def frame_offset(setup, total_sci_ext, fits_number):
#The fits_number counter serves to help us select which rows in the .tab file we want to use in our median evaluation. We want to be taking the median value of the XX slit median values for the given frame. Since the .tab file is appended to for all Z number of files we need to determine which rows to use with which file <- the fits_number iterator and knowing the number of science extensions determine which rows to use.
end_row = total_sci_ext * fits_number
beg_row = (total_sci_ext * fits_number) - (total_sci_ext-1)
print 'Taking the median value from rows: %s - %s in the %s file for file #%d of the file list' % (beg_row, end_row, '*_lambdaoff.tab', fits_number)
#This is reading the median column of the unrestricted dlambda table.
#It determines the number of rows and runs statistics over all the rows selected
#The statistics (mean, stddev, median, min, max) will be run on the median values of each slit to give an overall offset value
iraf.tstat('%s_lambdaoff.tab' % config,'median',outtable='%s_lambdaoffmed.tab' % config, row='%s - %s' % (beg_row, end_row), Stdout=0)
#This is printing out the final offset value (median from *lambdaoffall.tab) which is to be applied to all slits in the same file
iraf.tprint('%s_lambdaoffmed.tab' % config, col='median',showr='no',showh='no',row=str(fits_number))
#here I'm printing out the offset value from the table and assigning it to 'offset'; it's a list so I'll change it to a float next
offset = iraf.tprint('%s_lambdaoffmed.tab' % config, col='median',showr='no',showh='no',row=str(fits_number), Stdout=1)
#offset comes out as redirected output from tprint and needs to be changed to the appropriate form
offset_value = [line.strip() for line in offset]
if offset_value[0] == 'INDEF':
IPython.embed() #INDEF comes from the lines not being found
offset_value = float(offset_value[0])
return offset_value
def run_elli(input, xcntr, ycntr, eg, pa, sma):#,radd,background):
iraf.stsdas(_doprint=0)
iraf.tables(_doprint=0)
iraf.stsdas.analysis(_doprint=0)
iraf.stsdas.analysis.isophote(_doprint=0)
image_exist = 1
if(str(input)[:3] == 'ima'):
output = 'elli_' + input[6:-4] + 'txt'
if(str(input)[:3] == 'out'):
output = 'out_elli_' + str(input)[4:-7] + 'txt'
#unlearn geompar controlpar samplepar magpar ellipse
iraf.geompar(x0=xcntr, y0=ycntr, ellip0=eg, pa0=pa, sma0=10, minsma=0.1, \
maxsma=sma*5.0, step=0.1,recente="yes")
iraf.controlpar(conver=0.05, minit=10, maxit=50, hcenter="no", hellip="no",\
hpa="no", wander="", maxgerr=0.5, olthres=1,soft="no")
iraf.samplepar(integrm="bi-linear", usclip=3,lsclip=3, nclip=0, fflag=0.5)
iraf.magpar(mag0=0, refer=1, zerolev=0)
iraf.ellipse("".join(input), output="test", interac="no",Stdout="ellip", \
Stderr="err")
iraf.tprint("test.tab", prparam="no", prdata="yes", pwidth=80, plength=0, \
showrow="no", orig_row="no", showhdr="no", showunits="no", \
columns="SMA, INTENS, INT_ERR, MAG, MAG_LERR, MAG_UERR",\
rows="-", \
option="plain", align="yes", sp_col="", lgroup=0, Stdout=output)
for myfile in ['ellip','err','test.tab']:
if os.access(myfile,os.F_OK):
os.remove(myfile)
def run_elli_full(cutimage, output, xcntr, ycntr, eg, pa, sma,
sky): #,radd,background):
"""The function responsible for fit ellipse"""
EllGal = c.outdir + 'GalEllFit.fits'
fEl = pyfits.open(os.path.join(c.datadir, cutimage))
GaLaXy = fEl[0].data
fEl.close()
GaLaXy = GaLaXy - sky
hdu = pyfits.PrimaryHDU(GaLaXy.astype(n.float32))
hdu.writeto(EllGal)
try:
iraf.stsdas(_doprint=0)
iraf.tables(_doprint=0)
iraf.stsdas.analysis(_doprint=0)
iraf.stsdas.analysis.isophote(_doprint=0)
except:
iraf.stsdas()
iraf.tables()
iraf.stsdas.analysis()
iraf.stsdas.analysis.isophote()
image_exist = 1
iraf.unlearn('geompar')
iraf.geompar.x0 = xcntr
iraf.geompar.y0 = ycntr
iraf.geompar.ellip0 = eg
iraf.geompar.pa0 = pa
iraf.geompar.sma0 = 6.0
iraf.geompar.minsma = 0.1
iraf.geompar.maxsma = sma * 5.0
iraf.geompar.step = 0.1
iraf.geompar.recente = "no"
iraf.geompar.xylearn = "no"
iraf.unlearn('controlpar')
iraf.controlpar.conver = 0.05
iraf.controlpar.minit = 10
iraf.controlpar.maxit = 50
iraf.controlpar.hcenter = "no"
iraf.controlpar.hellip = "no"
iraf.controlpar.hpa = "no"
iraf.controlpar.wander = "INDEF"
iraf.controlpar.maxgerr = 0.5
iraf.controlpar.olthres = 1
iraf.controlpar.soft = "no"
iraf.samplepar.integrm = "bi-linear"
iraf.samplepar.usclip = 3
iraf.samplepar.lsclip = 3
iraf.samplepar.nclip = 0
iraf.samplepar.fflag = 0.5
iraf.unlearn('ellipse')
iraf.ellipse("".join(EllGal), output="test", interac="no",Stdout="ellip", \
Stderr="err")
iraf.tprint("test.tab", prparam="no", prdata="yes", pwidth=80, plength=0, \
showrow="no", orig_row="no", showhdr="no", showunits="no", \
columns="SMA, INTENS, INT_ERR, ELLIP, ELLIP_ERR, PA, PA_ERR, \
MAG, MAG_LERR, MAG_UERR, TMAG_E, TMAG_C, A3, \
A3_ERR, B3, B3_ERR, A4, A4_ERR, B4_ERR" , rows="-", \
option="plain", align="yes", sp_col="", lgroup=0, Stdout=output)
for myfile in ['ellip', 'err', 'test.tab', EllGal]:
if os.access(c.outdir + myfile, os.F_OK):
os.remove(c.outdir + myfile)
def run_ell(file_in, file_tab, file_dat, mag, **ellipse_par):
# prochaine etape : mettre en argument sous une certaine forme les parametres associes epar des taches 1) strict minimum sous forme de dico fixe 2) tout pouvoir changer sous forme de dictionnaire et tester les cles ...
# import iraf packages
iraf.stsdas()
iraf.analysis()
iraf.isophote()
p = Popen("ds9", shell = True)
time.sleep(5)
iraf.display(file_in, 1)
set_iraf_param(ellipse_par)
# iraf.lpar(iraf.geompar)
iraf.ellipse(file_in, file_tab, mag0 = str(mag), verbose = "no")
# iraf.lpar(iraf.isoimap)
iraf.isoimap(file_in, file_tab)
iraf.tproject(file_tab, "temp.fits", "SMA,INTENS,INT_ERR,ELLIP,ELLIP_ERR, PA, PA_ERR, X0, Y0, TFLUX_C, TMAG_E,NPIX_E")
iraf.tprint("temp.fits", pwidth = 200, Stdout = file_dat)
iraf.imdel("temp.fits")
p.kill()
def run_elli_full(input, output, xcntr, ycntr, eg, pa, sma, sky):#,radd,background):
"""The function responsible for fit ellipse"""
EllGal = 'GalEllFit.fits'
fEl = pyfits.open(input)
GaLaXy = fEl[0].data
fEl.close()
GaLaXy = GaLaXy - sky
hdu = pyfits.PrimaryHDU(GaLaXy.astype(n.float32))
hdu.writeto(EllGal)
try:
iraf.stsdas(_doprint=0)
iraf.tables(_doprint=0)
iraf.stsdas.analysis(_doprint=0)
iraf.stsdas.analysis.isophote(_doprint=0)
except:
iraf.stsdas()
iraf.tables()
iraf.stsdas.analysis()
iraf.stsdas.analysis.isophote()
image_exist = 1
iraf.unlearn('geompar')
iraf.geompar.x0=xcntr
iraf.geompar.y0=ycntr
iraf.geompar.ellip0=eg
iraf.geompar.pa0=pa
iraf.geompar.sma0=6.0
iraf.geompar.minsma=0.1
iraf.geompar.maxsma=sma*5.0
iraf.geompar.step=0.1
iraf.geompar.recente="no"
iraf.geompar.xylearn="no"
iraf.unlearn('controlpar')
iraf.controlpar.conver=0.05
iraf.controlpar.minit=10
iraf.controlpar.maxit=50
iraf.controlpar.hcenter="no"
iraf.controlpar.hellip="no"
iraf.controlpar.hpa="no"
iraf.controlpar.wander="INDEF"
iraf.controlpar.maxgerr=0.5
iraf.controlpar.olthres=1
iraf.controlpar.soft="no"
iraf.samplepar.integrm="bi-linear"
iraf.samplepar.usclip=3
iraf.samplepar.lsclip=3
iraf.samplepar.nclip=0
iraf.samplepar.fflag=0.5
iraf.unlearn('ellipse')
iraf.ellipse("".join(EllGal), output="test", interac="no",Stdout="ellip", \
Stderr="err")
iraf.tprint("test.tab", prparam="no", prdata="yes", pwidth=80, plength=0, \
showrow="no", orig_row="no", showhdr="no", showunits="no", \
columns="SMA, INTENS, INT_ERR, ELLIP, ELLIP_ERR, PA, PA_ERR, \
MAG, MAG_LERR, MAG_UERR, TMAG_E, TMAG_C, A3, \
A3_ERR, B3, B3_ERR, A4, A4_ERR, B4_ERR", rows="-", \
option="plain", align="yes", sp_col="", lgroup=0, Stdout=output)
for myfile in ['ellip','err','test.tab', EllGal]:
if os.access(myfile,os.F_OK):
os.remove(myfile)
def run_elli(input, output, xcntr, ycntr, eg, pa, sma):#,radd,background):
"""The function resposible for fit ellipse"""
iraf.stsdas(_doprint=0)
iraf.tables(_doprint=0)
iraf.stsdas.analysis(_doprint=0)
iraf.stsdas.analysis.isophote(_doprint=0)
image_exist = 1
# if(str(input)[:3] == 'ima'):
# output = 'elli_' + input[6:-4] + 'txt'
# if(str(input)[:3] == 'out'):
# output = 'out_elli_' + str(input)[4:-7] + 'txt'
# else:
# output = 'elli_' + input[:-5] + '.txt'
#unlearn geompar controlpar samplepar magpar ellipse
iraf.unlearn('geompar')
iraf.geompar.x0=xcntr
iraf.geompar.y0=ycntr
iraf.geompar.ellip0=eg
iraf.geompar.pa0=pa
iraf.geompar.sma0=10
iraf.geompar.minsma=0.1
iraf.geompar.maxsma=sma*5.0
iraf.geompar.step=0.1
iraf.geompar.recente="no"
iraf.geompar.xylearn="no"
iraf.unlearn('controlpar')
iraf.controlpar.conver=0.05
iraf.controlpar.minit=10
iraf.controlpar.maxit=50
iraf.controlpar.hcenter="no"
iraf.controlpar.hellip="no"
iraf.controlpar.hpa="no"
iraf.controlpar.wander="INDEF"
iraf.controlpar.maxgerr=0.5
iraf.controlpar.olthres=1
iraf.controlpar.soft="no"
iraf.samplepar.integrm="bi-linear"
iraf.samplepar.usclip=3
iraf.samplepar.lsclip=3
iraf.samplepar.nclip=0
iraf.samplepar.fflag=0.5
iraf.magpar.mag0=c.mag_zero
iraf.magpar.refer=1
iraf.magpar.zerolev=0
iraf.ellipse("".join(input), output="test", interac="no",Stdout="ellip", \
Stderr="err")
iraf.tprint("test.tab", prparam="no", prdata="yes", pwidth=80, plength=0, \
showrow="no", orig_row="no", showhdr="no", showunits="no", \
columns="SMA, INTENS, INT_ERR, MAG, MAG_LERR, MAG_UERR, \
TFLUX_E", rows="-", \
option="plain", align="yes", sp_col="", lgroup=0, Stdout=output)
for myfile in ['ellip','err','test.tab']:
if os.access(myfile,os.F_OK):
os.remove(myfile)
except getopt.error as e:
print(str(e))
usage()
_out_width = 80
_show_row = no
_column_names = no
_align_cols = no
if optlist:
for opt, value in optlist:
if opt in( "-s", "--showrow"):
_show_row = yes
elif opt in ("-c", "--colnames"):
_column_names = yes
elif opt in ("-a", "--align"):
_align_cols = yes
elif opt in ("-h", "--help"):
usage()
else:
print("Program bug, uninterpreted option", opt)
raise SystemExit
del getopt
iraf.tprint(args[0],prparam=no,prdata=yes,pwidth=_out_width,
plength=0,showrow=_show_row,orig_row=yes,showhdr=_column_names,
showunits=yes,columns="",rows="-",option="plain",align=_align_cols,
sp_col="",lgroup=0,mode="h")
#!/usr/bin/env python
print('This version of galTables works for *cutout-24-rot.tab files and *cutout-sdss.tab files. If you are not using rotated 24m files then use galTablesv2.py')
from pylab import *
import glob
from pyraf import iraf
import os
iraf.stsdas()
iraf.analysis()
iraf.toolbox()
iraf.ttools()
flag = str(raw_input('Which files? a=24 b=sdss '))
flag = str(flag)
if flag.find('a') > -1:
tabfiles = glob.glob('*cutout-24-rot.tab')
if flag.find('b') > -1:
tabfiles = glob.glob('*cutout-sdss.tab')
#tabfiles=glob.glob('*.tab')
#print tabfiles
for i in range(len(tabfiles)):
tfile = tabfiles[i]
nfile = tfile.split('.')
dfile = nfile[0]+'.dat'
print tfile,' -> ',dfile
iraf.tprint(table=tfile,pwidth='INDEF',showhdr='no',showunits='no',Stdout=dfile)
def runellipse(files,
xcenter,
ycenter,
minr,
ipa,
initialr,
maxr,
iellip,
nframe=1,
myradius=15):
initialradius = myradius
for i in range(len(files)):
myradius = initialradius
mfile = files[i]
#mask image
outfile1 = 'm' + mfile
continueWithProgram, continueWithObject = runimedit(
mfile, outfile1, nframe)
if not continueWithProgram:
print "quitting program"
return
if not continueWithObject:
print "going on to next image"
continue
#run ellipse
t = mfile.split('.')
efile = t[0] + '.tab'
imprefix = t[0]
print mfile, imprefix
print 'Running ellipse to fit isophotes to galaxy:'
try:
os.remove(efile)
except OSError:
print 'everything is ok'
print "First pass, letting PA and e vary"
iraf.ellipse(input=outfile1,
output=efile,
x0=xcenter,
y0=ycenter,
hcenter='no',
sma0=initialr,
minsma=minr,
maxsma=maxr,
pa=ipa,
hpa='no',
ellip=iellip,
hellip='no')
print 'Displaying isophotes from first pass. Hit q in DS9 window to quit'
iraf.isoexam(table=efile)
os.system('rm junk.txt')
iraf.tprint(table=efile,
pwidth='INDEF',
showhdr='no',
Stdout='junk.txt')
os.system("awk '{print $2, $7, $9, $11, $13}' < junk.txt > junk2.txt")
#run ellipse a second time, keeping PA and ellip fixed
#allow user to adjust the radius where PA and ellip are measured
repeatflag = 1
while (repeatflag > 0.1):
infile = open('junk2.txt', 'r')
for line in infile:
t = line.split()
if float(t[0]) > myradius:
newellip = float(t[1])
if newellip < .05: #min value that ellipse can handle
newellip = .05
newPA = float(t[2])
if newPA < -90:
newPA = newPA + 180
elif newPA > 90:
newPA = newPA - 180
#11 - X0, 13 - Y0
newxcenter = float(t[3])
newycenter = float(t[4])
break
s = 'rm ' + efile
os.system(s)
iraf.ellipse(input=outfile1,
output=efile,
x0=newxcenter,
y0=newycenter,
hcenter='yes',
sma0=initialr,
minsma=minr,
maxsma=maxr,
pa=newPA,
hpa='yes',
ellip=newellip,
hellip='yes')
print 'Displaying isophotes from second pass using r = ', myradius
print 'Hit q in the DS9 window to quit'
iraf.isoexam(table=efile)
flag = str(
raw_input('Are you happy with the fit? y=yes n=no x=quit '))
flag = str(flag)
print 'this is what I think you typed ', flag
if flag.find('n') > -1:
flag2 = str(
raw_input(
'What is the problem? c=off-center r=set new radius x=quit '
))
flag2 = str(flag2)
if flag2.find('r') > -1:
myr = input('Enter new radius to use ')
myradius = float(myr)
s = 'rm ' + efile
os.system(s)
repeatflag = 1
elif flag2.find('x') > -1:
repeatflag = 0
return
elif flag2.find('c') > -1:
s = 'mv *' + imprefix + '* OffCenter/'
print s
os.system(s)
repeatflag = 0
print "repeatflag = ", repeatflag
elif flag.find('x') > -1:
repeatflag = 0
print 'i think repeatflag = 0', repeatflag
return
else:
s = 'mv *' + imprefix + '* Finished/'
os.system(s)
repeatflag = 0
print 'i think repeatflag = 0 ', repeatflag
print 'repeatflag = ', repeatflag
def runellipseold(files,xcenter,ycenter,minr,ipa,initialr,maxr,iellip,nframe=1,myradius=15):
initialradius=myradius
for i in range(len(files)):
myradius=initialradius
mfile=files[i]
#mask image
outfile1='m'+mfile
continueWithProgram,continueWithObject=runimedit(mfile,outfile1,nframe)
if not continueWithProgram:
print "quitting program"
return
if not continueWithObject:
print "going on to next image"
continue
#run ellipse
t=mfile.split('.')
efile=t[0]+'.tab'
imprefix=t[0]
print mfile, imprefix
print 'Running ellipse to fit isophotes to galaxy:'
try:
os.remove(efile)
except OSError:
print 'everything is ok'
print "First pass, letting PA and e vary"
iraf.ellipse(input=outfile1,output=efile,x0=xcenter,y0=ycenter,hcenter='no',sma0=initialr,minsma=minr,maxsma=maxr,pa=ipa,hpa='no',ellip=iellip,hellip='no')
print 'Displaying isophotes from first pass. Hit q in DS9 window to quit'
iraf.isoexam(table=efile)
os.system('rm junk.txt')
iraf.tprint(table=efile,pwidth='INDEF',showhdr='no', Stdout='junk.txt')
os.system("awk '{print $2, $7, $9, $11, $13}' < junk.txt > junk2.txt")
#run ellipse a second time, keeping PA and ellip fixed
#allow user to adjust the radius where PA and ellip are measured
repeatflag=1
while (repeatflag > 0.1):
infile=open('junk2.txt','r')
for line in infile:
t=line.split()
if float(t[0]) > myradius:
newellip=float(t[1])
if newellip < .05:#min value that ellipse can handle
newellip=.05
newPA=float(t[2])
if newPA < -90:
newPA=newPA+180
elif newPA > 90:
newPA = newPA-180
#11 - X0, 13 - Y0
newxcenter=float(t[3])
newycenter=float(t[4])
break
s='rm '+efile
os.system(s)
iraf.ellipse(input=outfile1,output=efile,x0=newxcenter,y0=newycenter,hcenter='yes',sma0=initialr,minsma=minr,maxsma=maxr,pa=newPA,hpa='yes',ellip=newellip,hellip='yes')
print 'Displaying isophotes from second pass using r = ',myradius
print 'Hit q in the DS9 window to quit'
iraf.isoexam(table=efile)
flag=str(raw_input('Are you happy with the fit? y=yes n=no x=quit '))
flag=str(flag)
print 'this is what I think you typed ',flag
if flag.find('n') > -1:
flag2=str(raw_input('What is the problem? c=off-center r=set new radius x=quit '))
flag2=str(flag2)
if flag2.find('r') > -1:
myr=input('Enter new radius to use ')
myradius=float(myr)
s='rm '+efile
os.system(s)
repeatflag=1
elif flag2.find('x') > -1:
repeatflag=0
return
elif flag2.find('c') > -1:
s='mv *'+imprefix+'* OffCenter/'
print s
os.system(s)
repeatflag=0
print "repeatflag = ",repeatflag
elif flag.find('x') > -1:
repeatflag=0
print 'i think repeatflag = 0', repeatflag
return
else:
s='mv *'+imprefix+'* Finished/'
os.system(s)
repeatflag=0
print 'i think repeatflag = 0 ', repeatflag
print 'repeatflag = ',repeatflag
def runellipse(files,xcenter,ycenter,minr,ipa,initialr,maxr,iellip,nframe=1,myradius=15):
initialradius=myradius
#print 'got here'
#print files
for i in range(len(files)):
myradius=initialradius
mfile=files[i]
#mask image
outfile1='m'+mfile
if os.path.isfile(outfile1):
print "found masked file ",outfile1
print "skipping imedit and running ellipse interactively"
continueWithProgram=1
continueWithObject=1
else:
print "can't find masked file ",outfile1
print "running imedit"
continueWithProgram,continueWithObject=runimedit(mfile,outfile1,nframe)
if not continueWithProgram:
print "quitting program"
return
if not continueWithObject:
print "going on to next image"
continue
#run ellipse
t=mfile.split('.')
efile=t[0]+'.tab'
imprefix=t[0]
try:
os.remove(efile)
except OSError:
print 'everything is ok'
#continue
print "First pass through ellipse to find center"
iraf.ellipse(input=outfile1,output=efile,x0=xcenter,y0=ycenter,hcenter='no',sma0=initialr,minsma=minr,maxsma=maxr,pa=ipa,hpa='no',ellip=iellip,hellip='no',interactive='no')
#print 'Displaying isophotes from first pass. Hit q in DS9 window to quit'
#iraf.isoexam(table=efile)
os.system('rm junk.txt')
iraf.tprint(table=efile,pwidth='INDEF',showhdr='no', Stdout='junk.txt')
os.system("awk '{print $2, $7, $9, $11, $13}' < junk.txt > junk2.txt")
#run ellipse a second time, keeping PA and ellip fixed
#allow user to adjust the radius where PA and ellip are measured
infile=open('junk2.txt','r')
for line in infile:
t=line.split()
if float(t[0]) > myradius:
newxcenter=float(t[3])
newycenter=float(t[4])
break
s='rm '+efile
os.system(s)
#draw ellipse with ds9
iraf.display(outfile1,1)
(myellip,mypa)=findellipse(outfile1,newxcenter,newycenter)
flag2=str(raw_input('Do you want to skip this one? y=skip, any other key to continue '))
if flag2.find('y') > -1:
s='mv *'+imprefix+'* ../PeculiarGalaxies/'
print s
os.system(s)
continue
#run ellipse interactively
#allow user to repeat until satisfied with script
repeatflag=1
while repeatflag:
s='rm '+efile
os.system(s)
iraf.ellipse(input=outfile1,output=efile,x0=newxcenter,y0=newycenter,hcenter='yes',sma0=initialr,minsma=minr,maxsma=maxr,pa0=mypa,hpa='yes',ellip0=myellip,hellip='yes',interactive='no')
print 'Displaying isophotes from second pass using r = ',myradius
print 'Hit q in the DS9 window to quit'
iraf.isoexam(table=efile)
flag=str(raw_input('Are you happy with the fit? y=yes n=no x=quit '))
flag=str(flag)
print 'this is what I think you typed ',flag
if flag.find('n') > -1:
s='rm '+efile
os.system(s)
repeatflag=1
elif flag.find('x') > -1:
repeatflag=0
print 'i think repeatflag = 0', repeatflag
return
else:
s='mv *'+imprefix+'* ../Finished/'
os.system(s)
repeatflag=0
print 'i think repeatflag = 0 ', repeatflag
print 'repeatflag = ',repeatflag
def measure_disk(input_image,
xcenter,
ycenter,
ipa,
iellip,
initialr,
minr,
maxr,
zp,
band=0,
nframe=1,
myradius=25,
keepfixed=0,
einteractive=0,
mask_image=None):
print 'inside measure disk'
print 'mask image = ', mask_image
myradius = initialr
recentervalue = 'yes'
interactivevalue = 'no'
print '\n Running ellipse on ', input_image, '\n'
mfile = input_image
xcenter_cutout = xcenter
ycenter_cutout = ycenter
t = mfile.split('.')
efile = t[0] + '.tab'
efile_ascii = t[0] + '.dat'
imprefix = t[0]
print 'Running ellipse to fit isophotes to galaxy:', mfile
if os.path.exists(efile):
os.remove(efile)
if keepfixed:
print input_image, efile, xcenter_cutout, ycenter_cutout, initialr, minr, maxr, ipa
iraf.ellipse(input=input_image,
output=efile,
dqf=mask_image,
x0=xcenter_cutout,
y0=ycenter_cutout,
hcenter='yes',
recenter=recentervalue,
sma0=initialr,
minsma=minr,
maxsma=maxr,
pa=ipa,
hpa='yes',
ellip=iellip,
hellip='yes',
interactive='yes',
step=0.1,
linear='no')
else:
print "First pass, letting PA and e vary"
print input_image, efile, xcenter_cutout, ycenter_cutout, initialr, minr, maxr, ipa,
if mask_image == None:
iraf.ellipse(input=input_image,
output=efile,
x0=xcenter_cutout,
y0=ycenter_cutout,
hcenter='no',
recenter=0,
sma0=initialr,
minsma=minr,
maxsma=maxr,
pa=ipa,
hpa='no',
ellip=iellip,
hellip='no',
interactive=einteractive,
step=0.1,
linear='no')
else:
iraf.ellipse(input=input_image,
output=efile,
dqf=mask_image,
x0=xcenter_cutout,
y0=ycenter_cutout,
hcenter='no',
recenter=0,
sma0=initialr,
minsma=minr,
maxsma=maxr,
pa=ipa,
hpa='no',
ellip=iellip,
hellip='no',
interactive='yes',
step=0.1,
linear='no')
print 'Displaying isophotes from first pass. Hit q in DS9 window to quit'
iraf.isoexam(table=efile)
try:
os.system('rm tp.00*')
except:
print 'no tp.00? files to remove'
iraf.isoimap(input_image, table=efile)
# get final ellipse parameters to return to the user
if os.path.exists('junk.txt'):
os.remove('junk.txt')
iraf.tprint(table=efile, pwidth='INDEF', showhdr='no', Stdout='junk.txt')
s = "awk '{print $2, $7, $9, $11, $13}' < " + "junk.txt > " + "junk2.txt"
os.system(s)
infile = open('junk2.txt', 'r')
for line in infile:
t = line.split()
if float(t[0]) > myradius:
newellip = float(t[1])
if newellip < .05: # min value that ellipse can handle
newellip = .05
newPA = float(t[2])
if newPA < -90:
newPA = newPA + 180
elif newPA > 90:
newPA = newPA - 180
newxcenter = float(t[3])
newycenter = float(t[4])
if os.path.exists(efile_ascii):
os.remove(efile_ascii)
iraf.tprint(table=efile, pwidth='INDEF', showhdr='no', Stdout=efile_ascii)
return newxcenter, newycenter, newellip, newPA
def ellipse(image, outname, verbose=False, **kwargs):
"""run ellipse task
image : input image name
outname : output filename
Keywords:
*geompar*
x0, y0 -- required
ellip0 : initial ellipticity (default=0.2)
pa0 : initial PA in degrees ccw from +y (default=20)
sma0 : initial semi-major axis (default=10)
minsma : minimum sma (default=1)
maxsma : maximum sma (default='INDEF')
step : sma step size (default=0.1)
linear : linear sampling of sma? (default='no')
*controlpar*
conver :
"""
# verify input
if 'x0' not in kwargs.keys() or 'y0' not in kwargs.keys():
raise KeyError('x0 or y0 is not found')
# load packages
iraf.stsdas(_doprint=0, motd=False)
iraf.analysis(_doprint=0)
iraf.isophote(_doprint=0)
# reset all parameters
iraf.unlearn('ellipse', 'geompar', 'controlpar', 'samplepar')
iraf.ellipse.interactive = False
iraf.ellipse.xylearn = False # if True, it prompts input upon faling to find center
# geompar
iraf.ellipse.x0 = kwargs.pop('x0')
iraf.ellipse.y0 = kwargs.pop('y0')
iraf.ellipse.ellip0 = kwargs.pop('ellip0', 0.2)
iraf.ellipse.pa0 = kwargs.pop('pa0', 20.0)
iraf.ellipse.sma0 = kwargs.pop('sma0', 10.0)
iraf.ellipse.minsma = kwargs.pop('minsma', 1.)
iraf.ellipse.maxsma = kwargs.pop('maxsma', 'INDEF')
iraf.ellipse.step = kwargs.pop('step', 0.1)
iraf.ellipse.linear = kwargs.pop('linear', 0)
iraf.ellipse.verbose = verbose
# controlpar
iraf.ellipse.conver = kwargs.pop('conver', 0.05)
iraf.ellipse.minit = kwargs.pop('minit', 10)
iraf.ellipse.maxit = kwargs.pop('maxit', 50)
iraf.ellipse.hcenter = kwargs.pop('hcenter', 'no')
# samplepar
iraf.ellipse.tsample = kwargs.pop('tsample', 'none')
iraf.ellipse.harmonics = kwargs.pop('harmonics', 'none')
if verbose:
iraf.lparam('ellipse')
iraf.lparam('geompar')
iraf.lparam('controlpar')
iraf.lparam('samplepar')
# run ellipse
tempname = shorten_iauname(image) + str(uuid.uuid4()) + '.tab'
try:
iraf.ellipse(image, tempname)
# print ascii table
iraf.tprint(tempname, pwidth='INDEF', Stdout=outname)
os.remove(tempname)
except:
print 'ellipse failed'
def runEllipse24UsingSDSS(self):
agcnumber=self.agcnumber[self.ellipseflag]
#mcutoutpath='/home/rfinn/research/LocalClusters/MaskedCutouts/'+self.prefix+'/'
mcutoutpath='/home/rfinn/research/LocalClusters/MaskedCutouts/'+self.prefix+'/'
os.chdir(mcutoutpath)
s=outpathroot+'research/LocalClusters/Ellipse24UsingSDSS/'+self.prefix
try:
os.mkdir(s)
except OSError:
pass
for i in range(len(agcnumber)):
print agcnumber[i]
sdssEllipseTable= '/home/rfinn/research/LocalClusters/EllipseTables/'+self.prefix+'/'+self.prefix+'-'+str(agcnumber[i])+'-cutout-sdss.tab'
#mipsImage=mcutoutpath+'m'+self.prefix+'-'+str(agcnumber[i])+'-cutout-24-rot.fits'
mipsImage='m'+self.prefix+'-'+str(agcnumber[i])+'-cutout-24-rot.fits'
#outim=cutoutpath+self.prefix+'-'+str(agcSpiral[i])+'-cutout-sdss.fits \n'
os.system('rm junk.txt')
if os.path.isfile(sdssEllipseTable):
iraf.tprint(table=sdssEllipseTable,pwidth='INDEF',showhdr='no', Stdout='junk.txt')
os.system("awk '{print $2, $7, $9, $11, $13}' < junk.txt > junk2.txt")
else:
print 'Warning: ',sdssEllipseTable,' does not exist'
sdssEllipseTable= '/home/rfinn/research/LocalClusters/EllipseTables/'+self.prefix+'/'+self.prefix+'-'+str(agcnumber[i])+'-cutout-sdss.dat'
s="awk '{print $2, $7, $9, $11, $13}' <"+sdssEllipseTable+" > junk2.txt"
os.system(s)
#run ellipse a second time, keeping PA and ellip fixed
infile=open('junk2.txt','r')
for line in infile:
t=line.split()
if float(t[0]) > myradius:
newellip=float(t[1])
if newellip < .05:#min value that ellipse can handle
newellip=.05
newPA=float(t[2])
if newPA < -90:
newPA=newPA+180
elif newPA > 90:
newPA = newPA-180
#11 - X0, 13 - Y0
newxcenter=float(t[3])
newycenter=float(t[4])
t=mipsImage.split('.')
efile=self.prefix+'-'+str(agcnumber[i])+'.24UsingSDSS.tab'
copyefile=outpathroot+'research/LocalClusters/Ellipse24UsingSDSS/'+self.prefix+'/'+self.prefix+'-'+str(agcnumber[i])+'.24UsingSDSS.tab'
#iraf.ellipse(input=mipsImage,output=efile,inellip=sdssEllipseTable)#trying to use sdss input
if os.path.exists(efile):
s=efile+' exists. Rerun? (y=yes, any key to skip)'
rerunFlag=raw_input(s)
if rerunFlag.find('y') > -1:
os.remove(efile)
iraf.ellipse(input=mipsImage,output=efile,x0=xcenter,y0=ycenter,hcenter='yes',recenter='no',sma0=initialr,minsma=minr,maxsma=maxr,pa=newPA,hpa='yes',ellip=newellip,hellip='yes')
else:
continue
else:
iraf.ellipse(input=mipsImage,output=efile,x0=xcenter,y0=ycenter,hcenter='yes',recenter='no',sma0=initialr,minsma=minr,maxsma=maxr,pa=newPA,hpa='yes',ellip=newellip,hellip='yes')
#outfile24=homedir+'research/LocalClusters/EllipseTables/'+self.prefix+'/'+self.prefix+'-'+str(agcSpiral[i])+'-cutout-24-rot.dat \n'
print 'Displaying isophotes from ellipse fit. Hit q in DS9 window to quit'
iraf.isoexam(table=efile)
s='cp '+efile+' '+copyefile
print s
os.system(s)
def measure_disk(input_image,xcenter,ycenter,ipa,iellip,initialr,minr,maxr,zp,band=0,nframe=1,myradius=20,keepfixed=0,einteractive=0,mask_image=None):
print 'inside measure disk'
print 'mask image = ',mask_image
#myradius=initialr
recentervalue='yes'
interactivevalue='yes'
print '\n Running ellipse on ',input_image,'\n'
print ' Enter ? for a list of options \n'
print ' Enter c to continue fitting ellipses automatically \n'
mfile=input_image
xcenter_cutout=xcenter
ycenter_cutout=ycenter
t=mfile.split('.')
efile=t[0]+'.tab'
efile_ascii=t[0]+'.dat'
imprefix=t[0]
print 'Running ellipse to fit isophotes to galaxy:',mfile
if os.path.exists(efile):
os.remove(efile)
if keepfixed:
print input_image,efile,xcenter_cutout,ycenter_cutout,initialr,minr,maxr,ipa
iraf.ellipse(input=input_image,output=efile,dqf=mask_image,x0=xcenter_cutout,y0=ycenter_cutout,hcenter='yes',recenter=recentervalue,sma0=initialr,minsma=minr,maxsma=maxr,pa=ipa,hpa='yes',ellip=iellip,hellip='yes',interactive='yes',step=0.1,linear='no')
else:
print "First pass, letting PA and e vary"
print input_image,efile,xcenter_cutout,ycenter_cutout,initialr,minr,maxr,ipa,
if mask_image == None:
iraf.ellipse(input=input_image,output=efile,x0=xcenter_cutout,y0=ycenter_cutout,hcenter='no',recenter='yes',sma0=initialr,minsma=minr,maxsma=maxr,pa=ipa,hpa='no',ellip=iellip,hellip='no',interactive='yes',step=0.1,linear='no')
else:
iraf.ellipse(input=input_image,output=efile,dqf=mask_image,x0=xcenter_cutout,y0=ycenter_cutout,hcenter='no',recenter=0,sma0=initialr,minsma=minr,maxsma=maxr,pa=ipa,hpa='no',ellip=iellip,hellip='no',interactive='yes',step=0.1,linear='no')
print 'Displaying isophotes from first pass. Hit q in DS9 window to quit'
iraf.isoexam(table=efile)
try:
os.system('rm tp.00*')
except:
print 'no tp.00? files to remove'
iraf.isoimap(input_image,table=efile)
# get final ellipse parameters to return to the user
if os.path.exists('junk.txt'):
os.remove('junk.txt')
iraf.tprint(table=efile,pwidth='INDEF',showhdr='no', Stdout='junk.txt')
s="awk '{print $2, $7, $9, $11, $13}' < "+"junk.txt > "+"junk2.txt"
os.system(s)
redo = 1
while redo:
infile=open('junk2.txt','r')
print 'within redo loop'
for line in infile:
t=line.split()
if float(t[0]) > myradius:
#print 'got here',myradius, t[0]
newellip=float(t[1])
if newellip < .05: # min value that ellipse can handle
newellip=.05
newPA=float(t[2])
if newPA < -90:
newPA=newPA+180
elif newPA > 90:
newPA = newPA-180
newxcenter=float(t[3])
newycenter=float(t[4])
break
infile.close()
print 'ellipse values at r = ',myradius
print ' ellip = ',newellip
print ' PA = ',newPA
t=raw_input('are you happy? (n = no, enter to continue) ')
if t.find('n') >-1:
newr=raw_input('Enter radius where ellipse best represents galaxy ')
myradius=float(newr)
else:
redo = 0
continue
if os.path.exists(efile_ascii):
os.remove(efile_ascii)
iraf.tprint(table=efile,pwidth='INDEF',showhdr='no', Stdout=efile_ascii)
return newxcenter,newycenter,newellip,newPA
import os, sys
iraf.stsdas()
iraf.analysis()
iraf.toolbox()
iraf.ttools()
matchstring = sys.argv[1]
#flag = str(raw_input('Which files? a=24 b=sdss '))
#flag = str(flag)
#if flag.find('a') > -1:
# tabfiles = glob.glob('*cutout-24-rot.tab')
#if flag.find('b') > -1:
# tabfiles = glob.glob('*cutout-sdss.tab')
tabfiles = glob.glob(matchstring)
#tabfiles=glob.glob('*.tab')
print matchstring
#print tabfiles
for i in range(len(tabfiles)):
tfile = tabfiles[i] #
nfile = tfile.split('.tab')
dfile = nfile[0] + '.dat'
print tfile, ' -> ', dfile
iraf.tprint(table=tfile,
pwidth='INDEF',
showhdr='no',
showunits='no',
Stdout=dfile)
def measure_disk(input_image,
xcenter,
ycenter,
ipa,
iellip,
initialr,
minr,
maxr,
zp,
band=0,
nframe=1,
myradius=20,
keepfixed=0,
einteractive=0,
mask_image=None):
print 'inside measure disk'
print 'mask image = ', mask_image
#myradius=initialr
recentervalue = 'yes'
interactivevalue = 'yes'
print '\n Running ellipse on ', input_image, '\n'
print ' Enter ? for a list of options \n'
print ' Enter c to continue fitting ellipses automatically \n'
mfile = input_image
xcenter_cutout = xcenter
ycenter_cutout = ycenter
t = mfile.split('.')
efile = t[0] + '.tab'
efile_ascii = t[0] + '.dat'
imprefix = t[0]
print 'Running ellipse to fit isophotes to galaxy:', mfile
if os.path.exists(efile):
os.remove(efile)
if keepfixed:
print input_image, efile, xcenter_cutout, ycenter_cutout, initialr, minr, maxr, ipa
iraf.ellipse(input=input_image,
output=efile,
dqf=mask_image,
x0=xcenter_cutout,
y0=ycenter_cutout,
hcenter='yes',
recenter=recentervalue,
sma0=initialr,
minsma=minr,
maxsma=maxr,
pa=ipa,
hpa='yes',
ellip=iellip,
hellip='yes',
interactive='yes',
step=0.1,
linear='no')
else:
print "First pass, letting PA and e vary"
print input_image, efile, xcenter_cutout, ycenter_cutout, initialr, minr, maxr, ipa,
if mask_image == None:
iraf.ellipse(input=input_image,
output=efile,
x0=xcenter_cutout,
y0=ycenter_cutout,
hcenter='no',
recenter='yes',
sma0=initialr,
minsma=minr,
maxsma=maxr,
pa=ipa,
hpa='no',
ellip=iellip,
hellip='no',
interactive='yes',
step=0.1,
linear='no')
else:
iraf.ellipse(input=input_image,
output=efile,
dqf=mask_image,
x0=xcenter_cutout,
y0=ycenter_cutout,
hcenter='no',
recenter=0,
sma0=initialr,
minsma=minr,
maxsma=maxr,
pa=ipa,
hpa='no',
ellip=iellip,
hellip='no',
interactive='yes',
step=0.1,
linear='no')
print 'Displaying isophotes from first pass. Hit q in DS9 window to quit'
iraf.isoexam(table=efile)
try:
os.system('rm tp.00*')
except:
print 'no tp.00? files to remove'
iraf.isoimap(input_image, table=efile)
# get final ellipse parameters to return to the user
if os.path.exists('junk.txt'):
os.remove('junk.txt')
iraf.tprint(table=efile, pwidth='INDEF', showhdr='no', Stdout='junk.txt')
s = "awk '{print $2, $7, $9, $11, $13}' < " + "junk.txt > " + "junk2.txt"
os.system(s)
redo = 1
while redo:
infile = open('junk2.txt', 'r')
print 'within redo loop'
for line in infile:
t = line.split()
if float(t[0]) > myradius:
#print 'got here',myradius, t[0]
newellip = float(t[1])
if newellip < .05: # min value that ellipse can handle
newellip = .05
newPA = float(t[2])
if newPA < -90:
newPA = newPA + 180
elif newPA > 90:
newPA = newPA - 180
newxcenter = float(t[3])
newycenter = float(t[4])
break
infile.close()
print 'ellipse values at r = ', myradius
print ' ellip = ', newellip
print ' PA = ', newPA
t = raw_input('are you happy? (n = no, enter to continue) ')
if t.find('n') > -1:
newr = raw_input(
'Enter radius where ellipse best represents galaxy ')
myradius = float(newr)
else:
redo = 0
continue
if os.path.exists(efile_ascii):
os.remove(efile_ascii)
iraf.tprint(table=efile, pwidth='INDEF', showhdr='no', Stdout=efile_ascii)
return newxcenter, newycenter, newellip, newPA
