Re: [scipion-users] Xmipp tests

[Grigory S. <sha...@gm...>]

Hi,

I'm pretty sure xmipp works okay (other tests are working), just a few
tests have errors which you can ignore (thanks for reporting!).
I usually check if xmipp has been compiled properly by importing e.g. 3d
volumes of different formats (mrc, spi, hdf5) and make sure I can display
them with scipion viewer.

Best regards,
Grigory

--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.

MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. +44 (0) 1223 267228 <+44%201223%20267228>
e-mail: gs...@mr...


On Thu, Nov 4, 2021 at 3:57 PM Lynn Radamaker <lyn...@un...>
wrote:

> Dear Scipion community,
>
> I'm having some problems with Xmipp. It installed without errors, but it
> gives a warning that it cannot find the image library. When I run this test:
>
> scipion3 tests
> pwem.tests.workflows.test_workflow_xmipp_ctf_consensus.TestCtfConsensus
>
> Then it gives me the following error message:
>
> [   FAILED ] TestCtfConsensus.test1
>
> Traceback (most recent call last):
>   File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py",
> line 60, in testPartExecutor
>     yield
>   File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py",
> line 676, in run
>     self._callTestMethod(testMethod)
>   File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py",
> line 633, in _callTestMethod
>     method()
>   File
> "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/pwem/tests/workflows/test_workflow_xmipp_ctf_consensus.py",
> line 186, in test1
>     self.checkCTFs(protCTFcons3,
>   File
> "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/pwem/tests/workflows/test_workflow_xmipp_ctf_consensus.py",
> line 71, in checkCTFs
>     self.assertAlmostEqual(avgCTF['defocusU'], firstCTF.getDefocusU(),
> delta=100,
>   File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py",
> line 966, in assertAlmostEqual
>     raise self.failureException(msg)
> AssertionError: 24140.0898 != 24025.673242 within 100 delta
> (114.4165580000008 difference) : DefocusU doesn't match when defocus
> averaging.
>
> Also, the similar test:
>
> scipion3 tests pwem.tests.workflows.test_workflow_xmipp
>
> Gives the error message:
>
> [   FAILED ] TestXmippWorkflow.testXmippWorkflow
>
> Traceback (most recent call last):
>   File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py",
> line 60, in testPartExecutor
>     yield
>   File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py",
> line 676, in run
>     self._callTestMethod(testMethod)
>   File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py",
> line 633, in _callTestMethod
>     method()
>   File
> "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/pwem/tests/workflows/test_workflow_xmipp.py",
> line 198, in testXmippWorkflow
>
> self.assertAlmostEqual(protExtractCoordsShifts.outputCoordinates.getFirstItem().getPosition(),
>   File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/unittest/case.py",
> line 943, in assertAlmostEqual
>     diff = abs(first - second)
> TypeError: unsupported operand type(s) for -: 'tuple' and 'tuple'
>
>
>
> All the other tests (basic and medium) that I ran completed without
> problems. I'm hoping that you can give me some advice on how to fix these
> error and get Xmipp running properly.
>
> Kind regards,
>
> Lynn Radamaker
>
>
>
>
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