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scipion-em / scipion-em-warp

Plugin to use Warp programs within the Scipion framework
GNU General Public License v3.0
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test deconv 3d fails #3

Closed MohamadHarastani closed 1 year ago

MohamadHarastani commented 1 year ago 
[   FAILED ] TestDeconvolve3D.test_run

Traceback (most recent call last):
  File "/shared/miniconda3/envs/scipion3/lib/python3.8/unittest/case.py", line 60, in testPartExecutor
    yield
  File "/shared/miniconda3/envs/scipion3/lib/python3.8/unittest/case.py", line 676, in run
    self._callTestMethod(testMethod)
  File "/shared/miniconda3/envs/scipion3/lib/python3.8/unittest/case.py", line 633, in _callTestMethod
    method()
  File "/shared/scipion3/plugins/scipion-em-warp/warp/tests/test_protocols_tomo.py", line 105, in test_run
    self.assertSetSize(outputTomos, 4)
  File "/shared/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/tests/tests.py", line 224, in assertSetSize
    self.assertEqual(setObjSize, size)
  File "/shared/miniconda3/envs/scipion3/lib/python3.8/unittest/case.py", line 912, in assertEqual
    assertion_func(first, second, msg=msg)
  File "/shared/miniconda3/envs/scipion3/lib/python3.8/unittest/case.py", line 905, in _baseAssertEqual
    raise self.failureException(msg)
AssertionError: 2 != 4
azazellochg commented 1 year ago

can't reproduce this. check if your imod plugin is up to date

MohamadHarastani commented 1 year ago

I will try to reproduce it on another computer right now

MohamadHarastani commented 1 year ago

Reproduced on another computer right away. In the runstd.err I see a warning, but I am not sure if that is relevant.

00001:   /home/harastam/scipion3/scipion-em-warp/warp/utils.py:101: RuntimeWarning: divide by zero encountered in true_divide
00002:     wiener = ctf / (ctf * ctf + np.divide(1, snr))
azazellochg commented 1 year ago

You are not using the latest code from devel branch.

MohamadHarastani commented 1 year ago

You are right about the devel branch! The warning is gone. But the test still fails.

MohamadHarastani commented 1 year ago

There is no problem other than there are only two tilt series in the test data tutorialDataSusan and the assert is looking for 4 tomograms.. check your local ~/scipion3/data/tests/tutorialDataSusan/ Here is what I see image

azazellochg commented 1 year ago

aah, you are right. I think I have added more files to my folder for development reason. I'll fix the test