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Today

floca added a comment to T25804: Set 'selected' property when using the new selection concept.

OK. But we definetly should talk about it before it is approached.

Wed, Aug 21, 7:10 PM · MITK
neher closed T26421: [CmdInterface] process special characters as Wontfix.
Wed, Aug 21, 2:21 PM

Yesterday

floca added a project to T26636: Repo for sourcecode of upload infrastructure for DICOM and non-DICOM files: Request for Discussion.
Tue, Aug 20, 4:26 PM · Request for Discussion, d:cipher
reicht created T26636: Repo for sourcecode of upload infrastructure for DICOM and non-DICOM files.
Tue, Aug 20, 10:50 AM · Request for Discussion, d:cipher
reicht changed the visibility for T26299: [Webbased DICOM parsing and file handling].
Tue, Aug 20, 10:31 AM · CSI-HD
reicht assigned T26301: Browserbased parsing and identification of DICOM files to d485r.
Tue, Aug 20, 10:24 AM · CSI-HD

Mon, Aug 19

floca added a comment to T24766: Last time step of 3D+t data with arbitrary time geometry not selectable by image navigator spinbox.

@kalali: Sharp eyes and good work. As far as I can see this is a proper solution to fix a state a had not covered in my implementation. The handling of invalid timepoints is still okay. As the documentation only guaranties that negative invalids will be 0. For all others there are no garanties and developers use GetTimeBounds() to check wether they request legal time points or not.

Mon, Aug 19, 2:07 PM · MITK
kraeuter added a comment to T26269: [image statistics plugin] refactor to use new node selection widget.

Pushed new branch T26269-ChangeSelectionInStatisticsPlugin.

Mon, Aug 19, 12:07 PM · MITK

Sat, Aug 17

reicht changed the visibility for T26306: Identify a web-framework to operate a Server.
Sat, Aug 17, 11:05 PM · CSI-HD
reicht changed the visibility for T26301: Browserbased parsing and identification of DICOM files.
Sat, Aug 17, 11:05 PM · CSI-HD
reicht closed T26306: Identify a web-framework to operate a Server as Resolved.

Koa.js is the way to go in this case

Sat, Aug 17, 11:03 PM · CSI-HD
reicht closed T26307: Identify a proper Transfer technology as Resolved.

First initialize a TLS based websocket connection between browser and server. In addition encrypt the files using AES-GCM 256. Key to encrypt files is computed using ECDH P-384. Private/Public Key for ECDH is generated independently from the TLS secured websocket connection.

Sat, Aug 17, 11:02 PM · CSI-HD
reicht changed the visibility for T26307: Identify a proper Transfer technology.
Sat, Aug 17, 10:58 PM · CSI-HD
reicht moved T26306: Identify a web-framework to operate a Server from DKFZ ToDo to Doing on the CSI-HD board.
Sat, Aug 17, 10:57 PM · CSI-HD
reicht moved T26307: Identify a proper Transfer technology from DKFZ ToDo to Doing on the CSI-HD board.
Sat, Aug 17, 10:57 PM · CSI-HD
reicht changed the visibility for T26301: Browserbased parsing and identification of DICOM files.
Sat, Aug 17, 10:56 PM · CSI-HD
reicht closed T26301: Browserbased parsing and identification of DICOM files, a subtask of T26299: [Webbased DICOM parsing and file handling], as Resolved.
Sat, Aug 17, 10:56 PM · CSI-HD
reicht closed T26301: Browserbased parsing and identification of DICOM files as Resolved.

cannot be accomplished using cornerstone, since errors are thrown if non-dicom filesize is below "proper" DICOM file. Therefore we implemented our own routine to check if incoming filesize is below 132 bits, otherwise check if bits from 128 to 132 represent "DICM".

Sat, Aug 17, 10:56 PM · CSI-HD
pfjaeger <p.jaeger@dkfz.de> committed rMDTPUBLIC5b6bea6884ec: fixed channel dimension in lidc dataloader. Fixed unknown input argument in… (authored by pfjaeger <p.jaeger@dkfz.de>).
fixed channel dimension in lidc dataloader. Fixed unknown input argument in…
Sat, Aug 17, 3:55 PM

Fri, Aug 16

eisenman closed T26632: Saved calibrated IGT tool cannot be loaded anymore as Resolved.
Fri, Aug 16, 4:22 PM · IGT, MITK
eisenman committed rMITKdc8f1d5204b9: Merge branch 'T26632-EnsureFileSuffixForCalibratedTool' (authored by eisenman).
Merge branch 'T26632-EnsureFileSuffixForCalibratedTool'
Fri, Aug 16, 4:21 PM
eisenman added a comment to T26632: Saved calibrated IGT tool cannot be loaded anymore.

Pushed new branch T26632-EnsureFileSuffixForCalibratedTool.

Fri, Aug 16, 4:19 PM · IGT, MITK
kalali added a comment to T24766: Last time step of 3D+t data with arbitrary time geometry not selectable by image navigator spinbox.

I think the problem is here: https://phabricator.mitk.org/source/mitk/browse/master/Modules/Core/src/DataManagement/mitkArbitraryTimeGeometry.cpp$124
The m_MaximumTimePoints for the 3D+t-Heart image is [103, 160, 160]. The last timePoint argument is 160. So in the first iteration if (timePoint < *pos) will be false. Next two iterations it will be false as well since 160 is not less than 160. This will lead to result being 0 at the end of the function.
Normally the m_MaximumTimePoints for another time-image is something like [41, 46, 51] and the timePoint argument will be 46 for the last timestep.
This could be solved by using something like this:

mitk::TimeStepType mitk::ArbitraryTimeGeometry::TimePointToTimeStep(TimePointType timePoint) const
{
  mitk::TimeStepType result = 0;
Fri, Aug 16, 4:00 PM · MITK
eisenman moved T26632: Saved calibrated IGT tool cannot be loaded anymore from Backlog to In Progress on the IGT board.
Fri, Aug 16, 3:44 PM · IGT, MITK
eisenman closed T26635: IGT tools from loaded tool storage are not rendered automatically as Resolved.
Fri, Aug 16, 3:43 PM · IGT, MITK
eisenman committed rMITKb434c99c6919: Merge branch 'T26635-RenderToolsLoadedFromToolStorageFile' (authored by eisenman).
Merge branch 'T26635-RenderToolsLoadedFromToolStorageFile'
Fri, Aug 16, 3:42 PM
eisenman added a comment to T26635: IGT tools from loaded tool storage are not rendered automatically.

Pushed new branch T26635-RenderToolsLoadedFromToolStorageFile.

Fri, Aug 16, 3:40 PM · IGT, MITK
steint reopened T18450: Inconsistent data selection between Measurement and Statistic as "Open".

Solved when T26269 is solved.

Fri, Aug 16, 3:37 PM · Bugzilla, MITK
eisenman moved T26635: IGT tools from loaded tool storage are not rendered automatically from Backlog to In Progress on the IGT board.
Fri, Aug 16, 3:33 PM · IGT, MITK
eisenman closed T26634: Loaded IGT tool is not rendered automatically as Resolved.
Fri, Aug 16, 3:33 PM · IGT, MITK
kausch added a comment to T26630: Batchgenerators: Access transformation parameters used in batchgenerator augmentations.

It has been resolved in branch T26630-AccessAugmParams

Fri, Aug 16, 3:22 PM · Deep Learning
eisenman committed rMITKd1d4ddab5760: Merge branch 'T26634-RenderLoadedIGTTool' (authored by eisenman).
Merge branch 'T26634-RenderLoadedIGTTool'
Fri, Aug 16, 3:04 PM
eisenman added a comment to T26634: Loaded IGT tool is not rendered automatically.

Pushed new branch T26634-RenderLoadedIGTTool.

Fri, Aug 16, 3:02 PM · IGT, MITK
eisenman moved T26634: Loaded IGT tool is not rendered automatically from Backlog to In Progress on the IGT board.
Fri, Aug 16, 2:30 PM · IGT, MITK
eisenman triaged T26635: IGT tools from loaded tool storage are not rendered automatically as Normal priority.
Fri, Aug 16, 2:17 PM · IGT, MITK
eisenman triaged T26634: Loaded IGT tool is not rendered automatically as Normal priority.
Fri, Aug 16, 2:02 PM · IGT, MITK
kalali renamed T26633: [mxn multi widget] Show different time points of data from [mxn multi widget] Shof different time points of data to [mxn multi widget] Show different time points of data.
Fri, Aug 16, 1:58 PM · Restricted Project, MITK
kalali added a project to T26633: [mxn multi widget] Show different time points of data: Restricted Project.
Fri, Aug 16, 1:58 PM · Restricted Project, MITK
kalali triaged T26633: [mxn multi widget] Show different time points of data as Normal priority.
Fri, Aug 16, 1:58 PM · Restricted Project, MITK
kalali added a comment to T25030: Image navigator time slider moves twice.

See T24766.
I also experienced the two-step when debugging but using only console-output this does not happen with other time-data than 3D+t-Heart

Fri, Aug 16, 1:41 PM · Restricted Project, MITK
eisenman added a comment to T26632: Saved calibrated IGT tool cannot be loaded anymore.

The issue with the missing file extension only occurs on Linux.

Fri, Aug 16, 1:41 PM · IGT, MITK
kalali added a comment to T24766: Last time step of 3D+t data with arbitrary time geometry not selectable by image navigator spinbox.

This does not happen with the new mxn multi widget. Maybe connected to the render windows being synchronized / plane nodes when using the StdMultiWidget?

Fri, Aug 16, 1:40 PM · MITK
kalali added a comment to T25930: [Segmentation] Fill/Erase crashes at non-zero timestep / Issue with ArbitraryTimeGeometry.

Is this still valid? I looked at it but couldn't reproduce the bug.
If you can reproduce it, could you try to reproduce it with Pic2DplusT and MITK-Data/3D+t-ITKIO-TestData as well?

Fri, Aug 16, 12:36 PM · MITK (2018-04-4)
kalali added a comment to T26276: Segmentation created for multiple timepoints on 3D+t images.

I created such a segmentation on the 3D+t-heart dataset and stored the segmentation as *.nrrd. The I loaded the *.nrrd-segmentation again and I now I can only see the segmentation on the first timestep.
Important: The timesteps of the *.nrrd-segmentation are now from 0 - 3 and with a duration of 1ms. The original 3D+t-Heart was [0,103] [103,160] [160, 160]. This was also true for the original segmentation. If I store the 3D+t-Heart image as *.nrrd and reopen it again the original timesteps are preserved.

Fri, Aug 16, 12:19 PM · MITK (2018-04-4)
kraeuter claimed T26269: [image statistics plugin] refactor to use new node selection widget.
Fri, Aug 16, 12:06 PM · MITK
kalali updated subscribers of T18450: Inconsistent data selection between Measurement and Statistic.

Please talk to @kraeuter to as she is currently working on T26269

Fri, Aug 16, 12:04 PM · Bugzilla, MITK
eisenman triaged T26632: Saved calibrated IGT tool cannot be loaded anymore as Normal priority.
Fri, Aug 16, 11:58 AM · IGT, MITK
kalali added a comment to T26276: Segmentation created for multiple timepoints on 3D+t images.

I also tried it with MITK-Data/3D+t-ITKIO-TestData and everything works fine (segmentation and time-slider). However, a difference between all these time-images and the 3D+t-Heart// image is, that the Heart-image does not actually have a third timepoint, as the third timepoint is of length 0ms.
So maybe there is a problem with the matching of time points and the segmentation is displayed for the last time point, as the lats time point is actually non-existent and wraps around to the time point 0.

Fri, Aug 16, 11:49 AM · MITK (2018-04-4)
kalali added a comment to T26276: Segmentation created for multiple timepoints on 3D+t images.

I just tried this and I can reproduce it with MITK-Data/3D+t-Heart. But when I used Pic2DplusT the segmentation was only created on a single timestep.
Additionally, when I clicked on the arrows of the time-slider of the image navigation plugin the time slider sometimes wraps around the last time step and returns to timestep 0. This was already mentioned here T25030. However, this does not happen If I use the Pic2DplusT image so maybe the 3D+t-Heart image is corrupt?

Fri, Aug 16, 11:40 AM · MITK (2018-04-4)
steint closed T18450: Inconsistent data selection between Measurement and Statistic as Resolved.

The new implementation of the image statistics plugin offers a pulldown menu for image and mask image. This avoids the inconsistent data selection.

Fri, Aug 16, 11:22 AM · Bugzilla, MITK
eisenman triaged T26631: Tool not correctly visualized when tool tip edited in IGT Navigation Tool Manager as Normal priority.
Fri, Aug 16, 10:57 AM · IGT, MITK
kausch created T26630: Batchgenerators: Access transformation parameters used in batchgenerator augmentations.
Fri, Aug 16, 10:50 AM · Deep Learning
eisenman triaged T26629: Workbench in inconsistent state after trying to save a tool storage file with insufficient permissions as High priority.
Fri, Aug 16, 10:31 AM · IGT, MITK

Thu, Aug 15

neher closed T26628: IVIM View does not react to crosshair change as Resolved.
Thu, Aug 15, 3:09 PM · MITK Diffusion
adler added a member for Deep Learning: d246a.
Thu, Aug 15, 3:08 PM
adler added a member for CAMI: d246a.
Thu, Aug 15, 3:08 PM
neher committed rMITKDIFF98e9a601a162: Merge branch 'T26628-Ivim' (authored by neher).
Merge branch 'T26628-Ivim'
Thu, Aug 15, 3:03 PM
neher committed rMITKDIFF19e70e4317fc: App description (authored by neher).
App description
Thu, Aug 15, 3:02 PM
neher committed rMITKDIFF3b9d6d0b49f0: Merge branch 'T26628-Ivim' (authored by neher).
Merge branch 'T26628-Ivim'
Thu, Aug 15, 3:01 PM
neher committed rMITKDIFFd160ee880aff: IVIM cmd app (authored by neher).
IVIM cmd app
Thu, Aug 15, 3:00 PM
neher added a comment to T26628: IVIM View does not react to crosshair change.

Pushed new branch T26628-Ivim.

Thu, Aug 15, 3:00 PM · MITK Diffusion
neher triaged T26628: IVIM View does not react to crosshair change as Normal priority.
Thu, Aug 15, 2:22 PM · MITK Diffusion
neher closed T26386: [MITK Diffusion] Reader should recognize bval and bvec files, not only bvals and bvecs as Resolved.

it actually does already

Thu, Aug 15, 1:50 PM · MITK
bonekamp committed rPROUNET0810945924c4: updating README (authored by bonekamp).
updating README
Thu, Aug 15, 1:25 PM
bonekamp committed rPROUNET47696e20d6d3: updating README (authored by bonekamp).
updating README
Thu, Aug 15, 1:25 PM
neher closed T26602: Dipy reconstruction does not work as Resolved.
Thu, Aug 15, 11:32 AM · MITK Diffusion
neher committed rMITKDIFF3b90a517f609: Merge branch 'T26602-DipyRecon' (authored by neher).
Merge branch 'T26602-DipyRecon'
Thu, Aug 15, 11:25 AM
neher committed rMITKDIFFc78042aa846e: Correct file location. Use dipy SH convention (authored by neher).
Correct file location. Use dipy SH convention
Thu, Aug 15, 11:18 AM
neher added a comment to T26602: Dipy reconstruction does not work.

Pushed new branch T26602-DipyRecon.

Thu, Aug 15, 11:18 AM · MITK Diffusion
eisenman updated the task description for T24228: Restructure CreateTrackingDeviceSource method in TrackerDeviceTypeInformation implementations.
Thu, Aug 15, 9:21 AM · MITK, IGT

Wed, Aug 14

sridhara updated subscribers of T26611: Edit tool tip function in IGT Tracking doesn't apply the correction.

Compared ManualEditToolTip functions of IGTNavigationToolManager and IGTNavigationToolCalibration plugin which works correctly. In former, the storage is disconnected before editing the tool and when a new tracking connection is made the edited tool tip and orientation is lost. But in calibration plugin the editing of tool is done while tracking device is connected, so the information is preserved.
@eisenman @franza Can we remove the condition that the tracker has to disconnected before editing the tool or is there another work around for this.

Wed, Aug 14, 5:51 PM · Restricted Project, MITK
bonekamp committed rPROUNET418ea14fd07a: updating README (authored by bonekamp).
updating README
Wed, Aug 14, 5:13 PM
bonekamp committed rPROUNET0c10b1a6b666: nothing (authored by bonekamp).
nothing
Wed, Aug 14, 2:13 PM
kislinsk added a member for Deep Learning: bonekamp.
Wed, Aug 14, 12:51 PM
sridhara triaged T26611: Edit tool tip function in IGT Tracking doesn't apply the correction as Normal priority.
Wed, Aug 14, 10:59 AM · Restricted Project, MITK

Tue, Aug 13

franza added a comment to T26609: US Navigation / Tracked US: CT Registration Demo.

T26609-2018.04.beta.CT-Registration-Demo is based on a old 2018.04.beta version, CT registration is working.

Tue, Aug 13, 6:56 PM · IGT, MITK
franza added a comment to T26609: US Navigation / Tracked US: CT Registration Demo.

Pushed new branch T26609-2018.04.beta.CT-Registration-Demo.

Tue, Aug 13, 6:55 PM · IGT, MITK
franza added a comment to T26609: US Navigation / Tracked US: CT Registration Demo.

T26609-2019-08-USNavigationFix is based on 2019-05 MITK master, US Navigation is working, but CT registration is buggy.

Tue, Aug 13, 6:54 PM · IGT, MITK
franza added a comment to T26609: US Navigation / Tracked US: CT Registration Demo.

Pushed new branch T26609-2019-08-USNavigationFix.

Tue, Aug 13, 6:53 PM · IGT, MITK
franza triaged T26609: US Navigation / Tracked US: CT Registration Demo as Wishlist priority.
Tue, Aug 13, 6:28 PM · IGT, MITK
kalali added a revision to T24215: Refactor classes to use the QmitkAbstractMultiWidget(Editor): Unknown Object (Differential Revision).
Tue, Aug 13, 3:06 PM · Noteworthy, MITK
schererj moved T23030: Create a Docker Screenshot Tool from Backlog to Review on the d:cipher board.
Tue, Aug 13, 10:06 AM · d:cipher
schererj moved T24106: Merge a stable docker container for Dicom-Kibana from Backlog to Review on the d:cipher board.
Tue, Aug 13, 10:06 AM · d:cipher

Mon, Aug 12

kalali closed T26495: [mxn multi widget] Not able to chose level-window presets as Resolved.
Mon, Aug 12, 3:51 PM · Restricted Project, MITK
kalali added a comment to T26495: [mxn multi widget] Not able to chose level-window presets.

Level window widget has been added to both multi widget editors, presets work.
Using the context-menu of the level window slider the user can select the node he or she wants to modify. Using the multi-node selection approach from T25804 requires the selected-property to be set by the render window manager.
However, the multi-node-selection approach is included as the data manager is currently always available.

Mon, Aug 12, 3:50 PM · Restricted Project, MITK
kalali added a comment to T26495: [mxn multi widget] Not able to chose level-window presets.

Pushed new branch T26495-Enable-level-window-slider-and-presets.

Mon, Aug 12, 3:50 PM · Restricted Project, MITK
kalali added a comment to T25804: Set 'selected' property when using the new selection concept.

I came across this as I re-added the level window slider to the MxNMultiWidget (we didn't include this before as we used the PACS mode inside the MxNMultiWidget - which allows to change the level window via mouse moving). Now our user wants to use the level-window-presets available from the context menu of the level window slider.

Mon, Aug 12, 3:25 PM · MITK
floca added a comment to T25804: Set 'selected' property when using the new selection concept.

This would be necessary if we want to use the render window manager with the mxnmultiwidget and the mentioned task (T25483).

Mon, Aug 12, 3:22 PM · MITK
kalali added a comment to T25804: Set 'selected' property when using the new selection concept.

This would be necessary if we want to use the render window manager with the mxnmultiwidget and the mentioned task (T25483).

Mon, Aug 12, 3:11 PM · MITK
kalali moved T26485: PACS mode is active while segmentation is drawn from Restricted Project Column to Restricted Project Column on the Restricted Project board.
Mon, Aug 12, 1:52 PM · Restricted Project, MITK
kalali added a comment to T26485: PACS mode is active while segmentation is drawn.

For test purposes this has been solved for the segmentation module / plugin in 450d57dd of T24215.

Mon, Aug 12, 1:51 PM · Restricted Project, MITK
kalali claimed T26485: PACS mode is active while segmentation is drawn.
Mon, Aug 12, 1:15 PM · Restricted Project, MITK
kalali added a comment to T26485: PACS mode is active while segmentation is drawn.

Also when changing the interaction mode (PACS <-> MITK) while the segmentation tool (e.g. Add) is active, the changed interaction mode will overwrite the segmentation interaction and the render window changes again while drawing the segmentation.

Mon, Aug 12, 1:14 PM · Restricted Project, MITK
vemuri added a member for SuSI: hempe.
Mon, Aug 12, 11:58 AM
kalali added a comment to T26485: PACS mode is active while segmentation is drawn.

There seems to be a problem with the mitkDisplayActionEventBroadcast-class in general. Some classes have legacy code that disables the default display interactor to load a scenario-specific state machine and config file (see e.g. https://phabricator.mitk.org/source/mitk/browse/master/Modules/Segmentation/Interactions/mitkTool.cpp$121).
This is done in other classes. The problem is that the function does not reset the display action event broadcast instance but only display interactor instances.

Mon, Aug 12, 11:22 AM · Restricted Project, MITK
neher triaged T26602: Dipy reconstruction does not work as Normal priority.
Mon, Aug 12, 10:47 AM · MITK Diffusion
steint committed rMITK8092dc81e768: Merge branch 'T26599-add-dicomweb-module' (authored by steint).
Merge branch 'T26599-add-dicomweb-module'
Mon, Aug 12, 8:18 AM

Fri, Aug 9

kalali raised the priority of T24215: Refactor classes to use the QmitkAbstractMultiWidget(Editor) from Wishlist to Normal.
Fri, Aug 9, 4:11 PM · Noteworthy, MITK
kalali closed T25605: New concept for changing the view direction of render windows, a subtask of T25603: Combine render window manager with custom multi widget, as Resolved.
Fri, Aug 9, 4:00 PM · Restricted Project, MITK
kalali closed T25605: New concept for changing the view direction of render windows as Resolved.

The modified render window has been added and can be used by the StdMultiWidget and the MxNMulwiWidget (see T24215).
This is used here and a new entry for the render window menu has been added.

Fri, Aug 9, 4:00 PM · Restricted Project, MITK