acil-bwh / slicercip Goto Github PK

Detected when switching to Cmake 3.5 (although it has nothing to do with it)

@lassoan @rjosest

To remove the "noise" associated with the project, I suggest disabling the following unused features if it still applies:

Go to General settings and disable the Wiki, Projects and Discussions tabs	If empty or unused, hide Releases and Packages section on the right side

_{This comment was adapted from my GitHub saved replies, it is licensed under a Creative Commons Attribution 4.0 International License and you were welcome to reuse it.}

See

When loading all modules (observed on a local build using Slicer r24904 on Ubuntu 15.10), the following is reported:

Algorithm vtkAssignAttribute(0x439bac0) returned failure for request: vtkInformation (0x43ab630)
  Debug: Off
  Modified Time: 244466
  Reference Count: 1
  Registered Events: (none)
  Request: REQUEST_DATA_OBJECT
  ALGORITHM_AFTER_FORWARD: 1
  FORWARD_DIRECTION: 0




Algorithm vtkAssignAttribute(0x439bac0) returned failure for request: vtkInformation (0x43ac220)
  Debug: Off
  Modified Time: 244471
  Reference Count: 1
  Registered Events: (none)
  Request: REQUEST_DATA_OBJECT
  FROM_OUTPUT_PORT: 0
  ALGORITHM_AFTER_FORWARD: 1
  FORWARD_DIRECTION: 0




Algorithm vtkAssignAttribute(0x439bac0) returned failure for request: vtkInformation (0x43abeb0)
  Debug: Off
  Modified Time: 244479
  Reference Count: 1
  Registered Events: (none)
  Request: REQUEST_DATA_OBJECT
  FROM_OUTPUT_PORT: 0
  ALGORITHM_AFTER_FORWARD: 1
  FORWARD_DIRECTION: 0

As seen at https://slicer.cdash.org/build/2831700/configure this extension is not building successfully for Slicer 5.1 which will soon become a stable Slicer 5.2 version.

@pieper switched to using this upstream repo in Slicer/ExtensionsIndex@36a9284, but this repo doesn't appear to have the necessary compatibility fixes that were issued at https://github.com/Slicer/SlicerCIP/tree/develop.

Could you associate the 3d-slicer-extension GitHub topic so that it is listed here: https://github.com/topics/3d-slicer-extension

To learn more about topic, read https://help.github.com/en/articles/about-topics

_{This comment was adapted from my GitHub saved replies, it is licensed under a Creative Commons Attribution 4.0 International License and you were welcome to reuse it.}

The module "RegionTypeModule" doesn't seem to be working ok.
As a complement/workaround, a Colormap with all the possible Region-Type combinations could be used, so that any labelmap could use it.
I developed and tested code that creates the colormap from a file when the module starts. However, ideally, the node should be created dynamically using the ChestConventions. This is more or less what it's done in the module as of today, but in a new labelmap and only with 256 combinations.

Hi,

A radiologist colleague of mine is using your CIP extension in Slicer 4.10.2 on Windows. He has noticed a bug when trying to segment multiple pulmonary nodules in a single session. Here is his description to me (verbatim):

Yes, I upgraded to 4.10.2 and installed the CIP extension, but I’m not satisfied with the performance till now. I segmented 6 scans and I faced this problem twice: When I have a scan with multiple nodules to segment, after I segment the first one and choose a second nodule, the segment button stops working. So I have to save the mask I already finished, close the program and start it again to complete the segmentation of other nodules.

I just wanted to pass this information forward since he is not a GitHub user. Thanks for your help.

Header files is available in both:

• Loadable/RegionTypeDisplay/MRML/vtkMRMLChestRTColorTableNode.h
• Loadable/RegionType/MRML/vtkMRMLChestRTColorTableNode.h

Seems the module RegionType is not build and could be remove.

Cc: @jonieva

Test CIP_LesionModel is failing because this data file is not available:

http://midas.chestimagingplatform.org/download/item/667/1001_UVM_CANCER.nrrd

Here is the error reported when trying to access it

An error occurred

The system has encountered the following error:
Unable to find file on the disk
In /var/www/Midas3/core/controllers/components/DownloadBitstreamComponent.php, line: 50
At 14:52:54 2017-08-31

If needed, we could help you transition to http://girder.readthedocs.io to organize and manage your data.

Running qSlicerParticlesDisplayModuleGenericTest allows to reproduce the problem.

23: Class "vtkCellData" has 2 instances still around.
23: Class "vtkTransformPolyDataFilter" has 1 instance still around.
23: Class "vtkInformationVector" has 11 instances still around.
23: Class "vtkPointData" has 2 instances still around.
23: Class "vtkCompositeDataPipeline" has 3 instances still around.
23: Class "vtkMatrix4x4" has 2 instances still around.
23: Class "vtkSimpleTransform" has 1 instance still around.
23: Class "vtkPoints" has 2 instances still around.
23: Class "vtkInformation" has 33 instances still around.
23: Class "vtkInformationStringVectorValue" has 1 instance still around.
23: Class "vtkPolyData" has 2 instances still around.
23: Class "vtkCylinderSource" has 1 instance still around.
23: Class "vtkAlgorithmOutput" has 1 instance still around.
23: Class "vtkInformationIntegerValue" has 56 instances still around.
23: Class "vtkCellArray" has 1 instance still around.
23: Class "vtkFloatArray" has 5 instances still around.
23: Class "vtkInformationStringValue" has 2 instances still around.
23: Class "vtkInformationExecutivePortVectorValue" has 1 instance still around.
23: Class "vtkIdTypeArray" has 1 instance still around.
23: Class "vtkTransform" has 1 instance still around.
23: Class "vtkFieldData" has 2 instances still around.
23: Class "vtkSphereSource" has 1 instance still around.
23: Class "vtkCommand or subclass" has 2 instances still around.
23: Class "vtkInformationExecutivePortValue" has 2 instances still around.

We are planning to remove Slicer core modules that have been superseded by other modules.
https://discourse.slicer.org/t/removing-legacy-modules-in-slicer5/11371

We have noticed that this extension currently uses legacy editor module, and charts infrastructure (instead of Segment editor, Plots, and Tables modules).

If you want your extension to be available for the upcoming Slicer5 release, please remove dependency to these modules. If you have any questions or need any help with the upgrade, you can write here or post to the Slicer forum. Thank you for your contribution.

See

Installing the latest CIP fails with messages like the one below (on linux, but probably the same everywhere).

Key error is:
ImportError: No module named Colors

I manually copied the Colors.py file into the logic folder and this resolved the problem for my installation.

The fix would be to explicitly include the Colors.py file in the installation:

https://github.com/acil-bwh/SlicerCIP/blob/develop/Scripted/CIP_Common/CMakeLists.txt#L5

Looks like the problem arose with this commit: 62afe4c

@acil-bwh @rjosest

The following path was manually added to the PythonPath in CIP_TracheaStentPlanning: /home/researcher/.config/NA-MIC/Extensions-25011/Chest_Imaging_Platform/lib/Slicer-4.5/qt-scripted-modules/CIP
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/home/researcher/.config/NA-MIC/Extensions-25011/Chest_Imaging_Platform/lib/Slicer-4.5/qt-scripted-modules/CIP_TracheaStentPlanning.py", line 26, in <module>
    from CIP.logic.SlicerUtil import SlicerUtil
  File "/home/researcher/.config/NA-MIC/Extensions-25011/Chest_Imaging_Platform/lib/Slicer-4.5/qt-scripted-modules/CIP/logic/__init__.py", line 6, in <module>
    from Colors import *
ImportError: No module named Colors
loadSourceAsModule - Failed to load file "/home/researcher/.config/NA-MIC/Extensions-25011/Chest_Imaging_Platform/lib/Slicer-4.5/qt-scripted-modules/CIP_TracheaStentPlanning.py"  as module "CIP_TracheaStentPlanning" ! 
Fail to instantiate module "CIP_TracheaStentPlanning" 

See

environment:
OS: Windows11
Slicer Ver: 5.2.1 stable release
CIP: install from slicer extension manager

I used this lung lesion analyzer in the tutorial to segmnet lung nodule.
I patched seed point and clicked "Segment nodule" button, the program ran for a while and displayed "Status: Completed with errors"

Lesion Segmentation terminated with an unknown exception.

Traceback (most recent call last):
File "C:/Users/uu/AppData/Local/NA-MIC/Slicer 5.2.1/NA-MIC/Extensions-31317/Chest_Imaging_Platform/lib/Slicer-5.2/qt-scripted-modules/CIP_LesionModel.py", line 2181, in
result.AddObserver("ModifiedEvent", lambda caller, event: self.onNoduleSegmentationCLIStateUpdated(
File "C:/Users/uu/AppData/Local/NA-MIC/Slicer 5.2.1/NA-MIC/Extensions-31317/Chest_Imaging_Platform/lib/Slicer-5.2/qt-scripted-modules/CIP_LesionModel.py", line 2420, in onNoduleSegmentationCLIStateUpdated
raise Exception("The Nodule Segmentation CLI failed")
Exception: The Nodule Segmentation CLI failed

I have done the same things on Ubuntu, the task also failed with:

Lesion Segmentation standard error:
terminate called after throwing an instance of 'slicer_itk::ExceptionObject'
what(): /work/Stable/Slicer-0-build/ITK/Modules/Core/SpatialObjects/include/itkSpatialObjectPoint.hxx:59:
ITK ERROR: SpatialObjectPoint(0x1218f10): The SpatialObject must be set prior to calling.

Traceback (most recent call last):
File "/home/uu/Slicer-5.2.1-linux-amd64/NA-MIC/Extensions-31317/Chest_Imaging_Platform/lib/Slicer-5.2/qt-scripted-modules/CIP_LesionModel.py", line 2181, in
result.AddObserver("ModifiedEvent", lambda caller, event: self.onNoduleSegmentationCLIStateUpdated(
File "/home/uu/Slicer-5.2.1-linux-amd64/NA-MIC/Extensions-31317/Chest_Imaging_Platform/lib/Slicer-5.2/qt-scripted-modules/CIP_LesionModel.py", line 2420, in onNoduleSegmentationCLIStateUpdated
raise Exception("The Nodule Segmentation CLI failed")
Exception: The Nodule Segmentation CLI failed

I try to reinstall Slicer with 5.1.0 and 5.0.0, the the same issue occured
Finally, I download SlicerCIP integrated(4.10.2), everything is OK.
So I guess CIP is not compatible with Slicer5.x, right?

@lassoan it would be great if you could check and change the Linux/Mac build instructions in readme.md as they refer to Slicer 4.

Thank you.

Issue imported from https://issues.slicer.org/view.php?id=4390

From Jinglong Chen:

I am doing some research with airway inspector in chest imaging platform. I get the result ,but I can't export the result.I try the" write CVS file",no respond.Then select,copy,paste in a excel table,failed.Would you like to tell me how to export the result ?Previously,when running the parenchyma analysis for emphysema,so does the result.

Is the Slicer CIP extension no longer being actively supported? I recently installed the nightly build version of Slicer (version 4.11.0) and the CIP extension is no longer available for installation. Any idea why?

Previously I had Slicer 4.8.1 and CIP extension worked fine.

I am on a Mac with Mojave 10.14.4.

Thanks for your help.

Apparently there's been a change at some point in SubjectHierarchyNode. Depending on the Slicer version (/settings?) there are different settings for the SubjectHierarchyNode. This seems to be related with some change in the API, because it provokes an error when getting the root node with: slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(slicer.mrmlScene)

Interestingly, this happens in the Release and in the last nightly, but not with some intermediate versions. So my take is that it may be related to some settings.

When loading all modules (observed on a local build using Slicer r24904 on Ubuntu 15.10), the following is reported:

Warning: In /home/jcfr/Projects/Slicer/Libs/MRML/DisplayableManager/vtkMRMLDisplayableManagerFactory.cxx, line 132
vtkMRMLThreeDViewDisplayableManagerFactory (0xe07b50): RegisterDisplayableManager - vtkMRMLTractographyDisplayDisplayableManager already registered