Drishti v.2.6.5 crashes

rootsinpeat commented 5 years ago

Hi, I'm new to 3D modelling and working on my master's thesis with this. I'm trying to calculate the volumetric information for my rootsystem-model, which is displayed well in Drishti. Whenever I try to measure the volume or the surface area, the program instantly crashes and the window is closed. Otherwise, it works fine. I'm currently using v.2.6.5 and tryed the same with v.2.6.4 as well. Might there be a a memory problem? Or is there another way to obtain the volumetric information besides 'Functions>Measurements>Volume'? Any help would be welcome

AjayLimaye commented 5 years ago

Hi rootsinpeat, What is the size of the volume and size of texture memory on your graphics card? Cheers, Ajay

On Mon, May 6, 2019 at 7:55 PM rootsinpeat notifications@github.com wrote:

Hi, I'm new to 3D modelling and working on my master's thesis with this. I'm trying to calculate the volumetric information for my rootsystem-model, which is displayed well in Drishti. Whenever I try to measure the volume or the surface area, the program instantly crashes and the window is closed. Otherwise, it works fine. I'm currently using v.2.6.5 and tryed the same with v.2.6.4 as well. Might there be a a memory problem? Or is there another way to obtain the volumetric information besides 'Functions>Measurements>Volume'? Any help would be welcome

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The Australian National University

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T: +61 2 6125 4616

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rootsinpeat commented 5 years ago

Hello Ajay,

thanks for the fast reply!

My two volumes are derived from image stacks, that differ considerably in size.

A consists of 101 slices, that make up a 310 MB .raw file, the pvl.nc file made from it has 391 Bytes.

B consists of 769 slices, which make up a 1,97 GB .raw file, pvl.nc for B is 389 Bytes.

The graphics card is a Nivida GeForce RTX 2080 Ti, that has 11 GB of texture memory according to the Nivida website.

I had several problems with image segmentation due to memory-problems before, so I fear this is a similar problem with Drishti. Our working group bought a new computer for these kind of tasks and was advised by people from the zoology department who work with commerical 3D imaging software, which components to buy (e.g. 64 RAM). They were kind of hoping to replace Amira, but had no time diving straight into freeware. Which is, to some extend, my part now.

Kind regards Stella

Am Dienstag, den 07-05-2019 um 2:29 schrieb AjayLimaye:

Hi rootsinpeat, What is the size of the volume and size of texture memory on your graphics card? Cheers, Ajay

On Mon, May 6, 2019 at 7:55 PM rootsinpeat wrote:

Hi, I'm new to 3D modelling and working on my master's thesis with this. I'm trying to calculate the volumetric information for my rootsystem-model, which is displayed well in Drishti. Whenever I try to measure the volume or the surface area, the program instantly crashes and the window is closed. Otherwise, it works fine. I'm currently using v.2.6.5 and tryed the same with v.2.6.4 as well. Might there be a a memory problem? Or is there another way to obtain the volumetric information besides 'Functions>Measurements>Volume'? Any help would be welcome

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.

--

Ajay Limaye

VIsualization Programmer, NCI Australia

The Australian National University

143 Ward Road

Acton, ACT, 2601

T: +61 2 6125 4616

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AjayLimaye commented 5 years ago

Hi Stella, You have an excellent setup, there should be no problem with Drishti. In order to check whether it is a bug in the software would it be possible to send me the smaller of the two in order to test it here. Please send processed files (.pvl.nc and .pvl.nc.001) as well as project (and keyframe) files if you have them. Cheers, Ajay

On Wed, May 8, 2019 at 3:14 AM rootsinpeat notifications@github.com wrote:

Hello Ajay,

thanks for the fast reply!

My two volumes are derived from image stacks, that differ considerably in size.

A consists of 101 slices, that make up a 310 MB .raw file, the pvl.nc file made from it has 391 Bytes.

B consists of 769 slices, which make up a 1,97 GB .raw file, pvl.nc for B is 389 Bytes.

The graphics card is a Nivida GeForce RTX 2080 Ti, that has 11 GB of texture memory according to the Nivida website.

I had several problems with image segmentation due to memory-problems before, so I fear this is a similar problem with Drishti. Our working group bought a new computer for these kind of tasks and was advised by people from the zoology department who work with commerical 3D imaging software, which components to buy (e.g. 64 RAM). They were kind of hoping to replace Amira, but had no time diving straight into freeware. Which is, to some extend, my part now.

Kind regards Stella

Am Dienstag, den 07-05-2019 um 2:29 schrieb AjayLimaye:

Hi rootsinpeat, What is the size of the volume and size of texture memory on your graphics card? Cheers, Ajay

On Mon, May 6, 2019 at 7:55 PM rootsinpeat wrote:

Hi, I'm new to 3D modelling and working on my master's thesis with this. I'm trying to calculate the volumetric information for my rootsystem-model, which is displayed well in Drishti. Whenever I try to measure the volume or the surface area, the program instantly crashes and the window is closed. Otherwise, it works fine. I'm currently using v.2.6.5 and tryed the same with v.2.6.4 as well. Might there be a a memory problem? Or is there another way to obtain the volumetric information besides 'Functions>Measurements>Volume'? Any help would be welcome

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub , or mute the thread

.

--

Ajay Limaye

VIsualization Programmer, NCI Australia

The Australian National University

143 Ward Road

Acton, ACT, 2601

T: +61 2 6125 4616

Want the latest news from NCI?

Find out more about NCI: YouTube / Facebook / Twitter / LinkedIn

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[1] https://github.com/nci/drishti/issues/33#issuecomment-489860012 [2]

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rootsinpeat commented 5 years ago

Hi Ajay,

thanks a lot for checking my data. All the requested files are in the appendix.

In case you are wondering: it's a model of the first 40cm of the root system within a peat core. It was our first try, so the images we took for input were not really taken that well.

Thanks again

Stella

Am Mittwoch, den 08-05-2019 um 0:54 schrieb AjayLimaye:

Hi Stella, You have an excellent setup, there should be no problem with Drishti. In order to check whether it is a bug in the software would it be possible to send me the smaller of the two in order to test it here. Please send processed files (.pvl.nc and .pvl.nc.001) as well as project (and keyframe) files if you have them. Cheers, Ajay

On Wed, May 8, 2019 at 3:14 AM rootsinpeat wrote:

Hello Ajay,

thanks for the fast reply!

My two volumes are derived from image stacks, that differ considerably in size.

A consists of 101 slices, that make up a 310 MB .raw file, the pvl.nc file made from it has 391 Bytes.

B consists of 769 slices, which make up a 1,97 GB .raw file, pvl.nc for B is 389 Bytes.

The graphics card is a Nivida GeForce RTX 2080 Ti, that has 11 GB of texture memory according to the Nivida website.

I had several problems with image segmentation due to memory-problems before, so I fear this is a similar problem with Drishti. Our working group bought a new computer for these kind of tasks and was advised by people from the zoology department who work with commerical 3D imaging software, which components to buy (e.g. 64 RAM). They were kind of hoping to replace Amira, but had no time diving straight into freeware. Which is, to some extend, my part now.

Kind regards Stella

Am Dienstag, den 07-05-2019 um 2:29 schrieb AjayLimaye:

Hi rootsinpeat, What is the size of the volume and size of texture memory on your graphics card? Cheers, Ajay

On Mon, May 6, 2019 at 7:55 PM rootsinpeat wrote:

Hi, I'm new to 3D modelling and working on my master's thesis with this. I'm trying to calculate the volumetric information for my rootsystem-model, which is displayed well in Drishti. Whenever I try to measure the volume or the surface area, the program instantly crashes and the window is closed. Otherwise, it works fine. I'm currently using v.2.6.5 and tryed the same with v.2.6.4 as well. Might there be a a memory problem? Or is there another way to obtain the volumetric information besides 'Functions>Measurements>Volume'? Any help would be welcome

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub , or mute the thread

.

--

Ajay Limaye

VIsualization Programmer, NCI Australia

The Australian National University

143 Ward Road

Acton, ACT, 2601

T: +61 2 6125 4616

Want the latest news from NCI?

Find out more about NCI: YouTube / Facebook / Twitter / LinkedIn

[image: cid:image002.png@01D449EE.B750D8C0]

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub [1], or mute the thread [2].

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[1] https://github.com/nci/drishti/issues/33#issuecomment-489860012 [2]

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rootsinpeat commented 5 years ago

Hello Ajay, have you found any time to look at the data yet? Cheers, Stella

AjayLimaye commented 5 years ago

Hi Stella, Have not received the files yet. Cheers, Ajay

On Tue, May 21, 2019 at 9:57 PM rootsinpeat notifications@github.com wrote:

Hello Ajay, have you found any time to look at the data yet? Cheers, Stella

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rootsinpeat commented 5 years ago

Hello Ajay, I'm sorry, my compression-type was apparently not accepted by GitHub before. I Hope it works now. Rootsinpeat project.zip Thanks, Stella

AjayLimaye commented 5 years ago

Hi Stella, Attached is the screen capture for calculating volume. Your data is segmented and the part the you want calculated is at the extreme right. Due to linear interpolation you can see stuff on the screen even when extreme right is not selected in the transfer function. You would get 0 volume if you use that transfer function. Change it so that you select the contributing voxels and you should get the correct volume. Cheers, Ajay rootsInPeat.webm https://drive.google.com/file/d/1NYCETl5peNeNV6v0V5Vzsg4I9mSkw4Kz/view?usp=drive_web

On Wed, May 22, 2019 at 8:14 PM rootsinpeat notifications@github.com wrote:

Hello Ajay, I'm sorry, my compression-type was apparently not accepted by GitHub before. I Hope it works now. Rootsinpeat project.zip https://github.com/nci/drishti/files/3206885/Rootsinpeat.project.zip Thanks, Stella

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AjayLimaye commented 5 years ago

Try this one - http://sf.anu.edu.au/~acl900/drishti_perpetualbeta/2.6.6/Drishti-2.6.6_beta.zip

On Thu, May 23, 2019 at 1:20 PM Ajay Limaye limaye.ajay@gmail.com wrote:

Hi Stella, Attached is the screen capture for calculating volume. Your data is segmented and the part the you want calculated is at the extreme right. Due to linear interpolation you can see stuff on the screen even when extreme right is not selected in the transfer function. You would get 0 volume if you use that transfer function. Change it so that you select the contributing voxels and you should get the correct volume. Cheers, Ajay rootsInPeat.webm https://drive.google.com/file/d/1NYCETl5peNeNV6v0V5Vzsg4I9mSkw4Kz/view?usp=drive_web

On Wed, May 22, 2019 at 8:14 PM rootsinpeat notifications@github.com wrote:

Hello Ajay, I'm sorry, my compression-type was apparently not accepted by GitHub before. I Hope it works now. Rootsinpeat project.zip https://github.com/nci/drishti/files/3206885/Rootsinpeat.project.zip Thanks, Stella

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/nci/drishti/issues/33?email_source=notifications&email_token=ABMVVLVK7KLMMSJNMDRFFCDPWUMG3A5CNFSM4HK6UVTKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODV6SSVI#issuecomment-494741845, or mute the thread https://github.com/notifications/unsubscribe-auth/ABMVVLU4OG6FP76HTEVMHULPWUMG3ANCNFSM4HK6UVTA .

rootsinpeat commented 5 years ago

Thank you so much!! It works perfectly

nci / drishti