Slicer custom application deployment to many computers

spycolyf · August 6, 2021, 7:23pm

Yes, that would work. Can that static progress dialog be done in Python? I don’t have much time. At this point example code would be most helpful. Thanks.

spycolyf · August 6, 2021, 8:05pm

Has anyone ever seen this error. Don’t spend much time researching right now please. Just want to know if this rings a bell or have a rough guess. Thanks!

[ERROR][Python] 06.08.2021 14:04:58 [Python] (...\lib\SlicerQReads-4.13\qt-scripted-modules\DICOMLib\DICOMUtils.py:728) - DICOM plugin failed to load '3: MR AXIAL FLAIR' as a 'Image sequence'.
Traceback (most recent call last):
  File "...\lib\SlicerQReads-4.13\qt-scripted-modules\DICOMLib\DICOMUtils.py", line 722, in loadLoadables
    loadSuccess = plugin.load(loadable)
  File "... /bin/../lib/SlicerQReads-4.13/qt-scripted-modules/DICOMImageSequencePlugin.py", line 363, in load
    self.addSequenceBrowserNode(loadable.name, outputSequenceNodes, playbackRateFps, loadable)
  File "... /bin/../lib/SlicerQReads-4.13/qt-scripted-modules/DICOMImageSequencePlugin.py", line 230, in addSequenceBrowserNode
    outputSequenceBrowserNode = slicer.vtkMRMLSequenceBrowserNode()

mikebind · August 6, 2021, 9:15pm

I have occasionally had the DICOM loader erroneously identify a series as a “Sequence” instead of a volume, and then try to load it that way. It looks like that might be what have run into. Alternatively, it sounds like you have been mucking around in DICOMUtils.py, so perhaps some of the logic there is no longer valid and is leading to this error.

spycolyf · August 6, 2021, 9:49pm

Yes, this occurred only with MR series which I have not done much testing. PET, CT and NM works fine. Also, I undid the DicomUtils changes, so I don’t think it’s that.

Thanks

pieper · August 6, 2021, 9:59pm

If you aren’t planning to use Sequences you can also try turning off the Sequences plugin. Easiest would be to take it out of the CMakeLists.txt so it doesn’t get included in your installation. (Need to also remove it from the build tree if you are re-building in place). Be aware though that there can be many MR acquisitions that don’t map cleanly to volumes, so sometimes loading a sequence is correct. In this case it’s not clear what your MR data is so probably best to just catch any errors and say that the series type is not supported.

Here’s one option. Replace time.sleep with your call.

import time; d = qt.QMessageBox(qt.QMessageBox.Icon(qt.QMessageBox.Information), "SlicerQReads", "Working...", qt.QMessageBox.NoButton); d.setStandardButtons(0); d.show(); slicer.app.processEvents(); time.sleep(2); d.hide()

spycolyf · August 7, 2021, 9:50pm

Thanks @pieper,

Do you think it could be programmed in such a way as to show the dialog during the image load time when no images are showing and there is a white background in the 3D view, and then hide when the images are displayed? I’m trying to place the d.show() and d.hide() in various sections of the code to have this effect. Haven’t found it yet tho.

Thanks

spycolyf · August 9, 2021, 6:49pm

@pieper: I’m assuming that’s a no.
It seems wherever I put the code, it comes up and immediately disappears. If you blink, you’d miss it.

Thanks

spycolyf · August 9, 2021, 6:59pm

@jcfr

Hello JC, could you tell me where to place the above code to display the dialog box so that it appears when SlicerQREADS’ main window displays and goes away when the images appear?

Thanks

pieper · August 9, 2021, 8:22pm

Hi Doug - that example uses the 2 second delay (the time.sleep(2) part) to emulate calling the load routine. So if you put the first part, up to slicer.app.processEvents() before your call to load the imags and the d.hide() after the load call returns then the “Working…” dialog should stay up for as long as it takes for the reading process to complete. Does that make sense to you?

jcfr · August 9, 2021, 8:44pm

Relevant changes have been implemented in the following pull request:
See https://github.com/KitwareMedical/SlicerQReads/pull/107

spycolyf · August 11, 2021, 4:16am

@jcfr, @lassoan, that was perfect. I did put it in a try / except block to avoid it hanging up because the DICOM import fails a lot. Otherwise, task manager is the only way to kill it.

Thank y’all so much.

lassoan · August 11, 2021, 4:19am

Slicer may need extra plugins for loading exotic information objects, but I don’t find that it fails a lot for commonly occurring data sets. What specific problems did you encounter?

spycolyf · August 11, 2021, 5:09am

Oh probably it’s because some of my DICOM headers are faulty. I have not specifically identified the cause yet. But it seems to be mainly my MR file headers that I need to fix. QREADS itself is very forgiving of DICOM header imperfections. But when it fails, the patient demographics don’t show up in the title bar and the W/L is not set to the header values. Anyway I’ll try to solve that soon.

Hey @lassoan, how do I disable or eliminate the main window minimize button. We need to disallow minimizing SlicerQREADS because it behaves as a modal dialog. Probably a QT command. Correct?

Thanks.

jcfr · August 11, 2021, 6:57am

I did put it in a try / except block to avoid it hanging up because the DICOM import fails a lot. Otherwise, task manager is the only way to kill it.

Following the coomment of @pieper , the corresponding PR has been updated with an additional commit introducing the context manager inProgressDialog, this allows to cleanly handle the case when exception are raised without preventing the exception from being caught. See https://github.com/KitwareMedical/SlicerQReads/pull/107

how do I disable or eliminate the main window minimize button.

This is implemented in the following PR.
See https://github.com/KitwareMedical/SlicerQReads/pull/108

spycolyf · August 23, 2021, 9:40pm

@lassoan @pieper @jcfr @jamesobutler

I think everything is looking good for the release. One thing that could get us a lot of service calls though:

Does anyone know how to programmatically detect whether the correct version of OpenGL is installed on the systems for SlicerQREADS to run. Currently, on systems with OpenGL version 1.0, the module displays a dialog indicating insufficient graphics capability, and then does not exit properly, leaving QREADS in a hung state waiting for SlicerQREADS to exit. Maybe there’s somewhere I can place a Try/Catch to avoid this abnormal exit. I believe SlicerQReadsApp-real.exe hangs around in task manager as well.

Thanks

pieper · August 23, 2021, 9:53pm

The code that checks that is below. It should be cleaning up nicely, but perhaps for your purposes you want to check the graphics resources earlier and exit right away.

github.com

Slicer/Slicer/blob/0094e9a35bd266cc8b0e677858dabce797c9928f/Base/QTApp/qSlicerApplicationHelper.txx#L96-L109

    
      
          // qSlicerApplicationHelper::checkRenderingCapabilities() seems only work reliably
          // on Windows, therefore we skip it on other platforms.
          // See details at https://issues.slicer.org/view.php?id=4252
          #if defined(_WIN32)
            if (enableMainWindow && !app.testAttribute(qSlicerCoreApplication::AA_EnableTesting))
              {
              // Warn the user if rendering requirements are not met and offer
              // exiting from the application.
              if (!qSlicerApplicationHelper::checkRenderingCapabilities())
                {
                return 1;
                }
              }
          #endif

github.com

Slicer/Slicer/blob/ae2e56b493138eaa9d9082951f49bb3d693a2a9d/Base/QTApp/qSlicerApplicationHelper.cxx#L240-L300

    
      
          bool qSlicerApplicationHelper::checkRenderingCapabilities()
          {
            vtkNew<vtkSystemInformation> systemInfo;
            systemInfo->RunRenderingCheck();
            if (systemInfo->GetRenderingCapabilities() & vtkSystemInformation::OPENGL)
              {
              return true;
              }
          
          
  qWarning("Graphics capability of this computer is not sufficient to run this application");
          
          
  QString message = tr("Graphics capability of this computer is not sufficient to "
              "run this application. The application most likely will not function properly.");
          
          
  QString details = tr(
              "See more information and help at:\n{1}/user_guide/get_help.html#slicer-application-does-not-start\n\n"
              "Graphics capabilities of this computer:\n\n")
              .arg(qSlicerApplication::application()->documentationBaseUrl());
            details += systemInfo->GetRenderingCapabilitiesDetails().c_str();

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lassoan · October 12, 2021, 2:11pm

For computers that don’t have GPU (or not accessible due to using the computer via remote desktop connection) then it is possible to run Slicer using a software renderer. See details here. Switching to a software renderer would require copying about 20 DLLs to the bin folder and set two environment variables, so it would not be hard to automate it.

spycolyf · October 12, 2021, 8:58pm

Oh wow! Thanks. I’ll consider that @lassoan. Appreciate it

spycolyf · October 12, 2021, 9:04pm

@lassoan,

In my 3D view, I’m doing 3D rendering and ROI cropping, and I’m using presets like CT-Cardiac, CT-Xray, CT-Lung, etc. Is there a preset for CT Bone?

Thanks

lassoan · October 12, 2021, 9:08pm

Yes, there is a preset called “CT-bone”:

These presets are relatively hard to find (the user needs to go to Volumes module and select a volume). Suggestions are welcome for making them more easily accessible. Maybe in the dropdown menu of the window/level mouse mode selector? Or in the right-click menu of a view?

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