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Oct 10 2023

floca edited projects for T29454: Clarify the versions/editions we publish as installer, added: MITK (v2023.12); removed MITK (v2023.04).
Oct 10 2023, 12:07 PM · MITK (v2024.06), Request for Discussion
floca edited projects for T29454: Clarify the versions/editions we publish as installer, added: MITK (v2023.04); removed MITK.
Oct 10 2023, 12:06 PM · MITK (v2024.06), Request for Discussion

Sep 27 2023

floca added a comment to T30207: Add org.mitk.gui.qt.dicominspector to release.

I think in doubt I would just move but not merge it for now. If we see that it is needed or wanted we can make the effort and merge it. It would be better than not offering this feature at all.

Sep 27 2023, 11:01 AM · Request for Discussion, MITK (v2023.12)
floca added a project to T30207: Add org.mitk.gui.qt.dicominspector to release: Request for Discussion.

The dicom inspector has one additional dependency to module MITKDICOM. Therefore if we merge the inspector plugins also our normal inspector could only be build if DICOM module is activated. (Which it currently is per default).

Sep 27 2023, 10:56 AM · Request for Discussion, MITK (v2023.12)
floca claimed T30210: [SEG] Add dedicated reader for label image stack support.
Sep 27 2023, 10:50 AM · Moved to git.dkfz.de, MITK (v2024.12)
floca claimed T30209: [SEG] Add a writer for label image stack support.
Sep 27 2023, 10:49 AM · Moved to git.dkfz.de, MITK (v2024.12)
floca claimed T27718: Miniapp for basic DICOM testing.
Sep 27 2023, 10:39 AM · MITK (v2023.12), Kaapana (internal)

Sep 19 2023

floca added a project to T30186: PixelDumper view in MITK release: Request for Discussion.
Sep 19 2023, 11:39 AM · Moved to git.dkfz.de, MITK
floca updated the task description for T30186: PixelDumper view in MITK release.
Sep 19 2023, 11:38 AM · Moved to git.dkfz.de, MITK
floca added a comment to T30186: PixelDumper view in MITK release.

Is there some additional functionality involved or could we just add it as another MIME type for images instead of a dedicated plugin?

Yes there is. As only (potentially) the pixel values of image parts with an mask should be exported. And you can select multiple image (as long as they have the same geometry), there pixel values will be exported into the same table.

Sep 19 2023, 11:38 AM · Moved to git.dkfz.de, MITK

Sep 11 2023

floca placed T29392: [SEG] Add dedicated writer to store multi-label images in nifti up for grabs.
Sep 11 2023, 3:01 PM · Moved to git.dkfz.de, MITK (v2024.12)
floca triaged T30210: [SEG] Add dedicated reader for label image stack support as Normal priority.
Sep 11 2023, 3:00 PM · Moved to git.dkfz.de, MITK (v2024.12)
floca updated the task description for T30209: [SEG] Add a writer for label image stack support.
Sep 11 2023, 2:36 PM · Moved to git.dkfz.de, MITK (v2024.12)
floca triaged T30209: [SEG] Add a writer for label image stack support as Normal priority.
Sep 11 2023, 2:36 PM · Moved to git.dkfz.de, MITK (v2024.12)
floca triaged T30208: [SEG] Add support to read/write stack of label images from/to a mitk label image as Normal priority.
Sep 11 2023, 2:34 PM · Moved to git.dkfz.de, MITK (v2024.12)
floca renamed T29392: [SEG] Add dedicated writer to store multi-label images in nifti from [Segmentation] Add dedicated writer to store multi-label images in nifti to [SEG] Add dedicated writer to store multi-label images in nifti.
Sep 11 2023, 1:58 PM · Moved to git.dkfz.de, MITK (v2024.12)
floca moved T30207: Add org.mitk.gui.qt.dicominspector to release from Backlog to MITK Meeting on the Request for Discussion board.
Sep 11 2023, 11:43 AM · Request for Discussion, MITK (v2023.12)
floca triaged T30207: Add org.mitk.gui.qt.dicominspector to release as Normal priority.
Sep 11 2023, 11:43 AM · Request for Discussion, MITK (v2023.12)

Sep 8 2023

floca triaged T30194: [SEG] Refactor LabelSetImage to MultiLabelSegmentation class as High priority.
Sep 8 2023, 12:15 PM · Next Milestone
floca added a comment to T26397: Multilabel Segmentation file cannot be converted to multilabel segmentation in MITK.

@full Is this still an issue (with the current release)?

Sep 8 2023, 11:59 AM · MITK

Sep 7 2023

floca added a comment to T30157: [DCM][SEG] potential in compliance to DICOM segmentation: clarify correct use of pixel value/segment number.

offer the feature to take an instance UID that is an int as the pixel value.

Not sure if I understand it correctly, but ... DICOM UID cannot have int as the value - this would violate VR constraints.

Sep 7 2023, 5:40 PM · Moved to git.dkfz.de, MITK (v2024.12), Missing Info, Request for Discussion
floca claimed T29204: [SEG] Rework properties of Label class + add instance information.
Sep 7 2023, 12:38 PM · Moved to git.dkfz.de, MITK (v2024.12), Breaking Change
floca added a comment to T30157: [DCM][SEG] potential in compliance to DICOM segmentation: clarify correct use of pixel value/segment number.

T29204 should be done before as we need to store the information in an appropriate way. The most important thing is that we have then a property to store the instance UID. The default UID is the pixelvalue if not overwritten by the user or another configuration. Regarding the persistance of the pixel value I see two option:
a) Live with the fact (and document it) that DICOM Seg is not "loss less" regarding the pixel value. So after saving to and loading from DICOM Seg your label will have the same (class) name and instance UID but might have a different pixel value.
b) offer the feature to take an instance UID that is an int as the pixel value. But this is only possible if we assure in our UI that you cannot use/change into an instance UID in a Segmentation that is alrready used there by another label.
Currently I would lean to a) and generate a new ticket for b) and see if we need it in the future.

Sep 7 2023, 12:37 PM · Moved to git.dkfz.de, MITK (v2024.12), Missing Info, Request for Discussion
floca added a subtask for T30157: [DCM][SEG] potential in compliance to DICOM segmentation: clarify correct use of pixel value/segment number: T29204: [SEG] Rework properties of Label class + add instance information.
Sep 7 2023, 12:29 PM · Moved to git.dkfz.de, MITK (v2024.12), Missing Info, Request for Discussion
floca added a parent task for T29204: [SEG] Rework properties of Label class + add instance information: T30157: [DCM][SEG] potential in compliance to DICOM segmentation: clarify correct use of pixel value/segment number.
Sep 7 2023, 12:29 PM · Moved to git.dkfz.de, MITK (v2024.12), Breaking Change
floca closed T30161: [DCM][SEG] First label data gets lost if multilables are stored as DCM Seg as Resolved.
Sep 7 2023, 12:18 PM · Missing Info, MITK (v2023.12)
floca closed T30161: [DCM][SEG] First label data gets lost if multilables are stored as DCM Seg, a subtask of T30157: [DCM][SEG] potential in compliance to DICOM segmentation: clarify correct use of pixel value/segment number, as Resolved.
Sep 7 2023, 12:18 PM · Moved to git.dkfz.de, MITK (v2024.12), Missing Info, Request for Discussion

Aug 12 2023

floca updated the task description for T30186: PixelDumper view in MITK release.
Aug 12 2023, 5:09 PM · Moved to git.dkfz.de, MITK
floca triaged T30186: PixelDumper view in MITK release as Normal priority.
Aug 12 2023, 5:04 PM · Moved to git.dkfz.de, MITK
floca closed T26368: [ModelFitInspector] Performance if multiple bookmark points are added as Wontfix.

After we have moved to Qt6, we then have QtCharts to our disposal and migrate to that.

Aug 12 2023, 3:19 PM · Restricted Project, Restricted Project, MITK
floca closed T26368: [ModelFitInspector] Performance if multiple bookmark points are added, a subtask of T25832: Migrate ModelFit inspector plugin to MitkChart, as Wontfix.
Aug 12 2023, 3:19 PM · Moved to git.dkfz.de, Restricted Project, Restricted Project, MITK
floca closed T26367: [ModelFitInspector] Remove bookmark doesn't work, a subtask of T25832: Migrate ModelFit inspector plugin to MitkChart, as Wontfix.
Aug 12 2023, 3:17 PM · Moved to git.dkfz.de, Restricted Project, Restricted Project, MITK
floca closed T26367: [ModelFitInspector] Remove bookmark doesn't work as Wontfix.

After we have moved to Qt6, we then have QtCharts to our disposal and migrate to that.

Aug 12 2023, 3:17 PM · Restricted Project, Restricted Project, MITK
floca closed T26366: [ModelFitInspector] Fixed scaling doesn't work yet as Wontfix.

After we have moved to Qt6, we then have QtCharts to our disposal and migrate to that.

Aug 12 2023, 3:17 PM · Restricted Project, Restricted Project, MITK
floca closed T26366: [ModelFitInspector] Fixed scaling doesn't work yet, a subtask of T25832: Migrate ModelFit inspector plugin to MitkChart, as Wontfix.
Aug 12 2023, 3:17 PM · Moved to git.dkfz.de, Restricted Project, Restricted Project, MITK
floca added a comment to T25832: Migrate ModelFit inspector plugin to MitkChart.

Should be done after(!) we have moved to Qt6 as we then have QtCharts to our disposal and migrate to that.

Aug 12 2023, 3:15 PM · Moved to git.dkfz.de, Restricted Project, Restricted Project, MITK
floca closed T27306: [statistics] Errors caused in MitkChart when using histogram and intensity profile widgets. as Wontfix.

After we have moved to Qt6, we then have QtCharts to our disposal and migrate to that.

Aug 12 2023, 3:14 PM · MITK (v2023.12)
floca added a comment to T27285: [Image Statistics] QmitkChart widget should support ID or allow control over labels.

Should be done after(!) we have moved to Qt6 as we then have QtCharts to our disposal and migrate to that.

Aug 12 2023, 3:12 PM · Moved to git.dkfz.de, MITK (v2024.12)
floca added a parent task for T29406: Make MITK compatible with Qt 6: T26473: Optimize QmitkChartWidget interface.
Aug 12 2023, 3:11 PM · MITK (v2024.06)
floca added a subtask for T26473: Optimize QmitkChartWidget interface: T29406: Make MITK compatible with Qt 6.
Aug 12 2023, 3:11 PM · Moved to git.dkfz.de, MITK
floca added a comment to T26473: Optimize QmitkChartWidget interface.

Should be done after(!) we have moved to Qt6 as we then have QtCharts to our disposal and migrate to that.

Aug 12 2023, 3:11 PM · Moved to git.dkfz.de, MITK
floca added a comment to T27284: [Image Statistic] Histogram is only supported with one image and <=1 ROI.

Should be done after(!) we have moved to Qt6 as we then have QtCharts to our disposal and migrate to that.

Aug 12 2023, 3:10 PM · Moved to git.dkfz.de, MITK (v2024.12)

Aug 4 2023

floca committed rMITK5918b7bf914d: Also store the label name in the segment label tag. (authored by floca).
Also store the label name in the segment label tag.
Aug 4 2023, 10:24 AM
floca committed rMITKe40c812ae502: Remove the drop of the first label (background label are not existing anymore). (authored by floca).
Remove the drop of the first label (background label are not existing anymore).
Aug 4 2023, 10:24 AM
floca committed rMITKb3652d42a119: T30161 Fixe saving of DCM Seg (authored by floca).
T30161 Fixe saving of DCM Seg
Aug 4 2023, 10:24 AM
floca triaged T30183: [REG] Add Elastix support to MITK as Normal priority.
Aug 4 2023, 10:22 AM · Moved to git.dkfz.de, MITK
floca added a subtask for T30182: [SEG] Storing segmentation as DICOM Seg failes if reference image is not a valid DICOM: T26951: DICOM SEG - DicomSegIO should just use properties of the passed segmentation object.
Aug 4 2023, 10:18 AM · Moved to git.dkfz.de, MITK (v2024.12)
floca added a parent task for T26951: DICOM SEG - DicomSegIO should just use properties of the passed segmentation object: T30182: [SEG] Storing segmentation as DICOM Seg failes if reference image is not a valid DICOM.
Aug 4 2023, 10:18 AM · Moved to git.dkfz.de, MITK (v2024.12)
floca triaged T30182: [SEG] Storing segmentation as DICOM Seg failes if reference image is not a valid DICOM as Normal priority.
Aug 4 2023, 10:17 AM · Moved to git.dkfz.de, MITK (v2024.12)

Aug 3 2023

floca added a project to T30181: Add option for a "mean" line profile in statistics view: Request for Discussion.
Aug 3 2023, 3:54 PM · Moved to git.dkfz.de, Restricted Project, MITK
floca triaged T30181: Add option for a "mean" line profile in statistics view as Normal priority.
Aug 3 2023, 3:50 PM · Moved to git.dkfz.de, Restricted Project, MITK

Aug 1 2023

floca added a comment to T30148: MITK FlowBench v2023.04 - crashes on "Accept segmentation".

@kislinsk Where does the crash originate from?

Aug 1 2023, 6:03 PM · MITK (v2023.12)
floca added a comment to T30148: MITK FlowBench v2023.04 - crashes on "Accept segmentation".

@gaoh Maybe you got it wrong. Saving DICOM seg is broken like always. The there is no version before v2023.04.02 that could store multi lable segmentations correctly and 4D will always crash. If you find a earlier version that does not crash on your data, then it is highliy likely to a change in DCMTK over time.

Aug 1 2023, 6:03 PM · MITK (v2023.12)
floca added a project to T29640: Verboseness in MatchPoint Algorithm Control: Missing Info.
Aug 1 2023, 12:09 PM · MITK (v2024.12), Missing Info

Jul 31 2023

floca added a comment to T29640: Verboseness in MatchPoint Algorithm Control.

@holzwart Which version of MITK and which plugin do you use?

Jul 31 2023, 8:11 PM · MITK (v2024.12), Missing Info
floca renamed T30175: [Py] UC1.4 - All images in data storage that are visible are set opacity 50% in a specific render window from [Py] UC2 - All images in data storage that are visible are set opacity 50% in a specific render window to [Py] UC4 - All images in data storage that are visible are set opacity 50% in a specific render window.
Jul 31 2023, 8:04 PM · Moved to git.dkfz.de, MITK
floca renamed T30175: [Py] UC1.4 - All images in data storage that are visible are set opacity 50% in a specific render window from [Py] UC2 - All images in data storage that are visible are stored to [Py] UC2 - All images in data storage that are visible are set opacity 50% in a specific render window.
Jul 31 2023, 8:04 PM · Moved to git.dkfz.de, MITK
floca created T30175: [Py] UC1.4 - All images in data storage that are visible are set opacity 50% in a specific render window.
Jul 31 2023, 7:56 PM · Moved to git.dkfz.de, MITK
floca updated the task description for T30173: [Py] UC1.2 - Selected image are stored.
Jul 31 2023, 7:55 PM · Moved to git.dkfz.de, MITK
floca renamed T30173: [Py] UC1.2 - Selected image are stored from [Py] Selected image are stored to [Py] UC2 - Selected image are stored.
Jul 31 2023, 7:47 PM · Moved to git.dkfz.de, MITK
floca created T30174: [Py] UC1.3 - Selected image can be manipulated with simpleITK and added to data storage.
Jul 31 2023, 7:46 PM · Moved to git.dkfz.de, MITK
floca renamed T30172: [Py] UC1.1 - Selected image can be manipulated with simpleITK and updated from [Py] Selected image can be manipulated with simpleITK and updated to [Py] UC1 - Selected image can be manipulated with simpleITK and updated.
Jul 31 2023, 7:44 PM · Moved to git.dkfz.de, MITK
floca renamed T30173: [Py] UC1.2 - Selected image are stored from [Py] Selected image and stored. to [Py] Selected image are stored.
Jul 31 2023, 7:34 PM · Moved to git.dkfz.de, MITK
floca created T30173: [Py] UC1.2 - Selected image are stored.
Jul 31 2023, 7:34 PM · Moved to git.dkfz.de, MITK
floca created T30172: [Py] UC1.1 - Selected image can be manipulated with simpleITK and updated.
Jul 31 2023, 7:30 PM · Moved to git.dkfz.de, MITK
floca created T30171: [Py] View to execute scripts that interact with the rest of the workbench.
Jul 31 2023, 7:09 PM · Moved to git.dkfz.de, MITK
floca updated the task description for T30170: [Py] Python in MITK.
Jul 31 2023, 7:03 PM · Moved to git.dkfz.de, MITK
floca added a parent task for T27923: Integrate possibility to execute Python Code in MITK : T30170: [Py] Python in MITK.
Jul 31 2023, 7:02 PM · MITK
floca added a subtask for T30170: [Py] Python in MITK: T27923: Integrate possibility to execute Python Code in MITK .
Jul 31 2023, 7:02 PM · Moved to git.dkfz.de, MITK
floca created T30170: [Py] Python in MITK.
Jul 31 2023, 7:02 PM · Moved to git.dkfz.de, MITK
floca created T30169: Hot keys for iterating through slices (while segmenting).
Jul 31 2023, 4:17 PM · Moved to git.dkfz.de, Request for Discussion, MITK

Jul 28 2023

floca triaged T30168: Fail to load NIFTI images due to error "itk only supports orthonormal direction cosines" as Normal priority.
Jul 28 2023, 4:57 PM · Moved to git.dkfz.de, MITK

Jul 26 2023

floca added a comment to T29631: Integration of an updated Feature Branch.

@goetzm Thank you for the patch. We will look into it and merge it for parts that we keep (see T29649). If change your mind and want to maintain the rest of the classification code base in an extension, we can revisit it and see how we can help with merging the rest. Best Ralf

Jul 26 2023, 12:01 PM · MITK

Jul 25 2023

floca added a comment to T30164: [Segmentation] [Bug] 2D RGB image not correctly handled by SegPreviewTool API tool.

Your "solution" is not a real fix. It just exploits a bug/undefined behavior. So do not do it

Jul 25 2023, 1:59 PM · Moved to git.dkfz.de, MITK (v2024.12), Request for Discussion

Jul 24 2023

floca added a comment to T30164: [Segmentation] [Bug] 2D RGB image not correctly handled by SegPreviewTool API tool.

Be carefull. RGB channels of an RGB image are not stored in different mitk::Image channels currently. Every thing is stored in one channel. But the channel has the pixel type "rgba". So the channels are encoded in each pixel.

Jul 24 2023, 2:24 PM · Moved to git.dkfz.de, MITK (v2024.12), Request for Discussion

Jul 13 2023

floca triaged T30161: [DCM][SEG] First label data gets lost if multilables are stored as DCM Seg as Unbreak Now! priority.
Jul 13 2023, 3:37 PM · Missing Info, MITK (v2023.12)
floca lowered the priority of T29396: [Segmentation] Newly created labelset image has wrong image type from High to Normal.
Jul 13 2023, 10:15 AM · MITK (v2024.12)
floca lowered the priority of T29535: Reinit of scene with planar figure while the Display is closed leads to crash from High to Normal.
Jul 13 2023, 10:14 AM · Moved to git.dkfz.de, MITK (v2024.12), Known Issue

Jul 11 2023

floca triaged T30158: [DCM][SEG] Check why unittests did not detect breaking support of DCM Seg and fix the (unit) test as Unbreak Now! priority.
Jul 11 2023, 7:54 PM · Moved to git.dkfz.de, MITK (v2024.12)
floca raised the priority of T30157: [DCM][SEG] potential in compliance to DICOM segmentation: clarify correct use of pixel value/segment number from High to Unbreak Now!.

@fedorov Thank you for your quick reply and verification for my assumption (I hoped, that I might have overlooked some broader interpretablility...)

Jul 11 2023, 7:51 PM · Moved to git.dkfz.de, MITK (v2024.12), Missing Info, Request for Discussion
floca added a comment to T30157: [DCM][SEG] potential in compliance to DICOM segmentation: clarify correct use of pixel value/segment number.
Jul 11 2023, 10:53 AM · Moved to git.dkfz.de, MITK (v2024.12), Missing Info, Request for Discussion
floca added a comment to T30155: Bounding boxes / ROIs in MITK.

👍
I would propose to also standardizeand align some of the properties for the frames to be either in sync with MITK terminology or with DICOM.

Jul 11 2023, 9:14 AM · MITK (v2024.06)
floca triaged T30157: [DCM][SEG] potential in compliance to DICOM segmentation: clarify correct use of pixel value/segment number as High priority.
Jul 11 2023, 9:06 AM · Moved to git.dkfz.de, MITK (v2024.12), Missing Info, Request for Discussion

Jul 9 2023

floca added a comment to T30155: Bounding boxes / ROIs in MITK.

@kislinsk thank you for the explanations. They do make sense.

Jul 9 2023, 4:49 PM · MITK (v2024.06)

Jul 8 2023

kislinsk awarded T30152: Create an MITK extension for IGT&co and move code a Love token.
Jul 8 2023, 8:35 AM · MITK (v2024.06)
kislinsk awarded T29649: Classification Module clean up a Love token.
Jul 8 2023, 8:35 AM · MITK (v2023.12), Request for Discussion

Jul 7 2023

floca added a comment to T30155: Bounding boxes / ROIs in MITK.

Thank you for the first draft. I had the following first thoughts:

Jul 7 2023, 3:36 PM · MITK (v2024.06)
floca updated subscribers of T29649: Classification Module clean up.

from @neher : clscreenshot sounds like something that might be useful, but i never used it

Jul 7 2023, 11:53 AM · MITK (v2023.12), Request for Discussion

Jul 6 2023

floca moved T29649: Classification Module clean up from Backlog to Cycle on the MITK (v2023.12) board.
Jul 6 2023, 1:07 PM · MITK (v2023.12), Request for Discussion
floca edited projects for T29649: Classification Module clean up, added: MITK (v2023.12); removed MITK.
Jul 6 2023, 1:07 PM · MITK (v2023.12), Request for Discussion
floca added a comment to T29649: Classification Module clean up.

So far only CLGlobalImageFeatures is claimed to be needed.

Jul 6 2023, 10:16 AM · MITK (v2023.12), Request for Discussion
floca updated the task description for T29649: Classification Module clean up.
Jul 6 2023, 10:16 AM · MITK (v2023.12), Request for Discussion
floca updated subscribers of T30152: Create an MITK extension for IGT&co and move code.
Jul 6 2023, 8:47 AM · MITK (v2024.06)
floca triaged T30152: Create an MITK extension for IGT&co and move code as High priority.
Jul 6 2023, 8:47 AM · MITK (v2024.06)

Jul 4 2023

floca closed T28139: [LabelSetImage] Ambigious meaning of "layer" in LabelSetImage, a subtask of T28525: Design refactoring of LabelSetImage and associated classes, as Resolved.
Jul 4 2023, 5:22 PM · Next Milestone
floca closed T28139: [LabelSetImage] Ambigious meaning of "layer" in LabelSetImage as Resolved.

Valid. Will be /is regarded in the refactoring.

Jul 4 2023, 5:22 PM · MITK (v2023.12), Request for Discussion
floca added a project to T28181: [Segmentation] Should warning messages be passed on to the UI?: Request for Discussion.
Jul 4 2023, 5:21 PM · Moved to git.dkfz.de, MITK (v2024.12)
floca closed T27182: Extend CLMatchPointReg MiniApp and move from Classification to Matchpoint module as Wontfix.

There is now a dedicated mini app for matching.

Jul 4 2023, 5:17 PM · MITK (v2023.12), Restricted Project
floca moved T27718: Miniapp for basic DICOM testing from Backlog to Cycle on the MITK (v2023.12) board.
Jul 4 2023, 5:16 PM · MITK (v2023.12), Kaapana (internal)
floca moved T27809: [Segmentation Utilities] "Labels" tabs in operations of Utilities view is empty from Backlog to Cycle on the MITK (v2023.12) board.
Jul 4 2023, 5:15 PM · MITK (v2023.12), Request for Discussion