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Sep 11 2023

kompan triaged T30198: Update checklist for Perfusion Concentration Curve Converter as Normal priority.
Sep 11 2023, 7:43 AM · MITK (v2023.12)
kompan removed a project from T27350: Refactoring of T1 map calculation/selection for perfusion and CEST: Cleared.
Sep 11 2023, 7:39 AM · MITK (v2024.06)
kompan claimed T29638: ModelFit Inspector crahes sometimes on data selection.
Sep 11 2023, 7:07 AM · MITK (v2024.12)
kompan edited projects for T29638: ModelFit Inspector crahes sometimes on data selection, added: MITK (v2023.12); removed MITK.
Sep 11 2023, 7:04 AM · MITK (v2024.12)

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
kompan committed rMITK25c62e83bd6f: Add unit tests for exponential saturation model. (authored by kompan).
Add unit tests for exponential saturation model.
Sep 8 2023, 9:07 AM
kompan committed rMITK1f439d767d43: Add unit tests for exponential saturation model. (authored by kompan).
Add unit tests for exponential saturation model.
Sep 8 2023, 9:07 AM
kompan committed rMDd50538d93140: Update PK unit tests according to changes in T29632. (authored by kompan).
Update PK unit tests according to changes in T29632.
Sep 8 2023, 8:06 AM
kompan committed rMD15b2bde56694: Update PK PET unit tests according to changes in T29632. (authored by kompan).
Update PK PET unit tests according to changes in T29632.
Sep 8 2023, 8:06 AM
kompan committed rMDf7815e51a8d1: Update ModelFit unit tests according to changes in T29632. (authored by kompan).
Update ModelFit unit tests according to changes in T29632.
Sep 8 2023, 7:54 AM
kompan committed rMITK62ce68f3a3ed: Rework of general and PK models regarding naming, units and model… (authored by kompan).
Rework of general and PK models regarding naming, units and model…
Sep 8 2023, 7:23 AM
kompan committed rMITK5d124b67c62c: Remove GetNumberOfDerivedParameters() from Extended One Tissue Compartment… (authored by kompan).
Remove GetNumberOfDerivedParameters() from Extended One Tissue Compartment…
Sep 8 2023, 7:23 AM
kompan committed rMITK9279201c13d9: Remove GetNumberOfDerivedParameters() from Two Tissue Compartment FDG Model. (authored by kompan).
Remove GetNumberOfDerivedParameters() from Two Tissue Compartment FDG Model.
Sep 8 2023, 7:23 AM
kompan committed rMITKaf48ae9d2397: Remove GetNumberOfDerivedParameters() from Two Tissue Compartment Model. (authored by kompan).
Remove GetNumberOfDerivedParameters() from Two Tissue Compartment Model.
Sep 8 2023, 7:23 AM
kompan committed rMITK6246c28e0ac5: Remove FUNCTION_STRING and NUMBER_OF_DERIVED_PARAMETERS from 2CXM. (authored by kompan).
Remove FUNCTION_STRING and NUMBER_OF_DERIVED_PARAMETERS from 2CXM.
Sep 8 2023, 7:23 AM
kompan committed rMITKa774835ad92e: Remove GetNumberOfDerivedParameters() from One Tissue Compartment Model. (authored by kompan).
Remove GetNumberOfDerivedParameters() from One Tissue Compartment Model.
Sep 8 2023, 7:23 AM
kompan committed rMITK9634752ede61: Remove function string from Standard Tofts Model. (authored by kompan).
Remove function string from Standard Tofts Model.
Sep 8 2023, 7:23 AM
kompan committed rMITK5b09efc324d0: Remove function string from Extended Tofts Model. (authored by kompan).
Remove function string from Extended Tofts Model.
Sep 8 2023, 7:23 AM
kompan committed rMITK1610d0267c89: Remove NUMBER_OF_DERIVED_PARAMETERS and GetNumberOfDerivedParameters() from… (authored by kompan).
Remove NUMBER_OF_DERIVED_PARAMETERS and GetNumberOfDerivedParameters() from…
Sep 8 2023, 7:23 AM
kompan committed rMITKd06ecadc692b: Remove NUMBER_OF_DERIVED_PARAMETERS and GetNumberOfDerivedParameters() from… (authored by kompan).
Remove NUMBER_OF_DERIVED_PARAMETERS and GetNumberOfDerivedParameters() from…
Sep 8 2023, 7:23 AM
kompan committed rMITKa1446a88cea4: Remove GetDerivedParameterNames() from Exponential Decay Offset Model. (authored by kompan).
Remove GetDerivedParameterNames() from Exponential Decay Offset Model.
Sep 8 2023, 7:23 AM
kompan committed rMITK60a12e64dff5: Remove GetDerivedParameterNames() from Exponential Saturation Model. (authored by kompan).
Remove GetDerivedParameterNames() from Exponential Saturation Model.
Sep 8 2023, 7:23 AM
kompan committed rMITK0cca42de7a98: Remove GetStaticParameterUnits() from Two Step Linear Model. (authored by kompan).
Remove GetStaticParameterUnits() from Two Step Linear Model.
Sep 8 2023, 7:23 AM
kompan committed rMITK236184e53b92: Remove GetDerivedParameterUnits() from Exponential Saturation Model. (authored by kompan).
Remove GetDerivedParameterUnits() from Exponential Saturation Model.
Sep 8 2023, 7:23 AM
kompan committed rMITKae380c4c9cc6: Remove GetDerivedParameterUnits() from Exponential Decay Offset Model. (authored by kompan).
Remove GetDerivedParameterUnits() from Exponential Decay Offset Model.
Sep 8 2023, 7:23 AM
kompan committed rMITK8d0366673790: Remove GetStaticParameterUnits() from Three Step Linear Model. (authored by kompan).
Remove GetStaticParameterUnits() from Three Step Linear Model.
Sep 8 2023, 7:23 AM
kompan committed rMITK2e43b447f596: Remove GetStaticParameterUnits() from Exponential Saturation Model. (authored by kompan).
Remove GetStaticParameterUnits() from Exponential Saturation Model.
Sep 8 2023, 7:23 AM
kompan committed rMITK69e78b1859c3: Remove GetStaticParameterUnits() from Linear Model. (authored by kompan).
Remove GetStaticParameterUnits() from Linear Model.
Sep 8 2023, 7:23 AM
kompan committed rMITKfd48f80c6cea: Remove GetStaticParameterUnits() from Exponential Decay Offset Model. (authored by kompan).
Remove GetStaticParameterUnits() from Exponential Decay Offset Model.
Sep 8 2023, 7:23 AM
kompan committed rMITKce1b4809d162: Remove GetStaticParameterUnits() from Exponential Decay Model. (authored by kompan).
Remove GetStaticParameterUnits() from Exponential Decay Model.
Sep 8 2023, 7:23 AM
kompan committed rMITK8aa020ca2e16: Remove unused variable. (authored by kompan).
Remove unused variable.
Sep 8 2023, 7:23 AM
kompan committed rMITKcda9ac0ba222: Rework Descriptive Pharmacokinetic Brix Model. (authored by kompan).
Rework Descriptive Pharmacokinetic Brix Model.
Sep 8 2023, 7:23 AM
kompan committed rMITK0fe6f771381f: Rework Two Tissue Compartment FDG Model. (authored by kompan).
Rework Two Tissue Compartment FDG Model.
Sep 8 2023, 7:23 AM
kompan committed rMITK85892c552182: Remove 2SL and 3SL model from Fit DCE documentation. (authored by kompan).
Remove 2SL and 3SL model from Fit DCE documentation.
Sep 8 2023, 7:23 AM
kompan committed rMITK50766039ad1b: Rework Extended One Tissue Compartment Model. (authored by kompan).
Rework Extended One Tissue Compartment Model.
Sep 8 2023, 7:23 AM
kompan committed rMITK0fc1f67630bb: Rework Two Tissue Compartment Model. (authored by kompan).
Rework Two Tissue Compartment Model.
Sep 8 2023, 7:23 AM
kompan committed rMITK378b0f8e29f7: Rework One Tissue Compartment Model. (authored by kompan).
Rework One Tissue Compartment Model.
Sep 8 2023, 7:23 AM
kompan committed rMITK7495e6a3d86c: Rework Two Compartment Exchange Model. (authored by kompan).
Rework Two Compartment Exchange Model.
Sep 8 2023, 7:23 AM
kompan committed rMITK8783a4829e61: Rework Extended Tofts Model. (authored by kompan).
Rework Extended Tofts Model.
Sep 8 2023, 7:23 AM
kompan committed rMITK264b58bf21a9: Rework Standard Tofts Model. (authored by kompan).
Rework Standard Tofts Model.
Sep 8 2023, 7:23 AM
kompan committed rMITK2d3ed650e4bd: Update model formnulas in generic fitting plugin F1 help. (authored by kompan).
Update model formnulas in generic fitting plugin F1 help.
Sep 8 2023, 7:23 AM
kompan committed rMITKbd7eb018be9a: Rework AIF model base. (authored by kompan).
Rework AIF model base.
Sep 8 2023, 7:23 AM
kompan committed rMITK11ede9c97214: Improve human readability of parameters in Exponential Saturation Model. (authored by kompan).
Improve human readability of parameters in Exponential Saturation Model.
Sep 8 2023, 7:23 AM
kompan committed rMITK3bbf345fb838: Correction of documentation in comment of Exponential Saturation Model. (authored by kompan).
Correction of documentation in comment of Exponential Saturation Model.
Sep 8 2023, 7:23 AM
kompan committed rMITK84fc69133427: Improve human readability of parameter in Exp Decay Offset Model. (authored by kompan).
Improve human readability of parameter in Exp Decay Offset Model.
Sep 8 2023, 7:23 AM
kompan committed rMITKd6848f394091: Correction of documentation in comments of Exponential Decay Offset Model. (authored by kompan).
Correction of documentation in comments of Exponential Decay Offset Model.
Sep 8 2023, 7:23 AM
kompan committed rMITK8d95bd73499f: Correction of documentation in comments of Exponential Decays Model. (authored by kompan).
Correction of documentation in comments of Exponential Decays Model.
Sep 8 2023, 7:23 AM
kompan committed rMITKb23464b3e614: Improve human readability of parameters for Linear Model. (authored by kompan).
Improve human readability of parameters for Linear Model.
Sep 8 2023, 7:23 AM
kompan committed rMITK441b873fa43d: Improve human readability of parameters for Exponential Decay Model. (authored by kompan).
Improve human readability of parameters for Exponential Decay Model.
Sep 8 2023, 7:23 AM
kompan committed rMITKa734a2604762: Improve human readability of parameters for Two Step Linear Model. (authored by kompan).
Improve human readability of parameters for Two Step Linear Model.
Sep 8 2023, 7:23 AM
kompan committed rMITK09e52e32ee5f: Move Three Step Linear Model to ModelFit and generic datafit view. (authored by kompan).
Move Three Step Linear Model to ModelFit and generic datafit view.
Sep 8 2023, 7:23 AM
kompan committed rMITKe75959248f40: Rework Three Step Linear Model. (authored by kompan).
Rework Three Step Linear Model.
Sep 8 2023, 7:23 AM
kompan committed rMITKad93e1643fd5: Improve human readability of parameter names for Three Step Linear Model. (authored by kompan).
Improve human readability of parameter names for Three Step Linear Model.
Sep 8 2023, 7:23 AM
kompan committed rMITKa236f9f2133a: Move Two Step Linear Model to ModelFit and generic data fit view. (authored by kompan).
Move Two Step Linear Model to ModelFit and generic data fit view.
Sep 8 2023, 7:23 AM
kompan committed rMITKccec37190a04: Rework Two Step Linear Model. (authored by kompan).
Rework Two Step Linear Model.
Sep 8 2023, 7:23 AM
kompan committed rMITKd6b31761449f: Rework Exponential Saturation Model (authored by kompan).
Rework Exponential Saturation Model
Sep 8 2023, 7:23 AM
kompan committed rMITK0fc547c52f63: Rework Exponential Decay Offset model (authored by kompan).
Rework Exponential Decay Offset model
Sep 8 2023, 7:23 AM
kompan committed rMITKa75ae6576826: Rework T2 decay model (now exponential decay model). (authored by kompan).
Rework T2 decay model (now exponential decay model).
Sep 8 2023, 7:23 AM
kompan committed rMITKae52316d1081: Rework linear model. (authored by kompan).
Rework linear model.
Sep 8 2023, 7:22 AM

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
fedorov 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.

Sep 7 2023, 5:19 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
s434n moved T29302: Movie maker plugin does not work correctly with the new mxn multi widget from Cycle to Backlog on the MITK (v2023.12) board.
Sep 7 2023, 10:33 AM · Moved to git.dkfz.de, MITK (v2024.12)
s434n removed a project from T29369: [Segmentation Utilities] Handle / select different labels independently: Request for Discussion.
Sep 7 2023, 10:31 AM · MITK (v2024.06)
s434n added a comment to T29369: [Segmentation Utilities] Handle / select different labels independently.
  • Boolean Operations
    • chosen: high effort
    • Can be used so that the other functions can do everything
    • Work only on one image, select two labels
  • Contour to Image & Surface to Image
    • chosen: low effort seems more senseful. The functionality can be achieved via other tools (e.g. boolean)
  • Image Masking
    • chosen: low effort
  • Morphological Operations
    • as proposed
    • Pick an image & pick a label
    • Include options like in picking tool, i.e. generate a new layer when doing an operation, lock labels (to make sure other labels are not overwritten e.g. for a dilution)
  • Add a new tool: Transfer Label could be used to transfer a label from one image to another (if the same image is selected twice, it's just a rename)
Sep 7 2023, 10:30 AM · MITK (v2024.06)
s434n removed a project from T30192: [MxN] UI elements not visible on Mac: Request for Discussion.
Sep 7 2023, 9:57 AM · MITK (v2023.12)
s434n moved T30192: [MxN] UI elements not visible on Mac from Backlog to MITK Meeting on the Request for Discussion board.
Sep 7 2023, 9:14 AM · MITK (v2023.12)
s434n added a project to T30192: [MxN] UI elements not visible on Mac: Request for Discussion.
Sep 7 2023, 9:14 AM · MITK (v2023.12)

Sep 6 2023

kompan committed rMITKccfdc487f4c0: Add model constraints checker in case no default constraints are set. (authored by kompan).
Add model constraints checker in case no default constraints are set.
Sep 6 2023, 11:00 AM
kompan committed rMITK267628a28f92: Add model constraints checker in case no dafault contraints are set. (authored by kompan).
Add model constraints checker in case no dafault contraints are set.
Sep 6 2023, 11:00 AM

Aug 31 2023

a178n added a comment to T29652: [Preferences] Cannot open SAM preference page after tool activation.

After suspecting whether python process using std::async would be causing the issue, like below:

m_Future = std::async(std::launch::async, &mitk::SegmentAnythingPythonService::start_python_daemon, this);

I tried starting python process using basic std::thread like shown below:

std::thread([&](){mitk::SegmentAnythingPythonService::start_python_daemon();}).detach();

there is no change in behavior.
The issue root cause still eludes me.

Aug 31 2023, 2:45 PM · Moved to git.dkfz.de, MITK (v2024.12)
s434n triaged T30192: [MxN] UI elements not visible on Mac as High priority.
Aug 31 2023, 2:31 PM · MITK (v2023.12)

Aug 29 2023

s434n added a comment to T28491: [Segmentation] Slice interpolation 'confirm for all slices' sometimes crahes.

I tested this again with the current version of MITK (develop branch) and can see no problems. Interpolation works without problems on my laptop (Windows 10, 32GB RAM)

Aug 29 2023, 4:07 PM · MITK (v2023.12)

Aug 24 2023

s434n committed rMITK013da8c575c1: remove unused/outdated QmitkFFmpegWriter import (authored by s434n).
remove unused/outdated QmitkFFmpegWriter import
Aug 24 2023, 4:30 PM
s434n committed rMITK77eaee663ab1: Decouple TimeNavigation from SliceNavigationController (authored by s434n).
Decouple TimeNavigation from SliceNavigationController
Aug 24 2023, 4:30 PM
s434n committed rMITKf9cb09180c85: Use concrete variable type and const (authored by kalali).
Use concrete variable type and const
Aug 24 2023, 4:30 PM
s434n committed rMITKc8c7a75725c3: Update the time nc before the slice nc (authored by kalali).
Update the time nc before the slice nc
Aug 24 2023, 4:30 PM
s434n committed rMITK40b57ea76624: adapt new SNC occurences introduced since merging and fix remaining bugs (authored by s434n).
adapt new SNC occurences introduced since merging and fix remaining bugs
Aug 24 2023, 4:30 PM
s434n committed rMITK0dab5fe5f1ac: Refactor class to work with the new TimeNavigationController (authored by kalali).
Refactor class to work with the new TimeNavigationController
Aug 24 2023, 4:30 PM
s434n committed rMITK80bda9107823: Refactor class to work with the new TimeNavigationController (authored by kalali).
Refactor class to work with the new TimeNavigationController
Aug 24 2023, 4:30 PM
s434n committed rMITKf314ae99a2f5: Remove TimeNavigationController parameter / member (authored by kalali).
Remove TimeNavigationController parameter / member
Aug 24 2023, 4:30 PM
s434n committed rMITKfcd58f5173b5: Remove unnecessary controller / controller-connections (authored by kalali).
Remove unnecessary controller / controller-connections
Aug 24 2023, 4:30 PM
s434n committed rMITK5c3b7c799bf3: Refactor class to work with the new TimeNavigationController (authored by kalali).
Refactor class to work with the new TimeNavigationController
Aug 24 2023, 4:30 PM
s434n committed rMITKd58b817f6178: Replace SliceNavigationController with TimeNavigationController (authored by kalali).
Replace SliceNavigationController with TimeNavigationController
Aug 24 2023, 4:30 PM
s434n committed rMITKfe90eadd9150: Refactor class to work with the new TimeNavigationController (authored by kalali).
Refactor class to work with the new TimeNavigationController
Aug 24 2023, 4:30 PM
s434n committed rMITKcc1dda7884d6: Replace the SliceNavigationController inside the RenderingManager (authored by kalali).
Replace the SliceNavigationController inside the RenderingManager
Aug 24 2023, 4:30 PM
s434n committed rMITK0fd0318820f2: Modify BaseController to only hold a single stepper (authored by kalali).
Modify BaseController to only hold a single stepper
Aug 24 2023, 4:30 PM
s434n committed rMITK79829b658496: Modify the SliceNavigationController to remove time-related data (authored by kalali).
Modify the SliceNavigationController to remove time-related data
Aug 24 2023, 4:30 PM
s434n committed rMITKed8c3c8ee4a8: Remove unnecessary / unused functions / variable (authored by kalali).
Remove unnecessary / unused functions / variable
Aug 24 2023, 4:30 PM
s434n committed rMITK742c0a0f3e7e: Add TimeNavigationController (authored by kalali).
Add TimeNavigationController
Aug 24 2023, 4:29 PM

Aug 23 2023

kompan committed rMDe1c386aa8f47: Add JSON files for unit tests of exponential saturation model. (authored by kompan).
Add JSON files for unit tests of exponential saturation model.
Aug 23 2023, 7:25 AM

Aug 21 2023

kompan committed rMITK03ce52d72b6c: Manually add content of D646. (authored by kompan).
Manually add content of D646.
Aug 21 2023, 10:21 AM
kompan committed rMITK1d0d458f7bf2: Simplify ternary operator in ComputeSignalFromParameters. (authored by kompan).
Simplify ternary operator in ComputeSignalFromParameters.
Aug 21 2023, 10:21 AM
kompan committed rMITK0ffc66e2bb66: Remove MitkTestingHelper module from CMakeLists. (authored by kompan).
Remove MitkTestingHelper module from CMakeLists.
Aug 21 2023, 10:21 AM