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norajitr (Tobias Norajitra)
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Projects (9)

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User Since
Aug 1 2016, 12:10 PM (205 w, 5 d)

Recent Activity

Tue, Jun 30

norajitr added a comment to T27085: 2D region growing tool fails for low intensity regions.

@floca @nolden At this point I would say the task is still a blocker from a clinical point of view. The tool is somewhat usable, but still not always working as expected thus making it inconvenient and non-intuitive. Sometimes for example, the region growing cannot be further expanded in contrast to the similarity of nearby image intensities, sometimes it takes several trials at different seed points. Altogether, this makes the tool work differently than one would expect. Also sometimes, the tool displays some kind of 'lag' when waiting for region updates (i.e. mouse position updates that had just worked suddenly have no more effect).

Tue, Jun 30, 4:16 PM · Cleared, MITK (2020)

Wed, Jun 17

norajitr added a project to T27483: DICOM import of multi-channel data not working: Request for Discussion.
Wed, Jun 17, 8:00 PM · MITK (2020), Restricted Project, DICOM
norajitr added a comment to T27483: DICOM import of multi-channel data not working.

A current blocker for use of NAKO data, therefore set as high priority.

Wed, Jun 17, 7:50 PM · MITK (2020), Restricted Project, DICOM
norajitr added a comment to T27483: DICOM import of multi-channel data not working.

Issue as shown in the attachment

Wed, Jun 17, 7:49 PM · MITK (2020), Restricted Project, DICOM
norajitr triaged T27483: DICOM import of multi-channel data not working as High priority.
Wed, Jun 17, 7:46 PM · MITK (2020), Restricted Project, DICOM

May 7 2020

norajitr added a comment to T27085: 2D region growing tool fails for low intensity regions.

Done (pm)

May 7 2020, 2:41 PM · Cleared, MITK (2020)
norajitr added a comment to T27085: 2D region growing tool fails for low intensity regions.

do you know when this stopped working?

The error was first noticed recently while working with clinical partners on MRI lung data from the NAKO. I checked the old installer from 2015, where it also did not work.

or someone else: is there an example image in MITK Data to show this behavior?

I could not find a suitable lung example in MITK Data. I checked on two old lung MRI datasets in the department, where the problem did not occur.

May 7 2020, 1:33 PM · Cleared, MITK (2020)

Feb 10 2020

norajitr triaged T27086: Long file names force segmentation plugin to expand in order to be usable. as High priority.
Feb 10 2020, 6:12 PM · MITK (2020)
norajitr triaged T27085: 2D region growing tool fails for low intensity regions as High priority.
Feb 10 2020, 4:53 PM · Cleared, MITK (2020)

Dec 8 2017

norajitr committed rMITK0d5d2c4b9525: Merge branch 'T23923-NonDiffusionDicomImportRedundancy' (authored by norajitr).
Merge branch 'T23923-NonDiffusionDicomImportRedundancy'
Dec 8 2017, 3:26 PM
norajitr committed rMITK8972edd03431: Keep track of the read files in the mitkBaseDICOMReaderService. (authored by norajitr).
Keep track of the read files in the mitkBaseDICOMReaderService.
Dec 8 2017, 11:55 AM

Oct 27 2017

norajitr committed rMITK6a8a8e4c789a: Merge branch 'T23165-simple-volume-import-testing' (authored by norajitr).
Merge branch 'T23165-simple-volume-import-testing'
Oct 27 2017, 11:42 AM
norajitr committed rMITK5f286931c67e: Compiler issue stuff (authored by norajitr).
Compiler issue stuff
Oct 27 2017, 11:42 AM
norajitr committed rMITK9bcda1498a76: Merge branch 'T23165-simple-volume-import-testing' (authored by norajitr).
Merge branch 'T23165-simple-volume-import-testing'
Oct 27 2017, 11:31 AM
norajitr committed rMITKe385101e827b: Compiler issue stuff (authored by norajitr).
Compiler issue stuff
Oct 27 2017, 11:30 AM
norajitr committed rMITK289099b645d9: Merge branch 'T23165-simple-volume-import-testing' (authored by norajitr).
Merge branch 'T23165-simple-volume-import-testing'
Oct 27 2017, 11:00 AM
norajitr committed rMITK0cfa2bdd2af4: Only involve test helper if any input is provided. (authored by norajitr).
Only involve test helper if any input is provided.
Oct 27 2017, 10:58 AM
norajitr committed rMITK217808a4a38d: Cleanup (authored by norajitr).
Cleanup
Oct 27 2017, 10:57 AM

Oct 16 2017

norajitr added a comment to T23165: DICOM reader provides image fragments where a coherent image volume is desired..

Test data is up now

Oct 16 2017, 4:41 PM · Restricted Project, MITK
norajitr committed rMD2bf1039410a0: DICOM dataset with sloppy tag entries for reader tests. (authored by norajitr).
DICOM dataset with sloppy tag entries for reader tests.
Oct 16 2017, 4:39 PM

Oct 13 2017

norajitr added a comment to T23165: DICOM reader provides image fragments where a coherent image volume is desired..

Added a new test for the simple volume import. The test is run on a small DICOM dataset with sloppy entries for the affected DICOM tags. Also, functionality of the mitk::DICOMFileReaderTestHelper has been extended to check for single block output.

Oct 13 2017, 4:00 PM · Restricted Project, MITK
norajitr committed rMITK449603e409a9: Simple volume import test added; DICOMFileReaderTestHelper extended for the… (authored by norajitr).
Simple volume import test added; DICOMFileReaderTestHelper extended for the…
Oct 13 2017, 3:51 PM
norajitr added a comment to T23165: DICOM reader provides image fragments where a coherent image volume is desired..

Pushed new branch T23165-simple-volume-import-testing.

Oct 13 2017, 3:51 PM · Restricted Project, MITK
norajitr committed rMITK269a0c8b8b9e: Label adapted for simple DICOM import configuration. (authored by norajitr).
Label adapted for simple DICOM import configuration.
Oct 13 2017, 1:51 PM

Sep 29 2017

norajitr added a comment to T23165: DICOM reader provides image fragments where a coherent image volume is desired..

Two built-in features of the DICOMITKSeriesGDCMReader cause the false import of this dataset: the number of frames splitting criterion, and the equidistant block sorting step. The problem has been solved by adding a less-strict DICOM import option (MITK Simple Volume Importer), that disables the features in the class. The case is then handled with the new simpleinstancenumber_soft configuration. On reader selection, the resource is fetched from the DICOM Reader Module through the micro services.

Sep 29 2017, 10:45 AM · Restricted Project, MITK
norajitr committed rMITKf1681f66edc8: Added a modified configuration of simpleinstancenumber_soft that solves the… (authored by norajitr).
Added a modified configuration of simpleinstancenumber_soft that solves the…
Sep 29 2017, 10:38 AM
norajitr committed rMITK4998bda70282: temp (authored by norajitr).
temp
Sep 29 2017, 10:38 AM
norajitr added a comment to T23165: DICOM reader provides image fragments where a coherent image volume is desired..

Pushed new branch T23165-image-fragments-from-DICOM-import.

Sep 29 2017, 10:38 AM · Restricted Project, MITK

Aug 4 2017

norajitr committed rMITK230ac6332937: Merge branch 'T22901-IntensityProfileStatisticsCalculation' (authored by norajitr).
Merge branch 'T22901-IntensityProfileStatisticsCalculation'
Aug 4 2017, 4:48 PM
norajitr committed rMITK6bf344854850: Directly work on the mask indices. (authored by norajitr).
Directly work on the mask indices.
Aug 4 2017, 4:47 PM
norajitr committed rMITK627208c548c7: Merge branch 'T22901-IntensityProfileStatisticsCalculation' (authored by norajitr).
Merge branch 'T22901-IntensityProfileStatisticsCalculation'
Aug 4 2017, 3:18 PM
norajitr committed rMITKac278ffb3176: Unused type removal. (authored by norajitr).
Unused type removal.
Aug 4 2017, 3:16 PM
norajitr closed T22839: Label Noise in the Clipping Plane Plugin. as Resolved.
Aug 4 2017, 2:19 PM · MITK
norajitr committed rMITKdb6eba51b440: Merge branch 'T22901-IntensityProfileStatisticsCalculation' (authored by norajitr).
Merge branch 'T22901-IntensityProfileStatisticsCalculation'
Aug 4 2017, 2:05 PM
norajitr added a comment to T22901: Image Statistics calculator intensity profile statistics not computed.

Until further restructuring, image statistics can now be calculated for line profiles, and for non-closed planar figures in general. To this end, the mask generator was extended by poly-line rasterisation.

Aug 4 2017, 1:59 PM · Restricted Project, MITK
norajitr committed rMITK6f216473100e: Mask calculator functionality extended for non-closed planar figures. (authored by norajitr).
Mask calculator functionality extended for non-closed planar figures.
Aug 4 2017, 1:46 PM
norajitr added a comment to T22901: Image Statistics calculator intensity profile statistics not computed.

Pushed new branch T22901-IntensityProfileStatisticsCalculation.

Aug 4 2017, 1:46 PM · Restricted Project, MITK
norajitr added a comment to T23165: DICOM reader provides image fragments where a coherent image volume is desired..

Result from DICOM import.

Aug 4 2017, 11:14 AM · Restricted Project, MITK
norajitr added a comment to T23165: DICOM reader provides image fragments where a coherent image volume is desired..

A dicom example can be found in the internal projects drive: /E132-Projekte/Old/DICOM-MIX-DTH/norajitra/GeometryIssues/i40/anoi40.

Aug 4 2017, 10:58 AM · Restricted Project, MITK
norajitr added a project to T22901: Image Statistics calculator intensity profile statistics not computed: Restricted Project.
Aug 4 2017, 10:50 AM · Restricted Project, MITK
norajitr added a project to T23165: DICOM reader provides image fragments where a coherent image volume is desired.: Restricted Project.
Aug 4 2017, 10:49 AM · Restricted Project, MITK
norajitr created T23165: DICOM reader provides image fragments where a coherent image volume is desired..
Aug 4 2017, 10:42 AM · Restricted Project, MITK

Jul 21 2017

norajitr claimed T22901: Image Statistics calculator intensity profile statistics not computed.
Jul 21 2017, 3:19 PM · Restricted Project, MITK
norajitr closed T22900: Don't compute image statistics if segmentation is empty as Resolved.
Jul 21 2017, 2:06 PM · MITK

Jun 26 2017

hentsch awarded T22900: Don't compute image statistics if segmentation is empty a Grey Medal token.
Jun 26 2017, 10:42 AM · MITK

Jun 23 2017

norajitr committed rMITKfc2ed06c6bec: Merge branch 'T22900-NoStatisticsCalculationForEmptySegmentation' (authored by norajitr).
Merge branch 'T22900-NoStatisticsCalculationForEmptySegmentation'
Jun 23 2017, 3:56 PM
norajitr committed rMITK0b321356c1cb: Make sure the segmentation pointer is not empty. (authored by norajitr).
Make sure the segmentation pointer is not empty.
Jun 23 2017, 3:55 PM
norajitr committed rMITKec2c4fcf1a6c: Add empty segmentation check and handle empty segmentation. (authored by norajitr).
Add empty segmentation check and handle empty segmentation.
Jun 23 2017, 3:55 PM
norajitr added a comment to T22900: Don't compute image statistics if segmentation is empty.

Pushed new branch T22900-NoStatisticsCalculationForEmptySegmentation.

Jun 23 2017, 3:54 PM · MITK
norajitr added a comment to T22900: Don't compute image statistics if segmentation is empty.

Added a fix where the segmentation mask is checked for non-zero entries prior to calculation. If the segmentation is empty, an error message will be displayed without starting the calculation.

Jun 23 2017, 2:56 PM · MITK
norajitr updated subscribers of T22900: Don't compute image statistics if segmentation is empty.
Jun 23 2017, 2:54 PM · MITK
norajitr claimed T22900: Don't compute image statistics if segmentation is empty.
Jun 23 2017, 2:53 PM · MITK

May 15 2017

norajitr added a comment to T22254: Render windows show *not* the corresponding orientation after reinit with permuted axes.

Thanks for the hint. It turned out in the end that the default cubic interpolation simply messed with labels on the rotated view planes...

May 15 2017, 2:38 PM · Pull Request, MITK (2016-11)

May 12 2017

norajitr added a comment to T22839: Label Noise in the Clipping Plane Plugin..

This issue is resolved by setting the nearest neighbor interpolation in the clipped labeling image by default.

May 12 2017, 2:58 PM · MITK
norajitr added a comment to T22839: Label Noise in the Clipping Plane Plugin..

The bug occurs for image geomtries with axes non-parallel to the world coordinate system. The reason for this is that after a global-reinit, voxels and viewplanes are non-perpendicular, and with the previous cubic interpolation of the segmentation labels, the observed mis-labeling occurs.

May 12 2017, 2:58 PM · MITK
norajitr committed rMITK5370157901f2: Merge branch 'T22839-LabelNoiseInTheClippingPlanePlugin' (authored by norajitr).
Merge branch 'T22839-LabelNoiseInTheClippingPlanePlugin'
May 12 2017, 2:49 PM
norajitr committed rMITK79a6bc0e5d55: Set nearest neighbor interpolation as default in the clipped data node. (authored by norajitr).
Set nearest neighbor interpolation as default in the clipped data node.
May 12 2017, 2:32 PM
norajitr added a comment to T22839: Label Noise in the Clipping Plane Plugin..

Pushed new branch T22839-LabelNoiseInTheClippingPlanePlugin.

May 12 2017, 2:32 PM · MITK
norajitr added a project to T22839: Label Noise in the Clipping Plane Plugin.: MITK.
May 12 2017, 2:32 PM · MITK
norajitr triaged T22839: Label Noise in the Clipping Plane Plugin. as Normal priority.
May 12 2017, 2:30 PM · MITK
norajitr committed rMITK02830524bc39: Merge branch 'T22620-RegionGrowerInHighIntensityRegions' (authored by norajitr).
Merge branch 'T22620-RegionGrowerInHighIntensityRegions'
May 12 2017, 2:21 PM
norajitr committed rMITK23c5f5a09a22: typename added for linux compiler issues. (authored by norajitr).
typename added for linux compiler issues.
May 12 2017, 2:21 PM
norajitr added a comment to T22254: Render windows show *not* the corresponding orientation after reinit with permuted axes.

Thanks for the clarification, that explains the rotation of course. We are having problems with some other tools (e.g. with the clipping plane plugin) that came up just in these cases with (permuted) non-unity matrices. Apparently, that is then unrelated with these fixes.

May 12 2017, 12:46 PM · Pull Request, MITK (2016-11)
norajitr committed rMITK5989c1a91f73: Merge branch 'T22620-RegionGrowerInHighIntensityRegions' (authored by norajitr).
Merge branch 'T22620-RegionGrowerInHighIntensityRegions'
May 12 2017, 11:57 AM
norajitr added a comment to T22620: Region growing doesn't work within high intensity regions.

The first fix allows the region growing segmentation to start in high-intensity regions in the first place. Now, there is a remaining issue with the usability, that is, extreme scrolling is required to generate segmentations to span higher differences of image intensities.

May 12 2017, 11:47 AM · Auto-closed, MITK
norajitr reopened T22254: Render windows show *not* the corresponding orientation after reinit with permuted axes as "Open".

In some cases, the fix leads to unexpected results (see attached). That is, re-init / global re-inits cause image rotations.@Miklos, maybe you have an idea where to start fixing this issue?

May 12 2017, 11:35 AM · Pull Request, MITK (2016-11)
norajitr added a comment to T22839: Label Noise in the Clipping Plane Plugin..

The reason for the bug seems to be associated with image geometries issues that were also addressed in T22254. That is, after loading clipping planes, orig and segmentations, the problem disappears after a manual reinit.

May 12 2017, 10:13 AM · MITK
norajitr added a comment to T22839: Label Noise in the Clipping Plane Plugin..

See attachments.

May 12 2017, 9:35 AM · MITK
norajitr created T22839: Label Noise in the Clipping Plane Plugin..
May 12 2017, 9:32 AM · MITK

Apr 28 2017

norajitr committed rMITKc0eaee533048: Setting a smaller iso contour value for in-bounds contour creation. (authored by norajitr).
Setting a smaller iso contour value for in-bounds contour creation.
Apr 28 2017, 4:02 PM
norajitr added a comment to T19580: Region grower seed point sometimes jumps.

Pushed new branch T19580-RegionGrowerOutOfBoundsContourCreation.

Apr 28 2017, 4:02 PM · Auto-closed, MITK, Bugzilla
norajitr claimed T19580: Region grower seed point sometimes jumps.

The reason for the out-of-bounds contour creation lies in the iso contour value of 0.5. The latter causes the contour to be just outside of the image slice geometry for the upper indices, which is then also output in the warning message.

Apr 28 2017, 2:50 PM · Auto-closed, MITK, Bugzilla

Feb 17 2017

norajitr committed rMITKf71aac030d69: Merge branch 'T22494-region-growing-fix-mitk' (authored by norajitr).
Merge branch 'T22494-region-growing-fix-mitk'
Feb 17 2017, 3:53 PM
norajitr added a comment to T22494: Region growing becomes unusable after several usages.

Pushed new branch T22494-region-growing-fix-mitk.

Feb 17 2017, 3:53 PM · Pull Request, MITK

Aug 2 2016

norajitr added a comment to T19578: Crosshair freezes after de-activating segmentation tools.

Has been fixed in T19467.

Aug 2 2016, 10:23 AM · MITK (2016-03), Bugzilla
norajitr added a comment to T19519: Region growing tool does not close after confirm segmentation.

[0fe95e]: Merge branch 'bug-19519-closeAdaptiveRegionGrowingToolOnSegmentationCo

Merged commits:

2016-06-15 17:30:17 Tobias Norajitra [304641]
Deactivate the tool if the segmentation is confirmed.

Aug 2 2016, 10:22 AM · MITK (2016-03), Bugzilla
norajitr added a comment to T19519: Region growing tool does not close after confirm segmentation.

Deactivate the tool via tool manager on ConfirmSegmentation().

Aug 2 2016, 10:22 AM · MITK (2016-03), Bugzilla
norajitr added a comment to T19467: ToolManager reloads display configuration on tool deactivation.

[1bb183]: Merge branch 'bug-19467-ToolManagerDisplayConfiguration'

Merged commits:

2016-03-30 14:33:03 Tobias Norajitra [0b4262]
Style changes.

Aug 2 2016, 10:22 AM · Bugzilla, MITK
norajitr added a comment to T19467: ToolManager reloads display configuration on tool deactivation.

At the moment, there is one hard-coded configuration for all tools, i.e. the one that is set in the Tool::Activated method. This can be fixed by a configuration member which can be modified by the according tool subclasses.
To this end, we have set the "DisplayConfigMITK" configuration as a default setting in the Tool-class, and the "DisplayConfigMITKNoCrosshair" configuration for all 2D tools.

Aug 2 2016, 10:22 AM · Bugzilla, MITK
norajitr added projects to T19449: Render window not updated on non-auto-topmost data node selection.: MITK, Bugzilla.
Aug 2 2016, 10:22 AM · Bugzilla, MITK
norajitr added a comment to T19436: Auto top most image for Level Window Slider fails for identical images..

Reason for the bug is within mitk::LevelWindowManager::SetLevelWindowProperty, where node selection according to the handed-over levelWindowProperty is made using NodePredicateProperty. If all loaded images are identical, the node predicate property simply delivers the first node with regard to the otherwise identical level window properties of the identical nodes.

Aug 2 2016, 10:22 AM · Bugzilla, MITK
norajitr added a comment to T19436: Auto top most image for Level Window Slider fails for identical images..

The issue is resolved using an explicit pointer-based comparison of the level window property.

Aug 2 2016, 10:22 AM · Bugzilla, MITK
norajitr added projects to T19436: Auto top most image for Level Window Slider fails for identical images.: MITK, Bugzilla.
Aug 2 2016, 10:22 AM · Bugzilla, MITK
norajitr added a comment to T19359: Insufficient gray value range captured by lower threshold auto setting in 3D Region Growing Tool..

Lower threshold is set to one standard deviation below mean gray value for the upwards growth case, in order to fix the issue.

Aug 2 2016, 10:22 AM · Bugzilla, MITK
norajitr added projects to T19359: Insufficient gray value range captured by lower threshold auto setting in 3D Region Growing Tool.: MITK, Bugzilla.
Aug 2 2016, 10:22 AM · Bugzilla, MITK
norajitr added a comment to T19359: Insufficient gray value range captured by lower threshold auto setting in 3D Region Growing Tool..

More specifically, from the seedpoint neighborhood, the mean gray value is chosen as lower threshold for 3D region growing. Thus, gray value variance is not taken into account, leading to an excluding behaviour of the subsequent region growing.

Aug 2 2016, 10:22 AM · Bugzilla, MITK
norajitr added a comment to T19359: Insufficient gray value range captured by lower threshold auto setting in 3D Region Growing Tool..

[fa6ed3]: Merge branch 'bug-19359-lowerThresholdAutoChoiceAdaptation'

Merged commits:

2015-10-07 16:07:23 Tobias Norajitra [16771b]
Adjust lower threshold by neighborhood gray value standard deviation. In addition, replace hard coded out-of-bounds value by according numeric trait bounds.

Aug 2 2016, 10:22 AM · Bugzilla, MITK
norajitr added a comment to T19319: 3d region growing, weird interaction with level window.

The stated observations are in accordance with the desired behaviour: the segmentation preview is generated via shifting the level window according to the region growing bar in the tool controls.

Aug 2 2016, 10:21 AM · Bugzilla, MITK
norajitr added a comment to T19277: Unclear documentation for GetScalarValueMin/Max in image statistics holder..

[8228c7]: Merge branch 'bug-19277-GetScalarValueMinMax-Recomputation-Documentati

Merged commits:

2015-09-02 16:36:07 Tobias Norajitra [94d88f]
Misspelling corrected.

Aug 2 2016, 10:21 AM · Bugzilla, MITK
norajitr added a comment to T19277: Unclear documentation for GetScalarValueMin/Max in image statistics holder..

Proper documentation suggested.

Aug 2 2016, 10:21 AM · Bugzilla, MITK
norajitr added projects to T19277: Unclear documentation for GetScalarValueMin/Max in image statistics holder.: MITK, Bugzilla.
Aug 2 2016, 10:21 AM · Bugzilla, MITK
norajitr added projects to T19276: Threshold segmentation result invisible for large scale float image.: MITK, Bugzilla.
Aug 2 2016, 10:21 AM · Bugzilla, MITK
norajitr added a comment to T19276: Threshold segmentation result invisible for large scale float image..

The according test image is attached in T19250.

Aug 2 2016, 10:21 AM · Bugzilla, MITK
norajitr added a comment to F1262: floatImage.nrrd.

Float image exhibiting faulty binary threshold segmentation.

Aug 2 2016, 10:21 AM
norajitr added projects to T19250: Binary threshold tool produces unexpected results on float images.: MITK, Bugzilla.
Aug 2 2016, 10:21 AM · MITK (2016-03), Bugzilla
norajitr added a comment to T19250: Binary threshold tool produces unexpected results on float images..

Float image exhibiting faulty binary threshold segmentation.

Aug 2 2016, 10:21 AM · MITK (2016-03), Bugzilla
norajitr added a comment to T19250: Binary threshold tool produces unexpected results on float images..

The segmentation result appears to be valid, but the preview is faulty in the given case. This seems to be strongly related to T14652, as a very small level window range is being set in the binary threshold tool on threshold changes.

Aug 2 2016, 10:21 AM · MITK (2016-03), Bugzilla
norajitr added a comment to T19250: Binary threshold tool produces unexpected results on float images..

For both bugs, small level window ranges are problematic. Dependency can be upheld until there is further clarity on 14652.

Aug 2 2016, 10:21 AM · MITK (2016-03), Bugzilla
norajitr added a comment to T19193: Pointset not displayed in list after loading.

[0cbc70]: Merge branch 'bug-19193-PointSetNotDisplayedAfterReading'

Merged commits:

2015-08-12 14:37:39 Tobias Norajitra [ab9e83]
Proper model reset for point list widget update.

Aug 2 2016, 10:21 AM · Bugzilla, MITK
norajitr added a comment to T19193: Pointset not displayed in list after loading.

Erroneous point list model reset calls in QmitkPointListModel::SetPointSetNode() led to the inproper update behaviour of the point list widget. Bug has been fixed by proper adjustment of point list model reset.

Aug 2 2016, 10:21 AM · Bugzilla, MITK