Hi Stefan, I just wanted to check if there are any updates on its implementation. No rush—just curious to know how it's progressing.
Best, Mujassim On Mon, 24 Mar 2025 at 13:52, Dinkelacker, Stefan < s.dinkelac...@dkfz-heidelberg.de> wrote: > > Hi Mujassim, > > yes, an approach in that direction is reasonable. I think I would write a > function that traverses from the hover point in both directions along the > contour for a certain distance D (should be easy since two points are > always connected by a straight line). Each contour vertex that is within D > I would pair with a weight like a vertex at the hover point would have > weight 1, a vertex in distance D/2 would have weight 0.5 and a vertex in > distance D would have weight 0. The returned list of pairs (probably made > up of vertex index and weight) I would use to decide on which points the > move operation has influence on and how much. The weight can also be > directly used to calculate a color for rendering like in my example picture. > > There's an edge case for tiny contours, though, when basically more or > less all points are within distance D. So probably I would also take the > contour's complete circumferrence into account to decide if D should be > decreased to never cover more than a certain percentage of a contour's > circumferrence, or simething similar. A strategy for this is greatly > dependent on the contour's you are expecting in the first place, like will > they have dense or sparse vertices, what is the typical ratio of distance > between vertices and the whole circumferrence etc... > > Best, > Stefan > > ________________________________________ > Von: Mujassim Jamal <mujassimjama...@gmail.com> > Gesendet: Freitag, 21. März 2025 12:21 > An: Dinkelacker, Stefan > Cc: mitk-users@lists.sourceforge.net > Betreff: Re: [Extern] - [mitk-users] Contour Editing in MITK > > Hi Stefan, > > While implementing the custom mapper for neighbor highlighting, I realized > that I first need to identify the neighboring points before I can highlight > them. This means that creating and identifying neighbor points within the > contour itself is an essential prerequisite. > > It might be more effective to focus on neighbor detection first before > moving on to the rendering and appearance aspects. For reference, I have > attached a picture showing the contour I am working on, which consists of > six vertices. Here’s the basic approach I have in mind: > > 1. A position is hovered over on the contour (marked in red at vertex 1 > or between vertices 5 and 4). > 2. If a vertex is found at that position, proceed to the next step; > otherwise, first add a point at that location. > 3. The algorithm will then attempt to find neighboring points on both > sides of the hovered position within a specified radius (marked in green). > 4. If no neighboring points are found, 'X' number of points will be added > in both directions of the hovered position within the radius. > 5. Finally, the identified points to be highlighted will be passed to the > rendering process. > > Does this approach make sense to you? I’d appreciate your thoughts on it. > > Best, > Mujassim > > > On Mon, 17 Mar 2025 at 19:36, Dinkelacker, Stefan < > s.dinkelac...@dkfz-heidelberg.de<mailto:s.dinkelac...@dkfz-heidelberg.de>> > wrote: > Hi Mujassim, > > interactors typically just change state/properties of data. The > transformation into render primitives happens in mapper classes, which > (re-)generate the VTK (or OpenGL in legacy cases) primitives on any > data/property updates. Long story short: if you want to change anything > regarding the appearance of data, you would need to write (potentially > derive) your own mapper. Unfortunately mappers in the regime of > PlanarFigures or ContourModelSets are, let's say, part of a technical dept > that were never resolved, and while they are working, they shouldn't > probably be used as examples for new implementations. You still can do so, > of course, but in general new mappers should be derived from > mitk::VtkMapper. > > Best regards, > Stefan > ________________________________________ > Von: Mujassim Jamal <mujassimjama...@gmail.com<mailto: > mujassimjama...@gmail.com>> > Gesendet: Montag, 17. März 2025 13:10 > An: Dinkelacker, Stefan > Cc: mitk-users@lists.sourceforge.net<mailto: > mitk-users@lists.sourceforge.net> > Betreff: Re: [Extern] - [mitk-users] Contour Editing in MITK > > Hi Stefan, > > Yes, the Lasso tool better aligns with my needs. I tested > ContourModelInteractor, set up the MITK-ProjectTemplate, created a custom > interactor class inheriting from ContourModelInteractor, and implemented a > function to enable interaction on the saved contour node, following your > instructions. I also prefer this approach from scratch rather than the > vtkCutter approach you mentioned in your other post. > > Before implementing the OnMovePoint function, I plan to first develop a > neighbor highlighting feature for the contour. This feature will highlight > the neighboring areas of a point when hovered over with the mouse. Users > will also be able to adjust the highlighted area, allowing modifications to > only that portion of the contour rather than the entire area between two > points (which I believe is the default behavior). Currently, > ContourModelInteractor highlights the entire contour when hovered over. > > Could you share your thoughts on this approach? > > Best regards, > Mujassim > > On Fri, 21 Feb 2025 at 12:14, Dinkelacker, Stefan < > s.dinkelac...@dkfz-heidelberg.de<mailto:s.dinkelac...@dkfz-heidelberg.de > ><mailto:s.dinkelac...@dkfz-heidelberg.de<mailto: > s.dinkelac...@dkfz-heidelberg.de>>> wrote: > Hi Mujassim, > > let's assume you would start with the lasso tool [1] instead of the > livewire tool, which uses the same base class but seems to fit your needs > even better. The base class EditableContourTool [2] sets up the state > machine "EditableContourTool.xml" for the creation of the contour and > connects most of the functions. The derived LassoTool class then only > connects the MovePoint action in addition. But all of this interaction is > for the creation of the contour, not for editing. In > LassoTool::FinishTool() you will see, however, that another > DataInteractor/StateMachine is associated with the created contour data > node: ContourModelInteractor [3] with > ContourModelModificationInteractor.xml as state machine. In this class you > find the OnMovePoint() method which is called when moving a point of the > contour. That's where you want to hook in to add your functionality. You > can do this for example by subclassing ContourModelInteractor and > overriding the OnMovePoint() method. > > To understand/test the ContourModelInteractor in the MITK Workbench first, > activate the Segmentation plugin, create a segmentation, select the Lasso > tool from the 2D tools and remove the checkmark from "Auto-confirm > contour". This is crucial. Start a contour with a double click, add points > with single clicks and add the last point again with a double click. Now > the editable contour should still be on the screen and you can test the > ContourModelnteractor by moving an existing point of the contour for > example. > > To start with such a contour right from the beginning I recommend to save > the contour so you can simply open it later without having to use the > segmentation plugin. The contour node from the lasso tool is invisible by > default, though. To make it visible, open the preferences (Ctrl+P), click > on Data Manager on the very top and set the checkmark for "Show helper > objects". While the Lasso tool is active with an editable contour, you will > see a "working contour node" node in the Data Manager now. You can > right-click on it and "Save..." it to a .cnt file, that you can later open > again. > > When you implement your subclass you can activate the interaction by > calling either DataInteractor::SetDataNode() or > DataNode::SetDataInteractor() on a contour node. A good starting point for > that is probably your own plugin/view and to wire up a button to do so. > Start best with the MITK-ProjectTemplate [4] where you could modify the > Example View for your first prototype [5]. > > [1] https://docs.mitk.org/2024.12/classmitk_1_1LassoTool.html > [2] https://docs.mitk.org/2024.12/classmitk_1_1EditableContourTool.html > [3] https://docs.mitk.org/2024.12/classmitk_1_1ContourModelInteractor.html > [4] https://github.com/MITK/MITK-ProjectTemplate/blob/master/README.md > [5] > https://github.com/MITK/MITK-ProjectTemplate/blob/master/Plugins/org.mitk.gui.qt.exampleplugin/src/internal/QmitkExampleView.cpp > > Best, > Stefan > ________________________________________ > Von: Mujassim Jamal <mujassimjama...@gmail.com<mailto: > mujassimjama...@gmail.com><mailto:mujassimjama...@gmail.com<mailto: > mujassimjama...@gmail.com>>> > Gesendet: Dienstag, 18. Februar 2025 13:41 > An: Dinkelacker, Stefan > Cc: mitk-users@lists.sourceforge.net<mailto: > mitk-users@lists.sourceforge.net><mailto:mitk-users@lists.sourceforge.net > <mailto:mitk-users@lists.sourceforge.net>> > Betreff: Re: [Extern] - [mitk-users] Contour Editing in MITK > > Hi Stefan, > > I followed your instructions and explored the LiveWire tool, which helped > me understand how it leverages ContourModelLiveWireInteractor for various > interactions. I also reviewed its corresponding state machine and > configuration XML files, which were quite easy to follow. > > Next, I traced the inheritance hierarchy of ContourModelLiveWireInteractor > up to DataInteractor, where each class has a ConnectActionsAndFunctions > function responsible for linking state machine actions to interactor > functions (as you mentioned in an earlier response). The description of the > DataInteractor class also states that new interactor classes can be derived > from it. > > From this point, what would you recommend as my next step? Should I > proceed with creating a new interactor and its associated XML files, or is > there anything else I should refer to before diving into the implementation? > > Looking forward to your guidance. > > Best, > Mujassim > > On Tue, 11 Feb 2025 at 15:33, Dinkelacker, Stefan < > s.dinkelac...@dkfz-heidelberg.de<mailto:s.dinkelac...@dkfz-heidelberg.de > ><mailto:s.dinkelac...@dkfz-heidelberg.de<mailto: > s.dinkelac...@dkfz-heidelberg.de>><mailto:s.dinkelac...@dkfz-heidelberg.de > <mailto:s.dinkelac...@dkfz-heidelberg.de><mailto: > s.dinkelac...@dkfz-heidelberg.de<mailto:s.dinkelac...@dkfz-heidelberg.de>>>> > wrote: > Hi Mujassim, > > I think at this stage an example-based exploration is probably the most > efficient way of going forward. For the Live Wire tool, see [1] for example > and move up the inheritance until you find the code using an Interactor. An > Interactor is connected to a state machine and a separate config for that > statemachine. Both are written as .xml files. The Interactor code connects > actions and conditions of a statemachine to its methods. > > Best, > Stefan > > [1] https://docs.mitk.org/2024.12/classmitk_1_1LiveWireTool2D.html > ________________________________________ > Von: Mujassim Jamal <mujassimjama...@gmail.com<mailto: > mujassimjama...@gmail.com><mailto:mujassimjama...@gmail.com<mailto: > mujassimjama...@gmail.com>><mailto:mujassimjama...@gmail.com<mailto: > mujassimjama...@gmail.com><mailto:mujassimjama...@gmail.com<mailto: > mujassimjama...@gmail.com>>>> > Gesendet: Dienstag, 11. Februar 2025 04:46 > An: Dinkelacker, Stefan > Cc: mitk-users@lists.sourceforge.net<mailto: > mitk-users@lists.sourceforge.net><mailto:mitk-users@lists.sourceforge.net > <mailto:mitk-users@lists.sourceforge.net>><mailto: > mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net > ><mailto:mitk-users@lists.sourceforge.net<mailto: > mitk-users@lists.sourceforge.net>>> > Betreff: Re: [Extern] - [mitk-users] Contour Editing in MITK > > Hi, > > Yes, I previously built MITK v2023.12, but I encountered several compiler > errors related to ITK (conversion type errors) and POCO (OpenSSL version > mismatch). > > Thank you for suggesting these four tools. I have explored all of them and > found that the Draw Polygon and LiveWire tools closely match my use case, > though I will still need to make significant customizations. I plan to > refer to the code of these two tools to get an initial understanding of > point adding, dragging, picking, etc. > > I would appreciate it if you could share any resources on developing a > custom interactor in MITK. > > Best, > Mujassim > > On Wed, 5 Feb 2025 at 17:28, Dinkelacker, Stefan < > s.dinkelac...@dkfz-heidelberg.de<mailto:s.dinkelac...@dkfz-heidelberg.de > ><mailto:s.dinkelac...@dkfz-heidelberg.de<mailto: > s.dinkelac...@dkfz-heidelberg.de>><mailto:s.dinkelac...@dkfz-heidelberg.de > <mailto:s.dinkelac...@dkfz-heidelberg.de><mailto: > s.dinkelac...@dkfz-heidelberg.de<mailto:s.dinkelac...@dkfz-heidelberg.de > >>><mailto:s.dinkelac...@dkfz-heidelberg.de<mailto: > s.dinkelac...@dkfz-heidelberg.de><mailto:s.dinkelac...@dkfz-heidelberg.de > <mailto:s.dinkelac...@dkfz-heidelberg.de>><mailto: > s.dinkelac...@dkfz-heidelberg.de<mailto:s.dinkelac...@dkfz-heidelberg.de > ><mailto:s.dinkelac...@dkfz-heidelberg.de<mailto: > s.dinkelac...@dkfz-heidelberg.de>>>>> wrote: > Hi and welcome to MITK! > > The last version of MITK that supported Qt 5 was MITK v2023.12, as far as > I know. Starting with later versions, Qt 6.6+ is a strict requirement. > > To get started, I recommend running the MitkWorkbench application and > exploring the contour interaction functionalities available in two > different plugins: > > - Measurement [1]: The Draw Polygon and Draw Subdivision Polygon tools > demonstrate how contours can be interacted with. > > - Segmentation [2]: The Lasso and LiveWire tools are both based on contour > interaction. > > MITK provides at least two approaches for working with contours and > interacting with them. However, you will need to write some code—for > example, handling a Modified event to map contour changes back to a 3D > model (referred to as a Surface in MITK). Additionally, MITK's current > interactors only operate on individual contour vertices. > > If you aim to implement an approach similar to what you showed in your > video—where multiple neighboring vertices of a contour are modified > simultaneously—you will need to develop a custom interactor. While this is > certainly possible, it is not the simplest task for a first MITK project. > > Best, > Stefan > > [1] https://docs.mitk.org/2024.12/org_mitk_views_measurement.html > [2] > https://docs.mitk.org/2024.12/org_mitk_views_segmentation.html#org_mitk_views_segmentationlivewiretool > > ________________________________________ > Von: Mujassim Jamal <mujassimjama...@gmail.com<mailto: > mujassimjama...@gmail.com><mailto:mujassimjama...@gmail.com<mailto: > mujassimjama...@gmail.com>><mailto:mujassimjama...@gmail.com<mailto: > mujassimjama...@gmail.com><mailto:mujassimjama...@gmail.com<mailto: > mujassimjama...@gmail.com>>><mailto:mujassimjama...@gmail.com<mailto: > mujassimjama...@gmail.com><mailto:mujassimjama...@gmail.com<mailto: > mujassimjama...@gmail.com>><mailto:mujassimjama...@gmail.com<mailto: > mujassimjama...@gmail.com><mailto:mujassimjama...@gmail.com<mailto: > mujassimjama...@gmail.com>>>>> > Gesendet: Mittwoch, 5. Februar 2025 11:27 > An: mitk-users@lists.sourceforge.net<mailto: > mitk-users@lists.sourceforge.net><mailto:mitk-users@lists.sourceforge.net > <mailto:mitk-users@lists.sourceforge.net>><mailto: > mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net > ><mailto:mitk-users@lists.sourceforge.net<mailto: > mitk-users@lists.sourceforge.net>>><mailto: > mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net > ><mailto:mitk-users@lists.sourceforge.net<mailto: > mitk-users@lists.sourceforge.net>><mailto:mitk-users@lists.sourceforge.net > <mailto:mitk-users@lists.sourceforge.net><mailto: > mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net > >>>> > Betreff: [Extern] - [mitk-users] Contour Editing in MITK > > Hi, > > First of all, I am new to using MITK. I am working with Qt 5.15.2, but I > couldn't find an MITK version compatible with this Qt version. Therefore, I > built the latest version of MITK (v2024.12). > > My question is: Can I use the MITK toolkit to create a contour editing > feature such that, after projecting a 3D model as a contour onto the 2D > segmentation, I can pick and drag the points on the contour in 2D and see > the effect directly on the 3D model? I found that MITK provides various > contour-related classes, but I am unsure whether they can be used for my > specific use case. > > I am attaching a Google Drive link that contains a video showcasing what I > want to achieve using MITK. > Video: > https://drive.google.com/file/d/1Wu3UJmQQeewlR0Thvx7TPP0iYLEmfu1J/view?usp=sharing > > Thank you. >
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