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Mar 31 2022

s434n triaged T29106: [Segmentation Options] "show only selected nodes" is not immediately applied as Low priority.
Mar 31 2022, 12:55 PM · MITK (v2022.10), Checklist
s349i created T29105: [3D Surface Interpolation] 3D+t Interpolation Preview Crashes When Going Through Different Time Steps.
Mar 31 2022, 12:00 PM · Breaking Change, MITK (v2024.06), Checklist

Mar 30 2022

s349i renamed T29088: [Checklist] 3D Segmentation - Checklist and MITK UI Inconsistencies from [3D Segmentation] 3D Segmentation Tools - Checklist and MITK UI Inconsistencies to [3D Segmentation] 3D Segmentation Checklist - Checklist and MITK UI Inconsistencies.
Mar 30 2022, 4:24 PM · MITK (v2022.04), Checklist
s349i created T29102: [3D Segmentation] Picking Tool - Problem deleting picked regions..
Mar 30 2022, 4:24 PM · Cleared, Checklist, MITK (v2022.04)
s349i renamed T29088: [Checklist] 3D Segmentation - Checklist and MITK UI Inconsistencies from [Segmentation] 3D Segmentation Tools - Checklist and MITK UI Inconsistencies to [3D Segmentation] 3D Segmentation Tools - Checklist and MITK UI Inconsistencies.
Mar 30 2022, 4:17 PM · MITK (v2022.04), Checklist
s349i renamed T29089: [3D Segmentation] 3D Segmentation - Color cycle resets with the new layer. from [Segmentation] 3D Segmentation - Color cycle resets with the new layer. to [3D Segmentation] 3D Segmentation - Color cycle resets with the new layer..
Mar 30 2022, 4:17 PM · MITK (v2022.04), Checklist
s349i renamed T29096: [3D Segmentation] Threshold Tool - Does not handle multiple labels. from [Segmentation] Threshold Tool - Does not handle multiple labels. to [3D Segmentation] Threshold Tool - Does not handle multiple labels..
Mar 30 2022, 4:17 PM · Checklist, MITK (v2022.04)
s349i renamed T29097: [3D Segmentation] UL Threshold Tool - Does not handle multiple labels. from [Segmentation] UL Threshold Tool - Does not handle multiple labels. to [3D Segmentation] UL Threshold Tool - Does not handle multiple labels..
Mar 30 2022, 4:17 PM · Checklist, MITK (v2022.04)
s349i renamed T29098: [3D Segmentation] UL Threshold Tool - 0 intensity value not include in slider range? from [Segmentation] UL Threshold Tool - 0 intensity value not include in slider range? to [3D Segmentation] UL Threshold Tool - 0 intensity value not include in slider range?.
Mar 30 2022, 4:17 PM · MITK (v2024.06), Restricted Project, Checklist
s349i updated the task description for T29101: [3D Segmentation] Region Growing Tool - Generated Segmentation darkens the ambient image.
Mar 30 2022, 4:15 PM · MITK, Checklist
s349i created T29101: [3D Segmentation] Region Growing Tool - Generated Segmentation darkens the ambient image.
Mar 30 2022, 4:14 PM · MITK, Checklist
s349i created T29100: [3D Segmentation] Otsu Tool - Better Preview Region Clicking Behaviour.
Mar 30 2022, 4:03 PM · Checklist, MITK (v2022.04)
s349i created T29099: [3D Segmentation] Otsu Tool - Does not handle multiple labels..
Mar 30 2022, 4:00 PM · Checklist, MITK (v2022.04)
s349i created T29098: [3D Segmentation] UL Threshold Tool - 0 intensity value not include in slider range?.
Mar 30 2022, 3:51 PM · MITK (v2024.06), Restricted Project, Checklist
s349i created T29097: [3D Segmentation] UL Threshold Tool - Does not handle multiple labels..
Mar 30 2022, 3:45 PM · Checklist, MITK (v2022.04)
s349i created T29096: [3D Segmentation] Threshold Tool - Does not handle multiple labels..
Mar 30 2022, 3:40 PM · Checklist, MITK (v2022.04)
s434n triaged T29095: [Image Cropper] Moving of the bounding box can not be undone as Wishlist priority.
Mar 30 2022, 3:37 PM · MITK, Checklist
s434n triaged T29094: Deleting a data node causes global reset as Normal priority.
Mar 30 2022, 3:37 PM · MITK, Checklist
s434n triaged T29093: [Image Cropper] Warning of rotated geometry not removed after reinit as Low priority.
Mar 30 2022, 3:36 PM · MITK (v2022.10), Checklist
s434n triaged T29092: [Image Cropper] Image name repeated in created nodes as Low priority.
Mar 30 2022, 3:35 PM · MITK (v2022.04), Checklist
s349i updated the task description for T29091: [3DSegmentation] [Threshold Tool] Spinbox entry does not allow entry of more than one number before update..
Mar 30 2022, 3:25 PM · Cleared, Checklist, MITK (v2022.04)
s349i updated the task description for T29091: [3DSegmentation] [Threshold Tool] Spinbox entry does not allow entry of more than one number before update..
Mar 30 2022, 3:25 PM · Cleared, Checklist, MITK (v2022.04)
s349i created T29091: [3DSegmentation] [Threshold Tool] Spinbox entry does not allow entry of more than one number before update..
Mar 30 2022, 3:24 PM · Cleared, Checklist, MITK (v2022.04)
s349i renamed T29089: [3D Segmentation] 3D Segmentation - Color cycle resets with the new layer. from 3D Segmentation - Color cycle resets with the new layer. to [Segmentation] 3D Segmentation - Color cycle resets with the new layer..
Mar 30 2022, 2:55 PM · MITK (v2022.04), Checklist
s349i renamed T29088: [Checklist] 3D Segmentation - Checklist and MITK UI Inconsistencies from 3D Segmentation Tools Checklist and MITK UI Inconsistencies to [Segmentation] 3D Segmentation Tools - Checklist and MITK UI Inconsistencies.
Mar 30 2022, 2:54 PM · MITK (v2022.04), Checklist
s349i renamed T29089: [3D Segmentation] 3D Segmentation - Color cycle resets with the new layer. from Color cycle resets with the new layer. to 3D Segmentation - Color cycle resets with the new layer..
Mar 30 2022, 2:44 PM · MITK (v2022.04), Checklist
s349i created T29089: [3D Segmentation] 3D Segmentation - Color cycle resets with the new layer..
Mar 30 2022, 2:43 PM · MITK (v2022.04), Checklist
s349i created T29088: [Checklist] 3D Segmentation - Checklist and MITK UI Inconsistencies.
Mar 30 2022, 2:39 PM · MITK (v2022.04), Checklist
floca closed T29062: MITK Flow as Resolved.
Mar 30 2022, 12:48 PM · Cleared, MITK (v2022.04)
kislinsk closed T28493: Multilabel color map colors are not very nice as Resolved.

Reordered palette from above to see similar colors next to each other to simulate the worst case:

palette_sorted.png (698×858 px, 4 KB)

Mar 30 2022, 11:35 AM · Checklist, Request for Discussion, MITK (v2022.04)
kislinsk closed T28493: Multilabel color map colors are not very nice, a subtask of T27807: [MultiLabel Segmentation] Inspection of module and plugin, as Resolved.
Mar 30 2022, 11:35 AM · MITK (v2024.06)
floca claimed T29062: MITK Flow.
Mar 30 2022, 11:01 AM · Cleared, MITK (v2022.04)

Mar 29 2022

kislinsk closed T28804: [Help] Hard to read color scheme (blue on dark background) as Resolved.

Since all colors in the widget are tuned to be in front of a white background I explicitly set the help search results background to be white.

Mar 29 2022, 11:36 PM · MITK (v2022.04), Checklist
kislinsk claimed T28804: [Help] Hard to read color scheme (blue on dark background).
Mar 29 2022, 10:28 PM · MITK (v2022.04), Checklist
kislinsk added a comment to T28585: The MITK-Tutorial Step 9 missing inheritence.

I already started to implement a new plugin generator (T27701) but it still is delayed because of priority reasons. When the plugin generator is back, step 9 should be revised/fixed.

Mar 29 2022, 10:03 PM · MITK (v2024.06)
franza added a comment to T28585: The MITK-Tutorial Step 9 missing inheritence.

A fix for this bug is available here: https://github.com/Alfred-Franz/MITK/tree/T28585-Included_inheritence (thanks to @kannberg!). However, I did not create a pull request yet because the plugin generator as used in tutorial step 9 should be completely replaced by the project template (see discussion in T27701). This means that tutorial step 9 will have to be completely revised, which would probably be quite a bit of work. But I think especially the example code for using a region grower in this tutorial step is worth to keep it.

Mar 29 2022, 3:37 PM · MITK (v2024.06)
kislinsk closed T27260: Spacing points still remain in data manager after closing calibration view as Resolved.
Mar 29 2022, 12:06 PM · MITK (v2022.04), Pull Request, IGT
kislinsk closed T28811: [Volume Visualization] [UX] Missing labels for dropdowns as Resolved.

I used the opportunity to get rid of some unused legacy classes and properties regarding volume visualization. According to our minimum requirements of the rendering backend, I removed the rendering mode combobox (GPU vs CPU) as we can assume capable GPUs. The blend mode combobox is now labeled and its items are fully spelled.

Mar 29 2022, 11:53 AM · Breaking Change, MITK (v2022.04), Checklist
franza edited projects for T27260: Spacing points still remain in data manager after closing calibration view, added: MITK (v2022.04); removed MITK.
Mar 29 2022, 11:13 AM · MITK (v2022.04), Pull Request, IGT
kompan added a comment to T27339: Provide public MITK ModelFit installer on a regular basis.

Current to dos to provide an MITK perfusion/modelFit installer:

  • Unit tests
    • Determine test coverage (T30195)
    • Unit tests for debug parameter images (T30196)
Mar 29 2022, 10:37 AM · MITK (v2024.06)
kislinsk claimed T28811: [Volume Visualization] [UX] Missing labels for dropdowns.

Was mentioned again in the current testing cycle by other testers.

Mar 29 2022, 9:36 AM · Breaking Change, MITK (v2022.04), Checklist
kahl added a comment to T28607: [Segmentation] LiveWire tool issues and improvements.

Regarding the comment of closing the contour with a double click: I also realized this during my work on the new add tool and I think the way I fixed it was to modify the OnFinish() function in the mitkLiveWireTool2D to check whether the click was performed on the first point which was also how it was done before the closure contour was added to the LiveWire tool.
Here is the code of my new add tool branch where I changed it:
https://phabricator.mitk.org/source/mitk/browse/feature%252FT28464-new-add-tool-2/Modules/Segmentation/Interactions/mitkLiveWireTool2D.cpp$344

Mar 29 2022, 9:35 AM · MITK (v2022.10), Cleared, Checklist

Mar 28 2022

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

This is my shot at it mainly based on the palettes above with extra effort regarding neighboring color contrasts (top-left to bottom-right). But it is impossible to get 25 perfectly distinguishable colors. Also I took into account that the human eye has the highest sensitivity in the green spectrum.

Mar 28 2022, 9:10 PM · Checklist, Request for Discussion, MITK (v2022.04)
kislinsk added a comment to T28493: Multilabel color map colors are not very nice.

Kelly is nice because it is not overly saturated as most other palettes, but I think the most useful is indeed glasbey, when the two black-ish and one grey-ish colors are removed for our context. Red and magenta both appears pretty similar twice. Also, the colors should be a reordered a little bit and for the sake of compatibility/expectations start with red. More or less the same for polychrome but there we would also need to get rid of more grey colors.

Mar 28 2022, 8:36 PM · Checklist, Request for Discussion, MITK (v2022.04)
kislinsk added a comment to T28493: Multilabel color map colors are not very nice.

I procrastinated on the colors tonight for quite some time and finally found something that really stood out - the standard distinguishable color palettes of R:

Mar 28 2022, 8:32 PM · Checklist, Request for Discussion, MITK (v2022.04)
kislinsk lowered the priority of T29076: [Segmentation] Pressing DEL should delete a label from Normal to Wishlist.

Same for F2 regarding renaming of labels. I would also say double-click, but as it turned out, double-click is already used to jump to the center of the label.

Mar 28 2022, 8:23 PM · MITK (v2024.06), Checklist
kislinsk edited projects for T28607: [Segmentation] LiveWire tool issues and improvements, added: Cleared; removed Request for Discussion.

The first two comments should be targeted for this release. The last comment is something that also happens sometimes with the new implementation of the polygon tool that uses the same base class. But fixing is too complex to be worth spending time before the release, so whoever grabs this task, focus on the first two comments.

Mar 28 2022, 8:21 PM · MITK (v2022.10), Cleared, Checklist
kalali edited projects for T28768: Region Growing in its current state is unintuitive, added: MITK (v2022.04); removed MITK.
Mar 28 2022, 5:47 PM · MITK (v2022.04), Checklist
kalali updated the task description for T29079: [Segmentation] Test tools on different anatomical planes.
Mar 28 2022, 5:44 PM · Checklist, MITK (v2022.04)
kalali updated the task description for T29079: [Segmentation] Test tools on different anatomical planes.
Mar 28 2022, 5:44 PM · Checklist, MITK (v2022.04)
kalali triaged T29079: [Segmentation] Test tools on different anatomical planes as High priority.
Mar 28 2022, 5:44 PM · Checklist, MITK (v2022.04)
kalali triaged T29078: [Segmentation] Erase tool has unclear edge cases as High priority.
Mar 28 2022, 5:23 PM · Next Milestone, Checklist
kalali added a comment to T27506: Extend checklists for segmentation view.

All checklists have been refactored and used again for testing MITK 2022.04.
Some issues with the checklists still exist, so I will use this task to fix these for the upcoming release:

Mar 28 2022, 5:10 PM · MITK (v2022.04), Cleared
kalali triaged T29077: [Segmentation] Showing / hiding labels using the labelsetwidget selects them as Normal priority.
Mar 28 2022, 4:34 PM · MITK (v2023.04), Checklist
kalali triaged T29076: [Segmentation] Pressing DEL should delete a label as Normal priority.
Mar 28 2022, 4:27 PM · MITK (v2024.06), Checklist
kalali added projects to T28607: [Segmentation] LiveWire tool issues and improvements: Checklist, Request for Discussion.

@floca, @kislinsk: Both @kahl and @kleina won't be able to work on this anymore, but this task is still open. We also received some feedback regarding the usability from the last test day, so we should discuss how to proceed:

Mar 28 2022, 4:18 PM · MITK (v2022.10), Cleared, Checklist
kislinsk closed T28777: Resetting Standard Multi Widget preferences leads to other colors than the default ones as Resolved.

It is not worth currently to spend much time on this so I fixed it as fast as possible by syncing the default colors instead of creating a single source of truth. This code location was barely touched in the past decade and I don't see why this would receive suddenly much more attention than that.

Mar 28 2022, 3:51 PM · MITK (v2022.04), Checklist
kislinsk added a comment to T28777: Resetting Standard Multi Widget preferences leads to other colors than the default ones.

Deleted branch from rMITK MITK: bugfix/T28777-DefaultDecorationColors.

Mar 28 2022, 3:47 PM · MITK (v2022.04), Checklist
kislinsk added a comment to T28777: Resetting Standard Multi Widget preferences leads to other colors than the default ones.

Pushed new branch to rMITK MITK: bugfix/T28777-DefaultDecorationColors.

Mar 28 2022, 3:46 PM · MITK (v2022.04), Checklist
kalali added a project to T28493: Multilabel color map colors are not very nice: Checklist.

The problem was mentioned again in the tested checklists:

  • image.png (123×978 px, 13 KB)
Mar 28 2022, 3:16 PM · Checklist, Request for Discussion, MITK (v2022.04)
kalali closed T28110: Extend checklists for multilabel segmentation view as Resolved.

MultiLabel Checklists have been removed and the content has been merged into the basic segmentation checklists (because of T28142: [Segmentation] Remove plugin redundancy with MultiLabelSegmentation).
Only the ML Utilities checklist exists so I will close this task.

Mar 28 2022, 3:11 PM · MITK (v2022.04)
kalali closed T28110: Extend checklists for multilabel segmentation view, a subtask of T28108: [Release Checklists] Prepare release checklists, as Resolved.
Mar 28 2022, 3:11 PM · MITK
kislinsk claimed T28777: Resetting Standard Multi Widget preferences leads to other colors than the default ones.

Also, as reported by @s434n , the decoration colors in the Image Navigator only update after there was a render window update / click in one of the render windows.

Mar 28 2022, 1:42 PM · MITK (v2022.04), Checklist
a178n added a comment to T29066: Change GUI order for "Task" and "Configuration".

Pushed new branch to rMITK MITK: feature/T29066-after-hackathon-changes.

Mar 28 2022, 12:10 PM · MITK, Next Milestone
kislinsk closed T29072: Fix various minor segmentation issues as Resolved.
Mar 28 2022, 11:21 AM · Checklist, MITK (v2022.04)
kislinsk added a comment to T29072: Fix various minor segmentation issues.

Deleted branch from rMITK MITK: bugfix/T29072-VariousSegmentationViewFixes.

Mar 28 2022, 11:21 AM · Checklist, MITK (v2022.04)
kislinsk updated the task description for T29072: Fix various minor segmentation issues.
Mar 28 2022, 11:16 AM · Checklist, MITK (v2022.04)
a178n closed T29059: [BUG] Prediction not working for Mono Modal data as Resolved.
Mar 28 2022, 10:30 AM · MITK (v2022.04)
a178n added a comment to T29059: [BUG] Prediction not working for Mono Modal data.

Deleted branch from rMITK MITK: feature/T29059-nnUnet-monomodal-bugfix.

Mar 28 2022, 10:28 AM · MITK (v2022.04)
kislinsk updated the task description for T29072: Fix various minor segmentation issues.
Mar 28 2022, 10:28 AM · Checklist, MITK (v2022.04)
kislinsk updated the task description for T29072: Fix various minor segmentation issues.
Mar 28 2022, 10:12 AM · Checklist, MITK (v2022.04)
kislinsk added a comment to T29072: Fix various minor segmentation issues.

Pushed new branch to rMITK MITK: bugfix/T29072-VariousSegmentationViewFixes.

Mar 28 2022, 10:11 AM · Checklist, MITK (v2022.04)
kislinsk triaged T29072: Fix various minor segmentation issues as Normal priority.
Mar 28 2022, 9:56 AM · Checklist, MITK (v2022.04)
a178n triaged T29071: Update Checklist as Normal priority.
Mar 28 2022, 9:49 AM · MITK, Next Milestone
kislinsk closed T29070: Create (smoothed) polygon model crashes as Resolved.
Mar 28 2022, 9:27 AM · Checklist, MITK (v2022.04)
kislinsk added a comment to T29070: Create (smoothed) polygon model crashes.

Deleted branch from rMITK MITK: bugfix/T29070-CreatePolygonModelCrashes.

Mar 28 2022, 9:25 AM · Checklist, MITK (v2022.04)
kislinsk added a comment to T29070: Create (smoothed) polygon model crashes.

Pushed new branch to rMITK MITK: bugfix/T29070-CreatePolygonModelCrashes.

Mar 28 2022, 9:24 AM · Checklist, MITK (v2022.04)
kislinsk triaged T29070: Create (smoothed) polygon model crashes as High priority.
Mar 28 2022, 9:21 AM · Checklist, MITK (v2022.04)

Mar 25 2022

a178n added a comment to T29059: [BUG] Prediction not working for Mono Modal data.

Pushed new branch to rMITK MITK: feature/T29059-nnUnet-monomodal-bugfix.

Mar 25 2022, 5:16 PM · MITK (v2022.04)
floca edited projects for T29062: MITK Flow, added: MITK (v2022.04), Cleared; removed MITK.

This is due to the change in the plugin ID . MultiLabel Segmentation View does not exist any more.

Mar 25 2022, 4:06 PM · Cleared, MITK (v2022.04)
a178n triaged T29068: Multi-Modal Prediction : Auto load no.of modalities and modal order on the GUI from pickle file as Normal priority.
Mar 25 2022, 3:03 PM · MITK, Next Milestone
a178n triaged T29067: Introduce option to save the segmentation in the nnUNet tool GUI itself. as Normal priority.
Mar 25 2022, 2:54 PM · MITK
a178n triaged T29066: Change GUI order for "Task" and "Configuration" as Normal priority.
Mar 25 2022, 2:42 PM · MITK, Next Milestone
a178n triaged T29065: Check if RESULTS_FOLDER environment variable exist and get the directory as Normal priority.
Mar 25 2022, 2:40 PM · MITK, Next Milestone
a178n triaged T29064: Remember last used Python Path as Normal priority.
Mar 25 2022, 2:36 PM · MITK, Next Milestone
a178n claimed T29061: Validate the manually selected Python virtual environments.
Mar 25 2022, 2:32 PM · MITK, Next Milestone
a178n triaged T29063: When all the folds are selected in "Folds" dropdown box, then show "All Folds" instead of "All" as Normal priority.
Mar 25 2022, 2:32 PM · MITK (v2024.06)
a178n triaged T29061: Validate the manually selected Python virtual environments as Low priority.
Mar 25 2022, 2:27 PM · MITK, Next Milestone
kislinsk triaged T29060: [Segmentation] Glitch in label color after 3d-interpolation as Normal priority.
Mar 25 2022, 11:14 AM · MITK (v2023.04), Checklist
a178n triaged T29059: [BUG] Prediction not working for Mono Modal data as Unbreak Now! priority.
Mar 25 2022, 10:22 AM · MITK (v2022.04)
kalali closed T29055: [Segmentation] Update checklists accordingly, a subtask of T28142: [Segmentation] Remove plugin redundancy with MultiLabelSegmentation, as Resolved.
Mar 25 2022, 9:30 AM · MITK (v2022.04), Breaking Change
kalali closed T29055: [Segmentation] Update checklists accordingly as Resolved.
Mar 25 2022, 9:30 AM · MITK (v2022.04)
kalali updated the task description for T29055: [Segmentation] Update checklists accordingly.
Mar 25 2022, 9:30 AM · MITK (v2022.04)

Mar 24 2022

kalali updated the task description for T29055: [Segmentation] Update checklists accordingly.
Mar 24 2022, 2:22 PM · MITK (v2022.04)
kalali updated the task description for T29055: [Segmentation] Update checklists accordingly.
Mar 24 2022, 2:21 PM · MITK (v2022.04)
kalali moved T29055: [Segmentation] Update checklists accordingly from Backlog to Cycle on the MITK (v2022.04) board.
Mar 24 2022, 2:12 PM · MITK (v2022.04)
kalali added a revision to T29047: [MultiLabel Segmentation] Remove documentation: Restricted Differential Revision.
Mar 24 2022, 1:46 PM · MITK (v2022.04)
kalali triaged T29055: [Segmentation] Update checklists accordingly as High priority.
Mar 24 2022, 1:46 PM · MITK (v2022.04)
kalali moved T29047: [MultiLabel Segmentation] Remove documentation from Backlog to Cycle on the MITK (v2022.04) board.
Mar 24 2022, 1:20 PM · MITK (v2022.04)
kompan closed T27745: [MITKDoc] Revise Model Fit Generic View Documentation as Resolved.
Mar 24 2022, 12:39 PM · MITK (v2022.04)