[Gate-users] [BULK ?] Using parameters for mac files

Thu Mar 17 15:02:40 CET 2022

Thank you very much Tim and Helge, that is working now. I won’t tell you how embarrassingly long I spent trying to fix what was effectively just the wrong order.

I have a few other small bugs to iron out, such as it thinks the extension is missing from the PET data etc. now, but it is at least triggering Gate to open.

Thank you

Mark Baker
Principal Clinical Scientist (Interim)
Imaging Physics (Ionising)
The Clatterbridge Cancer Centre NHS Foundation Trust
(he, him)

CCCW Tel:  0151 556 5030
CCCL Tel: 0151 318 8438
Email: mark.baker23 at nhs.net<mailto:mark.baker23 at nhs.net>
Microsoft Teams (click here)<https://teams.microsoft.com/l/chat/0/0?users=mark.baker23@nhs.net>

From: Helge Pettersen <helge.e.s.pettersen at gmail.com>
Sent: 17 March 2022 13:37
To: Schneider Tim <Tim.Schneider at curie.fr>
Cc: BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION TRUST) <mark.baker23 at nhs.net>; gate-users at lists.opengatecollaboration.org
Subject: Re: [Gate-users] [BULK ?] Using parameters for mac files

Hi,

I don't know if this is the issue, but I usually have to escape the parameter list when I use bash $variables. See example below:

Gate -a "'[phantom,$phantom] [spotx,$x]
[spoty,$y] [theta,$theta] [axisx,$axis_x] [axisy,$axis_y]
[rotation,90]'" Main_phantom.mac

Good luck,

Helge Egil Seime Pettersen, PhD
Particle Therapy / Imaging / Proton CT
Department of Oncology and Medical Physics
Haukeland University Hospital
Bergen, Norway

On Thu, Mar 17, 2022 at 2:15 PM Schneider Tim <Tim.Schneider at curie.fr<mailto:Tim.Schneider at curie.fr>> wrote:
Hi Mark,

When I run macros with parameters, I call them like this:

Gate -a [param,value] mac/macro.mac

Not sure if your way of doing it is correct as well, but the above always worked for me.

Cheers,
Tim

Am 17/03/2022 um 13:11 schrieb BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION TRUST) <mark.baker23 at nhs.net<mailto:mark.baker23 at nhs.net>>:

Hi all

I am trying to run some parameters into my Gate simulation, but it doesn’t seem to be working and Gate sticks at the PreInit stage (although the CPU does ramp up to 100%). I am running multiple instances of Gate (up to 8 simultanouely), so it is laborious to go into each of the macs every time I want to change a parameter, so I was hoping this would help. My project is hoping to calculate dose distributions from PET scans using CT scans as the geometry. Previously it was working fine until I tried to add the parameters.

The relevant parts of my code are below (there is obviously a lot more so I’ve attached the files also in case anyone wants to look deeper, some bits commented out during the debugging)

In the main1.mac, I have changed the geometry to
/gate/world/daughters/name patientCT
/gate/world/daughters/insert ImageNestedParametrisedVolume
/gate/patientCT/geometry/setImage {CTData}

The main1.mac calls sourceF18.mac as its source, which contains the link to the PET data. The relevant part is
/gate/source/addSource patientPET voxel
/gate/source/patientPET/imageReader/readFile {PETData}

I also change the number of primaries on the fly, so I set that to the following in main1.mac
/gate/application/setTotalNumberOfPrimaries {NoOfPrimaries}

I’ve a got a script to run the multiple instances of Gate, alongside a lot of housework for moving files and merging them etc. I have checked the input to the parameters, and as far as I can tell, they are fine.

I call Gate using the following
Gate mac/main1.mac [CTData,$CTDataFile] [NoOfPrimaries,$NumberPrimaries] [PETData,$PTDataFile] &

where the user could select the following information, for example,
$CTDataFile is data/dcm/CT/br38f.mha
$PTDataFile is data/dcm/PT/brainmaskPET.mha
$NumberPrimaries is 1000

If I go back to my main1.mac etc. and manually change the parameters to the data above and change my run.sh script to Gate mac/main1.mac &  it works perfectly, so presumably I am doing something wrong with passing the parameters through.

I’d appreciate it if anyone had any thoughts on this?

Thank you

Mark Baker
Principal Clinical Scientist (Interim)
Imaging Physics (Ionising)
The Clatterbridge Cancer Centre NHS Foundation Trust
(he, him)

CCCW Tel:  0151 556 5030
CCCL Tel: 0151 318 8438
Email: mark.baker23 at nhs.net<mailto:mark.baker23 at nhs.net>
Microsoft Teams (click here)<https://teams.microsoft.com/l/chat/0/0?users=mark.baker23@nhs.net>

Honorary Lecturer, Dept. of Physics
University of Liverpool

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