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thomass (Sarina Thomas)
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Projects (10)

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User Since
Aug 1 2016, 12:10 PM (254 w, 4 d)

Recent Activity

Thu, Jun 17

thomass updated subscribers of T28267: [Visualization] Custom colormaps are not handeled correctly.

As discussed with @s434n, I will discard my diff D466 for now, because it caused some unwanted interactions with the LayoutAnnotationRenderer. The quick fix of D506 solves the problem that in Geldosimetry and OverlayManager the colorbarAnnotation is not displayed in the right center (placed too heigh and is cutoff in the render window).

Thu, Jun 17, 12:02 PM · MITK

Wed, Jun 2

thomass added a comment to T28514: [Multilabel Segmentation] Changing visibility of labels on higher layers does not trigger update.

I am indeed still reading since I still have tasks to do (I will not leave beforehand just as promised :-)). I think you are referring to T28383 / D477 ... maybe it didn’t fully do the trick.

Wed, Jun 2, 1:07 PM · MITK

Apr 27 2021

thomass closed T27067: ImageCropper cannot crop some images (4d?) as Resolved.

The task as such is resolved. Another task with open questions from D279 is created with T28466

Apr 27 2021, 4:34 PM · MITK
thomass triaged T28466: [Image Cropper] Bounding shape cropper behavior not clear as Normal priority.
Apr 27 2021, 4:32 PM · MITK

Apr 22 2021

thomass closed T28008: [Mapper] Levelwindow overwrites vtkLookUpTable Range with levelwindow range as Resolved.

Could be solved by @kislinsk suggestion to change rendering mode to LOOKUPTABLE_COLOR to not envoke the levelwindow to overwrite the range

Apr 22 2021, 1:30 PM · Request for Discussion, MITK
thomass committed rRTTBed98724bd7ae: Added tests for value comparison (authored by thomass).
Added tests for value comparison
Apr 22 2021, 10:52 AM

Apr 15 2021

thomass committed rRTTB377303e52d4f: include different sampling strategy based on absolute mm (authored by thomass).
include different sampling strategy based on absolute mm
Apr 15 2021, 2:49 PM

Apr 14 2021

thomass placed T27099: [MITKDoc] Revise Clipping Plane Plugin Documentation up for grabs.

Unassign myself because we removed the clipping plane from the release and have not discussed yet how to further proceed.

Apr 14 2021, 11:01 AM · Next Milestone, MITK, Cleared
thomass reassigned T28406: [Segmentation] Examine Live-wire tool for different costfunctions/behavior from thomass to kleina.
Apr 14 2021, 11:00 AM · MITK
thomass updated subscribers of T28406: [Segmentation] Examine Live-wire tool for different costfunctions/behavior.

The first user feedback of the patch above was positive, the users liked the behavior.
However, the patch did not work correctly in terms of modifying the points afterwards (users were warned before).

Apr 14 2021, 10:48 AM · MITK
thomass placed T27507: Check the current behavior of the segmentation tools according static and dynamic 4D segmentation up for grabs.
Apr 14 2021, 10:38 AM · MITK (v2021.10), Missing Info, Restricted Project

Apr 11 2021

thomass committed rRTTB051dec8f7167: try to make the test build work again wip (authored by thomass).
try to make the test build work again wip
Apr 11 2021, 5:49 PM
thomass committed rRTTBac212ba954f6: uncommented test snippet for now because not complete (authored by thomass).
uncommented test snippet for now because not complete
Apr 11 2021, 5:49 PM
thomass committed rRTTBaf580ef73263: Merge branch 'master' into feature/T27843-Add_gamma_index_to_RTTB (authored by thomass).
Merge branch 'master' into feature/T27843-Add_gamma_index_to_RTTB
Apr 11 2021, 5:49 PM
thomass committed rRTTBfe1e1968a7fc: fix for doseThreshold based on measuredDose instead of referenceDose (authored by thomass).
fix for doseThreshold based on measuredDose instead of referenceDose
Apr 11 2021, 5:49 PM

Mar 31 2021

thomass added a comment to T28406: [Segmentation] Examine Live-wire tool for different costfunctions/behavior.

Pushed new branch to rMITK MITK: feature/T28406-PatchForTestingLiveWireBehavior.

Mar 31 2021, 9:40 AM · MITK
thomass claimed T28406: [Segmentation] Examine Live-wire tool for different costfunctions/behavior.
Mar 31 2021, 9:30 AM · MITK
thomass added a comment to T28406: [Segmentation] Examine Live-wire tool for different costfunctions/behavior.

First patch to change following behavior (for user testing only):

  • The linesegments are added with each mouseclick of the users without the cost function but by connecting start and endpoint
  • If the user double-clicks on the image, the last point is connected with the first adding an additional segment.
Mar 31 2021, 9:20 AM · MITK

Mar 25 2021

thomass added a parent task for T28383: [Multilabel Segmentation] In case of two layers, a change of visibility is not updated automatically: Unknown Object (Maniphest Task).
Mar 25 2021, 12:31 PM · Next Milestone, MITK
thomass added a parent task for T28406: [Segmentation] Examine Live-wire tool for different costfunctions/behavior: Unknown Object (Maniphest Task).
Mar 25 2021, 12:30 PM · MITK
thomass triaged T28406: [Segmentation] Examine Live-wire tool for different costfunctions/behavior as Wishlist priority.
Mar 25 2021, 12:29 PM · MITK

Mar 19 2021

thomass triaged T28389: [Multilabelsegmentation] Locking all labels can only be reversed by unlock all as Normal priority.
Mar 19 2021, 11:08 AM · MITK
thomass claimed T28383: [Multilabel Segmentation] In case of two layers, a change of visibility is not updated automatically.
Mar 19 2021, 10:36 AM · Next Milestone, MITK

Mar 18 2021

thomass added a comment to T28385: [Segmentation Utilities] Erosion crashes the MITK Workbench after interpolation.

On a first glance, the interpolation seems to affect the result.

  1. Create the segmentation with interpolation -> save it -> reload segmentation -> erosion = no crash
  2. Create the segmentation with interpolation -> erosion = crash
Mar 18 2021, 2:24 PM · Missing Info, MITK (v2021.10)
thomass triaged T28385: [Segmentation Utilities] Erosion crashes the MITK Workbench after interpolation as High priority.
Mar 18 2021, 2:15 PM · Missing Info, MITK (v2021.10)
thomass added a comment to T28383: [Multilabel Segmentation] In case of two layers, a change of visibility is not updated automatically.

The issue can indeed be solved by a mitk::RenderingManager::GetInstance()->RequestUpdateAll(); in QmitkLabelsetWidget function OnVisibleButtonClicked() but there seems to be something wrong with the lock logic when "Lock All" "Unlock All" is clicked

Mar 18 2021, 8:53 AM · Next Milestone, MITK

Mar 17 2021

thomass added a project to T28383: [Multilabel Segmentation] In case of two layers, a change of visibility is not updated automatically: Next Milestone.
Mar 17 2021, 1:39 PM · Next Milestone, MITK
thomass triaged T28383: [Multilabel Segmentation] In case of two layers, a change of visibility is not updated automatically as Normal priority.
Mar 17 2021, 1:38 PM · Next Milestone, MITK

Mar 2 2021

thomass added a comment to T28341: Crashes when using plugin with documentation opened (in MatchPoint,Modelfit,..).

Since you also mentioned different editors: Not sure if this is also related but one of the terminal outputs of the testers was:

Mar 2 2021, 9:51 AM · MITK

Mar 1 2021

thomass updated the task description for T28341: Crashes when using plugin with documentation opened (in MatchPoint,Modelfit,..).
Mar 1 2021, 5:38 PM · MITK
thomass added a comment to T28341: Crashes when using plugin with documentation opened (in MatchPoint,Modelfit,..).

With the modelfit inspector it most often crashed, if the user clicked on a datanode in the datastorage

Mar 1 2021, 3:07 PM · MITK
thomass updated the task description for T28341: Crashes when using plugin with documentation opened (in MatchPoint,Modelfit,..).
Mar 1 2021, 3:02 PM · MITK
thomass renamed T28341: Crashes when using plugin with documentation opened (in MatchPoint,Modelfit,..) from [Docu] Crashes when using plugin with documentation opened to [Docu] Crashes when using plugin with documentation opened (in MatchPoint,Modelfit,..).
Mar 1 2021, 2:49 PM · MITK
thomass triaged T28341: Crashes when using plugin with documentation opened (in MatchPoint,Modelfit,..) as High priority.
Mar 1 2021, 2:48 PM · MITK

Feb 18 2021

thomass added a member for MIC: s434n.
Feb 18 2021, 3:38 PM

Feb 10 2021

thomass triaged T28294: [Documentation] std multiwidget does show a blank page on F1 as Normal priority.
Feb 10 2021, 2:58 PM · Missing Info, MITK (v2021.10)

Feb 4 2021

thomass added a comment to T28275: [Segmentation] AdaptiveRegionGrowingTool must be refactored / 4D Segmentation returns error message when point is not on the correct timestep.

Probably it would just help to replace the MITK Error by a warning? This is also done when there is no point set at all.

Feb 4 2021, 2:50 PM · MITK (v2021.10)
thomass added a parent task for T28275: [Segmentation] AdaptiveRegionGrowingTool must be refactored / 4D Segmentation returns error message when point is not on the correct timestep: T28000: MITK v2021.02.
Feb 4 2021, 2:48 PM · MITK (v2021.10)
thomass added a subtask for T28000: MITK v2021.02: T28275: [Segmentation] AdaptiveRegionGrowingTool must be refactored / 4D Segmentation returns error message when point is not on the correct timestep.
Feb 4 2021, 2:48 PM · MITK-ProjectTemplate, MITK (v2021.02)
thomass triaged T28275: [Segmentation] AdaptiveRegionGrowingTool must be refactored / 4D Segmentation returns error message when point is not on the correct timestep as High priority.
Feb 4 2021, 2:48 PM · MITK (v2021.10)
thomass added a comment to T24754: Volume Visualization crashes with some CT images.

I couldn't reproduce this bug in the latest Release installer on Windows. However, there is no volume visualization shown at all (no matter which timestep or which histogram I select).
If the crash does not occur anymore on Ubuntu etc. we can resolve the crash bug.

Feb 4 2021, 2:36 PM · Restricted Project, MITK
thomass edited projects for T28274: [Volume Visualization] Volume Rendering for 4D images does only work on timestep 0 or not at all, added: MITK (v2021.02); removed MITK.

Most likely something for the next release IMO, but please decide @kislinsk :)

Feb 4 2021, 2:35 PM · Next Milestone, MITK, Request for Discussion
thomass triaged T28274: [Volume Visualization] Volume Rendering for 4D images does only work on timestep 0 or not at all as Normal priority.
Feb 4 2021, 2:34 PM · Next Milestone, MITK, Request for Discussion

Feb 2 2021

thomass added a comment to T28267: [Visualization] Custom colormaps are not handeled correctly.

Since the default colormaps are overwritten by the levelwindow I added a Boolean property to give the user a possibility to prevent the custom colormap from being overwritten

Feb 2 2021, 11:11 AM · MITK
thomass updated the task description for T28267: [Visualization] Custom colormaps are not handeled correctly.
Feb 2 2021, 11:10 AM · MITK
thomass triaged T28267: [Visualization] Custom colormaps are not handeled correctly as Normal priority.
Feb 2 2021, 10:37 AM · MITK

Jan 29 2021

thomass moved T28243: [Segmentation] 3D Otsu does not show preview for a second time from Backlog to Segmentation on the MITK (v2021.02) board.
Jan 29 2021, 7:55 PM · MITK (v2021.02)
thomass moved T28248: [Segmentation] Picking 3D Tool creates a 3D segmentation out of a 4D image from Backlog to Segmentation on the MITK (v2021.02) board.
Jan 29 2021, 7:54 PM · MITK (v2021.10)
thomass moved T28247: [Segmentation] Watershed tool freezes when slider and threshold are set to a low value from Backlog to Segmentation on the MITK (v2021.02) board.
Jan 29 2021, 7:53 PM · Missing Info, MITK (v2021.10), Request for Discussion
thomass lowered the priority of T28248: [Segmentation] Picking 3D Tool creates a 3D segmentation out of a 4D image from High to Normal.

Sorry this was already mentioned in T27507. But I think we never discussed / decided what the purpose of picking on 4D tools should be. But not necessarily important for the release though.

Jan 29 2021, 7:53 PM · MITK (v2021.10)
thomass renamed T28248: [Segmentation] Picking 3D Tool creates a 3D segmentation out of a 4D image from Please enter a meaningful title to [Segmentation] Picking 3D Tool creates a 3D segmentation out of a 4D image.
Jan 29 2021, 7:49 PM · MITK (v2021.10)
thomass created T28248: [Segmentation] Picking 3D Tool creates a 3D segmentation out of a 4D image.
Jan 29 2021, 7:45 PM · MITK (v2021.10)
thomass triaged T28247: [Segmentation] Watershed tool freezes when slider and threshold are set to a low value as Unbreak Now! priority.
Jan 29 2021, 7:44 PM · Missing Info, MITK (v2021.10), Request for Discussion
thomass added a comment to T28245: [Segmentation] 3D Region Growing preview does not show a binary mask in Windows Installer.

Watershed tool also has very weird rendering flickers, whenever there is more than one image visible in the 2D view. Whenever the rendering bug is solved, the segmentation tools should be checked again.

Jan 29 2021, 7:18 PM · MITK (v2021.02)
thomass updated the task description for T28245: [Segmentation] 3D Region Growing preview does not show a binary mask in Windows Installer.
Jan 29 2021, 7:11 PM · MITK (v2021.02)
thomass triaged T28245: [Segmentation] 3D Region Growing preview does not show a binary mask in Windows Installer as Unbreak Now! priority.
Jan 29 2021, 7:09 PM · MITK (v2021.02)
thomass triaged T28244: [Segmentation] Fast Marching Tool not really responsive for large images as High priority.
Jan 29 2021, 6:39 PM · Missing Info, MITK (v2021.10)
thomass added a comment to T28243: [Segmentation] 3D Otsu does not show preview for a second time.

IMO not severe for the upcoming release since Otsu is not often used and it is not a show stopper...

Jan 29 2021, 5:43 PM · MITK (v2021.02)
thomass triaged T28243: [Segmentation] 3D Otsu does not show preview for a second time as Normal priority.
Jan 29 2021, 5:42 PM · MITK (v2021.02)
thomass added a comment to T28222: [ImageStatistics] Histogram is only shown for timestep 0.

Since you are already working on the histogram anyways, can you check the following:

Jan 29 2021, 3:03 PM · MITK (v2021.02)

Jan 27 2021

thomass added a parent task for T28219: [Image Cropper] Selection widget does not allow to create a new bounding box: T28000: MITK v2021.02.
Jan 27 2021, 3:45 PM · MITK (v2021.02)
thomass added a subtask for T28000: MITK v2021.02: T28219: [Image Cropper] Selection widget does not allow to create a new bounding box.
Jan 27 2021, 3:45 PM · MITK-ProjectTemplate, MITK (v2021.02)
thomass added a comment to T28223: [ImageStatistics] Deleting a datanode after statistics leads to no histogram update for the next node.

probably related to T28206

Jan 27 2021, 3:14 PM · Next Milestone, MITK
thomass added a subtask for T28000: MITK v2021.02: T28220: [Image Cropper] Masking a 4D image and overwrite the original one leads to strange result.
Jan 27 2021, 3:08 PM · MITK-ProjectTemplate, MITK (v2021.02)
thomass added a parent task for T28220: [Image Cropper] Masking a 4D image and overwrite the original one leads to strange result: T28000: MITK v2021.02.
Jan 27 2021, 3:08 PM · MITK (v2021.02)
thomass added a parent task for T28221: [ImageStatistics] Histogram is not updated when using ROI: T28000: MITK v2021.02.
Jan 27 2021, 3:07 PM · MITK (v2021.02)
thomass added a subtask for T28000: MITK v2021.02: T28221: [ImageStatistics] Histogram is not updated when using ROI.
Jan 27 2021, 3:07 PM · MITK-ProjectTemplate, MITK (v2021.02)
thomass added a subtask for T28000: MITK v2021.02: T28222: [ImageStatistics] Histogram is only shown for timestep 0.
Jan 27 2021, 3:06 PM · MITK-ProjectTemplate, MITK (v2021.02)
thomass added a parent task for T28222: [ImageStatistics] Histogram is only shown for timestep 0: T28000: MITK v2021.02.
Jan 27 2021, 3:06 PM · MITK (v2021.02)
thomass added a parent task for T28223: [ImageStatistics] Deleting a datanode after statistics leads to no histogram update for the next node: T28000: MITK v2021.02.
Jan 27 2021, 3:06 PM · Next Milestone, MITK
thomass added a subtask for T28000: MITK v2021.02: T28223: [ImageStatistics] Deleting a datanode after statistics leads to no histogram update for the next node.
Jan 27 2021, 3:06 PM · MITK-ProjectTemplate, MITK (v2021.02)
thomass updated the task description for T28223: [ImageStatistics] Deleting a datanode after statistics leads to no histogram update for the next node.
Jan 27 2021, 3:00 PM · Next Milestone, MITK
thomass triaged T28223: [ImageStatistics] Deleting a datanode after statistics leads to no histogram update for the next node as High priority.
Jan 27 2021, 3:00 PM · Next Milestone, MITK
thomass triaged T28222: [ImageStatistics] Histogram is only shown for timestep 0 as High priority.
Jan 27 2021, 2:53 PM · MITK (v2021.02)
thomass added a comment to T28221: [ImageStatistics] Histogram is not updated when using ROI.

However, checking "Show Subchart" always invokes an update and then you can see it

Jan 27 2021, 2:42 PM · MITK (v2021.02)
thomass triaged T28221: [ImageStatistics] Histogram is not updated when using ROI as High priority.
Jan 27 2021, 2:40 PM · MITK (v2021.02)
thomass edited projects for T28219: [Image Cropper] Selection widget does not allow to create a new bounding box, added: MITK (v2021.02); removed MITK.
Jan 27 2021, 2:37 PM · MITK (v2021.02)
thomass edited projects for T28220: [Image Cropper] Masking a 4D image and overwrite the original one leads to strange result, added: MITK (v2021.02); removed MITK.
Jan 27 2021, 2:36 PM · MITK (v2021.02)
thomass triaged T28220: [Image Cropper] Masking a 4D image and overwrite the original one leads to strange result as High priority.
Jan 27 2021, 2:34 PM · MITK (v2021.02)
thomass triaged T28219: [Image Cropper] Selection widget does not allow to create a new bounding box as Unbreak Now! priority.
Jan 27 2021, 2:31 PM · MITK (v2021.02)

Jan 4 2021

thomass added a comment to T27689: RTDose image can not be serialized and workbench crashes upon loading.

The scene is created successfully if following (deprecated) properties are disabled in mitkDICOMImageBlockDescriptor.cpp:

Jan 4 2021, 5:10 PM · Request for Discussion, MITK

Dec 16 2020

thomass added a comment to T27689: RTDose image can not be serialized and workbench crashes upon loading.

as name property, the name of the RT node is provided correctly.
I created a working example with Pic3D for comparison.
Looking at both caaaaa.xml files, the only difference I notice is that the corrupted one is encoded with UTF-8 but otherwise it looks similar (as far as I see).

Dec 16 2020, 9:12 AM · Request for Discussion, MITK
thomass added a comment to T27689: RTDose image can not be serialized and workbench crashes upon loading.

<?xml version="1.0" encoding="UTF-8"?>
<Version Writer="C:\Development\MITK-dev\src\Modules\SceneSerialization\src\mitkSceneIO.cpp" Revision="$Revision: 17055 $" FileVersion="1"/>

Dec 16 2020, 8:40 AM · Request for Discussion, MITK
thomass added a comment to T27689: RTDose image can not be serialized and workbench crashes upon loading.

sorry just saw the message. I put it in the shared folder.

Dec 16 2020, 8:07 AM · Request for Discussion, MITK

Dec 15 2020

thomass added a comment to T27689: RTDose image can not be serialized and workbench crashes upon loading.

As Ralf pointed out, it is actually not related to the GenericProperty as such but it seems that the scene does not even contain any nrrd files after saving and that is why it breaks

Dec 15 2020, 3:50 PM · Request for Discussion, MITK

Dec 14 2020

thomass added a comment to T27689: RTDose image can not be serialized and workbench crashes upon loading.

GenericProperty associated to key 'MITK.IO.reader.DICOM.PixelSpacingInterpretation'
GenericProperty associated to key 'MITK.IO.reader.DICOM.ReaderImplementationLevel'
GenericProperty associated to key 'dicomseriesreader.PixelSpacingInterpretation'
GenericProperty associated to key 'dicomseriesreader.ReaderImplementationLevel' still need to be changed

Dec 14 2020, 2:39 PM · Request for Discussion, MITK
thomass updated the task description for T28113: [Segmentation] LiveWire tool confirms segmentation upon tool or label change.
Dec 14 2020, 2:28 PM · MITK (v2021.10)
thomass triaged T28113: [Segmentation] LiveWire tool confirms segmentation upon tool or label change as Low priority.
Dec 14 2020, 2:26 PM · MITK (v2021.10)
thomass added a comment to T25152: Cannot compare TemporoSpatialStringProperty.

Since solution 1 worked well for me and seems to be more generic, I would vote for 1.

Dec 14 2020, 12:46 PM · MITK

Dec 10 2020

thomass added a comment to T27689: RTDose image can not be serialized and workbench crashes upon loading.

I tried it with my current develop (not the latest due to ongoing QT issues - wip) and it resolves the last warning (predescibed dose) but not the others. According to the D449 this is the one you changed, so as expected I suppose :) As soon as I get the latest develop up and running I will check the diff further.

Dec 10 2020, 7:23 PM · Request for Discussion, MITK

Dec 8 2020

thomass added a comment to T27689: RTDose image can not be serialized and workbench crashes upon loading.

Might be related to T25305

Dec 8 2020, 6:38 PM · Request for Discussion, MITK

Nov 25 2020

thomass closed T27696: Dicom loading does not work for some 4D data with the latest installer as Resolved.
Nov 25 2020, 8:25 AM · DICOM, Missing Info, MITK

Nov 24 2020

thomass added a project to T28008: [Mapper] Levelwindow overwrites vtkLookUpTable Range with levelwindow range : Request for Discussion.

apparently a vtkLoopUpTable is set automatically so the property as such cannot be used to handle custom vtkLookUpTables

Nov 24 2020, 4:07 PM · Request for Discussion, MITK
thomass triaged T28008: [Mapper] Levelwindow overwrites vtkLookUpTable Range with levelwindow range as Normal priority.
Nov 24 2020, 2:25 PM · Request for Discussion, MITK

Oct 22 2020

thomass added a comment to T27904: Feature request: Colorbars to interpret data in MITK.

In T26382 the recent developments are summarized.

Oct 22 2020, 3:04 PM · MITK
thomass triaged T27904: Feature request: Colorbars to interpret data in MITK as Normal priority.
Oct 22 2020, 12:59 PM · MITK

Oct 6 2020

thomass added a comment to T27507: Check the current behavior of the segmentation tools according static and dynamic 4D segmentation.

@thomass Thanks.
Now I might be nasty. Have you also checked everything wenn loading to 4D images with different time geometry? E.G. So that the selected time step in the navigator must not correspond to the same time step of the image you segment on?

With two 4D images 3D+t-Heart and US4Dcyl it crashes indeed when

  • using the Add tool on the static 3D+t Heart on timestep 0
  • changing the timestep and then use the Add tool again

I couldn't reproduce the crash when combining 4D_TEE_Data_MV and US4Dcyl (yet)

Could you please check (if not done already), if this scenario also crashes if you do it with a static segmentation?
This info is important for the decission, if we have to fix it directly or just partialy deactivate the dynamic option for this cycle. (Curently static segs on 4D images are more relevant then dynamic segs).

Oct 6 2020, 12:34 PM · MITK (v2021.10), Missing Info, Restricted Project
thomass closed T27825: Example MITK-Video on Measurements View as Resolved.
Oct 6 2020, 12:07 PM · Restricted Project
thomass triaged T27825: Example MITK-Video on Measurements View as Normal priority.
Oct 6 2020, 12:07 PM · Restricted Project
thomass added a comment to T27507: Check the current behavior of the segmentation tools according static and dynamic 4D segmentation.

@thomass Thanks.
Now I might be nasty. Have you also checked everything wenn loading to 4D images with different time geometry? E.G. So that the selected time step in the navigator must not correspond to the same time step of the image you segment on?

Oct 6 2020, 8:30 AM · MITK (v2021.10), Missing Info, Restricted Project