kislinsk renamed T29274: Label Loss on repeatedly loaded and saved segmentations from Label Loss on Saved Tasks for Flow Bench to Label Loss on repeatedly loaded and saved segmentations.

Sep 6 2022, 7:39 AM · MITK

Sep 5 2022

kalali closed T29266: Clean SliceNavigationController as Resolved.

Sep 5 2022, 12:23 PM · Breaking Change, MITK

kalali closed T29266: Clean SliceNavigationController, a subtask of T29264: Overhaul of the SliceNavigationController and the BaseRenderer, as Resolved.

Sep 5 2022, 12:23 PM · MITK

kalali renamed T29266: Clean SliceNavigationController from Clean SliceNavigationController to remove unnecessary data members / member functions to Clean SliceNavigationController.

Sep 5 2022, 12:23 PM · Breaking Change, MITK

kalali committed rMITK26410ab07619: Clean SliceNavigationController to remove unnecessary data members / member… (authored by kalali).

Clean SliceNavigationController to remove unnecessary data members / member…

Sep 5 2022, 12:22 PM

kalali committed rMITK3017e9312fb8: Manual formatting (authored by kalali).

Manual formatting

Sep 5 2022, 12:22 PM

kalali committed rMITKad1e8bd80740: Remove unnecessary / unused functions / variable (authored by kalali).

Remove unnecessary / unused functions / variable

Sep 5 2022, 12:22 PM

kalali committed rMITK78ef597e20ca: Apply clang format (authored by kalali).

Apply clang format

Sep 5 2022, 12:22 PM

kalali committed rMITK68e9d18831c0: Use auto (authored by kalali).

Use auto

Sep 5 2022, 12:22 PM

kalali committed rMITKd850cfafb15a: Remove namespace prefix (authored by kalali).

Remove namespace prefix

Sep 5 2022, 12:22 PM

kalali committed rMITK75774d46afc2: Clean includes (authored by kalali).

Clean includes

Sep 5 2022, 12:22 PM

kalali committed rMITKaf567057be98: Remove unexpected side-effect (authored by kalali).

Remove unexpected side-effect

Sep 5 2022, 12:22 PM

Sep 2 2022

kislinsk added a revision to T29274: Label Loss on repeatedly loaded and saved segmentations: Unknown Object (Differential Revision).

Sep 2 2022, 2:49 PM · MITK

kislinsk added a comment to T29274: Label Loss on repeatedly loaded and saved segmentations.

The solution is to ignore default properties when loading multilabel images as it was already intended:

Sep 2 2022, 2:02 PM · MITK

kislinsk added a comment to T29274: Label Loss on repeatedly loaded and saved segmentations.

Pushed new branch to rMITK MITK: bugfix/T29274-IgnoreDefaultPropertiesOnLoad.

Sep 2 2022, 2:01 PM · MITK

j115e added a member for MIC: s367a.

Sep 2 2022, 12:45 PM

kalali closed T29218: Remove deprecated SetInputWorldGeometry3D / GetInputWorldGeometry3D of SliceNavigationController, a subtask of T29269: Check geometries in SliceNavigationController and BaseRenderer, as Resolved.

Sep 2 2022, 10:27 AM · MITK (v2024.06)

kalali closed T29218: Remove deprecated SetInputWorldGeometry3D / GetInputWorldGeometry3D of SliceNavigationController as Resolved.

Sep 2 2022, 10:27 AM · MITK

kalali committed rMITKfb3fd3e8d6ca: Remove deprecated InputWorldGeometry3D of SliceNavigationController (authored by kalali).

Remove deprecated InputWorldGeometry3D of SliceNavigationController

Sep 2 2022, 10:26 AM

kalali committed rMITKc88c46f393a3: Remove function from test class (authored by kalali).

Remove function from test class

Sep 2 2022, 10:26 AM

kalali committed rMITK114aaa02b887: Remove / modify functions that require / use the InputWorldGeometry3D (authored by kalali).

Remove / modify functions that require / use the InputWorldGeometry3D

Sep 2 2022, 10:26 AM

kalali committed rMITK7f86276afd84: Remove InputWorldGeometry3D from the SliceNavigationController (authored by kalali).

Remove InputWorldGeometry3D from the SliceNavigationController

Sep 2 2022, 10:26 AM

kalali closed T29212: Remove "GetCurrentWorldGeometry2D" of BaseRenderer, a subtask of T29269: Check geometries in SliceNavigationController and BaseRenderer, as Resolved.

Sep 2 2022, 10:04 AM · MITK (v2024.06)

kalali closed T29212: Remove "GetCurrentWorldGeometry2D" of BaseRenderer as Resolved.

Sep 2 2022, 10:04 AM · MITK (v2022.10)

kalali committed rMITKfd3998e44a44: Remove "GetCurrentWorldGeometry2D" of BaseRenderer (authored by kalali).

Remove "GetCurrentWorldGeometry2D" of BaseRenderer

Sep 2 2022, 10:03 AM

kalali committed rMITK068c3ef3550c: Remove deprecated functions (authored by kalali).

Remove deprecated functions

Sep 2 2022, 10:03 AM

kalali committed rMITK86735eb070bc: Clean code (authored by kalali).

Clean code

Sep 2 2022, 10:03 AM

kislinsk added a revision to T29253: Update external projects: Restricted Differential Revision.

Sep 2 2022, 2:29 AM · MITK (v2022.10)

kislinsk added a comment to T29253: Update external projects.

Okay, this task is ready for review. I will create a Differential soon to test all the upgrades on Linux and macOS as well...

Sep 2 2022, 1:08 AM · MITK (v2022.10)

kislinsk updated the task description for T29253: Update external projects.

Sep 2 2022, 1:06 AM · MITK (v2022.10)

Sep 1 2022

kislinsk updated the task description for T29253: Update external projects.

Sep 1 2022, 10:24 PM · MITK (v2022.10)

kalali added a revision to T29273: Decouple TimeNavigation from SliceNavigationController: Restricted Differential Revision.

Sep 1 2022, 4:30 PM · MITK

Aug 31 2022

kalali placed T26399: Workbench crash on simple tree model update up for grabs.

Aug 31 2022, 11:34 AM · MITK, Request for Discussion

kalali moved T29090: [3D Segmentation] Threshold tool preview draws contours in green and not in the active label color. from MITK Meeting to Backlog on the Request for Discussion board.

Aug 31 2022, 11:34 AM · MITK (v2024.06), Request for Discussion, Checklist

kalali removed a project from T27613: Improve reinit behavior: Request for Discussion.

Aug 31 2022, 11:34 AM · Request for Discussion, MITK (v2023.04)

kalali moved T28989: [Segmentation] CanHandle functions seem to be inconsistent from MITK Meeting to Backlog on the Request for Discussion board.

Aug 31 2022, 11:33 AM · MITK, Request for Discussion

kalali edited projects for T29094: Deleting a data node causes global reset, added: MITK; removed MITK (v2022.10), Request for Discussion.

Aug 31 2022, 11:22 AM · MITK, Checklist

kalali edited projects for T26399: Workbench crash on simple tree model update, added: MITK; removed MITK (v2022.10).

Aug 31 2022, 11:17 AM · MITK, Request for Discussion

kalali removed a project from T28669: [Segmentation] QmitkSlicesInterpolator and QmitkSliceBasedInterpolatorWidget seem to be redundant: Request for Discussion.

Aug 31 2022, 11:15 AM · Breaking Change, MITK (v2022.10)

a178n closed T29239: Download models to new Results_Folder as Resolved.

Aug 31 2022, 9:35 AM · MITK (v2022.10)

a178n closed T29227: Remove vestigial UI element "No. of extra Modalities" spinbox as Resolved.

Aug 31 2022, 9:35 AM · MITK (v2022.10)

a178n triaged T29275: Test new nnUNet(v2) python codebase with MITK as Normal priority.

Aug 31 2022, 9:32 AM · MITK (v2024.06)

kislinsk added a comment to T29274: Label Loss on repeatedly loaded and saved segmentations.

Image header for the working case with 2 labels

NRRD0004
# Complete NRRD file format specification at:
# http://teem.sourceforge.net/nrrd/format.html
type: unsigned short
dimension: 3
space: left-posterior-superior
sizes: 256 256 49
space directions: (1,0,0) (0,1,0) (0,0,3)
kinds: domain domain domain
endian: little
encoding: gzip
space origin: (0,0,0)
DICOM_0008_0060:={"values":[{"z":0, "t":0, "value":"SEG"}]}
DICOM_0008_103E:={"values":[{"z":0, "t":0, "value":"MITK Segmentation"}]}
layer_000:=3
layers:=1
modality:=org.mitk.image.multilabel
org.mitk.label_000_00000:=<?xml version="1.0" encoding="UTF-8"?>\n<Label>\n    <property key="DICOM.0062.0002.0062.0004" type="TemporoSpatialStringProperty">\n        <temporo_spatial_string>{"values":[{"z":0, "t":0, "value":"0"}]}</temporo_spatial_string>\n    </property>\n    <property key="DICOM.0062.0002.0062.0005" type="TemporoSpatialStringProperty">\n        <temporo_spatial_string>{"values":[{"z":0, "t":0, "value":"Exterior"}]}</temporo_spatial_string>\n    </property>\n    <property key="DICOM.0062.0002.0062.0008" type="TemporoSpatialStringProperty">\n        <temporo_spatial_string>{"values":[{"z":0, "t":0, "value":"SEMIAUTOMATIC"}]}</temporo_spatial_string>\n    </property>\n    <property key="center.coordinates" type="Point3dProperty">\n        <point x="0" y="0" z="0"/>\n    </property>\n    <property key="center.index" type="Point3dProperty">\n        <point x="0" y="0" z="0"/>\n    </property>\n    <property key="color" type="ColorProperty">\n        <color r="0" g="0" b="0"/>\n    </property>\n    <property key="layer" type="UIntProperty">\n        <unsigned value="0"/>\n    </property>\n    <property key="locked" type="BoolProperty">\n        <bool value="false"/>\n    </property>\n    <property key="name" type="StringProperty">\n        <string value="Exterior"/>\n    </property>\n    <property key="opacity" type="FloatProperty">\n        <float value="0"/>\n    </property>\n    <property key="value" type="UShortProperty">\n        <unsigned value="0"/>\n    </property>\n    <property key="visible" type="BoolProperty">\n        <bool value="true"/>\n    </property>\n</Label>\n
org.mitk.label_000_00001:=<?xml version="1.0" encoding="UTF-8"?>\n<Label>\n    <property key="DICOM.0062.0002.0062.0003.0008.0100" type="TemporoSpatialStringProperty">\n        <temporo_spatial_string>{"values":[{"z":0, "t":0, "value":"T-D000A"}]}</temporo_spatial_string>\n    </property>\n    <property key="DICOM.0062.0002.0062.0003.0008.0102" type="TemporoSpatialStringProperty">\n        <temporo_spatial_string>{"values":[{"z":0, "t":0, "value":"SRT"}]}</temporo_spatial_string>\n    </property>\n    <property key="DICOM.0062.0002.0062.0003.0008.0104" type="TemporoSpatialStringProperty">\n        <temporo_spatial_string>{"values":[{"z":0, "t":0, "value":"Anatomical Structure"}]}</temporo_spatial_string>\n    </property>\n    <property key="DICOM.0062.0002.0062.0004" type="TemporoSpatialStringProperty">\n        <temporo_spatial_string>{"values":[{"z":0, "t":0, "value":"1"}]}</temporo_spatial_string>\n    </property>\n    <property key="DICOM.0062.0002.0062.0005" type="TemporoSpatialStringProperty">\n        <temporo_spatial_string>{"values":[{"z":0, "t":0, "value":"Liver"}]}</temporo_spatial_string>\n    </property>\n    <property key="DICOM.0062.0002.0062.0008" type="TemporoSpatialStringProperty">\n        <temporo_spatial_string>{"values":[{"z":0, "t":0, "value":"SEMIAUTOMATIC"}]}</temporo_spatial_string>\n    </property>\n    <property key="DICOM.0062.0002.0062.000F.0008.0100" type="TemporoSpatialStringProperty">\n        <temporo_spatial_string>{"values":[{"z":0, "t":0, "value":"T-62000"}]}</temporo_spatial_string>\n    </property>\n    <property key="DICOM.0062.0002.0062.000F.0008.0102" type="TemporoSpatialStringProperty">\n        <temporo_spatial_string>{"values":[{"z":0, "t":0, "value":"SRT"}]}</temporo_spatial_string>\n    </property>\n    <property key="DICOM.0062.0002.0062.000F.0008.0104" type="TemporoSpatialStringProperty">\n        <temporo_spatial_string>{"values":[{"z":0, "t":0, "value":"Liver"}]}</temporo_spatial_string>\n    </property>\n    <property key="center.coordinates" type="Point3dProperty">\n        <point x="0" y="0" z="0"/>\n    </property>\n    <property key="center.index" type="Point3dProperty">\n        <point x="0" y="0" z="0"/>\n    </property>\n    <property key="color" type="ColorProperty">\n        <color r="0.745098054" g="0" b="0.196078435"/>\n    </property>\n    <property key="layer" type="UIntProperty">\n        <unsigned value="0"/>\n    </property>\n    <property key="locked" type="BoolProperty">\n        <bool value="true"/>\n    </property>\n    <property key="name" type="StringProperty">\n        <string value="Liver"/>\n    </property>\n    <property key="opacity" type="FloatProperty">\n        <float value="0.600000024"/>\n    </property>\n    <property key="value" type="UShortProperty">\n        <unsigned value="1"/>\n    </property>\n    <property key="visible" type="BoolProperty">\n        <bool value="true"/>\n    </property>\n</Label>\n
org.mitk.label_000_00002:=<?xml version="1.0" encoding="UTF-8"?>\n<Label>\n    <property key="DICOM.0062.0002.0062.0004" type="TemporoSpatialStringProperty">\n        <temporo_spatial_string>{"values":[{"z":0, "t":0, "value":"2"}]}</temporo_spatial_string>\n    </property>\n    <property key="DICOM.0062.0002.0062.0005" type="TemporoSpatialStringProperty">\n        <temporo_spatial_string>{"values":[{"z":0, "t":0, "value":"Label 1"}]}</temporo_spatial_string>\n    </property>\n    <property key="DICOM.0062.0002.0062.0008" type="TemporoSpatialStringProperty">\n        <temporo_spatial_string>{"values":[{"z":0, "t":0, "value":"SEMIAUTOMATIC"}]}</temporo_spatial_string>\n    </property>\n    <property key="center.coordinates" type="Point3dProperty">\n        <point x="0" y="0" z="0"/>\n    </property>\n    <property key="center.index" type="Point3dProperty">\n        <point x="0" y="0" z="0"/>\n    </property>\n    <property key="color" type="ColorProperty">\n        <color r="0.952941179" g="0.764705896" b="0"/>\n    </property>\n    <property key="layer" type="UIntProperty">\n        <unsigned value="0"/>\n    </property>\n    <property key="locked" type="BoolProperty">\n        <bool value="true"/>\n    </property>\n    <property key="name" type="StringProperty">\n        <string value="Label 1"/>\n    </property>\n    <property key="opacity" type="FloatProperty">\n        <float value="0.600000024"/>\n    </property>\n    <property key="value" type="UShortProperty">\n        <unsigned value="2"/>\n    </property>\n    <property key="visible" type="BoolProperty">\n        <bool value="true"/>\n    </property>\n</Label>\n
org_mitk_uid:=2a0c52f7-1b2e-4a46-88ca-f4ff9344a7e4

Aug 31 2022, 1:31 AM · MITK

Aug 30 2022

kislinsk added a comment to T29274: Label Loss on repeatedly loaded and saved segmentations.

In my example I have an image with a predefined label which works as expected.
When I add labels in the Segmentation View and draw something, everything seems fine.
Save and load again the segmentation to see that all pixels of the drawn labels are there, but only the first label appears in the Segmentation View.
So it seems like all the meta data for the extra labels were dismissed when saving the segmentation.

Aug 30 2022, 11:49 AM · MITK

• s349i changed the visibility for F2564298: 5_manually_add_again.PNG.

Aug 30 2022, 11:40 AM

• s349i changed the visibility for F2564303: 3_back_create_new_label.PNG.

Aug 30 2022, 11:40 AM

• s349i changed the visibility for F2564302: 1_save_results.PNG.

Aug 30 2022, 11:40 AM

• s349i changed the visibility for F2564301: 2_open_new_task.PNG.

Aug 30 2022, 11:40 AM

• s349i changed the visibility for F2564300: 4_new_label_not_shown.PNG.

Aug 30 2022, 11:40 AM