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Maniphest T8910

META BUG Geometry Cleanup
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Description

  1. Create a new member matrix for rotation:

ITK images include a Matrix m_Direction, containing information about rotation. At the moment we do not have a similar member in our MITK Geometries. ATM we handle rotation by adjusting the index-to-world transform funciton directly, which is not always comprehensible (since it does contain spacing as well).
It is desirable to have a Matrix Membervariable for Rotation in MITK Geometry3D as well, with respective Set/Get Functions. When the matrix is changed, the world-to-index transform should be be recalculated.

  1. More Privacy for better comprehension

Editing the World-To-Index Transform directly should be avoided, instead you should set Spacing, Origin and DirectionMatrix. This is much more comprehensible!! The Geometry classes should take care of recalcuation of VTK and ITK Transform Matrixes itself!

  1. Remove unused and redundant members

There are unused and redundant methods and parameters (e.g. setSpacing, setFloatSpacing, Quaternion.. ) in the Geometry3D class. We should get rid of them to make the geometry class more comprehensible and smaller

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StatusAssignedTask
 ResolvedkislinskT11113 MITK doesn't visualize normalized and thus very small meshes in the expected way.
 DuplicateNoneT8910 META BUG Geometry Cleanup
 WontfixNoneT11948 ComputeBoundingGeometry3D grid wrong (world geometry calculation)
 WontfixNoneT10785 Spacing of a worldGeometry of several images is not the greatest common divisor of all spacings
 WontfixNoneT24071 Revisit 2-d image rendering
 WontfixNoneT17812 SlicedGeometry3D initialisation fix for non-image geometries
 ResolvedkislinskT20204 Provide public getter for reference geometry of sliced geometries
 ResolvedkislinskT20217 Equality checks when setting data storage for renderers
 ResolvedkislinskT20218 DataStorage::ComputeBoundingBox3D creates geometry with incorrect origin and bounding box
 WontfixkislinskT24080 Write visual debugging utilitiy for inspecting geometries
 WontfixkislinskT16288 Geometry3D::SetIndexToWorld(..) should apply some checks on the matrix
 WontfixkislinskT5282 Inconsistent methods parameter in Geometry3D
 InvalidNoneT16242 Crosshair visualization does not correspond to index coordinates in status bar
 ResolvedNoneT9109 Equalsfunction for geometries
 ResolvedNoneT6505 If setting a cloned geometry for an image via SetClonedGeometry(Geometry) the cloned Geometry can be slightly different from the original one
 ResolvedNoneT17209 4D datatypes are not rendered properly
 ResolvedNoneT9075 Inconsistent transformation of Vector3D and Point3D from Index- to World-Coordinates in Geometry3D
 ResolvedNoneT10937 Support TimeSlicedGeometry to handle non evenly timed timesteps
 WontfixkislinskT16473 0.5 offset in Fast Marching Segmentation Tool
 ResolvedNoneT16243 Create an IndexToWorld function with discrete Index (mitk::index3D) as parameter

Event Timeline

graser added projects: MITK, Bugzilla.Jul 27 2011, 6:04 PM
graser added a subscriber: graser.Sep 29 2011, 10:07 AM

There is a need for a IndexToWorld transform, that accepts mitk::index3d as input

• fetzer added subscribers: ivo, • fetzer.Oct 19 2011, 5:36 PM

Bastian and I started cleaning up the geometries. We created a wikipage in order to write down some definitions we had to make during the refactoring process and to have some kind of record about what we have done so far:

http://mbits/mbiwiki/mitk%3A%3AGeometry%20Refactoring#preview

@ivo, Marco, Daniel: It would be create if you could take a look at the wikipage from time to time and to check whether our definitions are consistent with the original intention of the geometries.

maleike added a subscriber: maleike.Oct 19 2011, 5:38 PM

(In reply to comment #2)

http://mbits/mbiwiki/mitk%3A%3AGeometry%20Refactoring#preview

@ivo, Marco, Daniel: It would be create if you could take a look at the
wikipage from time to time and to check whether our definitions are consistent
with the original intention of the geometries.

Could you please put this on mitk.org/wiki/internal or similar? mbits is DKFZ internal, which I am not anymore without VPN.

espak added a subscriber: espak.Feb 8 2012, 8:54 PM

Has the wiki page been moved to mitk.org?

• wildes added a subscriber: • wildes.Dec 3 2014, 4:35 PM

I'll close this bug as dublicate of 18034 and 17035, as a lot of these requests are already solved due to the new Geometry concepts. T18520 describes new tasks for cleaning up geometries.

kislinsk closed this task as a duplicate of T18034: BaseGeometry: investigate if redundant transformation data is really necessary.Aug 1 2016, 10:47 PM
kislinsk closed subtask T5282: Inconsistent methods parameter in Geometry3D as Wontfix.Jun 20 2018, 6:27 AM
kislinsk closed subtask T16473: 0.5 offset in Fast Marching Segmentation Tool as Wontfix.
kislinsk closed subtask T16288: Geometry3D::SetIndexToWorld(..) should apply some checks on the matrix as Wontfix.
kislinsk reopened this task as Open.Jun 27 2018, 12:44 PM
kislinsk closed this task as a duplicate of T18034: BaseGeometry: investigate if redundant transformation data is really necessary.
kislinsk changed the status of subtask T16242: Crosshair visualization does not correspond to index coordinates in status bar from Invalid to Spite.Jun 27 2018, 1:33 PM
kislinsk changed the status of subtask T16242: Crosshair visualization does not correspond to index coordinates in status bar from Spite to Invalid.Jun 27 2018, 1:37 PM
kislinsk mentioned this in T27033: Clean up stale remote branches.Jan 25 2020, 9:01 PM
kislinsk closed subtask T11948: ComputeBoundingGeometry3D grid wrong (world geometry calculation) as Wontfix.May 26 2020, 11:17 AM
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