SlicerQR Development

[spycolyf (Doug Porter)]

Yes, I installed TortoiseGit and it is really nice. I’ll tell my team about it for managing GIT for QREADS. Thanks for sharing that @lassoan

[spycolyf (Doug Porter)]

@lassoan @pieper @jcfr,

Is it possible to position the image scroll slider at the bottom of the images rather than the top?

[spycolyf (Doug Porter)]

I’m proud of myself. Thanks to @lassoan helping me today, with TortoiseGit, I was able create a branch, make minor changes, commit, push, and then create a pull request. Lots more to learn, but it’s a start.

[spycolyf (Doug Porter)]

@pieper @lassoan @jcfr

Can the mouse button event assignment be done in Python? For example, with the Python script, can I assign zoom to the mouse wheel down and drag, and pan to the left button, and W/L to simultaneous left and right buttons?

Maybe the SetEventTranslationClickAndDrag function?

[spycolyf (Doug Porter)]

@jcfr,

I built the latest code and the title information still does not work. I tried the following and nothing printed in Python interactor. Does this mean that the code never gets executed?. Here’s where I placed the print statements in the code…

def _update():
  slicer.app.processEvents()
  slicer.app.layoutManager().resetThreeDViews()
  QReadsLogic.setZoom(self._parameterNode.GetParameter("Zoom"))
  # Dictionary of name and values
  values = {QReadsLogic.DICOM_TAGS[tag]: value for tag, value in QReadsLogic.dicomTagValues(node).items()}

  print("*" * 40)
  print(values)
  print("*" * 40)

  # Update window title
  slicer.util.mainWindow().windowTitle = "CMRN: {PatientID}    Patient Name: {PatientName}     Study: {StudyDescription}     Series: {SeriesDescription}".format(**values)

[jcfr (Jean Christophe Fillion Robin (Kitware))]

To help others understand the context:

KitwareMedical/SlicerQReads/blob/7fcd4749c80ead46cbbe60829126c7a1814ae6b1/Modules/Scripted/QReads/QReads.py#L210-L232

This code is called after a node is created, failing to see the information reported in the log file or python interactor probably means there are other errors happen beforehand during the loading of the data.

[spycolyf (Doug Porter)]

@jamesobutler @lassoan @pieper @jcfr

How do I show and un-show the ruler at the bottom of the image?

I can’t find it in the Script Repository.

Thanks

[mau_igna_06 (Mauro I. Dominguez)]

This is how I do it:

#For the 3D view
ThreeDViewNode = slicer.mrmlScene.GetSingletonNode("1", "vtkMRMLViewNode")
ThreeDViewNode.SetRulerType(1)# Change 1 by 0, 2 to get no ruler or thick
ThreeDViewNode.SetRulerColor(0)# Change 0 to 1, 2 to get other colors

#For red slice
redSliceNode = slicer.mrmlScene.GetSingletonNode("Red", "vtkMRMLSliceNode")
redSliceNode.SetRulerType(1)
redSliceNode.SetRulerColor(2)

[spycolyf (Doug Porter)]

Thanks @mau_igna_06,

Do you also implement an interactive measuring tool? One where the user can draw a line on the image and a measurement is given?

[mau_igna_06 (Mauro I. Dominguez)]

I think you can implement it yourself using a vtkMRMLMarkupsLineNode, some event listeners and GUI buttons. But the experts may guide you further

[spycolyf (Doug Porter)]

@mau_igna_06

vtkMRMLMarkupsLineNode

Some info is here I believe. In case you want to know.

Help with orientation marker and ruler

Hello again, I spoke to the people who will be the end users of my Slicer module and they really do want something more precise than the built-in ruler tool I referred to in the first post in this thread. If you have any links to share that could help me figure out the syntax for adding a ruler tool to my module (using qSlicerSimpleMarkupsWidget?) that would be greatly appreciated.

[spycolyf (Doug Porter)]

@pieper @lassoan @jcfr @jamesobutler

My module works perfectly except if I push the “Set Thickness” button first. Then hardly anything works. If I push other buttons first, everything works perfectly. We beta test next Monday, so HELP!!!

This issue is listed in tracker here: https://github.com/KitwareMedical/SlicerQReads/issues/103

Here’s the deal. After I push the “Set Threshold” button I get this error…

Traceback (most recent call last):
  File "/home/jcfr/Projects/SlicerQReads-Release/Slicer-build/lib/SlicerQReads-4.13/qt-scripted-modules/QReads.py", line 389, in updateGUIFromParameterNode
    QReadsLogic.slabThicknessInMmToNumberOfSlices(volumeNode, slabThicknessInMm))
  File "/home/jcfr/Projects/SlicerQReads-Release/Slicer-build/lib/SlicerQReads-4.13/qt-scripted-modules/QReads.py", line 612, in slabThicknessInMmToNumberOfSlices
    assert tichknessInMm > 0
AssertionError

Here’s the code segments at 389 and 612

 def updateGUIFromParameterNode(self, caller=None, event=None):
      QReadsLogic.setSlab(       (line 389)
          QReadsLogic.slabModeFromString(slabModeStr),
          QReadsLogic.slabThicknessInMmToNumberOfSlices(volumeNode, slabThicknessInMm))

@staticmethod
  def slabThicknessInMmToNumberOfSlices(volumeNode, tichknessInMm):
     if volumeNode is None:
      return 1
    assert tichknessInMm > 0  (line 612)
    return int(tichknessInMm / max(volumeNode.GetSpacing()))

… and no jokes anout

[lassoan (Andras Lasso)]

Can you upload an Windows installation package and send the link so that we can test it?

You can also check it yourself by attaching a Python debugger and check where the 0 slice thickness value comes from.

[jcfr (Jean Christophe Fillion Robin (Kitware))]

To ensure messages posted on the forum benefit the community, we suggest to provide minimally reproducible example.

In that particular case, it turns out I started to look at this and it is a simple logic issue.

[spycolyf (Doug Porter)]

@lassoan

Yes, I would have done that if I could get my debugger to work. I’ve successfully attached the Python Debugger fro VS Code, and tried to set break points, but get this error…

pydev debugger: warning: trying to add breakpoint to file that does not exist: c:\programdata\na-mic\slicer 4.13.0-2021-04-22\qreads.py (will have no effect)
Traceback (most recent call last):
  File "C:/SlicerQReads-0.1.0-2021-04-27-win-amd64/lib/SlicerQReads-4.13/qt-scripted-modules/QReads.py", line 55, in eventFilter
    slicer.util.mainWindow().writeSettings()
AttributeError: qSlicerAppMainWindow has no attribute named 'writeSettings'

Although my SlicerQREADS module folder was set to “C:/SlicerQReads-0.1.0-2021-04-27-win-amd64/lib/SlicerQReads-4.13/qt-scripted-modules/QReads.py”, why is it trying to set break points in “c:\programdata\na-mic\slicer 4.13.0-2021-04-22\qreads.py?”

Thanks

[jcfr (Jean Christophe Fillion Robin (Kitware))]

started to look at this and it is a simple logic issue.

This has been fixed in BUG: Fix toggling of SlabThickness mode by jcfr · Pull Request #105 · KitwareMedical/SlicerQReads · GitHub

qSlicerAppMainWindow has no attribute named 'writeSettings'

Consider rebuilding the application, the error reported indicate you didn’t rebuilt. Changes have been integrated.

See BUG: Ensure window geometry and position is restored · KitwareMedical/SlicerQReads@2150063 · GitHub

[spycolyf (Doug Porter)]

Sorry @jcfr,

I’ll try to speak more in the context of addressing the Slicer community rather than the experts. Got it.

And thanks so much for the fix, I was losing a little sleep over this one. You just added a couple more days to my life I think.

Thanks

[lassoan (Andras Lasso)]

@spycolyf

Although my SlicerQREADS module folder was set to “C:/SlicerQReads-0.1.0-2021-04-27-win-amd64/lib/SlicerQReads-4.13/qt-scripted-modules/QReads.py”, why is it trying to set break points in “c:\programdata\na-mic\slicer 4.13.0-2021-04-22\qreads.py?”

This is a recent regression in Visual Studio Code’s Python debugger. On Windows, you need to remove pathMappings section from the default debugger configuration - see instruction here.

[spycolyf (Doug Porter)]

@lassoan

Wow! That fixed it. Thanks