Page MenuHomePhabricator
Feed All Stories

Jan 29 2021

a178n triaged T28242: Live Wire Segmentation bug as Normal priority.
Jan 29 2021, 5:25 PM · MITK-ProjectTemplate, MITK (v2021.02)
kalali added a comment to T27883: [Segmentation] Crash and interpolation issues in static segmentation on reference image with strange arbitrary time geometry (3d+t heart).

The last thing that happens is a crash.

Jan 29 2021, 3:59 PM · MITK (v2021.02)
floca added a comment to T28230: Issue with DICOM SEG -> NIFTI conversion: missing empty slices.

These parameter descriptions don't really make sense, no?

parser.addArgument("fix", "f", mitkCommandLineParser::Image, "Input Image", "Path to the input VTK polydata", us::Any(), false, false, false, mitkCommandLineParser::Input);
parser.addArgument("moving", "m", mitkCommandLineParser::File, "Output text file", "Target file. The output statistic is appended to this file.", us::Any(), false, false, false, mitkCommandLineParser::Output);
parser.addArgument("output", "o", mitkCommandLineParser::File, "Extension", "File extension. Default is .nii.gz", us::Any(), false, false, false, mitkCommandLineParser::Output);
Jan 29 2021, 3:57 PM · MITK
floca added a comment to T28230: Issue with DICOM SEG -> NIFTI conversion: missing empty slices.

Yes the easiest way would be arc diff and arc land.
Just a side note: As MITK also uses gitflow now, a compliant branch name would be feature/* or bugfix/*.

Jan 29 2021, 3:55 PM · MITK
floca added a comment to T28222: [ImageStatistics] Histogram is only shown for timestep 0.

It is a safety measure. As soon as more then to rows are in the table (so either >1 image or >1 roi) the histogram is deactivated at the moment, because you would not be able to discreminate them accordingly. See also Tasks mentioned above. Needs substential overhaul in the internals.

Jan 29 2021, 3:49 PM · MITK (v2021.02)
neher added a comment to T28230: Issue with DICOM SEG -> NIFTI conversion: missing empty slices.

I added the functionality to choose the interpolator. I forgot how to merge it :) Arcanist? And land on develop?

Jan 29 2021, 3:47 PM · MITK
kalali added a comment to T27883: [Segmentation] Crash and interpolation issues in static segmentation on reference image with strange arbitrary time geometry (3d+t heart).

Still valid - although it was not clearly defined what happened. Sorry, too many things going on at the same time. I will add a video to show some strange behavior.

Jan 29 2021, 3:36 PM · MITK (v2021.02)
neher added a comment to T28230: Issue with DICOM SEG -> NIFTI conversion: missing empty slices.

Pushed new branch to rMITK MITK: T28230-ResampleImageToReference.

Jan 29 2021, 3:21 PM · MITK
thomass added a comment to T28222: [ImageStatistics] Histogram is only shown for timestep 0.

Since you are already working on the histogram anyways, can you check the following:

Jan 29 2021, 3:03 PM · MITK (v2021.02)
neher added a comment to T28230: Issue with DICOM SEG -> NIFTI conversion: missing empty slices.

These parameter descriptions don't really make sense, no?

Jan 29 2021, 2:36 PM · MITK
schererj added a comment to T28230: Issue with DICOM SEG -> NIFTI conversion: missing empty slices.

Thank you very much for the super fast response!
For me this is only coupled to the training support within Kaapana.

Jan 29 2021, 2:16 PM · MITK
neher added a comment to T28230: Issue with DICOM SEG -> NIFTI conversion: missing empty slices.

For RACOON we need it in the next weeks. Sooner is better of course :)
We could simply adapt CLResampleImageToReference to optionally use NN. Should be easy enough. I will take a look today.

Jan 29 2021, 2:07 PM · MITK
kalali added a comment to T28239: Multilabel Segmentation - 3D Segmentation Confused about required outcome.

That's exactly what I wrote and defined in the checklist. The checklist is correct as it perfectly reflects what's happening in the workbench. This is - as described in the title of the corresponding section - valid for 4D test data.

Jan 29 2021, 2:02 PM · MITK-ProjectTemplate, MITK (v2021.02)
p212r lowered the priority of T28196: [Docs] Update Dev-Guide for 0.1.1-dev from Normal to Low.
Jan 29 2021, 1:21 PM · Kaapana (internal)
p212r moved T28196: [Docs] Update Dev-Guide for 0.1.1-dev from Discussion to Resolved on the Kaapana (internal) board.
Jan 29 2021, 1:21 PM · Kaapana (internal)
p212r removed a project from T28196: [Docs] Update Dev-Guide for 0.1.1-dev: Request for Discussion.
Jan 29 2021, 1:20 PM · Kaapana (internal)
gaoh added a comment to T28240: [MultiLabel Segmentierung] – Optionen.

The other options "Show as volume rendering" and "Enable auto-selection mode" are not working as described. Or I didn't get the description..

Jan 29 2021, 1:10 PM · MITK-ProjectTemplate, MITK (v2021.02)
gaoh updated the task description for T28239: Multilabel Segmentation - 3D Segmentation Confused about required outcome.
Jan 29 2021, 1:07 PM · MITK-ProjectTemplate, MITK (v2021.02)
gaoh added a comment to T28240: [MultiLabel Segmentierung] – Optionen.

Ah it seems I was mistaking, at least the transparent overlay works, the color mismatch remains.

Jan 29 2021, 12:50 PM · MITK-ProjectTemplate, MITK (v2021.02)
gaoh added a comment to T28240: [MultiLabel Segmentierung] – Optionen.

Ah, when changing the Preference of Segmenation, the mask is changed... How can I create a "Multilabel Mask"?

Jan 29 2021, 12:46 PM · MITK-ProjectTemplate, MITK (v2021.02)
gaoh triaged T28240: [MultiLabel Segmentierung] – Optionen as Normal priority.
Jan 29 2021, 12:42 PM · MITK-ProjectTemplate, MITK (v2021.02)
gaoh closed T28239: Multilabel Segmentation - 3D Segmentation Confused about required outcome, a subtask of T28000: MITK v2021.02, as Resolved.
Jan 29 2021, 12:25 PM · MITK-ProjectTemplate, MITK (v2021.02)
gaoh closed T28239: Multilabel Segmentation - 3D Segmentation Confused about required outcome as Resolved.

Yes, it is exactly as you described: static -> all timesteps, dynamic -> toolbox to apply to all timesteps or not.

Jan 29 2021, 12:25 PM · MITK-ProjectTemplate, MITK (v2021.02)
kislinsk added a comment to T28239: Multilabel Segmentation - 3D Segmentation Confused about required outcome.

I think it is the checklist. When creating a new segmentation based on a dynamic image you now can decide between a static segmentation that has a single timestep spanning over all reference image timesteps and a dynamic segmentation to have matching timesteps. In the latter case only the current timestep should be affected except the tool is explicitly giving the option to be applied to all timesteps at once. Can you confirm?

Jan 29 2021, 11:37 AM · MITK-ProjectTemplate, MITK (v2021.02)
kislinsk added a revision to T28204: Refactor LevelWindowManagerTest: Unknown Object (Differential Revision).
Jan 29 2021, 11:23 AM · MITK (v2021.10)
gaoh triaged T28239: Multilabel Segmentation - 3D Segmentation Confused about required outcome as Normal priority.
Jan 29 2021, 10:58 AM · MITK-ProjectTemplate, MITK (v2021.02)

Jan 28 2021

kislinsk updated the task description for T28000: MITK v2021.02.
Jan 28 2021, 10:29 PM · MITK-ProjectTemplate, MITK (v2021.02)
kalali added a comment to T28204: Refactor LevelWindowManagerTest.

I opened a review for my modifications / suggestions for a LevelWindowManagerTest. Please have a look at it: D461
I have explicitly two problems with the current test:

  1. I need to load the three images / datasets for each tests since it is not possible to keep those images in memory for every new tests. Does anyone know how to solve this problem?
  2. I randomly get a failed test in line 287 / 288
m_DataNode2->SetSelected(true);
CPPUNIT_ASSERT_MESSAGE("\"imageForLevelWindow\" property not correctly set", AssertImageForLevelWindowProperty(false, true, false));
Jan 28 2021, 10:28 PM · MITK (v2021.10)
kislinsk closed T28220: [Image Cropper] Masking a 4D image and overwrite the original one leads to strange result, a subtask of T28000: MITK v2021.02, as Resolved.
Jan 28 2021, 10:28 PM · MITK-ProjectTemplate, MITK (v2021.02)
kislinsk closed T28220: [Image Cropper] Masking a 4D image and overwrite the original one leads to strange result as Resolved.

For all cases the result now keeps the original level window. In case of Heart3D+t the level window property is lost otherwise. That's why it appeared in strange contrast and "lost" the level window widget.

Jan 28 2021, 10:28 PM · MITK (v2021.02)
floca triaged T28237: Refactor QmitkChart as High priority.
Jan 28 2021, 10:14 PM · Moved to git.dkfz.de, MITK (v2024.12)
floca added a comment to T26790: Workbench crashes when clearing chart data in ChartExample.

no it is not fixed. Happened today also in the QmitkHistogramWidget.

Jan 28 2021, 10:02 PM · Auto-closed, Restricted Project, MITK
floca claimed T28206: [Image Statistics] Renaming segmentation or planar figure based ROI nodes breaks histogram.
Jan 28 2021, 10:00 PM · MITK (v2024.12)
floca claimed T28222: [ImageStatistics] Histogram is only shown for timestep 0.
Jan 28 2021, 10:00 PM · MITK (v2021.02)
floca claimed T28221: [ImageStatistics] Histogram is not updated when using ROI.
Jan 28 2021, 10:00 PM · MITK (v2021.02)
floca added a comment to T28222: [ImageStatistics] Histogram is only shown for timestep 0.

Discussion already decided... *grrr*
The only way i was abel to find to quick fix T28221 and T28223, without rewritting the whole QmitChart and QmitkHistogramWidget (wich is currently out of question due to a lack of time), is by only using one fixed label name.
So at least this implicitly fixes T28206 somehow and decides the solution of this task.

Jan 28 2021, 9:59 PM · MITK (v2021.02)
kislinsk claimed T28220: [Image Cropper] Masking a 4D image and overwrite the original one leads to strange result.
Jan 28 2021, 9:53 PM · MITK (v2021.02)
kislinsk updated the task description for T28000: MITK v2021.02.
Jan 28 2021, 9:52 PM · MITK-ProjectTemplate, MITK (v2021.02)
kislinsk closed T28219: [Image Cropper] Selection widget does not allow to create a new bounding box as Resolved.
Jan 28 2021, 9:51 PM · MITK (v2021.02)
kislinsk closed T28219: [Image Cropper] Selection widget does not allow to create a new bounding box, a subtask of T28000: MITK v2021.02, as Resolved.
Jan 28 2021, 9:51 PM · MITK-ProjectTemplate, MITK (v2021.02)
kislinsk claimed T28219: [Image Cropper] Selection widget does not allow to create a new bounding box.
Jan 28 2021, 9:51 PM · MITK (v2021.02)
kislinsk updated the task description for T28000: MITK v2021.02.
Jan 28 2021, 9:46 PM · MITK-ProjectTemplate, MITK (v2021.02)
kislinsk closed T28213: [Point Set] Clear current time step does not work, a subtask of T28000: MITK v2021.02, as Resolved.
Jan 28 2021, 9:43 PM · MITK-ProjectTemplate, MITK (v2021.02)
kislinsk closed T28213: [Point Set] Clear current time step does not work as Resolved.

The context menu actions are either not implemented or dysfunctional. Disable the context menu for now.

Jan 28 2021, 9:43 PM · MITK (v2021.02)
kislinsk closed T28212: [Point Set] Only points for time step 0 are listed, a subtask of T28000: MITK v2021.02, as Invalid.
Jan 28 2021, 9:34 PM · MITK-ProjectTemplate, MITK (v2021.02)
kislinsk closed T28212: [Point Set] Only points for time step 0 are listed as Invalid.

Closing as "invalid". The secret is to use the mouse wheel to navigate between time steps in the point set widget. It is not in sync with the Image Navigator. The whole plugin and widgets need a complete rewrite to actually work reliably with dynamic images, though, but this is out of scope for this task and the upcoming release.

Jan 28 2021, 9:33 PM · MITK (v2021.02)
floca claimed T28223: [ImageStatistics] Deleting a datanode after statistics leads to no histogram update for the next node.
Jan 28 2021, 8:41 PM · Next Milestone, MITK
kalali added a comment to T28191: Refactor and extend LevelWindow unit tests.

I found several reasons to do a pseudo-UI test so I will come up with a draft for a test of the relevant classes.

Jan 28 2021, 8:36 PM · Auto-closed, MITK
floca updated subscribers of T28222: [ImageStatistics] Histogram is only shown for timestep 0.

Looked into it. So for quick fix we hace only the following options:

Jan 28 2021, 8:22 PM · MITK (v2021.02)
floca added a comment to T28230: Issue with DICOM SEG -> NIFTI conversion: missing empty slices.

OK. Following options/state:

Jan 28 2021, 7:01 PM · MITK
kleina committed rOBSHYPPOPY38bf9e41f9e5: Merge branch 'T26755_mpi4hyppopy' (authored by kleina).
Merge branch 'T26755_mpi4hyppopy'
Jan 28 2021, 4:55 PM
kleina committed rOBSHYPPOPYfd1e3a1ce194: Fexed tests. Parameter "normed" was updated to "density" in scipy.stats.norm (authored by kleina).
Fexed tests. Parameter "normed" was updated to "density" in scipy.stats.norm
Jan 28 2021, 4:55 PM
kleina committed rOBSHYPPOPY1a7a0544bf5e: Merge branch 'T26755_mpi4hyppopy' of https://github.com/MIC-DKFZ/Hyppopy into… (authored by kleina).
Merge branch 'T26755_mpi4hyppopy' of https://github.com/MIC-DKFZ/Hyppopy into…
Jan 28 2021, 4:55 PM
kleina committed rOBSHYPPOPY9e0e45582629: removed loss_function_call, which is depricated and was no longer used anyway. (authored by kleina).
removed loss_function_call, which is depricated and was no longer used anyway.
Jan 28 2021, 4:55 PM
kleina committed rOBSHYPPOPY63a9cb87d47e: Merge branch 'T26755_mpi4hyppopy' (authored by kleina).
Merge branch 'T26755_mpi4hyppopy'
Jan 28 2021, 4:55 PM
eisenman closed T28227: challangeR Patch v1.0.1 as Resolved.
Jan 28 2021, 1:04 PM · challengeR
eisenman closed T28201: Avoid blank pages in report as Resolved.
Jan 28 2021, 1:04 PM · challengeR
eisenman closed T28194: drop restriction at least 3 algorithms required for bootstrapping as Resolved.
Jan 28 2021, 1:04 PM · challengeR
eisenman closed T28193: bug in stabilityByAlgorithm.bootstrap.list as Resolved.
Jan 28 2021, 1:04 PM · challengeR
eisenman closed T28202: Error in stabilityByAlgorithm if only one case is used as Resolved.
Jan 28 2021, 1:03 PM · challengeR
eisenman closed T28210: update citation of paper to scientific reports as Resolved.
Jan 28 2021, 1:03 PM · challengeR
eisenman moved T28227: challangeR Patch v1.0.1 from In Progress to Done on the challengeR board.
Jan 28 2021, 11:22 AM · challengeR
floca added a parent task for T28230: Issue with DICOM SEG -> NIFTI conversion: missing empty slices: Unknown Object (Maniphest Task).
Jan 28 2021, 10:44 AM · MITK
floca added a comment to T28230: Issue with DICOM SEG -> NIFTI conversion: missing empty slices.

As discussed I would solve it by using a tool to resample/pad the segmentation to the same size like the image.
I will have a look on the most pragmatic way to provide the CLI.

Jan 28 2021, 10:44 AM · MITK
s669m triaged T28169: TFDA MVP v1 powered by Kaapana as Normal priority.
Jan 28 2021, 10:15 AM · Kaapana (internal)
s669m moved T28229: build getting failed after integration of tfda module from kaapana to Kaapana - Internal from Discussion to In Progress on the Kaapana (internal) board.
Jan 28 2021, 10:14 AM · Kaapana (internal)
neher closed T27974: Sarah requires an MITK installer containing the mitk file converter as Resolved.
Jan 28 2021, 9:51 AM · Missing Info, MITK
neher created T28232: Shapemodels.
Jan 28 2021, 9:47 AM · Auto-closed, Kaapana (internal), Request for Discussion, MITK
s669m updated the task description for T28229: build getting failed after integration of tfda module from kaapana to Kaapana - Internal .
Jan 28 2021, 9:37 AM · Kaapana (internal)
s669m updated the task description for T28229: build getting failed after integration of tfda module from kaapana to Kaapana - Internal .
Jan 28 2021, 9:37 AM · Kaapana (internal)
p212r moved T28196: [Docs] Update Dev-Guide for 0.1.1-dev from In Progress to Discussion on the Kaapana (internal) board.
Jan 28 2021, 9:33 AM · Kaapana (internal)
neher added a comment to T28230: Issue with DICOM SEG -> NIFTI conversion: missing empty slices.

As far as I know, this is crucial for the RACOON project. So for the Kaapana side, this has a high priority.

Jan 28 2021, 9:33 AM · MITK
gaoh moved T28196: [Docs] Update Dev-Guide for 0.1.1-dev from In Progress to Discussion on the Kaapana (internal) board.
Jan 28 2021, 9:31 AM · Kaapana (internal)
p212r raised the priority of T28196: [Docs] Update Dev-Guide for 0.1.1-dev from Low to Normal.
Jan 28 2021, 9:31 AM · Kaapana (internal)
p212r added a project to T28196: [Docs] Update Dev-Guide for 0.1.1-dev: Request for Discussion.
Jan 28 2021, 9:26 AM · Kaapana (internal)
s669m renamed T28229: build getting failed after integration of tfda module from kaapana to Kaapana - Internal from Kaapana - Internal build getting failed after integration of tfda to build getting failed after integration of tfda module from kaapana to Kaapana - Internal .
Jan 28 2021, 9:19 AM · Kaapana (internal)
s669m updated the task description for T28229: build getting failed after integration of tfda module from kaapana to Kaapana - Internal .
Jan 28 2021, 9:19 AM · Kaapana (internal)
schererj updated subscribers of T28230: Issue with DICOM SEG -> NIFTI conversion: missing empty slices.
Jan 28 2021, 9:18 AM · MITK
s669m updated the task description for T28229: build getting failed after integration of tfda module from kaapana to Kaapana - Internal .
Jan 28 2021, 9:18 AM · Kaapana (internal)
schererj triaged T28230: Issue with DICOM SEG -> NIFTI conversion: missing empty slices as High priority.
Jan 28 2021, 9:16 AM · MITK
s669m triaged T28229: build getting failed after integration of tfda module from kaapana to Kaapana - Internal as Normal priority.
Jan 28 2021, 9:07 AM · Kaapana (internal)
kislinsk closed T28224: [Point Set] List of points is not shown if plugin opened after data loading, a subtask of T28000: MITK v2021.02, as Resolved.
Jan 28 2021, 7:33 AM · MITK-ProjectTemplate, MITK (v2021.02)
kislinsk closed T28224: [Point Set] List of points is not shown if plugin opened after data loading as Resolved.
Jan 28 2021, 7:33 AM · MITK (v2021.02)
kislinsk claimed T28224: [Point Set] List of points is not shown if plugin opened after data loading.
Jan 28 2021, 7:17 AM · MITK (v2021.02)
kislinsk claimed T28213: [Point Set] Clear current time step does not work.
Jan 28 2021, 7:17 AM · MITK (v2021.02)
kislinsk claimed T28212: [Point Set] Only points for time step 0 are listed.
Jan 28 2021, 7:17 AM · MITK (v2021.02)

Jan 27 2021

kislinsk updated the task description for T28000: MITK v2021.02.
Jan 27 2021, 11:09 PM · MITK-ProjectTemplate, MITK (v2021.02)
kislinsk closed T28203: [Segmentation] 2-d correction tool does not work anymore and should be removed, a subtask of T28000: MITK v2021.02, as Resolved.
Jan 27 2021, 11:02 PM · MITK-ProjectTemplate, MITK (v2021.02)
kislinsk closed T28203: [Segmentation] 2-d correction tool does not work anymore and should be removed as Resolved.

Thanks for the hint.

Jan 27 2021, 11:02 PM · MITK (v2021.02)
kislinsk closed T22391: Correction tool doesn't work in empty slice as Invalid.

Since we removed the correction tool, this task is not valid anymore. The Add or Subtract tool can be used as a replacement. Remember that pressing CTRL inverts the logic of these tools.

Jan 27 2021, 11:00 PM · MITK, Restricted Project
kalali renamed T28203: [Segmentation] 2-d correction tool does not work anymore and should be removed from [Segmentation] 2-d correction tool does not work anymore to [Segmentation] 2-d correction tool does not work anymore and should be removed.
Jan 27 2021, 10:53 PM · MITK (v2021.02)
kalali added a comment to T28203: [Segmentation] 2-d correction tool does not work anymore and should be removed.

Ok, but then we can at least close T22391.

Jan 27 2021, 10:52 PM · MITK (v2021.02)
kislinsk claimed T28203: [Segmentation] 2-d correction tool does not work anymore and should be removed.

Is this obsolete know with the discussion results stated in D459?

Jan 27 2021, 10:50 PM · MITK (v2021.02)
kislinsk updated the task description for T28000: MITK v2021.02.
Jan 27 2021, 10:48 PM · MITK-ProjectTemplate, MITK (v2021.02)
kislinsk closed T28218: [Segmentation] The text in the "Create a static mask?" message box is way to technical, a subtask of T28000: MITK v2021.02, as Resolved.
Jan 27 2021, 10:46 PM · MITK-ProjectTemplate, MITK (v2021.02)
kislinsk closed T28218: [Segmentation] The text in the "Create a static mask?" message box is way to technical as Resolved.

Capture.PNG (187×502 px, 9 KB)

Jan 27 2021, 10:46 PM · MITK (v2021.02)
kislinsk updated the task description for T28000: MITK v2021.02.
Jan 27 2021, 10:26 PM · MITK-ProjectTemplate, MITK (v2021.02)
eisenman committed rCHALLENGERe9fe3abbeeee: Merge tag 'v1.0.1' into develop (authored by eisenman).
Merge tag 'v1.0.1' into develop
Jan 27 2021, 7:07 PM
eisenman committed rCHALLENGER9446685d5425: Merge branch 'release/T28227-v1.0.1' (authored by eisenman).
Merge branch 'release/T28227-v1.0.1'
Jan 27 2021, 7:07 PM
eisenman committed rCHALLENGER24eb5f4e9b9b: Add change notes (authored by eisenman).
Add change notes
Jan 27 2021, 7:02 PM