " " + self.calPath)
# TODO: place this in extractSpec
# view extracted spectra in detector plane
#for j in range(1, 3):
# print "\nDISPLAYING eqxbrg" + im + "[SCI," + str(j) + "]"
# iraf.display("eqxbrg" + im + "[SCI," + str(j) + "]")
# continue
# adjust the mask to cover cosmetics
if self.steps["maskSpec"]:
hdu = fits.open("eqxbrg" + im)
# create a separate mask for each science extension
for j in range(1, hdu[-1].header["EXTVER"] + 1):
txtMask = "mask_" + im[:im.find(".")] + "_" + str(
j) + ".txt"
ext = "[SCI," + str(j) + "]"
self.adjustDQ("eqxbrg" + im, ext, txtMask)
# rectify the extracted spectra
if self.steps["rectifySpec"]:
logFile = self.logRoot + "_rectifySpec.log"
# retrieve arc of matching central wavelength
arc = utils.matchCentWave(im, self.rawPath, self.arcList,
"arc/")
refIm = "erg" + arc
os.system("mv " + self.calPath + refIm + " ./")
# use first spectra to inform choice of final wavelength sampling
print "\nRECTIFYING SPECTRA IN", "xeqxbrg" + im
if i == 0:
self.rectifySpec("xeqxbrg" + im, wavtraname=refIm, \
fl_vardq="no", dw="INDEF", logfile=logFile, verbose="no")
dw = input("\nDesired wavelength sampling: ")
self.rectifySpec("xeqxbrg" + im, wavtraname=refIm, \
fl_vardq="yes", dw=dw, logfile=logFile, verbose="no")
# return arc from whence it came
os.system("mv " + refIm + " " + self.calPath)
# subtract the sky from the object fibers
if self.steps["subSky"]:
logFile = self.logRoot + "_subSky.log"
self.subSky("txeqxbrg" + im, fl_inter="no", logfile=logFile, \
verbose="no")
# flux calibrate the spectra
if self.steps["calibFlux"]:
logFile = self.logRoot + "_calibFlux.log"
self.calibFlux("stxeqxbrg" + im, fl_vardq="yes", fl_ext="yes", \
logfile=logFile, verbose="no")
# resample the data cube
if self.steps["resampCube"]:
logFile = self.logRoot + "_resampCube.log"
self.resampCube("cstxeqxbrg" + im, fl_atmdisp="yes", \
fl_var="yes", fl_dq="yes", logfile=logFile)
continue
# stack data cubes
if self.steps["stackCubes"]:
logFile = self.logRoot + "_stackCubes.log"
# make list of data cubes
cubeList = "cubeFiles.txt"
cmd = "ls dcstxeqxbrg* > " + cubeList
os.system(cmd)
# combine data cubes
self.stackCubes(cubeList)
# remove list
cmd = "rm -v " + cubeList
os.system(cmd)
return
def run(self):
# view bias exposures
#utils.viewIms(self.biasList, sat="yes")
# produce master bias
logFile = "v1895_reduceBias.log"
masterBias = "v1895_masterBias.fits"
#self.reduceBias(self.biasList, masterBias, rawpath="bias/", \
# fl_inter="no", fl_vardq="yes", logfile=logFile, verbose="no")
#util.viewIm(masterBias)
# view flat exposures
#utils.viewIms(self.flatList, sat="yes")
# check MDF (and modify, if necessary)
rawMDF = "gsifu_slits_mdf.fits"
logFile = "v1895_checkMDF.log"
#self.checkMDF(rawMDF, self.flatList, slits="both", rawpath="flat/", \
# bias=masterBias, logfile=logFile)
# create fiber trace reference (for each central wavelength)
# TODO: replace two calls to reduceIm with single call to reduceFlats
mdf = "gsifu_slits_mdf.fits"
logFile = "v1895_fiberTrace.log"
rawFlat = "S20080405S0066"
#v1895_cal.reduceIm(rawFlat, slits="both", rawpath="flat/", \
# fl_gscrrej="no", fl_wavtran="no", fl_skysub="no", fl_fluxcal="no", \
# fl_inter="no", fl_vardq="yes", mdffile=mdf, mdfdir="./", \
# bias=masterBias, logfile=logFile, verbose="no")
rawFlat = "S20080405S0070"
#v1895_cal.reduceIm(rawFlat, slits="both", rawpath="flat/", \
# fl_gscrrej="no", fl_wavtran="no", fl_skysub="no", fl_fluxcal="no", \
# fl_inter="no", fl_vardq="yes", mdffile=mdf, mdfdir="./", \
# bias=masterBias, logfile=logFile, verbose="no")
# determine wavelength solution for each central wavelength
logFile = "v1895_waveCal.log"
arcs = ["S20080405S0109", "S20080405S0110"]
extFlats = ["ergS20080405S0066", "ergS20080405S0070"]
for i in range(2):
#_ = v1895_cal.reduceIm(arcs[i], slits="both", rawpath="arc/", \
# fl_bias="no", fl_gscrrej="no", fl_wavtran="no", fl_skysub="no", \
# fl_fluxcal="no", fl_inter="no", mdffile=mdf, mdfdir="./", \
# reference=extFlats[i], recenter="no", trace="no", \
# logfile=logFile, verbose="no")
continue
arcList = "@arcFiles.txt"
#v1895_cal.calWave("erg" + arcList, coordlist="gmos$data/GCALcuar.dat", \
# fl_inter="yes", threshold=25., nlost=10, ntarget=15, \
# logfile=logFile, verbose="no")
# reduce the lamp flat (incl. removal of scattered light and QE correction)
logFile = "v1895_subScat.log"
#v1895_cal.reduceFlats(self.flatList, subscat="yes", rawpath="flat/", \
# slits="both", fl_gscrrej="no", fl_wavtran="no", fl_skysub="no", \
# fl_fluxcal="no", fl_inter="no", fl_vardq="yes", mdffile=mdf, \
# mdfdir="./", bias=masterBias, logfile=logFile, verbose="no")
# TODO: replace loop with call to reduceFlats
arc = "S20080405S0109"
imList = "flatFiles_473.txt"
logFile = "v1895_corrQE.log"
imPaths = utils.getImPaths(imList)
for im in imPaths:
#v1895_cal.reduceIm("brg" + im, slits="both", fl_addmdf="no", \
# fl_bias="no", fl_over="no", fl_trim="no", fl_qecorr="yes", \
# fl_gscrrej="no", fl_wavtran="no", fl_skysub="no", \
# fl_extract="yes", fl_fluxcal="no", fl_inter="no", \
# fl_vardq="yes", qe_refim="erg" + arc, mdffile=mdf, mdfdir='./', \
# logfile=logFile, verbose="no")
#v1895_cal.viewCube("eqbrg" + im)
continue
# TODO: replace loop with call to reduceFlats
arc = "S20080405S0110"
imList = "flatFiles_478.txt"
imPaths = utils.getImPaths(imList)
for im in imPaths:
#v1895_cal.reduceIm("brg" + im, slits="both", fl_addmdf="no", \
# fl_bias="no", fl_over="no", fl_trim="no", fl_qecorr="yes", \
# fl_gscrrej="no", fl_wavtran="no", fl_skysub="no", \
# fl_extract="yes", fl_fluxcal="no", fl_inter="no", \
# fl_vardq="yes", qe_refim="erg" + arc, mdffile=mdf, mdfdir='./', \
# logfile=logFile, verbose="no")
#v1895_cal.viewCube("eqbrg" + im)
continue
# calculate response function for each flat exposure
imList = "flatFiles.txt"
logFile = "v1895_respFunc.log"
imPaths = utils.getImPaths(imList)
for im in imPaths:
v1895_cal.compResp("eqbrg" + im, skyimage="", fl_inter="no", \
fl_fit="yes", function="spline3", order=45, sample="*", \
logfile=logFile, verbose="no")
continue
return
def reduceFlats(self, flatList, inPref="", arcList="", arcPath="", \
subscat="no", **kwargs):
print "\nREDUCING FLATS"
# retrieve filenames of individual exposures
flatPaths = utils.getImPaths(flatList)
# process flats one at a time
for flat in flatPaths:
# make additional preparations if QE correction requested
if "fl_qecorr" in kwargs.keys() and kwargs["fl_qecorr"] == "yes":
# move extracted arcs to working directory
refIm = "erg" + utils.matchCentWave(inPref + flat, "./", \
arcList, "arc/")
os.system("mv " + arcPath + refIm + " ./")
# add reference image to kwargs
kwargs["qe_refim"] = refIm
# model and remove the scattered light, if requested;
# otherwise, reduce the image
if subscat == "yes":
# TODO: display all science extensions
# find file holding extracted flat spectra
# TODO: determination of extFlat probably needs improvement
dirList = os.listdir("./")
descendList = [im for im in dirList if flat in im]
extFlat = [im for im in descendList if "erg" in im][0]
print extFlat
# find gaps between fiber bundles on detector
gapFile = "blkMask_" + flat[:flat.find(".")] + ".txt"
iraf.delete(gapFile)
iraf.gffindblocks(extFlat[1:], extFlat, gapFile)
# model and remove scattered light, if necessary
# (and repeat until satisfied)
utils.examIm(extFlat[1:] + "[SCI]", frame=1)
while True:
fixScat = bool(
input(
"Does subtraction of scattered light need improvement? (True/False): "
))
if fixScat:
xOrders = raw_input("X orders (csv): ")
yOrders = raw_input("Y orders (csv): ")
iraf.imdelete("b" + extFlat[1:])
iraf.gfscatsub(extFlat[1:], gapFile, fl_inter="yes", \
prefix="b", xorder=xOrders, yorder=yOrders, \
cross="yes")
utils.examIm("b" + extFlat[1:] + "[SCI]", frame=1)
else:
break
else:
# reduce the image
outPref = self.reduceIm(inPref + flat, **kwargs)
# TODO: for this to work, need to know the proper prefix ...
# (have reduceIm return the prefix?)
self.viewCube(outPref + inPref + flat)
pass
# return extracted arcs to their rightful place
if "fl_qecorr" in kwargs.keys() and kwargs["fl_qecorr"] == "yes":
os.system("mv " + refIm + " " + arcPath)
return