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isensee (Fabian Isensee)
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Aug 1 2016, 12:10 PM (286 w, 1 d)

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Dec 3 2021

isensee updated the task description for T28898: Cannot create new label in multilabel segmentation.
Dec 3 2021, 9:43 AM · MITK

Dec 2 2021

isensee updated subscribers of T28898: Cannot create new label in multilabel segmentation.
Dec 2 2021, 10:28 AM · MITK
isensee created T28898: Cannot create new label in multilabel segmentation.
Dec 2 2021, 10:19 AM · MITK

Nov 2 2021

isensee added a comment to T28769: Crash when loading two images with very different spacings.

Crazy stuff and good find 👍 Thanks Stefan!

Nov 2 2021, 5:01 PM · MITK

Oct 26 2021

isensee added a comment to T28769: Crash when loading two images with very different spacings.

Yes it looks like I am running OOM. Strange stuff. Loading each image individually MITK barely uses any RAM. As soon as I load both RAM usage jumps up to 20GB (out of my 32GB ) right before it crashes. Also CPU util is high just before that.

Oct 26 2021, 10:35 AM · MITK
isensee updated the task description for T28769: Crash when loading two images with very different spacings.
Oct 26 2021, 10:33 AM · MITK
isensee created T28769: Crash when loading two images with very different spacings.
Oct 26 2021, 10:32 AM · MITK

Oct 25 2021

isensee created T28768: Region Growing in its current state is unintuitive.
Oct 25 2021, 11:57 AM · Checklist, MITK
isensee added a comment to T28767: 2D (multi-label) segmentation tools -> paint/wipe unusable for larger images.

(I was painting in axial slice which was 2048x2048)

Oct 25 2021, 11:47 AM · Checklist, MITK
isensee created T28767: 2D (multi-label) segmentation tools -> paint/wipe unusable for larger images.
Oct 25 2021, 11:46 AM · Checklist, MITK

Oct 20 2021

isensee added a comment to T28758: Screenshot colors are not identical to 3D view.

strange... the color in here is displayed correctly. It's then my png viewer that must be messing things up...

Oct 20 2021, 5:16 PM · MITK
isensee closed T28758: Screenshot colors are not identical to 3D view as Resolved.
Oct 20 2021, 5:16 PM · MITK
isensee created T28758: Screenshot colors are not identical to 3D view.
Oct 20 2021, 5:15 PM · MITK

Oct 14 2021

isensee added a comment to T28493: Multilabel color map colors are not very nice.

The labels in my example are consecutive integers. And even if they weren't the color mapping should skip unused integer values. Use equivalent of np.unique(segmentation) to determine used labels and set the map accordingly.

Oct 14 2021, 12:41 PM · MITK
isensee added a comment to T28521: multilabel segmentation add switch to disable contour.

see T28736, does not really work for me

Oct 14 2021, 12:33 PM · MITK (v2021.10)
isensee updated the task description for T28736: Preferences for segmentation '2D display' are not properly utilized.
Oct 14 2021, 12:33 PM · MITK (v2022.04)
isensee created T28736: Preferences for segmentation '2D display' are not properly utilized.
Oct 14 2021, 12:32 PM · MITK (v2022.04)
isensee added a comment to T28675: Boolean Operations in Segmentation utilities are slow.

Unfortunately still slow. Just checked with 2021-10-01 shapshot on Ubuntu 18.04 (same system as tests above).
13.6s for intersection
14s for difference
didn't bother clocking union

Oct 14 2021, 12:23 PM · MITK (v2022.04)

Oct 4 2021

isensee closed T28717: Polygon model cannot be created from large segmentations as Resolved.
Oct 4 2021, 3:01 PM · MITK
isensee added a comment to T28717: Polygon model cannot be created from large segmentations.

Edit: After a long time the 3d Model appeared but no Data Manager object was created for it:

Screenshot from 2021-10-04 14-56-21.png (1×2 px, 220 KB)

Strange stuff (I deleted the segmentation tht's why the manager is empty)

Oct 4 2021, 2:57 PM · MITK
isensee created T28717: Polygon model cannot be created from large segmentations.
Oct 4 2021, 2:54 PM · MITK

Aug 24 2021

isensee reopened T28491: [Segmentation] Slice interpolation 'confirm for all slices' sometimes crahes as "Open".
Aug 24 2021, 10:38 AM · MITK (v2022.04)
isensee updated subscribers of T28491: [Segmentation] Slice interpolation 'confirm for all slices' sometimes crahes.

This is still not fixed, can we please re-open it?

Aug 24 2021, 10:38 AM · MITK (v2022.04)
isensee renamed T28675: Boolean Operations in Segmentation utilities are slow from Boolean Operations in Segmentation utilities are excruciatingly slow to Boolean Operations in Segmentation utilities are slow.
Aug 24 2021, 10:31 AM · MITK (v2022.04)
isensee created T28675: Boolean Operations in Segmentation utilities are slow.
Aug 24 2021, 10:28 AM · MITK (v2022.04)

Jun 4 2021

isensee updated the task description for T28500: Multilabel Segmentation Utilities do not work for multilabel segmentations.
Jun 4 2021, 12:19 PM · Missing Info, MITK (v2022.04)
isensee added a comment to T28491: [Segmentation] Slice interpolation 'confirm for all slices' sometimes crahes.

As it is an inexpensive operation my first guess would be an issue related to the amount of used memory. For example, the image above eats 3,5 GB, Activating the interpolation already triples it. Confirming adds at least another 3,5 GB. That could also explain why it is so slow (swapping). But at this point it is just a first assumption. On a 16 GB Windows machine I was able to complete the interpolation without crash but it took a while.

Jun 4 2021, 12:17 PM · MITK (v2022.04)
isensee created T28522: Segmentations are drawn differently depending on whether the segmentation tool is open or not.
Jun 4 2021, 12:15 PM · MITK
isensee created T28521: multilabel segmentation add switch to disable contour.
Jun 4 2021, 12:12 PM · MITK (v2021.10)

Jun 2 2021

isensee updated subscribers of T28491: [Segmentation] Slice interpolation 'confirm for all slices' sometimes crahes.

@kislinsk I know you have plenty of things to do, but this bug (along with T28516) is a blocker at the moment. I would like to recommend MITK as an annotation tool for our collaborators but cannot do that as along as the slice interpolation does not work (fast enough, T28516) for large images :-)

Jun 2 2021, 9:24 AM · MITK (v2022.04)
isensee created T28516: 2D slice interpolation should use multiprocessing.
Jun 2 2021, 9:22 AM · MITK (v2021.10)

Jun 1 2021

isensee added a comment to T28422: Multilabel color map does not produce unique colors.

@kislinsk sorry for the late reply. I am not using the convert to segmentation functionality because it draws contours by default and that is annoying because it obstructs too much from the image. Multilabel color map does exactly the right thing, is easy to use and does not require and additional mouse clicks. It is just more convenient :-)

Jun 1 2021, 5:02 PM · MITK (v2021.10)

May 25 2021

isensee updated the task description for T28500: Multilabel Segmentation Utilities do not work for multilabel segmentations.
May 25 2021, 11:14 AM · Missing Info, MITK (v2022.04)
isensee created T28500: Multilabel Segmentation Utilities do not work for multilabel segmentations.
May 25 2021, 11:13 AM · Missing Info, MITK (v2022.04)

May 20 2021

isensee added a comment to T28493: Multilabel color map colors are not very nice.
import numpy as np
import colorsys
from skimage import io
May 20 2021, 9:43 AM · MITK
isensee created T28493: Multilabel color map colors are not very nice.
May 20 2021, 9:19 AM · MITK

May 19 2021

isensee updated the task description for T28491: [Segmentation] Slice interpolation 'confirm for all slices' sometimes crahes.
May 19 2021, 10:12 AM · MITK (v2022.04)
isensee created T28491: [Segmentation] Slice interpolation 'confirm for all slices' sometimes crahes.
May 19 2021, 8:11 AM · MITK (v2022.04)
isensee updated the task description for T28490: Segmentation plugin: "new" segmentation should not run reinit!.
May 19 2021, 7:51 AM · Cleared, MITK (v2021.10)
isensee created T28490: Segmentation plugin: "new" segmentation should not run reinit!.
May 19 2021, 7:51 AM · Cleared, MITK (v2021.10)
isensee created T28489: int64 not supported.
May 19 2021, 7:40 AM · MITK