Slice view annotation controls

cpinter · July 17, 2024, 12:37pm

Hi all,

I just wanted to turn off slice view annotations in the latest Slicer and I found that it does not work. The main checkbox in the module does not have any effect:

Steps:

Load MRHead (see annotation in all slice views bottom left)
Go to DataProbe module
Uncheck checkbox shown above

Similarly, the code here also does not have any effect:
https://slicer.readthedocs.io/en/latest/developer_guide/script_repository.html#hide-slice-view-annotations

Has anything around the topic changed lately?

Update: Same behavior in 5.6.2. Looking at the SliceViewAnnotations code but it’s barely commented and a bit convoluted, so if someone knows it well any advice would be welcome. Thanks!

cpinter · July 17, 2024, 12:57pm

It seems to me that the update

github.com

Slicer/Slicer/blob/8c6219abd3f171f938fd5d003cd551db20842c7e/Modules/Scripted/DataProbe/DataProbeLib/SliceViewAnnotations.py#L327


      
                  return
          
              # Create corner annotations if have not created already
              if len(self.sliceViewNames) == 0:
                  self.createCornerAnnotations()
          
              for sliceViewName in self.sliceViewNames:
                  sliceWidget = self.layoutManager.sliceWidget(sliceViewName)
                  if sliceWidget:
                      sl = sliceWidget.sliceLogic()
                      self.updateCornerAnnotation(sl)
          
          def createGlobalVariables(self):
              self.sliceViewNames = []
              self.sliceWidgets = {}
              self.sliceViews = {}
              self.renderers = {}
          
          def createCornerAnnotations(self):
              self.createGlobalVariables()
              self.sliceViewNames = list(self.layoutManager.sliceViewNames())

is not called due to the early return

github.com

Slicer/Slicer/blob/8c6219abd3f171f938fd5d003cd551db20842c7e/Modules/Scripted/DataProbe/DataProbeLib/SliceViewAnnotations.py#L317


      
          
              self.cornerTextParametersCollapsibleButton.enabled = enabled
              self.activateCornersGroupBox.enabled = enabled
              self.fontPropertiesGroupBox.enabled = enabled
              self.annotationsAmountGroupBox.enabled = enabled
          
          def updateSliceViewFromGUI(self):
              if not self.sliceViewAnnotationsEnabled:
                  self.removeObservers(method=self.updateViewAnnotations)
                  self.removeObservers(method=self.updateGUIFromMRML)
                  return
          
              # Create corner annotations if have not created already
              if len(self.sliceViewNames) == 0:
                  self.createCornerAnnotations()
          
              for sliceViewName in self.sliceViewNames:
                  sliceWidget = self.layoutManager.sliceWidget(sliceViewName)
                  if sliceWidget:
                      sl = sliceWidget.sliceLogic()
                      self.updateCornerAnnotation(sl)

What I don’t understand

Why nobody noticed this in the past several months
Git log on this file shows basically no functional change for years

Although there is this commit that touches just what is broken:

I think for now I’ll use the workaround to call updateCornerAnnotation with each slice logic, but it would be good to get to the bottom of this.

lassoan · July 18, 2024, 4:29am

Disabling corner annotation has never worked for me. I always force update manually add you described.

The current implementation of this feature is so low quality (fragile, complicated, very limited functionality, poor visual appearance) that I would rewrite it from scratch. See details here:

github.com/Slicer/Slicer

Refactor Slice View Annotations infrastructure

opened 02:38AM - 22 Aug 23 UTC

jcfr

Type: Enhancement

## Is your feature request related to a problem? Please describe. Since its i…nception started in 2014, the support for rendering slice annotations has been very useful. It is ultimately done in the `SliceAnnotations`[^1] class instantiated based on the workflow described below. Once the `SliceAnnotations` is instantiated, it is then responsible to add observation on slice logics (see `addSliceViewObserver()`[^6]) by systematically checking if new slice viewer have been instantiated within the function `updateViewAnnotations()`[^7] it self called when any of the slice logic is modified. **Problem:** As outlined below by @lassoan, the current design is not extensible & flexible as it requires to hard-code module specific behavior into a single script. It for example, prevent extension from registering new annotation that should take precedence. [^6]: https://github.com/Slicer/Slicer/blob/8c92a12d6acecde092439981af70b1a27b6d2cf1/Modules/Scripted/DataProbe/DataProbeLib/SliceViewAnnotations.py#L346-L357 [^7]: https://github.com/Slicer/Slicer/blob/8c92a12d6acecde092439981af70b1a27b6d2cf1/Modules/Scripted/DataProbe/DataProbeLib/SliceViewAnnotations.py#L363-L380 ## Describe the solution you'd like * Re-implemented in C++ * Organize the content to display in `vtkMRMLTextNode` nodes with associated displayable manager * Allow customization of displayed fields * Support displaying * Slice position * Anatomical direction codes * Image display parameters (window, level, slice thickness, etc) * Patient/study/series metadata ## Describe alternatives you've considered NA ## Additional context ### Related posts & issues * https://discourse.slicer.org/t/how-to-show-orientation-marker-label-left-right-anterior-posterior/20231 * https://github.com/Slicer/Slicer/issues/4854 ### Excerpt copied from the prior comments and emails _Originally shared by @lassoan over email on August 19th, 2023_ > We want to display a lot of things around image sides and corners: > - Patient/study/series metadata (with much more flexibility than now) > - Anatomical direction codes (L, R, A, P, LA, LPI,... similarly to slice offset sliders) > - Image display parameters (window, level, slice thickness, etc) > - Slice position, maybe some data probe content > - Any text node content (that would allow a flexible way for modules to display custom content; which corner, color, etc. could be specified in display node) > > The current design is very limited, inflexible, non-extensible in any way. The implementation is also very fragile, low quality. > > The best would be to reimplement it in C++, using MRML nodes to store data, displayable manager to render, etc. > > Maybe all the corner text could be specified using HTML-like description using placeholders, for example: > > ```html > <PatientName/> <PatientAge/> <PatientSex format="short" /> > <StudyDate/> > <WindowWidthLevel/> > <TextNode id="vtkMRMLTextNode1" color="red" /> > ``` _Originally posted by @lassoan in https://github.com/Slicer/Slicer/issues/7176#issuecomment-1684865471_ > Slice view annotations is a mess. It was a quick prototype that got integrated to have this important feature in Slicer, but the design is really fragile and limited. We would need to rebuild it from scratch, using proper MRML-based design and flexibility and extensibility in mind, as overlay on image corners is very important space for displaying information. _Originally posted by @pieper in https://github.com/Slicer/Slicer/issues/7176#issuecomment-1685033306_ > Many viewers also use these as UI controls/widgets too (e.g. control reslice rotation or window/level tools by clicking on the corresponding corner annotation can be logical and ### Workflow: Instantiation of `DataProbeLib.SliceAnnotations` 1. `DataProbe` module constructor, `slicer.app.startupCompleted()` is connected to `DataProbe.DataProbe.addView()`[^2] 3. `DataProbe.DataProbe.addView()` instantiates[^3] `DataProbeInfoWidget.DataProbeInfoWidget`[^4] class 4. In `DataProbeInfoWidget` constructor, the function `DataProbeInfoWidget._createSmall()` which intern instantiates `DataProbeLib.SliceAnnotations()`[^5] [^1]: https://github.com/Slicer/Slicer/blob/main/Modules/Scripted/DataProbe/DataProbeLib/SliceViewAnnotations.py [^2]: https://github.com/Slicer/Slicer/blob/8c92a12d6acecde092439981af70b1a27b6d2cf1/Modules/Scripted/DataProbe/DataProbe.py#L40-L41 [^3]: https://github.com/Slicer/Slicer/blob/8c92a12d6acecde092439981af70b1a27b6d2cf1/Modules/Scripted/DataProbe/DataProbe.py#L59-L60 [^4]: https://github.com/Slicer/Slicer/blob/8c92a12d6acecde092439981af70b1a27b6d2cf1/Modules/Scripted/DataProbe/DataProbe.py#L68-L106 [^5]: https://github.com/Slicer/Slicer/blob/8c92a12d6acecde092439981af70b1a27b6d2cf1/Modules/Scripted/DataProbe/DataProbe.py#L401-L406

cpinter · July 19, 2024, 11:15am

Agreed, thanks. If this is not a recent regression then let’s leave any improvement or fix for the complete revamp.

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Slice view annotation controls

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