error of GSFLAT in gemini package

[bai]

Hi all,

I have the same error to jorge (http://iraf.net/forums/viewtopic.php?t=89972&start=0&postdays=0&postorder=asc&highlight=),
when I ran gsflat task.

----------------------------------------------------------------------------
GSREDUCE: Calling GMOSAIC
GLOGINIT ERROR: 101 Unable to access file 'gmos.log'..
GSREDUCE: returned from GMOSAIC.
Warning: cannot rename `tmpimage24510ec.fits' -> `gsflat.fits'
GSREDUCE: Calling GSAPPWAVE
--------------------------------------------------------------------------------

I have the write permissions in the current working directory and I delete all *.par files in .../uparm, but the problems still continue.

The version of IRAF is 2.14.1 and gemini is 1.11.1.

I hope someone can give me help.

Best regards,
Bai

[emma]

Hello Bai,

Please could you supply the following information:

1) your call to gsflat and the list of parameters you used
2) the output of "show home"
3) the output of "show uparm"
4) the path to your login.cl and uparm directory

Many thanks,

Emma

[bai]

Hi Emma,

Thanks for your reply.

I change the version to iraf 2.12.2 and Gemini 1.9 and add some lines into GMOSgratings.dat. The error never come again. I don't know why I have to use older version.

1) call to gsflat and the list of parameters

inflats,s,a,"flat*",,,"Input flatfields"
specflat,s,a,"nflat",,,"Output normalized flat (MEF)"
fl_slitcorr,b,h,no,,,"Correct output for Illumination/Slit-Function"
slitfunc,s,h,"",,,"Slit Function (MEF output of gsslitfunc)"
fl_keep,b,h,no,,,"Keep imcombined flat?"
combflat,s,h,"",,,"Filename for imcombined flat"
fl_over,b,h,no,,,"Subtract overscan level"
fl_trim,b,h,yes,,,"Trim off overscan region"
fl_bias,b,h,yes,,,"Subtract bias image"
fl_dark,b,h,no,,,"Subtract (scaled) dark image"
fl_qecorr,b,h,no,,,"QE correct the input images? (NOT YET IMPLEMENTED)"
fl_fixpix,b,h,yes,,,"Interpolate across chip gaps"
fl_vardq,b,h,no,,,"Create variance and data quality frames"
bias,s,h,"bias",,,"Bias image"
dark,s,h,"",,,"Dark image"
key_exptime,s,h,"EXPTIME",,,"Exposure time header keyword"
key_biassec,s,h,"BIASSEC",,,"Header keyword for overscan strip image section"
key_datasec,s,h,"DATASEC",,,"Header keyword for data section (excludes the overscan)"
rawpath,s,h,"",,,"GPREPARE: Path for input raw images"
sci_ext,s,h,"SCI",,,"Name of science extension"
var_ext,s,h,"VAR",,,"Name of variance extension"
dq_ext,s,h,"DQ",,,"Name of data quality extension"
key_mdf,s,h,"MASKNAME",,,"Header keyword for the MDF"
mdffile,s,h,"",,,"MDF to use if keyword not found"
mdfdir,s,h,"gmos$data/",,,"MDF database directory"
bpm,s,h,"",,,"Name of bad pixel mask file or image"
gaindb,s,h,"default",,,"Database with gain data"
gratingdb,s,h,"gmos$data/GMOSgratings.dat",,,"Gratings database file"
filterdb,s,h,"gmos$data/GMOSfilters.dat",,,"Filters database file"
bpmfile,s,h,"gmos$data/chipgaps.dat",,,"Info on location of chip gaps"
refimage,s,h,"",,,"Reference image for slit positions"
qe_refim,s,h,"",,,"QE wavelength reference image. (NOT YET IMPLEMENTED)"
fl_keep_qeim,b,h,yes,,,"Keep QE correction? (NOT YET IMPLEMENTED)"
qe_corrpref,s,h,"qecorr",,,"Prefix for QE correction files. (NOT YET IMPLEMENTED)"
qe_corrimages,s,h,"",,,"Name for QE correction data. (NOT YET IMPLEMENTED)"
qe_data,s,h,"gmosQEfactors.dat",,,"Data file that contains QE information. (NOT YET IMPLEMENTED)"
qe_datadir,s,h,"gmos$data/",,,"Directory containg QE data file. (NOT YET IMPLEMENTED)"
sat,s,h,"default",,,"Saturation level in raw images"
xoffset,r,h,INDEF,,,"X offset in wavelength [nm]"
yoffset,r,h,INDEF,,,"Y offset in unbinned pixels"
yadd,r,h,0.,,,"Additional pixels to add to each end of MOS slitlet lengths"
wave_limit,r,h,INDEF,,,"Upper wavelength limit of cut spectra (nm). Only for use with fl_detec=no."
fl_usegrad,b,h,no,,,"Use gradient method to find MOS slits"
fl_emis,b,h,no,,,"mask emission lines from lamp (affected pixels set to 1. in output)"
nbiascontam,s,h,"default",,,"Number of columns removed from overscan region"
biasrows,s,h,"default",,,"Rows to use for overscan region"
minval,r,h,INDEF,,1.,"Minimum pixel value in normalized flat"
fl_inter,b,h,no,,,"Fit response interactively?"
fl_answer,b,h,yes,,,"Continue interactive fitting?"
fl_detec,b,h,no,,,"Fit response detector by detector rather than slit by slit?"
fl_seprows,b,h,yes,,,"Fit and normalize each row separately?"
function,s,h,"spline3",spline3|legendre|chebyshev|spline1,,"Fitting function for response"
order,s,h,"15",,,"Order of fitting function, minimum value=1"
low_reject,r,h,3.,,,"Low rejection in sigma of response fit"
high_reject,r,h,3.,,,"High rejection in sigma of response fit"
niterate,i,h,2,,,"Number of rejection iterations in response fit"
combine,s,h,"average",,,"Combination operation"
reject,s,h,"avsigclip",,,"Rejection algorithm"
masktype,s,h,"goodvalue",none|goodvalue,,"Mask type"
maskvalue,r,h,0.,,,"Mask value"
scale,s,h,"mean",,,"Image scaling"
zero,s,h,"none",,,"Image zeropoint offset"
weight,s,h,"none",,,"Image weights"
statsec,s,h,"",,,"Statistics section"
lthreshold,r,h,INDEF,,,"Lower threshold"
hthreshold,r,h,INDEF,,,"Upper threshold"
nlow,i,h,1,0,,"minmax: Number of low pixels to reject"
nhigh,i,h,1,0,,"minmax: Number of high pixels to reject"
nkeep,i,h,0,0,,"Minimum to keep or maximum to reject"
mclip,b,h,yes,,,"Use median in sigma clipping algorithms?"
lsigma,r,h,3.,,,"Lower sigma clipping factor"
hsigma,r,h,3.,,,"Upper sigma clipping factor"
key_ron,s,h,"RDNOISE",,,"Keyword for readout noise in e-"
key_gain,s,h,"GAIN",,,"Keyword for gain in electrons/ADU"
ron,r,h,3.5,0.,,"Readout noise rms in electrons"
gain,r,h,2.2,1.0000000000000E-5,,"Gain in e-/ADU"
snoise,s,h,"0.0",,,"ccdclip: Sensitivity noise (electrons)"
sigscale,r,h,0.1,,,"Tolerance for sigma clipping scaling correction"
pclip,r,h,-0.5,,,"pclip: Percentile clipping parameter"
grow,r,h,0.,,,"Radius (pixels) for neighbor rejection"
ovs_flinter,b,h,no,,,"Interactive overscan fitting?"
ovs_med,b,h,no,,,"Use median instead of average in column bias?"
ovs_func,s,h,"chebyshev",spline3|legendre|chebyshev|spline1,,"Overscan fitting function"
ovs_order,i,h,1,,,"Order of overscan fitting function"
ovs_lowr,r,h,3.,,,"Low sigma rejection factor"
ovs_highr,r,h,3.,,,"High sigma rejection factor"
ovs_niter,i,h,2,,,"Number of rejection iterations"
fl_double,b,h,no,,,"Make double flats for nod-and-shuffle science"
nshuffle,i,h,0,,,"Number of shuffle pixels (unbinned)"
logfile,s,h,"/home/by/use_iraf/Q49/By_m101/tes/gmos.log",,,"Logfile name"
verbose,b,h,yes,,,"Verbose"
status,i,h,1,,,"Exit status (0=good)"
scanfile,*struct,h,"",,,"Internal use only"
mode,s,h,"ql",,,

2) the output of "show home"

/home/by/

3) the output of "show uparm"

home$uparm/

4) the path to my login.cl and uparm directory

/home/by/use_iraf/login.cl
/home/by/uparm



Thanks for your time.

Bai

[emma]

Hello Bai,

Thank you for the information. You should not have to resort to using old versions of IRAF and the Gemini IRAF package.

Your home and uparm variables look good, as does the path to your uparm directory. However, I'm not sure why your login.cl is located in a different directory to your uparm directory. Did you move the login.cl file? Did you edit that file in any way? When you started iraf, were you located in the /home/by/use_iraf/ directory?

Can you confirm that you have write permissions to the /home/by/use_iraf/Q49/By_m101/tes/ directory (i.e., where the logfile is written to)?

I just ran gsflat on some random GMOS flats using the same parameters that you are using (including using a path to the logfile) and everything worked fine. Do you get the same error if you just set gsflat.logfile="mylog.log"?

Many thanks,

Emma

[bai]

Hello Emma,

I still have the recent version of IRAF on my laptop.

I did not move login file. I just changed some parameters in login.cl.

set home ="/home/by/"
set uparm ="home$uparm"

I always start IRAF in the /home/by/use_iraf/ and I have the write permissions to /home/by/use_iraf/Q49/By_m101/tes/.

The logfile was reset to another name and the error still came out.

I do not know whether there are some compatibility bugs with my system (Fedora8), csh, or xgterm.

Thanks a lot,

Bai

[emma]

Hello again Bai,

There is a task in the Gemini IRAF package called install_check.cl that can be used to check a Gemini IRAF installation. You can define and execute the task by typing the following at the IRAF or PyRAF prompt:

[bai]

Hi Emma,

There are some errors when I run the install_check.cl.

1) It seems that I don't have extern_check.log.

/home/iraf/iraf/
redhat
NOAO/IRAF V2.14.1
/iraf/extern/gemini/
ERROR: No such environment variable
called as: `show (extern)'
"show extern | tee ("extern_check.log", out_type="text", append+)"
line 30: gemini$install_check_f.cl
called as: `install_check ()'


2) After I comment out the 30th line, it displays that some packages are not the most recent versions.

/home/iraf/iraf/
redhat
NOAO/IRAF V2.14.1
/iraf/extern/gemini/
IRAF installation 2.14.1 with patch is up to date. PASS
stsdas v3.14 installed. PASS
tables v3.14 installed. PASS
no files found
fitsutil package not up to date. FAIL.
gmisc package not up to date. FAIL
gemini version: v1.11.1
gemini package less than v1.11. Need to update. FAIL
Linux localhost.localdomain 2.6.23.1-42.fc8 #1 SMP Tue Oct 30 13:55:12 EDT 2007 i686 i686 i386 GNU/Linux


Should I reinstall the Fitsutil and the Gmisc?

Thanks,
Bai

[emma]

Hi Bai,

Apologies about the bug, I will fix that for the next release.

I noticed that your iraf installation is located in /home/iraf/iraf/ but the Gemini IRAF package is installed in /iraf/extern/gemini/. Do you have two installations of IRAF on your computer? Do you have an /iraf/iraf/ directory that contains another installation of IRAF? Where are all your other external packages located? Are they all in /home/iraf/extern/ or are they in /iraf/extern/? Which extern.pkg file did you edit?

The requirements for the Gemini IRAF package can be found at http://www.gemini.edu/sciops/data-and-results/processing-software/requirements. It is required that fitsutil and gmisc be installed for the Gemini IRAF package to work correctly.

Many thanks,

Emma

[bai]

Hi Emma,

I interlinked the folder /iraf to /home/iraf, so every user can use iraf.
I only have one IRAF, version 2.14.1, on the computer and all the IRAF packages are installed in the directory /iraf/extern/.
/home/iraf/extern/ and /iraf/extern/ are the same folders.

# External (non core-system) packages. To install a new package, add the
# two statements to define the package root directory and package task,
# then add the package helpdb to the `helpdb' list.

reset noao = iraf$noao/
task noao.pkg = noao$noao.cl

#reset tables = /iraf/extern/tables/
#task tables.pkg = tables$tables.cl

reset helpdb = "lib$helpdb.mip\
,noao$lib/helpdb.mip\
# ,tables$lib/helpdb.mip\
,fitsutil$lib/helpdb.mip\
,ctio$lib/helpdb.mip\
,gemini$lib/helpdb.mip\
,stsdas$lib/helpdb.mip\
,gmisc$lib/helpdb.mip\
"
reset zphot = /iraf/zphot/
task $zphot ="zphot$zphot.cl"

reset keck = /iraf/keck/
task $keck ="keck$keck.cl"

reset mscred = /iraf/extern/mscred/
task mscred.pkg = mscred$mscred.cl

reset fitsutil = /iraf/extern/fitsutil/
task fitsutil.pkg = fitsutil$fitsutil.cl

reset tables = /iraf/extern/tables/
task tables.pkg = tables$tables.cl

reset ctio = /iraf/extern/ctio/
task ctio.pkg = ctio$ctio.cl

reset gemini = /iraf/extern/gemini/
task gemini.pkg = gemini$gemini.cl

reset stsdas = /iraf/extern/stsdas/
task stsdas.pkg = stsdas$stsdas.cl
task apropos = stsdas$apropos.cl
#if (access("stsdas$lib")) reset helpdb= ( envget("helpdb") + ",stsdas$lib/helpdb.mip" )

reset gmisc = /iraf/extern/gmisc/
task gmisc.pkg = gmisc$gmisc.cl

reset nmisc = /iraf/extern/nmisc/
task $nmisc.pkg = nmisc$nmisc.cl


keep



The Gemini package is great. No error comes out in the old version. Data is processed accurately and efficiently. It is happy for me to use the package to deal with data.


Thanks for all your hard works on the package.

Bai

[emma]

Hi again Bai,

Are you able to provide me with details of your installation procedure? Did you get any errors when you ran the install script? I looked through http://iraf.net/irafdocs/pciraf.pdf and noted that the $iraf variable was set prior to running the install script. I assume this is when you set $iraf to /home/iraf/iraf/? Was the /iraf link set prior to running the install script?

Are you in a position to install IRAF in the standard location (i.e., /iraf) as a test to see if that solves the problem?

When you are testing the two different versions of the Gemini IRAF package, how are you switching between them? Do you have both versions installed somewhere on your machine or are you overwriting the installation in the gemini directory in the extern directory each time?

Finally, are you able to provide me with a copy of your ~/.cshrc file? It is possible that something is set in this file that could be causing the problem.

Many thanks,

Emma

[bai]

Hi Emma,

I can not remember the details of my procedure, but I am sure no error came when I installed IRAF. The procedure was something like:

(IRAF user)
mkdir /iraf/irafbin
mkdir /iraf/irafbin/bin.redhat
mkdir /iraf/irafbin/noao.bin.redhat
mkdir /iraf/extern
mkdir /iraf/extern/mscred
mkdir /iraf/extern/stsdas
mkdir /iraf/x11iraf
setenv iraf /iraf/iraf/local
cd /iraf/iraf/unix/hlib/
source irafuser.csh
./install -n
(root user)
su
Password:
./install
(IRAF user)
mkiraf

The older version of Gemini package was installed on my desktop, while resent version on my laptop.


The .cshrc contains:

# .cshrc

# User specific aliases and functions

alias rm 'rm -i'
alias cp 'cp -i'
alias mv 'mv -i'



Thanks a lot.

Bai

[emma]

Hi Bai,

Thank you for the information. I am a little confused ... you said that you have IRAF installed in /home/iraf ... if that was the case, then when you made all the IRAF directories, wouldn't you have made /home/iraf/irafbin etc? Also, the install_check output indicates that you set iraf to /home/iraf/iraf/ (rather than /iraf/iraf/local as you mentioned in your last message). I do think the problem is related to your IRAF installation (especially because I am unable to reproduce the problem).

Would it be possible for you to re-install IRAF on your laptop in the standard location (i.e., /iraf) to see if that solves the problem? I can help you through this, if required. Just let me know

Many thanks,

Emma

[emma]

Hi Bai,

I just wanted to let you know that I have been working with another user via the Gemini HelpDesk who had a very similar problem to you (they even had the same setup!), and a fresh install solved their problem

Many thanks,

Emma