def doit(fn,dp,mt):
""" JHT: this is the module that analyses an ALFOSC image of
a Vertical Slit, and recommends an alignment offset to the
current APERTURE WHEEL stepper motor units."""
## First check if data file exists
if not os.access(dp+fn+".fits",os.F_OK):
messageOut(mt,"File not found: "+dp+fn+".fits\n")
return "File not found: "+dp+fn+".fits"
messageOut(mt,"\nVertical-Slit analysis of file: "+dp+fn+".fits\n")
from pyraf import iraf
from pyraf import gwm
## Read current grism wheel position from image FITS header
iraf.images.imutil.imgets(dp+fn,"GRISM")
grismid=iraf.images.imutil.imgets.value
if grismid.find("pen")==-1:
messageOut(mt,"Vertical-Slit mode: grism wheel should be Open\n")
return "File %s: Vertical-Slit mode: grism wheel should be Open" % fn
## Read current aperture wheel position from image FITS header
iraf.images.imutil.imgets(dp+fn,"APERTUR")
slitid=iraf.images.imutil.imgets.value
if slitid.find("Vert")==-1:
messageOut(mt,"Vertical-Slit mode: no vertical slit in aperture wheel\n")
return "File %s: Vertical-Slit mode: no vertical slit in aperture wheel" % fn
slitwidth=float(slitid.split('_',9)[1].strip('\"'))
messageOut(mt,"Slit width "+str(slitwidth)+" "+slitid+"\n")
iraf.noao(_doprint=0)
iraf.noao.imred(_doprint=0)
iraf.noao.imred.specred(_doprint=0)
if not os.access("/tmp/tiasgat/",os.F_OK):
os.mkdir("/tmp/tiasgat/")
os.chmod("/tmp/tiasgat/",0777)
if os.access("/tmp/tiasgat/plot",os.F_OK): os.remove("/tmp/tiasgat/plot")
if os.access("/tmp/tiasgat/plot2",os.F_OK): os.remove("/tmp/tiasgat/plot2")
if os.access("/tmp/tiasgat/aplast",os.F_OK): os.remove("/tmp/tiasgat/aplast")
if os.access("/tmp/tiasgat/tvmarks",os.F_OK): os.remove("/tmp/tiasgat/tvmarks")
if os.access("/tmp/tiasgat/logfile",os.F_OK): os.remove("/tmp/tiasgat/logfile")
## Note that this will *not* update any uparm files !! (see pyraf documentation)
iraf.noao.imred.specred.dispaxis=2
iraf.noao.imred.specred.database="/tmp/tiasgat/"
iraf.noao.imred.specred.plotfile="/tmp/tiasgat/plot"
iraf.noao.imred.specred.logfile="/tmp/tiasgat/logfile"
width=6*slitwidth # x6 or else the widest slits go wrong
if width<4: width=4 # smaller than 4 and apfind will not find it
messageOut(mt,"Using width of "+str(width)+" pixels \n")
iraf.noao.imred.specred.apedit.width=width
## Display image on ds9
iraf.set(stdimage="imt512")
iraf.display(dp+fn,1,fill="no",Stdout="/dev/null")
# Suppress IRAF query for number of apertures to find
# This is only necesary for the widest slits: then the call to
# apfind results in an empty database file, as it cannot find an aperture.
# But aptrace works fine anyway (except for the annoying query) !?
iraf.noao.imred.specred.apfind.setParam('nfind.p_value', 1)
iraf.noao.imred.specred.apfind.setParam('nfind.p_mode','h')
## 'find' and trace spectrum; this will dump a plot to /tmp/tiasgat/plot
lines = iraf.noao.imred.specred.apfind(dp+fn,nfind=1,interactive="no", edit="no", nsum=20, Stdout=1)
for i in range (0,len(lines)): messageOut(mt,lines[i]+"\n")
lines = iraf.noao.imred.specred.aptrace(dp+fn,interactive="no",step=5,low_reject=2.5,
high_reject=2.5,function="leg",order=2,niterate=5,naverage=1, Stdout=1)
for i in range (0,len(lines)): messageOut(mt,lines[i]+"\n")
## Start graphics window; select the correct plot; show plot
gwm.window("Tiasgat! graphics")
iraf.plot.gkiextract("/tmp/tiasgat/plot",2,Stdout="/tmp/tiasgat/plot2")
gwm.getActiveGraphicsWindow().load("/tmp/tiasgat/plot2")
### how to read the aperture file, as output by aptrace ####
###
### center line 6 gives zero point
### max,min lines 24-25 n = (2 * x - (max + min)) / (max - min)
### c1,c2 lines 26-27
###
### The polynomial can be expressed as the sum
###
### poly = sum from i=1 to order {c_i * z_i}
###
### where the the c_i are the coefficients and the z_i are defined
### interatively as:
###
### z_1 = 1
### z_2 = n
### z_i = ((2*i-3) * n * z_{i-1} - (i-2) * z_{i-2}) / (i - 1)
###
### So for order=2 and for vertical slit/grism: X=center+c1+c2*n
### X=center + c1 + c2*(2 * Y - (max + min)) / (max - min)
### translated to X=a + bY
### a=center + c1 - c2*(max+min)/(max-min)
### b=2*C2/(max-min)
## Read the aperture definition file
apfile=open("/tmp/tiasgat/ap"+dp.replace('/','_')+fn,'r')
lines=apfile.readlines()
apfile.close()
#print lines[5], lines[23:]
c0 = float(lines[5].split(None,9)[1].strip())
lower = float(lines[23].strip())
upper = float(lines[24].strip())
c1 = float(lines[25].strip())
c2 = float(lines[26].strip())
a = c0 + c1 - c2*(upper+lower)/(upper-lower)
b = 2*c2/(upper-lower)
#print "zeropoint ", a, " slope ",b
## Remove aperture definition file
if os.access("/tmp/tiasgat/ap"+dp.replace('/','_')+fn,os.F_OK):
os.remove("/tmp/tiasgat/ap"+dp.replace('/','_')+fn)
## Mark the fit on the image display
if os.access("/tmp/tiasgat/tvmarks",os.F_OK): os.remove("/tmp/tiasgat/tvmarks")
tvmarkfile=open("/tmp/tiasgat/tvmarks",'w')
for i in range(int(lower),int(upper)+1,3):
tvmarkfile.write(str(a+b*i)+" "+str(i)+" 100 s \n")
tvmarkfile.close()
iraf.tv.tvmark(1,"",commands="/tmp/tiasgat/tvmarks",interactive="no")
## Read current grism wheel position from image FITS header
iraf.images.imutil.imgets(dp+fn,"ALAPRSTP")
oldwheelunits=float(iraf.images.imutil.imgets.value)
#print "APERSTEP", oldwheelunits
## Read binning FITS headers
iraf.images.imutil.imgets(dp+fn,"CDELT1")
xbin=float(iraf.images.imutil.imgets.value)
iraf.images.imutil.imgets(dp+fn,"CDELT2")
ybin=float(iraf.images.imutil.imgets.value)
iraf.images.imutil.imgets(dp+fn,"CRVAL1")
xstart=float(iraf.images.imutil.imgets.value)
messageOut(mt,"\nBinning factors "+str(int(xbin))+" x "+str(int(ybin))+"\n")
#messageOut(mt,"Xstart "+str(int(xstart))+"\n")
#messageOut(mt,"half "+str(int((lower+upper)/2))+"\n")
if xbin==1:
messageOut(mt,"\nSlitpos: X-position at CCD center "+str((xstart-1+a+b*(lower+upper)/2))+" according to fit\n")
else:
messageOut(mt,"\nSlitpos: X-binning is not 1: set wrongly in vsalign.run ?!\n\n")
## Correct the angle for the binning factors.
## A full wheel turn corresponds to 320000 units
offsetangle=320000 * math.atan(b*xbin/ybin) / (2*math.pi)
messageOut(mt,"Alignment: Offset to motor units "+str(offsetangle)+"\n")
newwheelunits=offsetangle + oldwheelunits
if newwheelunits < 0: newwheelunits+=320000
return "Result for %s : current APERTURE wheel units %d, suggested new value %d" % \
(fn, (0.5+oldwheelunits), (0.5+newwheelunits))
def doit(fn, dp, mt):
""" JHT: this is the module that analyses an ALFOSC image of
a Vertical Slit, and recommends an alignment offset to the
current APERTURE WHEEL stepper motor units."""
## First check if data file exists
if not os.access(dp + fn + ".fits", os.F_OK):
messageOut(mt, "File not found: " + dp + fn + ".fits\n")
return "File not found: " + dp + fn + ".fits"
messageOut(mt, "\nVertical-Slit analysis of file: " + dp + fn + ".fits\n")
from pyraf import iraf
from pyraf import gwm
## Read current grism wheel position from image FITS header
iraf.images.imutil.imgets(dp + fn, "GRISM")
grismid = iraf.images.imutil.imgets.value
if grismid.find("pen") == -1:
messageOut(mt, "Vertical-Slit mode: grism wheel should be Open\n")
return "File %s: Vertical-Slit mode: grism wheel should be Open" % fn
## Read current aperture wheel position from image FITS header
iraf.images.imutil.imgets(dp + fn, "APERTUR")
slitid = iraf.images.imutil.imgets.value
if slitid.find("Vert") == -1:
messageOut(
mt, "Vertical-Slit mode: no vertical slit in aperture wheel\n")
return "File %s: Vertical-Slit mode: no vertical slit in aperture wheel" % fn
slitwidth = float(slitid.split('_', 9)[1].strip('\"'))
messageOut(mt, "Slit width " + str(slitwidth) + " " + slitid + "\n")
iraf.noao(_doprint=0)
iraf.noao.imred(_doprint=0)
iraf.noao.imred.specred(_doprint=0)
if not os.access("/tmp/tiasgat/", os.F_OK):
os.mkdir("/tmp/tiasgat/")
os.chmod("/tmp/tiasgat/", 0777)
if os.access("/tmp/tiasgat/plot", os.F_OK): os.remove("/tmp/tiasgat/plot")
if os.access("/tmp/tiasgat/plot2", os.F_OK):
os.remove("/tmp/tiasgat/plot2")
if os.access("/tmp/tiasgat/aplast", os.F_OK):
os.remove("/tmp/tiasgat/aplast")
if os.access("/tmp/tiasgat/tvmarks", os.F_OK):
os.remove("/tmp/tiasgat/tvmarks")
if os.access("/tmp/tiasgat/logfile", os.F_OK):
os.remove("/tmp/tiasgat/logfile")
## Note that this will *not* update any uparm files !! (see pyraf documentation)
iraf.noao.imred.specred.dispaxis = 2
iraf.noao.imred.specred.database = "/tmp/tiasgat/"
iraf.noao.imred.specred.plotfile = "/tmp/tiasgat/plot"
iraf.noao.imred.specred.logfile = "/tmp/tiasgat/logfile"
width = 6 * slitwidth # x6 or else the widest slits go wrong
if width < 4: width = 4 # smaller than 4 and apfind will not find it
messageOut(mt, "Using width of " + str(width) + " pixels \n")
iraf.noao.imred.specred.apedit.width = width
## Display image on ds9
iraf.set(stdimage="imt512")
iraf.display(dp + fn, 1, fill="no", Stdout="/dev/null")
# Suppress IRAF query for number of apertures to find
# This is only necesary for the widest slits: then the call to
# apfind results in an empty database file, as it cannot find an aperture.
# But aptrace works fine anyway (except for the annoying query) !?
iraf.noao.imred.specred.apfind.setParam('nfind.p_value', 1)
iraf.noao.imred.specred.apfind.setParam('nfind.p_mode', 'h')
## 'find' and trace spectrum; this will dump a plot to /tmp/tiasgat/plot
lines = iraf.noao.imred.specred.apfind(dp + fn,
nfind=1,
interactive="no",
edit="no",
nsum=20,
Stdout=1)
for i in range(0, len(lines)):
messageOut(mt, lines[i] + "\n")
lines = iraf.noao.imred.specred.aptrace(dp + fn,
interactive="no",
step=5,
low_reject=2.5,
high_reject=2.5,
function="leg",
order=2,
niterate=5,
naverage=1,
Stdout=1)
for i in range(0, len(lines)):
messageOut(mt, lines[i] + "\n")
## Start graphics window; select the correct plot; show plot
gwm.window("Tiasgat! graphics")
iraf.plot.gkiextract("/tmp/tiasgat/plot", 2, Stdout="/tmp/tiasgat/plot2")
gwm.getActiveGraphicsWindow().load("/tmp/tiasgat/plot2")
### how to read the aperture file, as output by aptrace ####
###
### center line 6 gives zero point
### max,min lines 24-25 n = (2 * x - (max + min)) / (max - min)
### c1,c2 lines 26-27
###
### The polynomial can be expressed as the sum
###
### poly = sum from i=1 to order {c_i * z_i}
###
### where the the c_i are the coefficients and the z_i are defined
### interatively as:
###
### z_1 = 1
### z_2 = n
### z_i = ((2*i-3) * n * z_{i-1} - (i-2) * z_{i-2}) / (i - 1)
###
### So for order=2 and for vertical slit/grism: X=center+c1+c2*n
### X=center + c1 + c2*(2 * Y - (max + min)) / (max - min)
### translated to X=a + bY
### a=center + c1 - c2*(max+min)/(max-min)
### b=2*C2/(max-min)
## Read the aperture definition file
apfile = open("/tmp/tiasgat/ap" + dp.replace('/', '_') + fn, 'r')
lines = apfile.readlines()
apfile.close()
#print lines[5], lines[23:]
c0 = float(lines[5].split(None, 9)[1].strip())
lower = float(lines[23].strip())
upper = float(lines[24].strip())
c1 = float(lines[25].strip())
c2 = float(lines[26].strip())
a = c0 + c1 - c2 * (upper + lower) / (upper - lower)
b = 2 * c2 / (upper - lower)
#print "zeropoint ", a, " slope ",b
## Remove aperture definition file
if os.access("/tmp/tiasgat/ap" + dp.replace('/', '_') + fn, os.F_OK):
os.remove("/tmp/tiasgat/ap" + dp.replace('/', '_') + fn)
## Mark the fit on the image display
if os.access("/tmp/tiasgat/tvmarks", os.F_OK):
os.remove("/tmp/tiasgat/tvmarks")
tvmarkfile = open("/tmp/tiasgat/tvmarks", 'w')
for i in range(int(lower), int(upper) + 1, 3):
tvmarkfile.write(str(a + b * i) + " " + str(i) + " 100 s \n")
tvmarkfile.close()
iraf.tv.tvmark(1, "", commands="/tmp/tiasgat/tvmarks", interactive="no")
## Read current grism wheel position from image FITS header
iraf.images.imutil.imgets(dp + fn, "ALAPRSTP")
oldwheelunits = float(iraf.images.imutil.imgets.value)
#print "APERSTEP", oldwheelunits
## Read binning FITS headers
iraf.images.imutil.imgets(dp + fn, "CDELT1")
xbin = float(iraf.images.imutil.imgets.value)
iraf.images.imutil.imgets(dp + fn, "CDELT2")
ybin = float(iraf.images.imutil.imgets.value)
iraf.images.imutil.imgets(dp + fn, "CRVAL1")
xstart = float(iraf.images.imutil.imgets.value)
messageOut(
mt,
"\nBinning factors " + str(int(xbin)) + " x " + str(int(ybin)) + "\n")
#messageOut(mt,"Xstart "+str(int(xstart))+"\n")
#messageOut(mt,"half "+str(int((lower+upper)/2))+"\n")
if xbin == 1:
messageOut(
mt, "\nSlitpos: X-position at CCD center " + str(
(xstart - 1 + a + b * (lower + upper) / 2)) +
" according to fit\n")
else:
messageOut(
mt,
"\nSlitpos: X-binning is not 1: set wrongly in vsalign.run ?!\n\n"
)
## Correct the angle for the binning factors.
## A full wheel turn corresponds to 320000 units
offsetangle = 320000 * math.atan(b * xbin / ybin) / (2 * math.pi)
messageOut(mt,
"Alignment: Offset to motor units " + str(offsetangle) + "\n")
newwheelunits = offsetangle + oldwheelunits
if newwheelunits < 0: newwheelunits += 320000
return "Result for %s : current APERTURE wheel units %d, suggested new value %d" % \
(fn, (0.5+oldwheelunits), (0.5+newwheelunits))
gainlevel = float(iraf.images.imutil.imgets.value)
iraf.images.imutil.imgets(image1, "RDNOISE")
ron = float(iraf.images.imutil.imgets.value)
iraf.images.imutil.imgets(image1, "STFLTNM")
stfilter = iraf.images.imutil.imgets.value
print "Instrument setup:\nArm ", armpos
print "Mask ", maskpos
print "Top Halogen (0/1) ", tophalogen
print "Bottom Halogen (0/1) ", bothalogen
############ Start data reduction ###########
if interactive=="yes": gwm.window("FIES fluxstandard pipeline ;-)")
iraf.noao.imred(_doprint=0)
iraf.noao.imred.echelle(_doprint=0)
iraf.noao.imred.echelle.apedit.width=5.0
if (maskID==5):
mastertharlink="masterThArF1"
masterhalolink="masterHaloF1"
iraf.noao.imred.echelle.apedit.width=7.0
if (maskID==1):
mastertharlink="masterThArF2"
masterhalolink="masterHaloF2"
if (maskID==2):
mastertharlink="masterThArF3"
masterhalolink="masterHaloF3"
def doit(fn, dp, mt):
""" JHT: this is the module that analyses an ALFOSC pinhole spectrum
with a Horizontal Grism, and recommends an alignment offset to the
current GRISM WHEEL stepper motor units."""
## First check if data file exists
if not os.access(dp + fn + ".fits", os.F_OK):
messageOut(mt, "File not found: " + dp + fn + ".fits\n")
return "File not found: " + dp + fn + ".fits"
messageOut(mt, "\nHorizontal-Grism analysis of file: " + dp + fn + ".fits\n")
from pyraf import iraf
from pyraf import gwm
## Read current grism wheel position from image FITS header
iraf.images.imutil.imgets(dp + fn, "GRISM")
grismid = iraf.images.imutil.imgets.value
if grismid.find("Hori") == -1:
iraf.images.imutil.imgets(dp + fn, "FILTER") # maybe in filter wheel?
grismid = iraf.images.imutil.imgets.value
if grismid.find("Hori") == -1:
messageOut(mt, "Horizontal-Grism mode: no horizontal grism in wheel\n")
return "File %s: Horizontal-Grism mode: no horizontal grism in wheel" % fn
## Read current aperture wheel position from image FITS header
iraf.images.imutil.imgets(dp + fn, "APERTUR")
slitid = iraf.images.imutil.imgets.value
if slitid.find("inho") == -1:
messageOut(mt, "Horizontal-Grism mode: no pinhole in aperture wheel\n")
return "File %s: Horizontal-Grism mode: no pinhole in aperture wheel" % fn
iraf.noao(_doprint=0)
iraf.noao.imred(_doprint=0)
iraf.noao.imred.specred(_doprint=0)
if not os.access("/tmp/tiasgat/", os.F_OK):
os.mkdir("/tmp/tiasgat/")
os.chmod("/tmp/tiasgat/", 0777)
if os.access("/tmp/tiasgat/plot", os.F_OK):
os.remove("/tmp/tiasgat/plot")
if os.access("/tmp/tiasgat/plot2", os.F_OK):
os.remove("/tmp/tiasgat/plot2")
if os.access("/tmp/tiasgat/aplast", os.F_OK):
os.remove("/tmp/tiasgat/aplast")
if os.access("/tmp/tiasgat/tvmarks", os.F_OK):
os.remove("/tmp/tiasgat/tvmarks")
if os.access("/tmp/tiasgat/logfile", os.F_OK):
os.remove("/tmp/tiasgat/logfile")
## Note that this will *not* update any uparm files !! (see pyraf documentation)
iraf.noao.imred.specred.dispaxis = 1
iraf.noao.imred.specred.database = "/tmp/tiasgat/"
iraf.noao.imred.specred.plotfile = "/tmp/tiasgat/plot"
iraf.noao.imred.specred.logfile = "/tmp/tiasgat/logfile"
iraf.noao.imred.specred.apedit.width = 15
# iraf.lpar(iraf.noao.imred.specred.aptrace)
## Display image on ds9
iraf.set(stdimage="imt512")
iraf.display(dp + fn, 1, fill="no", Stdout="/dev/null")
# Suppress IRAF query for number of apertures to find
# This is only necesary for the widest slits: then the call to
# apfind results in an empty database file, as it cannot find an aperture.
# But aptrace works fine anyway (except for the annoying query) !?
iraf.noao.imred.specred.apfind.setParam("nfind.p_value", 1)
iraf.noao.imred.specred.apfind.setParam("nfind.p_mode", "h")
## 'find' and trace spectrum; this will dump a plot to /tmp/tiasgat/plot
lines = iraf.noao.imred.specred.apfind(dp + fn, nfind=1, interactive="no", Stdout=1)
for i in range(0, len(lines)):
messageOut(mt, lines[i] + "\n")
lines = iraf.noao.imred.specred.aptrace(
dp + fn,
interactive="no",
step=5,
low_reject=2.5,
high_reject=2.5,
function="leg",
order=2,
niterate=5,
naverage=1,
Stdout=1,
)
for i in range(0, len(lines)):
messageOut(mt, lines[i] + "\n")
## Start graphics window; select the correct plot; show plot
gwm.window("Tiasgat! graphics")
iraf.plot.gkiextract("/tmp/tiasgat/plot", 2, Stdout="/tmp/tiasgat/plot2")
gwm.getActiveGraphicsWindow().load("/tmp/tiasgat/plot2")
### how to read the aperture file, as output by aptrace ####
###
### center line 6 gives zero point
### max,min lines 24-25 n = (2 * x - (max + min)) / (max - min)
### c1,c2 lines 26-27
###
### The polynomial can be expressed as the sum
###
### poly = sum from i=1 to order {c_i * z_i}
###
### where the the c_i are the coefficients and the z_i are defined
### interatively as:
###
### z_1 = 1
### z_2 = n
### z_i = ((2*i-3) * n * z_{i-1} - (i-2) * z_{i-2}) / (i - 1)
###
### So for order=2 and for vertical slit/grism: Y=center+c1+c2*n
### Y=center + c1 + c2*(2 * X - (max + min)) / (max - min)
### translated to Y=a + bX
### a=center + c1 - c2*(max+min)/(max-min)
### b=2*C2/(max-min)
## Read the aperture definition file
apfile = open("/tmp/tiasgat/ap" + dp.replace("/", "_") + fn, "r")
lines = apfile.readlines()
apfile.close()
# print lines[5], lines[23:]
c0 = float(lines[5].split(None, 9)[2].strip())
lower = float(lines[23].strip())
upper = float(lines[24].strip())
c1 = float(lines[25].strip())
c2 = float(lines[26].strip())
a = c0 + c1 - c2 * (upper + lower) / (upper - lower)
b = 2 * c2 / (upper - lower)
# print "zeropoint ", a, " slope ",b
## Remove aperture definition file
if os.access("/tmp/tiasgat/ap" + dp.replace("/", "_") + fn, os.F_OK):
os.remove("/tmp/tiasgat/ap" + dp.replace("/", "_") + fn)
## Mark the fit on the image display
if os.access("/tmp/tiasgat/tvmarks", os.F_OK):
os.remove("/tmp/tiasgat/tvmarks")
tvmarkfile = open("/tmp/tiasgat/tvmarks", "w")
for i in range(int(lower), int(upper) + 1, 3):
tvmarkfile.write(str(i) + " " + str(a + b * i) + " 100 s \n")
tvmarkfile.close()
iraf.tv.tvmark(1, "", commands="/tmp/tiasgat/tvmarks", interactive="no")
## Read current grism wheel position from image FITS header
iraf.images.imutil.imgets(dp + fn, "ALGRSTP")
oldwheelunits = float(iraf.images.imutil.imgets.value)
# print "GRISMSTE", oldwheelunits
## Read binning FITS headers
iraf.images.imutil.imgets(dp + fn, "CDELT1")
xbin = float(iraf.images.imutil.imgets.value)
iraf.images.imutil.imgets(dp + fn, "CDELT2")
ybin = float(iraf.images.imutil.imgets.value)
messageOut(mt, "\nBinning factors " + str(int(xbin)) + " x " + str(int(ybin)) + "\n")
## Correct the angle for the binning factors.
## A full wheel turn corresponds to 320000 units
offsetangle = 320000 * math.atan(b * ybin / xbin) / (2 * math.pi)
messageOut(mt, "Offset to motor units " + str(offsetangle) + "\n")
newwheelunits = offsetangle + oldwheelunits
if newwheelunits < 0:
newwheelunits += 320000
return "Result for %s : current GRISM wheel units %d, suggested new value %d" % (
fn,
(0.5 + oldwheelunits),
(0.5 + newwheelunits),
)