Re: [scipion-users] Xmipp tests

[Alberto G. M. <alb...@cn...>]

Hi Lynn,

At this moment (on devel branch) the most of the test pass, included 
those what you refer. Just as a reminder; failure of a test in xmipp 
does not imply that Xmipp is failing.


On 10/11/21 12:36, Pablo Conesa wrote:
>
> Hi Lynn!
>
> Please do not worry about that error. The test is expecting a certain 
> CTF values and you are not getting them. Theses values may vary with 
> newer versions of the ctf estimation binaries (ccffind, gctf, ...and 
> so on) and the test might bot be updated.
>
> "AssertionError: 24140.0898 != 24025.673242 within 100 delta 
> (114.4165580000008 difference)"
>
> Means that we are expecting in the test a defocus value of 
> 24025.673242 +- 100 and you are getting 24140.0898.
>
> To me is a valid value.
>
> Actually, this test, like many create a project, in this case 
> "TestCtfConsensus". If you open the project I'd say boxes are green 
> and all worked fine, only the test (extrict) does not like the output.
>
> You should be able to ope the project with:
>
> scipion3 project TestCtfConsensus
>
>
>
>
> On 10/11/21 12:06, Lynn Radamaker wrote:
>> Dear Scipion community,
>>
>> the first of these errors was solved by expanding cistem in the 
>> plugin manager and installing Ctffind additionally.
>>
>> So far, I have not made any progress with the second error. When I 
>> open the workflow for this test project (TestXmippWorkflow) in 
>> Scipion, the last step is "extract coordinates applying shifts" which 
>> finishes successfully. Any help would be greatly appreciated.
>>
>> Kind regards,
>>
>> Lynn Radamaker
>>
>>
>>
>> On Thursday, November 04, 2021 15:33 CET, "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
>>>
>>>
>>>
>>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> scipion-users mailing list
>> sci...@li...
>> https://lists.sourceforge.net/lists/listinfo/scipion-users
> -- 
> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
-- 
- Alberto GM -