[fluka-discuss]: Re: ERROR:Impossible to open Voxel file

From: Horváth Dávid <David.Horvath_at_eli-beams.eu>
Date: Fri, 29 Mar 2019 20:26:51 +0000

Dear Stabb,

I tried to run your input, and it is working for me in Docker.

I had the S1.inp and vox.vxl in the same directory under docker_work (like: /docker_work/Stabb).
After I started FLUKA for Docker, I switched to this directory with the command: cd Stabb
And I issued the command: ln -srf vox.vxl /tmp/vxl.vxl
Finally I could run FLUKA with: $FLUPRO/flutil/rfluka -N0 -M1 S1
Or launch flair, and run that way: flair S1.inp

Note: I had to remove one of the duplicate USRBIN Energy scorings, it exceeded the memory limit.

Also, I made some changes to the F4D scripts. Now, if you are using Windows 10 HOME, you won't need this anymore. You can simply use "vox" on the VOXEL card as filename. You will need to download newest scripts, and run "install_win.bat" again.

I hope with this you can run is as well.

Kind regards,
Dávid Horváth

Junior Researcher
Radiation Protection
ELI Beamlines

E: david.horvath_at_eli-beams.eu
T: +420 266 051 283
M: Za Radnicí 835, 25241 Dolní Břeľany, Czech Republic


________________________________________
From: Sana Tabbasum <stabbass_at_purdue.edu>
Sent: 29 March 2019 20:39:28
To: Horváth Dávid; fluka-discuss_at_fluka.org
Subject: Re: ERROR:Impossible to open Voxel file

Sana Tabbasum has shared a OneDrive for Business file with you. To view it, click the link below.


<https://purdue0-my.sharepoint.com/:u:/g/personal/stabbass_purdue_edu/Ebxs3owLMAxMtCbJ6OuPaqUBCpZsQzEQFc7YRrfIwWusZg>
[https://r1.res.office365.com/owa/prem/images/dc-zip_20.png]<https://purdue0-my.sharepoint.com/:u:/g/personal/stabbass_purdue_edu/Ebxs3owLMAxMtCbJ6OuPaqUBCpZsQzEQFc7YRrfIwWusZg>

vox.zip<https://purdue0-my.sharepoint.com/:u:/g/personal/stabbass_purdue_edu/Ebxs3owLMAxMtCbJ6OuPaqUBCpZsQzEQFc7YRrfIwWusZg>




Thanks David,

Please find the attached file vox.vxl. You can rename it for vxl.vxl

and use for the input file. Let me know if anything else is required.

Thanks

Stabb

________________________________
From: Horváth Dávid <David.Horvath_at_eli-beams.eu>
Sent: Friday, March 29, 2019 3:22:40 PM
To: Sana Tabbasum; fluka-discuss_at_fluka.org
Subject: Re: ERROR:Impossible to open Voxel file

Dear Stabb,

I got the vxl.vxl and the input file in you email.

To send bigger files it is better to use some cloud sharing service, like https://send.firefox.com/

Kind regards,
Dávid Horváth

Junior Researcher
Radiation Protection
ELI Beamlines

E: david.horvath_at_eli-beams.eu
T: +420 266 051 283
M: Za Radnicí 835, 25241 Dolní Břeľany, Czech Republic


________________________________________
From: Sana Tabbasum <stabbass_at_purdue.edu>
Sent: 29 March 2019 20:17:53
To: Horváth Dávid; fluka-discuss_at_fluka.org
Subject: Re: ERROR:Impossible to open Voxel file

Hi David , I am trying to send you files but it seems that .vxl file is 22MB and upper limit

is 30 Mb still i am repeatedly getting message that its not delivered to any one.


Can you kindly confirm if you have got the files or not .?

Attached is the input and vxl file (/docker_work).


Stabb

________________________________
From: Horváth Dávid <David.Horvath_at_eli-beams.eu>
Sent: Tuesday, March 26, 2019 1:17:47 PM
To: Sana Tabbasum; fluka-discuss_at_fluka.org
Subject: Re: ERROR:Impossible to open Voxel file

Dear Stabb,

I don't see anything wrong, unfortunately.
Could you send me your input and voxel file?

Cheers,
Dávid Horváth

Junior Researcher
Radiation Protection
ELI Beamlines

E: david.horvath_at_eli-beams.eu
T: +420 266 051 283
M: Za Radnicí 835, 25241 Dolní Břeľany, Czech Republic


________________________________________
From: Sana Tabbasum <stabbass_at_purdue.edu>
Sent: 26 March 2019 18:12:48
To: Horváth Dávid; fluka-discuss_at_fluka.org
Subject: Re: ERROR:Impossible to open Voxel file

Hi David,

I have tried your suggestions, but apparently there is still some bug.

In order to avoid confusions This is what I have done,

1) In dicom /docker_work/ vxl.vxl, (same for bin as well)

2) In the input card, I have used /tmp/vxl

3) I have generated symlink using ln -srf vxl.vxl /tmp/vxl.vxl

4) My tmp contain, dicom.bnn , KS-script-xc..., vxl.vxl


Attached are pictures. Please let me know if there is anything wrong.

stabb

________________________________
From: Horváth Dávid <David.Horvath_at_eli-beams.eu>
Sent: Monday, March 25, 2019 6:21:43 PM
To: Sana Tabbasum; fluka-discuss_at_fluka.org
Subject: Re: ERROR:Impossible to open Voxel file

Dear Stabb,

1.) in Flair on the Dicom tab, you need to use the /docker_work/vxl.vxl file (and similarly the dicom.bnn should be also in /docker_work)

2.) Can you check again the content of the /tmp folder?

Cheers,
Dávid Horváth

Junior Researcher
Radiation Protection
ELI Beamlines

E: david.horvath_at_eli-beams.eu
T: +420 266 051 283
M: Za Radnicí 835, 25241 Dolní Břeľany, Czech Republic


________________________________________
From: Sana Tabbasum <stabbass_at_purdue.edu>
Sent: 25 March 2019 23:14:57
To: Horváth Dávid; fluka-discuss_at_fluka.org
Subject: Re: ERROR:Impossible to open Voxel file

Hi ,

I truly appreciate your help,

however its still not working,

I have run the cammand to generate the symlink, then went back to flair and opened my file,

1) An error message pops up when i try to click on Voxel command in the flair, Error DICOM to Voxel error

2) Out put still reflects same error can not open .vxl

________________________________
From: Horváth Dávid <David.Horvath_at_eli-beams.eu>
Sent: Monday, March 25, 2019 6:02:33 PM
To: Sana Tabbasum; fluka-discuss_at_fluka.org
Subject: Re: ERROR:Impossible to open Voxel file

Hi Stabb,

I think I see what is the problem.

Your voxel file in /docker_work is vxl.vxl, but when you created the symlink you used vox.vxl.
Try in /docker_work
ln -srf vxl.vxl /tmp/vxl.vxl

Cheers,
Dávid Horváth

Junior Researcher
Radiation Protection
ELI Beamlines

E: david.horvath_at_eli-beams.eu
T: +420 266 051 283
M: Za Radnicí 835, 25241 Dolní Břeľany, Czech Republic


________________________________________
From: Sana Tabbasum <stabbass_at_purdue.edu>
Sent: 25 March 2019 22:55:23
To: Horváth Dávid; fluka-discuss_at_fluka.org
Subject: Re: ERROR:Impossible to open Voxel file

Thanks !

Please find the attached.

________________________________
From: Horváth Dávid <David.Horvath_at_eli-beams.eu>
Sent: Monday, March 25, 2019 5:52:03 PM
To: Sana Tabbasum; fluka-discuss_at_fluka.org
Subject: Re: ERROR:Impossible to open Voxel file

Dear Stabb,

inside the docker container you can change directories with the "cd" command, like "cd /tmp" (without the apostrophes, space after the cd)
to show the content, use the "ls -al" command (without apostrophes, space after the ls)

Cheers,
Dávid Horváth

Junior Researcher
Radiation Protection
ELI Beamlines

E: david.horvath_at_eli-beams.eu
T: +420 266 051 283
M: Za Radnicí 835, 25241 Dolní Břeľany, Czech Republic


________________________________________
From: Sana Tabbasum <stabbass_at_purdue.edu>
Sent: 25 March 2019 22:45:27
To: Horváth Dávid; fluka-discuss_at_fluka.org
Subject: Re: ERROR:Impossible to open Voxel file

Thanks again David!


Attached find the content of /docker_work, how can i access the content of tmp,

if i am running FLUKA container ?


Stabb

________________________________
From: Horváth Dávid <David.Horvath_at_eli-beams.eu>
Sent: Monday, March 25, 2019 5:26:58 PM
To: Sana Tabbasum; fluka-discuss_at_fluka.org
Subject: Re: ERROR:Impossible to open Voxel file

Dear Stabb,

can you let me know what is the content of your /docker_work and /tmp folders with the "ls -al" command after you created the symlink?

Kind regards,
Dávid Horváth

Junior Researcher
Radiation Protection
ELI Beamlines

E: david.horvath_at_eli-beams.eu
T: +420 266 051 283
M: Za Radnicí 835, 25241 Dolní Břeľany, Czech Republic


________________________________________
From: Sana Tabbasum <stabbass_at_purdue.edu>
Sent: 25 March 2019 22:20:07
To: Horváth Dávid; fluka-discuss_at_fluka.org
Subject: Re: ERROR:Impossible to open Voxel file

Hi David,

 Thanks for the catch of space,

I have tried again, still no luck,

Any suggestion/help is appreciated.


please have a look at attached pictures.


________________________________
From: Horváth Dávid <David.Horvath_at_eli-beams.eu>
Sent: Monday, March 25, 2019 4:58:59 PM
To: Sana Tabbasum; fluka-discuss_at_fluka.org
Subject: Re: ERROR:Impossible to open Voxel file

Hi Stabb,

there is a space missing from the command creating the symbolic link, and make sure the filename on VOXEL card is /tmp/vxl

Kind regards,
Dávid Horváth

Junior Researcher
Radiation Protection
ELI Beamlines

E: david.horvath_at_eli-beams.eu
T: +420 266 051 283
M: Za Radnicí 835, 25241 Dolní Břeľany, Czech Republic


________________________________________
From: Sana Tabbasum <stabbass_at_purdue.edu>
Sent: 25 March 2019 21:50:26
To: Horváth Dávid; fluka-discuss_at_fluka.org
Subject: Re: ERROR:Impossible to open Voxel file

I appreciate your help David,

but it is still not working . Attached are the pictures.

________________________________
From: Horváth Dávid <David.Horvath_at_eli-beams.eu>
Sent: Monday, March 25, 2019 4:01:06 PM
To: Sana Tabbasum; fluka-discuss_at_fluka.org
Subject: Re: ERROR:Impossible to open Voxel file

Dear Stabb,

you need to create the symbolic link inside the Docker container after you started Fluka for Docker.

Kind regards,
Dávid Horváth

Junior Researcher
Radiation Protection
ELI Beamlines

E: david.horvath_at_eli-beams.eu
T: +420 266 051 283
M: Za Radnicí 835, 25241 Dolní Břeľany, Czech Republic


________________________________________
From: Sana Tabbasum <stabbass_at_purdue.edu>
Sent: 25 March 2019 20:54:48
To: Horváth Dávid; fluka-discuss_at_fluka.org
Subject: Re: ERROR:Impossible to open Voxel file

Hi , Thanks for your suggestion David,


I have tried it but unfortunately No luck!! I am still getting same error.

I have generated symbolic link in the folder, and provided the same path in the Voxel card.

Pictures attached, still I got the same error.


Any suggestions /help appreciated .


Thanks

Stabb

________________________________
From: Horváth Dávid <David.Horvath_at_eli-beams.eu>
Sent: Monday, March 25, 2019 11:08:03 AM
To: Sana Tabbasum; fluka-discuss_at_fluka.org
Subject: Re: ERROR:Impossible to open Voxel file

Dear Stabb,

I guessing based on your previous email, that you are trying to run using Docker.

There is a known issue with external files in Docker, you need to use the absolute path in the input for FLUKA to find them. While this is working with the OPEN card, the VOXEL card limits the filename to 10 character, where the absolute path doesn't fit.

But there is a workaround you can use:
1.) Go to the folder where your voxel file is.
2.) Create a smbolic link with the command:
ln -srf your_voxel_file.vxl /tmp/vxl.vxl
3.) In the FLUKA input / flair use the /tmp/vxl.vxl file in the VOXEL card.

Unfortunately you will need to recreate the symbolic link every time you run the FLUKA for Docker script.

I hope this helps.

Kind regards,
Dávid Horváth

Junior Researcher
Radiation Protection
ELI Beamlines

E: david.horvath_at_eli-beams.eu
T: +420 266 051 283
M: Za Radnicí 835, 25241 Dolní Břeľany, Czech Republic


________________________________________
From: owner-fluka-discuss_at_mi.infn.it <owner-fluka-discuss_at_mi.infn.it> on behalf of Sana Tabbasum <stabbass_at_purdue.edu>
Sent: 25 March 2019 14:01:39
To: fluka-discuss_at_fluka.org
Subject: [fluka-discuss]: ERROR:Impossible to open Voxel file

Hi,


I am trying to import a CT scan using DICOM, I have successfully generated the

voxel file, however when I try to run the file i have got an error "impossible to open .vxl

file . Given below.

Any suggestion , what could possibly be wrong ?


Thanks

Stabb


[cid:9ad67c35-7dbe-451e-8461-d44e0926a56c]


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Received on Fri Mar 29 2019 - 22:39:50 CET

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