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kalali (Amir Kalali)
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Aug 1 2016, 12:10 PM (159 w, 2 d)

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Fri, Aug 16

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
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
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)
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
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)

Tue, Aug 13

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

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
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
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

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
kalali added a comment to T25605: New concept for changing the view direction of render windows.

Pushed new branch T25605-View-direction-change-in-render-window-menu.

Fri, Aug 9, 3:56 PM · Restricted Project, MITK

Wed, Aug 7

kalali added a comment to T25595: Make classes work with the new render window access.

Pushed new branch T25595-New-render-window-access.

Wed, Aug 7, 12:53 PM · Restricted Project, MITK
kalali updated the task description for T25595: Make classes work with the new render window access.
Wed, Aug 7, 10:22 AM · Restricted Project, MITK
kalali renamed T25595: Make classes work with the new render window access from Make ImageNavigator work with the custom multi widget editor to Make classes work with the new render window access.
Wed, Aug 7, 9:56 AM · Restricted Project, MITK
kalali updated the task description for T24211: Multi widget editor responsibilities.
Wed, Aug 7, 9:46 AM · MITK
kalali added a comment to T24211: Multi widget editor responsibilities.

LayoutManager has been added in T24215.

Wed, Aug 7, 9:45 AM · MITK

Tue, Aug 6

kalali closed T26493: [mxn multi widget] Allow render window resizing as Resolved.

Render window menu is now available (T24215).
However, QSplitter were added to the MxNMultiWidget so that resizing via mouse-dragging is also possible.

Tue, Aug 6, 7:00 PM · Restricted Project, MITK
kalali added a comment to T24215: Refactor classes to use the QmitkAbstractMultiWidget(Editor).

Pushed new branch T24215-Remove-stdmultiwidget-dependency.

Tue, Aug 6, 6:59 PM · Noteworthy, MITK
kalali closed T24367: SetWidgetPlane-functions in QmitkStdMultiWidget not used, a subtask of T24356: Rework mouse mode switcher, as Resolved.
Tue, Aug 6, 6:57 PM · MITK
kalali closed T24367: SetWidgetPlane-functions in QmitkStdMultiWidget not used as Resolved.

Functions have been removed in T24215.
Additional functions to be removed: see T26542

Tue, Aug 6, 6:57 PM · Noteworthy, MITK
kalali updated the task description for T24215: Refactor classes to use the QmitkAbstractMultiWidget(Editor).
Tue, Aug 6, 6:56 PM · Noteworthy, MITK
kalali claimed T24215: Refactor classes to use the QmitkAbstractMultiWidget(Editor).
Tue, Aug 6, 6:53 PM · Noteworthy, MITK
kalali renamed T24215: Refactor classes to use the QmitkAbstractMultiWidget(Editor) from QmitkRenderWindow needs a StdMultiWidget to Refactor classes to use the QmitkAbstractMultiWidget(Editor).
Tue, Aug 6, 6:53 PM · Noteworthy, MITK
kalali added a project to T26572: Allow extension of QmitkRenderWindowMenu with custom layouts: Restricted Project.
Tue, Aug 6, 2:31 PM · Restricted Project, Restricted Project, MITK
kalali triaged T26572: Allow extension of QmitkRenderWindowMenu with custom layouts as Low priority.
Tue, Aug 6, 2:30 PM · Restricted Project, Restricted Project, MITK

Fri, Aug 2

kalali added a comment to T19683: "Show only selected node" changes the visibility of crosshair.

Could you elaborate on this? I don't get it: aren't we processing each single data node inside the data storage?

Fri, Aug 2, 5:46 PM · Bugzilla, Pull Request, MITK
kalali triaged T26555: [mxn multi widget] Provide different default layouts as Normal priority.
Fri, Aug 2, 3:07 PM · MITK

Thu, Aug 1

kalali added a comment to T26543: Enum for AXIAL, SAGITTAL, CORONAL 3D/ORIGINAL/NONE is provided at many different locations.

This will further allow to remove the string query (e.g. "axial") for render windows but allow a type-based request.

Thu, Aug 1, 2:04 PM · Request for Discussion, MITK
kalali moved T26543: Enum for AXIAL, SAGITTAL, CORONAL 3D/ORIGINAL/NONE is provided at many different locations from Backlog to MITK Meeting on the Request for Discussion board.
Thu, Aug 1, 2:03 PM · Request for Discussion, MITK
kalali triaged T26547: Clarify difference between QmitkPointListViewWidget and QmitkPointListView as Low priority.
Thu, Aug 1, 2:02 PM · Restricted Project, MITK
kalali triaged T26545: Make classes work with QmitkAbstractMultiWidget(Editor) as Normal priority.
Thu, Aug 1, 1:49 PM · Restricted Project, MITK
kalali added a comment to T26543: Enum for AXIAL, SAGITTAL, CORONAL 3D/ORIGINAL/NONE is provided at many different locations.

mitkBaseRenderer.h already contains the enum for Standard2D and Standard2D, which is needed if one wants to switch between 2D and 3D view.

Thu, Aug 1, 11:23 AM · Request for Discussion, MITK
kalali triaged T26542: Remove functions from StdMultiWidget(Editor) as Low priority.
Thu, Aug 1, 9:37 AM · MITK

Wed, Jul 31

kalali created T26543: Enum for AXIAL, SAGITTAL, CORONAL 3D/ORIGINAL/NONE is provided at many different locations.
Wed, Jul 31, 7:14 PM · Request for Discussion, MITK
kalali created T26542: Remove functions from StdMultiWidget(Editor).
Wed, Jul 31, 6:22 PM · MITK

Mon, Jul 29

kalali added members for SIDT: kislinsk, jungsi, steint, thomass.
Mon, Jul 29, 4:32 PM
kalali removed a member for SIDT: s635r.
Mon, Jul 29, 4:31 PM

Fri, Jul 26

kalali closed T26491: [Render window manager] Node renaming is not allowed as Resolved.
Fri, Jul 26, 5:05 PM · Restricted Project, MITK
kalali added a comment to T26491: [Render window manager] Node renaming is not allowed.

Pushed new branch T26491-Allow-node-renaming.

Fri, Jul 26, 5:05 PM · Restricted Project, MITK
kalali claimed T26491: [Render window manager] Node renaming is not allowed.
Fri, Jul 26, 12:56 PM · Restricted Project, MITK
kalali closed T26494: [Render window manager] Change view to currently active render window as Resolved.
Fri, Jul 26, 12:54 PM · Restricted Project, MITK
kalali added a comment to T26494: [Render window manager] Change view to currently active render window.

Has been resolved in T26492.

Fri, Jul 26, 12:54 PM · Restricted Project, MITK
kalali closed T26492: [mxn multi widget] Send active render window as Resolved.
Fri, Jul 26, 12:51 PM · Restricted Project, MITK
kalali added a comment to T26492: [mxn multi widget] Send active render window.

Pushed new branch T26492-Send-active-render-window.

Fri, Jul 26, 12:50 PM · Restricted Project, MITK

Wed, Jul 24

kalali closed T24161: Common interface for Custom-/Std-Multi widget (editor), a subtask of T24215: Refactor classes to use the QmitkAbstractMultiWidget(Editor), as Resolved.
Wed, Jul 24, 12:40 PM · Noteworthy, MITK
kalali closed T24161: Common interface for Custom-/Std-Multi widget (editor) as Resolved.

Branch has unpublished commits. Merging into T26492 to publish it.

Wed, Jul 24, 12:40 PM · Restricted Project, MITK

Tue, Jul 23

kalali renamed T26394: [Render window manager] Provide tree view / model from [Render window manager] Provide tree view / model for the to [Render window manager] Provide tree view / model.
Tue, Jul 23, 2:40 PM · Restricted Project, Restricted Project, MITK

Jul 22 2019

kalali claimed T24161: Common interface for Custom-/Std-Multi widget (editor).
Jul 22 2019, 5:03 PM · Restricted Project, MITK

Jul 19 2019

kalali claimed T26492: [mxn multi widget] Send active render window.
Jul 19 2019, 4:19 PM · Restricted Project, MITK
kalali added a comment to T26492: [mxn multi widget] Send active render window.

The active render window inside the multi widget editor is only set if the layout is changed.
It needs to be set if the user interacts with the render window.

Jul 19 2019, 4:19 PM · Restricted Project, MITK
kalali closed T26490: [mxn multi widget] Enable MITK mouse mode and allow mode switching as Resolved.
Jul 19 2019, 3:04 PM · MITK, Restricted Project
kalali committed rMITK6e4f328a4a22: Enable MITK mouse mode and allow mode switching (authored by kalali).
Enable MITK mouse mode and allow mode switching
Jul 19 2019, 3:00 PM
kalali committed rMITKc49c3cc67d23: Add function description (authored by kalali).
Add function description
Jul 19 2019, 3:00 PM
kalali committed rMITKbfcae17d3b8c: Add default interaction scheme (authored by kalali).
Add default interaction scheme
Jul 19 2019, 3:00 PM
kalali committed rMITK2f9722e259e2: Add exception if interaction event handler is not valid (authored by kalali).
Add exception if interaction event handler is not valid
Jul 19 2019, 3:00 PM
kalali closed T26487: After changing colormap, cannot return to grayscale as Resolved.
Jul 19 2019, 1:18 PM · Restricted Project, MITK
kalali committed rMITK9e687a1442ba: Initialize data members using the copy constructor (authored by kalali).
Initialize data members using the copy constructor
Jul 19 2019, 1:18 PM
kalali committed rMITK36bfa18f0d2b: Initialize data members using the copy constructor (authored by kalali).
Initialize data members using the copy constructor
Jul 19 2019, 1:18 PM
kalali added a revision to T26487: After changing colormap, cannot return to grayscale: Unknown Object (Differential Revision).
Jul 19 2019, 12:16 PM · Restricted Project, MITK

Jul 15 2019

kalali added a revision to T26490: [mxn multi widget] Enable MITK mouse mode and allow mode switching: Unknown Object (Differential Revision).
Jul 15 2019, 7:05 PM · MITK, Restricted Project
kalali committed rMITK45169a22abec: Enable changing the mouse mode via the configuration toolbar (authored by kalali).
Enable changing the mouse mode via the configuration toolbar
Jul 15 2019, 6:06 PM
kalali committed rMITK1f9bd5844acf: Enable changing the interaction scheme (authored by kalali).
Enable changing the interaction scheme
Jul 15 2019, 6:06 PM
kalali added a comment to T26490: [mxn multi widget] Enable MITK mouse mode and allow mode switching.

Pushed new branch T26490-Enable-MITK-mouse-mode-and-mode-switching.

Jul 15 2019, 6:05 PM · MITK, Restricted Project
kalali added a project to T26487: After changing colormap, cannot return to grayscale: Restricted Project.

The problem is with m_Type == type inside mitk::LookupTable::SetType. This variable is always GRAYSCALE when SetType is called inside the QmitkDataNodeColorMapAction. I guess this has something to do with the cloning of the lookup table.
I will take a closer look at this on Friday.

Jul 15 2019, 5:24 PM · Restricted Project, MITK
kalali moved T26490: [mxn multi widget] Enable MITK mouse mode and allow mode switching from Restricted Project Column to Restricted Project Column on the Restricted Project board.
Jul 15 2019, 11:18 AM · MITK, Restricted Project

Jul 11 2019

kalali renamed T26490: [mxn multi widget] Enable MITK mouse mode and allow mode switching from PACS mode is not preferred, allow MITK mode in BlackSwan to [mxn multi widget] Enable MITK mouse mode and allow mode switching.
Jul 11 2019, 1:09 PM · MITK, Restricted Project
kalali added a comment to T26486: PACS mouse mode does not allow scrolling with mouse wheel.

Ok but the simple solution would be to re-enable the MITK mouse mode.
This task is more of a general discussion how the PACS mode should work, according to common PACSes.

Jul 11 2019, 1:07 PM · Restricted Project, MITK
kalali moved T26486: PACS mouse mode does not allow scrolling with mouse wheel from Backlog to MITK Meeting on the Request for Discussion board.
Jul 11 2019, 11:50 AM · Restricted Project, MITK
kalali updated the task description for T25947: The data manager shows unreadable names.
Jul 11 2019, 11:19 AM · Request for Discussion, Restricted Project, MITK
kalali closed T24760: Restrictions and assumptions for the BlackSwan project, a subtask of T23758: Introduction of custom multi widget editor, as Invalid.
Jul 11 2019, 11:14 AM · Restricted Project, MITK
kalali closed T24760: Restrictions and assumptions for the BlackSwan project as Invalid.

We already got some feedback from users so this task is invalid. For the next version, check T26476.

Jul 11 2019, 11:14 AM · MITK
kalali added a parent task for T26496: [mxn multi widget] Re-initializations reset all render windows: Unknown Object (Maniphest Task).
Jul 11 2019, 11:10 AM · Restricted Project, MITK
kalali triaged T26496: [mxn multi widget] Re-initializations reset all render windows as High priority.
Jul 11 2019, 11:10 AM · Restricted Project, MITK
kalali renamed T26394: [Render window manager] Provide tree view / model from Provide tree view / model for the render window manager to [Render window manager] Provide tree view / model for the.
Jul 11 2019, 10:59 AM · Restricted Project, Restricted Project, MITK
kalali removed a subtask for T25601: Modernize render window manager: T26394: [Render window manager] Provide tree view / model.
Jul 11 2019, 10:59 AM · Restricted Project, MITK
kalali edited parent tasks for T26394: [Render window manager] Provide tree view / model, added: Unknown Object (Maniphest Task); removed: T25601: Modernize render window manager.
Jul 11 2019, 10:59 AM · Restricted Project, Restricted Project, MITK
kalali added a comment to T26394: [Render window manager] Provide tree view / model.

Sometimes adding a new segmentation will not show the segmentation -> layer / tree problem? Need to investigate further.

Jul 11 2019, 10:58 AM · Restricted Project, Restricted Project, MITK
kalali added a parent task for T25947: The data manager shows unreadable names: Unknown Object (Maniphest Task).
Jul 11 2019, 10:53 AM · Request for Discussion, Restricted Project, MITK
kalali moved T25947: The data manager shows unreadable names from Backlog to MITK Meeting on the Request for Discussion board.
Jul 11 2019, 10:50 AM · Request for Discussion, Restricted Project, MITK
kalali renamed T25947: The data manager shows unreadable names from The data manager does not show the data node name anymore to The data manager shows unreadable names.
Jul 11 2019, 10:50 AM · Request for Discussion, Restricted Project, MITK
kalali moved T19477: Select which dicom tags are used to create a nodes name from Backlog to MITK Meeting on the Request for Discussion board.
Jul 11 2019, 10:50 AM · Request for Discussion, Bugzilla, MITK
kalali added a project to T19477: Select which dicom tags are used to create a nodes name: Request for Discussion.

I'd like to discuss this as I am currently not happy with the node naming of DICOM images. The names are totally unreadable and changing each node name is unnecessary. It would be easier to define a name pattern and have this applied for all current and future nodes of the MITK session.

Jul 11 2019, 10:50 AM · Request for Discussion, Bugzilla, MITK
kalali added a comment to T26487: After changing colormap, cannot return to grayscale.

I cannot reproduce this using Windows.
I can reproduce this using Ubuntu 18.04, gcc 7.4.0.

Jul 11 2019, 10:29 AM · Restricted Project, MITK
kalali added a parent task for T26485: PACS mode is active while segmentation is drawn: Unknown Object (Maniphest Task).
Jul 11 2019, 10:25 AM · Restricted Project, MITK
kalali added a parent task for T26486: PACS mouse mode does not allow scrolling with mouse wheel: Restricted Maniphest Task.
Jul 11 2019, 10:25 AM · Restricted Project, MITK