segLg = slicer.modules.segmentations.logic() AttributeError: module 'modules' has no attribute 'segmentations'

Development
,
1

Are the modules not fully imported? What’s wrong in py?

segLg = slicer.modules.segmentations.logic()
AttributeError: module ‘modules’ has no attribute ‘segmentations’
print(dir(slicer.modules))
[‘AddManyMarkupsFiducialTestInstance’, ‘AtlasTestsInstance’, ‘BRAINSFitRigidRegistrationCrashIssue4139Instance’, ‘ColorLegendSelfTestInstance’, ‘CompareVolumesInstance’, ‘CropVolumeSelfTestInstance’, ‘CropVolumeSequenceInstance’, ‘DICOMEnhancedUSVolumePluginInstance’, ‘DICOMGeAbusPluginInstance’, ‘DICOMImageSequencePluginInstance’, ‘DICOMInstance’, ‘DICOMPatcherInstance’, ‘DICOMScalarVolumePluginInstance’, ‘DICOMSlicerDataBundlePluginInstance’, ‘DICOMVolumeSequencePluginInstance’, ‘DataProbeInstance’, ‘EndoscopyInstance’, ‘ExtensionWizardInstance’, ‘FiducialLayoutSwitchBug1914Instance’, ‘ImportItkSnapLabelInstance’, ‘JRC2013VisInstance’, ‘JupyterNotebooksInstance’, ‘LandmarkRegistrationInstance’, ‘MarkupsInCompareViewersSelfTestInstance’, ‘MarkupsInViewsSelfTestInstance’, ‘MultiVolumeImporterInstance’, ‘MultiVolumeImporterPluginInstance’, ‘NeurosurgicalPlanningTutorialMarkupsSelfTestInstance’, ‘doc’, ‘file’, ‘loader’, ‘name’, ‘package’, ‘spec’, ‘dicomPlugins’, ‘registrationPlugins’]

However in python console this situation does not occur.

image

2

Is it a build you did yourself or downloaded and installed?

Are there any errors on startup?

3

downloaded and installed from https://download.slicer.org/bitstream/67c52e9629825655577d0353

4

That is Slicer 5.8.1 for mac, and when I run it this works:

>>> slicer.modules.segmentations.logic()
<vtkSlicerSegmentationsModuleLogicPython.vtkSlicerSegmentationsModuleLogic(0x600003b38af0) at 0x1b4b7f100>
5

Please answer this question too, this is the more important one. Thanks

6

image
image800×447 79.6 KB

7

You’ll need to narrow down to something reproducible or we can’t help you out.

8 
# ...docs/segLg.py
import slicer
segLg = slicer.modules.segmentations.logic()

For example, add the above file docs/segLg.py to modules as follows:

image
image824×201 45.5 KB

**The error is as follows:**

image
image794×216 40.7 KB

9

Ah, okay. Your module is being discovered before the segmentations has loaded.

You need something like:

self.parent.dependencies = ["Segmentations"]

in your module’s main class.

2 Likes
10

@pieper For example, how to modify segLg.py :backhand_index_pointing_down:?

import slicer
# ? self.parent.dependencies = ["Segmentations"]
segLg = slicer.modules.segmentations.logic()
11

Since you added this docs path to the module path it needs to be in the scripted module format, like you get when you use the ExtensionWizard. That’s there the dependency is expressed.

12

@pieper Teacher, could you be more specific? Could you give an example🌰?

13

Like here:

2 Likes
14 
import slicer
# self.parent.dependencies = ["Segmentations"]
print(f'{dir(slicer.modules)=}')
segLg = slicer.modules.segmentations.logic()

dir(slicer.modules)=['AddManyMarkupsFiducialTestInstance', 'AtlasTestsInstance', 'BRAINSFitRigidRegistrationCrashIssue4139Instance', 'ColorLegendSelfTestInstance', 'CompareVolumesInstance', 'CropVolumeSelfTestInstance', 'CropVolumeSequenceInstance', 'DICOMEnhancedUSVolumePluginInstance', 'DICOMGeAbusPluginInstance', 'DICOMImageSequencePluginInstance', 'DICOMInstance', 'DICOMPatcherInstance', 'DICOMScalarVolumePluginInstance', 'DICOMSlicerDataBundlePluginInstance', 'DICOMVolumeSequencePluginInstance', 'DataProbeInstance', 'EndoscopyInstance', 'ExtensionWizardInstance', 'FiducialLayoutSwitchBug1914Instance', 'ImportItkSnapLabelInstance', 'JRC2013VisInstance', 'JupyterNotebooksInstance', 'LandmarkRegistrationInstance', 'MarkupsInCompareViewersSelfTestInstance', 'MarkupsInViewsSelfTestInstance', 'MultiVolumeImporterInstance', 'MultiVolumeImporterPluginInstance', 'NeurosurgicalPlanningTutorialMarkupsSelfTestInstance', 'PedicleScrewPlannerInstance', 'PedicleScrewSimulatorInstance', 'PedicleTrianglePlannerInstance', 'PerformanceTestsInstance', 'PlotsSelfTestInstance', 'PluggableMarkupsSelfTestInstance', 'PyTorchUtilsInstance', 'RSNA2012ProstateDemoInstance', 'RSNAQuantTutorialInstance', 'RSNAVisTutorialInstance', 'SampleDataInstance', 'ScenePerformanceInstance', 'ScreenCaptureInstance', 'SegmentEditorInstance', 'SegmentStatisticsInstance', 'SelfTestsInstance', 'SequencesSelfTestInstance', 'ShaderPropertiesInstance', 'SimpleFiltersInstance', 'SliceLinkLogicInstance', 'Slicer4MinuteInstance', 'SlicerBoundsTestInstance', 'SlicerDisplayNodeSequenceTestInstance', 'SlicerMRBMultipleSaveRestoreLoopTestInstance', 'SlicerMRBMultipleSaveRestoreTestInstance', 'SlicerMRBSaveRestoreCheckPathsTestInstance', 'SlicerNNUNetInstance', 'SlicerOrientationSelectorTestInstance', 'SlicerPythonTestRunnerInstance', 'SlicerScriptedFileReaderWriterTestInstance', 'SubjectHierarchyCorePluginsSelfTestInstance', 'SubjectHierarchyGenericSelfTestInstance', 'SurfaceToolboxInstance', 'TablesSelfTestInstance', 'TotalSegmentatorInstance', 'UtilTestInstance', 'VectorToScalarVolumeInstance', 'ViewControllersSliceInterpolationBug1926Instance', 'VolumeRenderingSceneCloseInstance', 'WebEngineInstance', 'WebServerInstance', '__doc__', '__file__', '__loader__', '__name__', '__package__', '__spec__', 'dicomPlugins', 'registrationPlugins', 'sampleDataSources', 'sceneImport2428Instance']
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/Applications/Slicer.app/Contents/lib/Python/lib/python3.9/imp.py", line 169, in load_source
    module = _exec(spec, sys.modules[name])
  File "<frozen importlib._bootstrap>", line 613, in _exec
  File "<frozen importlib._bootstrap_external>", line 850, in exec_module
  File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed
  File "/Users/liguimei/Documents/ppPrj/Resources/docs/segLg.py", line 4, in <module>
    segLg = slicer.modules.segmentations.logic()
AttributeError: module 'modules' has no attribute 'segmentations'
[Qt] loadSourceAsModule - Failed to load file "/Users/liguimei/Documents/ppPrj/Resources/docs/segLg.py"  as module "segLg" !
[Qt] Fail to instantiate module  "segLg"

Still don’t understand…

15

@lassoan ?…………………………………………….

16

Slicer has some expectations from files you try to use as modules. If you just drop some python code into a file, it can break, and that is what you see.

The particular expectation here is: It should be possible to import your file without it depending on other modules. Your code explicitly depends on other modules.

Re-writing the file so that it looks like the module shown by @pieper would help:

  • The code that uses slicer.modules.segmentations should be in one of the method of the class, so it doesn’t get executed at import time
  • Then you also have a place to declare dependencies, which will be respected

Trying to add one line to your existing code would not work.

1 Like
17

I would recommend to use the Extensions Wizard module to generate a module skeleton and add your code to it piece by piece. The STC-DEV-101 Tutorial should help.