Problem while opening stsdasbc

[sabyasachiiucaa]

Hi,

I am using iraf in a virtual ubuntu and inside Ureka.

When I am trying to open stsdasbc after installation it shows the following error:

**Initializing SAMP .... No Hub Available

  dataio.     language.   obsolete.   softools.   utilities.  
  dbms.       lists.      plot.       stsdasbc.   vo.         
  images.     noao.       proto.      system.     

vocl> stsdasbc/ : stsdasbc/ ^ ERROR: syntax error vocl> stsdasbc ERROR: task `stsdasbc' has no param file

What could be the reason?

[suvadip31]

Hi, I am new to ISOFIT. I am facing the same problem. Can anyone please tell me how to fix the error? Regards, Suvadip

[BogdanCiambur]

Hello,

In the 'stsdasbc' directory, rename all the files starting with 'stsdas...' by 'stsdasbc'. For example: 'stsdas.par' should be 'stsdasbc.par'. Do the same for the .cl, file, etc.

Then, to use cmodel, add the attached file (cmodel.cl) in stsdasbc/pkg/analysis/isophote/

This should work, please let me know if it does, so that I can update the repository with this information.

Good luck, cheers! cmodel.cl.tar.gz

[suvadip31]

Hi, Thank you very much for your reply. I tried but I get another error. vocl> stsdasbc

ERROR: task 'pyexecute' has no param file

"pyexecute("stsdas$addpath.py",verbose=no)"

line 33: stsdasbc$stsdasbc.cl

called as: 'stsdasbc ()'

regards, Suvadip

[suvadip31]

Hi Bogdan, Can you please advise me on how to fix the error?

Regards, Suvadip

[BogdanCiambur]

Hi Suvadip,

Hmm, that's strange. Try including the attached file (pyexecute.cl) in the /stsdasbc/ directory.

Did you install IRAF through Ureka? Note that I haven't tested Isofit on the Ureka installation, which may have additional/different things/settings than the standard installation, described in the readme above...

If the file attached still doesn't work, there are a few other steps we can try (don't worry, it can be done, I just reinstalled it on a new machine a few days ago):

1. If installed IRAF through Ureka, try instead the normal installation procedure (see step by step tutorial here for example: http://www.astronomy.ohio-state.edu/~khan/iraf/iraf_step_by_step_installation). This is the tested way, and it works.

2. If still getting errors like the one above, I will simply make available the entire /stsdas/ directory on the repository.

3. Alternatively, you can also try to re-generate the binaries with mkpkg. (Cross that bridge if we must...).

Anyway, do let me know if you manage to get it running, and what works, this is important feedback for me to improve the installation instructions.

Cheers, Bogdan

pyexecute.cl.tar.gz

[suvadip31]

Hi Bogdan,

Thank you very much. I tried with replacing the pyexecute.cl file but it shows the same error. Actually, first I installed IRAF normally. Then I installed iraf using ureka while installing PROFILER (Thank you very much for the software). Is that causing a problem? Can you please upload the whole stsdas directory in the repository? I am attaching a screenshot of my stsdasbc directory.

Regards, Suvadip

On Sat, Sep 16, 2017 at 2:46 PM, BogdanCiambur notifications@github.com wrote:

Hi Suvadip,

Hmm, that's strange. Try including the attached file (pyexecute.cl) in the /stsdasbc/ directory.

Did you install IRAF through Ureka? Note that I haven't tested Isofit on the Ureka installation, which may have additional/different things/settings than the standard installation, described in the readme above...

If the file attached still doesn't work, there are a few other steps we can try (don't worry, it can be done, I just reinstalled it on a new machine a few days ago):

1.

If installed IRAF through Ureka, try instead the normal installation procedure (see step by step tutorial here for example: http://www.astronomy.ohio-state.edu/~khan/iraf/iraf_ step_by_step_installation http://www.astronomy.ohio-state.edu/%7Ekhan/iraf/iraf_step_by_step_installation). This is the tested way, and it works. 2.

If still getting errors like the one above, I will simply make available the entire /stsdas/ directory on the repository. 3.

Alternatively, you can also try to re-generate the binaries with mkpkg. (Cross that bridge if we must...).

Anyway, do let me know if you manage to get it running, and what works, this is important feedback for me to improve the installation instructions.

Cheers, Bogdan

pyexecute.cl.tar.gz https://github.com/BogdanCiambur/ISOFIT/files/1308192/pyexecute.cl.tar.gz

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[suvadip31]

[BogdanCiambur]

It's OK to have Ureka installed as well in addition to the standard IRAF installation. Ureka installs everything in a separate place, and as long as you don't call the Ureka environment (ur_setup, I think) they should both work perfectly fine in parallel.

OK, there seem to be some wrong paths somewhere. Let's try some other steps, in order:

1.) Unpack the attachment and place all the files in its contents in /stsdasbc, replacing as required. Try it now.

stsdasbc_files.tar.gz

If you still get errors, try to re-compile the package:

2a.) Remove the file x_isophote.e from all your /bin.* folders in /stsdasbc, then:

2b.) Do the following in a terminal:

cd /path/to/stsdasbc (replace with actual path) isofit (load the isofit environment) mkpkg relink

2c.) Alternatively (or if it complains):

cd /path/to/stsdasbc/pkg/analysis/isophote isofit mkpkg relink

3.) If this doesn't work either, replace /stsdasbc with the one I will upload (it will be a web-link, since it's too large), and try. You may need to repeat steps 2* above.

4.) If you manage to get the task stsdasbc to work (one of the above steps SHOULD work), it may still be the case that when you try to run ellipse, you get the error message "error ... cannot open connected subprocess x_isophote.e" This is due to an incompatibility between the 32-bit x_isophote.e library and a 64 bit system. One possible workaround is to (re-)install iraf on 32-bit (from the link I sent you before), then in /iraf/iraf/ create a directory called /bin.linux64 (if you have a 64 bit system) and copy all the contents of /bin.linux inside.

[suvadip31]

Hi Bogdan,

Thank you for your reply. I copied all the files you attached in stsdasbc directory but now it says:

ERROR: task fitsio has no param file

called as: cl ()

My machine is 64 bit. So I reinstalled IRAF (64 bit) but the problem persists. One thing I noticed that after the command source ~/.bashrc, when I tried the isofit command, it says that the permission is denied.

And according to 2a. step, should I put the x.isophote.e file(provided by you in the repository) only in bin.linux64 or all bin.* files? I checked that in the bin.linux directory there is already a x.isophote.e file(whose size is different compared to what is provided by you in the repository. so I think that file is different.).

Anyway I removed all the x.isohote.e files from the stsdasbc directory. Opened a terminal inside stsdasbc directory and then did:

isofit

mkpkg relink

But it shows me some warning: Warning, mkpkg line 247: could not find mkpkg module or label 'relink'

Warning, mkpkg line 247: no entry in mkpkg file for 'relink'

So I opened a terminal inside isophote directory of stsdasbc and did:

isofit

mkpkg relink

but it says some warning:

Warning, mkpkg line 28: moduleisophote' not found or returned error`

Can you please tell me what should be the problem?

[BogdanCiambur]

Unfortunately, as I said before, Isofit won't work on a 64 bit installation. STScI have stopped development on the stsdas package, meaning it has remained it the 32-bit version. BUT, a 32 bit installation is what I have, and it is compatible with my 64-bit machine and OS.

So, I advise you to re-install IRAF 32 bit, from the website I gave you in an earlier post. Note, it is important to follow every step of the way. For example, the permissions to the /iraf directory are changed with the command:

sudo chmod u=rwx iraf

or, the "fitsio" error came from missing additional modules in the installation, which are the last steps in the tutorial, i.e.

---

cd /iraf/iraf/extern

sudo ./configure

[[The next two lines will take some time to complete, even with fast internet. Be patient.]]

sudo make adccdrom ctio cfh12k esowfi mscdb mscred stsdas nfextern optic

sudo make deitab euv mem0 mtools rvsao song sqiid stecf ucsclris upsqiid xdimsum

So, after you have fully installed iraf 32bit, you need to copy all libraries from /iraf/iraf/bin.linux into a new directory that you will create, called /iraf/iraf/bin.linux64.

Don't forget to place the environ.sh file in the /iraf directory.

Try now in /stsdasbc/analysis/isophote the commands

$ sudo mkpkg $ sudo mkpkg -relink (note thqt I had forgotten the dash)

[BogdanCiambur]

Do let me know if it's working out, so that I can close this issue and update the installation instructions.

Cheers

[suvadip31]

Hi Bogdan,

Thank you for your reply. I am trying to install 32 bit iraf now. Surely I will let you know if there is any problem. Thank you again for helping me out.

Yours sincerely, Suvadip

On 20-Sep-2017 2:17 PM, "BogdanCiambur" notifications@github.com wrote:

Do let me know if it's working out, so that I can close this issue and update the installation instructions.

Cheers

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[suvadip31]

Hi Bogdan,

Here is what I am doing. Please tell me if I am wrong.

1. Install IRAF 32 bit following every command of the command list.

2. Install the extra packages using the commands which are in the last few lines of the command list.

Now IRAF Installation is done

3. copy everything under /iraf/iraf/bin.linux directory.

4. Create a new directory /iraf/iraf/bin.linux64.

5. Paste the content inside /iraf/iraf/bin.linux.

6. Put environ.sh inside /iraf.

7. Go to /stsdasbc/analysis/isophote

8. Inside the isophote directory, do:

   $ sudo mkpkg

   $ sudo mkpkg -relink

Done

Please tell me if anything else is needed or anything wrong in the process.

Also, I think I have to do other steps as directed in the README.md file.

Regards, Suvadip

[BogdanCiambur]

As far as I can tell this is the correct process.

I would check that standard IRAF/ellipse works after step 5. Then yes, you need to place the environ.sh file in /iraf, place the function "isofit" (which calls it) in your /.bashrc file and source it, and then update the login.cl file (as per the README file).

Good luck!

[suvadip31]

Hi Bogdan,

In the step 5, I actually meant to paste the content of /iraf/iraf/bin.linux inside /iraf/iraf/bin.linux64(created by me). Sorry for mistake!!

Regards, Suvadip.

[BogdanCiambur]

Hi Suvadip,

Could you let me know if these steps worked? Again, it's important for me in order to update the installation instructions on the repository.

Cheers, Bogdan

[suvadip31]

Hi Bogdan,

Surely I will let you know the results. ISOFIT is very important for my research. I have to install it. Will it be problem if I let you know tomorrow? Because I have an exam tomorrow. Sorry for inconvenience. Thank you again for your help.

Regards, Suvadip

On 21-Sep-2017 6:58 PM, "BogdanCiambur" notifications@github.com wrote:

Hi Suvadip,

Could you let me know if these steps worked? Again, it's important for me in order to update the installation instructions on the repository.

Cheers, Bogdan

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[BogdanCiambur]

No worries, just let me know either way. Cheers

[suvadip31]

Thank you very much. 😊😊 I will mail you the results. Suvadip

On 21-Sep-2017 7:09 PM, "BogdanCiambur" notifications@github.com wrote:

No worries, just let me know either way. Cheers

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[suvadip31]

Hi Bogdan,

I apologize for late. I followed the procedure step by step as above but it shows me some errors.

$ isofit bash: /iraf/environ.sh: Permission denied $ cl /home/suvadip/.iraf/bin/cl: line 152: /iraf/iraf/bin.linux64/vocl.e: No such file or directory But I copied every content of /iraf/iraf/bin.linux folder inside /iraf/iraf/bin.linux64 Can you please help me?

Suvadip

[suvadip31]

[BogdanCiambur]

It looks like there isn't user permission for the file /iraf/iraf/environ.sh

This should have been taken care of with the command "sudo chmod u=rwx iraf", in the installation guide.

[BogdanCiambur]

Sorry, I meant /iraf/environ.sh

Once you sort out the permissions for this file, the command "isofit" should not return anything. When that's the case, you can type "cl", in the directory where you generated the uparm and login.cl file, with "mkiraf"

Also, for some reason, it's looking for vocl.e in /iraf/bin. This should be empty (it is for me...), I don't quite understand this error

[suvadip31]

Hi Bogdan, At last, it WORKS!! Here is what I did. Thank you very much.

1. Install 64-bit IRAF including those added packages. (I installed 64-bit because 32-bit was not running)
2. Put environ.sh in a different folder where I do not have to be root to change permissions.
3. Put the path of environ.sh in the .bashrc file and source it.
4. Put the provided x_isophote.e file inside bin.linux64 folder inside stsdasbc.
5. Put those files you provided inside stsdasbc.
6. Replace the isophote folder inside the stsdasbc/pkg/analysis/ with the one you provided.
7. Modify the login.cl file as per the README.md
8. $ isofit
9. $ cl
10. $ stsdasbc

Now, can you please tell me if I can have a manual of using ISOFIT? Thank you again for this software.

Suvadip

[suvadip31]

Hi Bogdan,

I am getting a new error. ERROR: Cannot open connected subprocess (./x_isophote.e) Can you please look into it?

Suvadip

[suvadip31]

Hi Bogdan, Can you please upload the stsdasbc directory?

Regards, Suvadip

[BogdanCiambur]

The error comes I think from the fact that the 32-bit library x_isophote.e is incompatible with a 64bit installation. The same thing happened to me, and was fixed by running 32bit IRAF...

The stsdasbc directory is too large to upload on GitHub (~1.5 Gb), but you should have all you need that's different from the standard IRAF version. The error above is related strictly to the x_isophote.e library, you can check this by replacing it with the standard stsdas version, and it will function (but won't run Isofit...).

Does 'mkpkg -relink' not help?

[suvadip31]

I tried installing the 32-bit IRAF but it did not run. it showed me the following error: /home/suvadip/.iraf/bin/cl: line 152: /iraf/iraf/bin.linux64/vocl.e: No such file or directory That is why I tried with 64-bit installation. Isofit works but it shows me an error related to x_ispphote.e. Where can I find the 64-bit version of x_isophote.e? I also did mkpkg -relink inside isophote directory (stsdasbc/pkg/analysis/isophote) but it did not work.

[BogdanCiambur]

There isn't a 64bit version, unfortunately, since stsdas have stopped development of this package a few years ago.

Looks like when you launch cl it's looking for the vocl.e in the /bin, rather than /bin.linux64 directory, which may be caused by a wrong path or IRAFARCH. The second should be set to linux64 in the environ.sh file, which is loaded when you type 'isofit'...

See here maybe?: http://iraf.net/forum/viewtopic.php?showtopic=1469447

[suvadip31]

Hi Bogdan,

I installed IRAF 32-bit and following the workaround in the forum, IRAF 32-bit now works. But I am still getting the same error. ERROR: Cannot open connected subprocess (./x_isophote.e)

After reinstalling IRAF, I created the /iraf/iraf/bin.linux64 directory and copied the contents of /iraf/iraf/bin.linux into /iraf/iraf/bin.linux64 and did sudo mkpkg mkpkg -relink inside stsdasbc/pkg/analysis/isophote/

And, there was no bin.linux64 folder inside stsdasbc(I copied the /iraf/iraf/extern/stsdas folder and renamed it). So I created it and placed the provided x_isophote.e inside it.

And, I tried sudo chmod u=rwx iraf to change the permission of /iraf but it still says that the permission is denied.

Can you please tell me why?

Regards, Suvadip

[greenyellowcat]

Hello, Dear Bogdan! Sorry for bothering you, but I got a problem with the installation of your package ``Isofit''. Even though I installed a 32bit version of IRAF the following error has appeared.

ERROR: Cannot open connected subprocess (./x_isophote.e)

I have taken the following steps: 1) Downloaded 32 bit version of iraf from http://iraf.noao.edu/ 2) Installed it: sudo ./install -s'' 3) Cd to extern and installed sdsdas:sudo ./configure ; sudo make stsdas'' 4) Copied stsdas to ~/stsdasbc 5) Replaced isophote folder with yours 6) Replaced x_isophote.e in bin.linux with yours 7) In dir IRAF, changed login.cl to use stsdasbc 8) Everything works, except the most needed x_isophote. 9) mkpkg does not compile: /usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: cannot find -lstxtools 10) Although I copied stxtools from tables dir to bin.linux in iraf directory and compled it again mkpkg still refuses to work: /usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: i386 architecture of input file `/home/greencat/iraf/bin.linux/libstxtools.a(checkdim.o)' is incompatible with i386:x86-64 output and etc (much more the same strings for each function) I do not understand why the output has to be in the form of 64 bit file... Is it the problem with IRAF, my system or something else? Could you please advice something?

Sincerely yours, Chupa ....

[suvadip31]

Hi Bogdan,

Will you please reconsider this issue again? I have installed 32-bit IRAF successfully in my 64-bit ubuntu machine and it is working fine. Now I am trying to install ISOFIT but it is giving me the error ERROR: Cannot open connected subprocess (./x_isophote.e) Will you mind making the stsdasbc folder available online?

Suvadip

[greenyellowcat]

Hi Suvadip, I am not using IRAF anymore due to it's poor maintance. But I remember that in the time I managed to resolve this problem by doing the following: 1) Find this binary file x_isophote.e in you IRAF distribution; 2) Try to load it from the console: "usr:PATHTOFILE$ ./x_isophote.e" where PATHTOFILE is result of a first step; 3) Check output; In my case, there were wrong paths for requsted ".so" libraries. 4) Check paths and create needed directories with needed libraries --- create path and then just copy the library in it; Hope It can help Best regards, Chupa

вт, 5 февр. 2019 г. в 09:36, suvadip31 notifications@github.com:

Hi Bogdan,

Will you please reconsider this issue again? I have installed 32-bit IRAF successfully in my 64-bit ubuntu machine and it is working fine. Now I am trying to install ISOFIT but it is giving me the error ERROR: Cannot open connected subprocess (./x_isophote.e) Will you mind making the stsdasbc folder available oniline?

Suvadip

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[suvadip31]

Hi Chupa,

In the first step, is this x_isophote.e the one Bogdan provided?

I just tried, locate x_isophote.e Output: /iraf/iraf/extern/stsdas/bin.linux/x_isophote.e /iraf/iraf/extern/stsdasbc/bin.linux64/x_isophote.e /iraf/iraf/extern/stsdasbc/pkg/analysis/isophote/stsdasbcbinx_isophote.e Regards, Suvadip

[greenyellowcat]

Hi Suvadip, Yes, that one, precisely. Check which IRAF version you are using. If it is 64bit version then use this choice: .(!NOTE POINT HERE TO EXECUTE THE FILE ITSELF )/iraf/iraf/extern/stsdasbc/bin.linux64/x_isophote.e Or just execute " /x_isophote.e" in /iraf/iraf/extern/stsdasbc/bin.linux64 dir. Analogous for 32bit version, just change bin.linux64-> bin.linux Regards, Chupa

вт, 5 февр. 2019 г. в 14:40, suvadip31 notifications@github.com:

Hi Chupa,

In the first step, is this x_isophote.e the one Bogdan provided?

I just tried, locate x_isophote.e Output: /iraf/iraf/extern/stsdas/bin.linux/x_isophote.e /iraf/iraf/extern/stsdasbc/bin.linux64/x_isophote.e /iraf/iraf/extern/stsdasbc/pkg/analysis/isophote/stsdasbcbinx_isophote.e Regards, Suvadip

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[greenyellowcat]

Remark:

• Or just execute " /x_isophote.e" in /iraf/iraf/extern/stsdasbc/bin.linux64 dir.

"/x_isophote.e" ---> ". /x_isophote.e" (AGAIN DO NOT MISS IMPORTANT POINT HERE)

[suvadip31]

Hi Chupa,

My iraf is 32 bit. This is the output: suvadip@lenovo:/iraf/iraf/extern/stsdasbc/bin.linux64$ ./x_isophote.e

os.zgtenv: cannot open `/usr/local/i686/gnu/iraf-2.16/include/iraf.h' os.zgtenv: cannot open `/usr/local/i686/gnu/iraf-2.16/include/iraf.h' os.zgtenv: cannot open `/usr/local/i686/gnu/iraf-2.16/include/iraf.h' os.zgtenv: cannot open `/usr/local/i686/gnu/iraf-2.16/include/iraf.h'

Suvadip

[suvadip31]

Hi Chupa,

I found that there is no directory like that. /usr/local/i686/gnu/iraf-2.16/include/iraf.h this does not exist actually.

Suvadip

[greenyellowcat]

Hi, Suvadip Yes, there is a problem with compiled binaries --- you can not change dependency paths. The solution here is to create this folder /usr/local/i686/gnu/iraf-2.16/include/iraf.h manually and copy your "iraf.h" there from wherever it has been installed on your system.

вт, 5 февр. 2019 г. в 16:16, suvadip31 notifications@github.com:

Hi Chupa,

I found that there is no directory like that. /usr/local/i686/gnu/iraf-2.16/include/iraf.h this does not exist actually.

Suvadip

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[suvadip31]

Thank you very much. Can you please tell me how to find where is this iraf.h installed?

Suvadip

[greenyellowcat]

The location should be dependent on your system. Try to use the following to find it yourself: sudo find / -name "*iraf.h" (sudo for better output readability)

вт, 5 февр. 2019 г. в 16:32, suvadip31 notifications@github.com:

Thank you very much. Can you please tell me how to find where is this iraf.h installed?

Suvadip

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[suvadip31]

Hi Chupa,

I just tried it but the same error comes up :( when I am running ellipse

[greenyellowcat]

вт, 5 февр. 2019 г. в 17:05, suvadip31 notifications@github.com:

Hi Chupa,

I just tried it but the same error comes up :( when I am running ellipse

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[greenyellowcat]

No worries, that's an iterative process :) Could you please copy the output of "./x_isophote.e" execution here. Probably, something is still wrong with dependencies. The goal is to run "./x_isophote.e" independently of IRAF.

вт, 5 февр. 2019 г. в 17:20, Смирнов Антон zeleniikot@gmail.com:

вт, 5 февр. 2019 г. в 17:05, suvadip31 notifications@github.com:

Hi Chupa,

I just tried it but the same error comes up :( when I am running ellipse

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[suvadip31]

Thank you, Chupa.

I executed earlier: suvadip@lenovo:/iraf/iraf/extern/stsdasbc/bin.linux64$ ./x_isophote.e

os.zgtenv: cannot open `/usr/local/i686/gnu/iraf-2.16/include/iraf.h' os.zgtenv: cannot open `/usr/local/i686/gnu/iraf-2.16/include/iraf.h' os.zgtenv: cannot open `/usr/local/i686/gnu/iraf-2.16/include/iraf.h' os.zgtenv: cannot open `/usr/local/i686/gnu/iraf-2.16/include/iraf.h'

Now after execution nothing comes up. suvadip@lenovo:/iraf/iraf/extern/stsdasbc/bin.linux64$ ./x_isophote.e >

[greenyellowcat]

Now, try using "ellipse" function in the opened console, just write "ellipse" after ">" symbol. Does it work in this mode?

вт, 5 февр. 2019 г. в 17:35, suvadip31 notifications@github.com:

Thank you, Chupa.

I executed earlier: suvadip@lenovo:/iraf/iraf/extern/stsdasbc/bin.linux64$ ./x_isophote.e

os.zgtenv: cannot open /usr/local/i686/gnu/iraf-2.16/include/iraf.h' os.zgtenv: cannot open/usr/local/i686/gnu/iraf-2.16/include/iraf.h' os.zgtenv: cannot open /usr/local/i686/gnu/iraf-2.16/include/iraf.h' os.zgtenv: cannot open/usr/local/i686/gnu/iraf-2.16/include/iraf.h'

Now after execution nothing comes up. suvadip@lenovo:/iraf/iraf/extern/stsdasbc/bin.linux64$ ./x_isophote.e

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[suvadip31]

In the opened console, after writing ellipse, it wants an input.

[greenyellowcat]

x_isophote.e works at least. Now the question is why IRAF cant connect to it. Are you sure that you are using 64 bit IRAF shell version? For insurance, repeat all previous step for 32 bit version and try to use "ellipse" from the IRAF shell again.

вт, 5 февр. 2019 г. в 18:24, suvadip31 notifications@github.com:

In the opned onsole, aftr writing ellipse, it wants an input. [image: screenshot from 2019-02-05 20-53-05] https://user-images.githubusercontent.com/31993648/52283302-3b60c700-2988-11e9-8f39-533a60fb3bc4.png

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[suvadip31]

Hi Chupa,

I am using 32-bit IRAF actually.

[greenyellowcat]

Then just repeat all the steps for this file: /iraf/iraf/extern/stsdasbc/bin.linux/x_isophote.e.

вт, 5 февр. 2019 г. в 19:12, suvadip31 notifications@github.com:

Hi Chupa,

I am using 32-bit IRAF actually.

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