Re: [scipion-users] Xmipp tests

[Pablo C. <pc...@cn...>]

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
>>
>>
>>
>>
>
>
>
>
>
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-- 
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*