Fixed Score coordinates and phantom subtomo tests #167
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# Conflicts: # xmipptomo/tests/test_protocols_xmipptomo.py
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… fix_test_score_coordinates # Conflicts: # xmipptomo/tests/test_protocols_xmipptomo.py
I have relaxed Regarding the warnings, I am not being able to replicate them on my machine. I guess they are related to the empty metadata generated by the tests (currently, one of the two metadata generated in the executions will be always empty). If this is the case, the warning should be expected. Again, the warning issue should be also solved with a better testing dataset. |
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The error buildbot report (the same I had in my mahcine) is: |
Hi @albertmena, I am trying on my laptop locally and I can't reproduce this issue... the tests run ok on my local installation with no Xmipp added to the bash. The changes in this PR should fix this issue (found on |
ok, we can consider this point as fixed. But the test is not robust (4 machines 4 fails) we may change the test data |
… params added to form, fixed protocol execution
I have modified the test and the protocol to improve its performance:
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| @@ -113,6 +121,7 @@ def detectOutliers(self): | |||
| self.scoreOutliers[idn][1] = z_scores[idn] | |||
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| def detectCarbonCloseness(self, coordinates): | |||
| pwutils.makePath(self._getExtraPath('carbonMask')) | |||
| self.scoreCarbon = [] | |||
| for tomoName in self.tomoNames: | |||
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The class has not self.tomoNames definition
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Hi @albertmena,
The attribute self.tomoNames is initialized in the method computeParams in line 101, which is called as a step inside the _insertAllSteps method (line 94). This step is called before detectCarbonCloseness, are you getting any error related to it? In my local installation, the test runs without issues. Thanks!
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looks like some local issue, the test works on galileo_shadow
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I think we are close to the solution! |
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Kudos, SonarCloud Quality Gate passed!
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Some checks to be done:
Check if score coordinate test is robust enough or extra changes are needed
Check micrograph cleaner scores (good particles should have a score closer to 0 or 1?)
Check if phantom subtomo tests runs fins (locally I am getting an error when doing a
--fourier wedgefilter with Xmipp, but it might be a local installation problem).