debug: pass failing unit test - Value errors from shape / num pixels mismatch

[geoffwoollard]

Can't reproduce failing unit test yet. Python 8 issue?

https://github.com/compSPI/simSPI/runs/4031149125?check_suite_focus=true

Run $CONDA/bin/pytest --cov-report term --cov-report xml:coverage.xml --cov=simSPI tests
  $CONDA/bin/pytest --cov-report term --cov-report xml:coverage.xml --cov=simSPI tests
  shell: /bin/bash -e {0}
  env:
    pythonLocation: /opt/hostedtoolcache/Python/3.8.12/x64
    LD_LIBRARY_PATH: /opt/hostedtoolcache/Python/3.8.12/x64/lib
============================= test session starts ==============================
platform linux -- Python 3.9.5, pytest-6.2.5, py-1.10.0, pluggy-1.0.0
rootdir: /home/runner/work/simSPI/simSPI, configfile: pytest.ini, testpaths: tests
plugins: cov-3.0.0
collected 8 items

tests/test_multislice.py ...F.                                           [ 62%]
tests/test_transfer.py ...                                               [100%]

=================================== FAILURES ===================================
________________________________ test_apply_dqe ________________________________

    def test_apply_dqe():
        """Test apply_dqe."""
        N_random = np.random.uniform(low=50, high=100)
        N = int(2 * (N_random // 2))
        ones = np.ones((N, N))
        freq_A_2d = transfer.ctf_freqs(N, dim=2)[0]
        mtf_const = 1.5
        mtf2 = (np.sinc(freq_A_2d * mtf_const)) ** 2
        ntf2 = np.sinc(freq_A_2d) ** 2
        dqe = mtf2 / ntf2
>       i0_dqe = multislice.apply_dqe(ones, dqe)

tests/test_multislice.py:85: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

i0_f = array([[1., 1., 1., ..., 1., 1., 1.],
       [1., 1., 1., ..., 1., 1., 1.],
       [1., 1., 1., ..., 1., 1., 1.],
       ...,
       [1., 1., 1., ..., 1., 1., 1.],
       [1., 1., 1., ..., 1., 1., 1.],
       [1., 1., 1., ..., 1., 1., 1.]])
dqe = array([[0.02518659, 0.01654163, 0.00994395, ..., 0.00994395, 0.01654163,
        0.02518659],
       [0.01654163, 0.00...16,
        0.01654163],
       [0.02518659, 0.01654163, 0.00994395, ..., 0.00994395, 0.01654163,
        0.02518659]])

    def apply_dqe(i0_f, dqe):
        """Convolution with detector's DQE.
    
        Convolution of (ctf applied) exit wave
        with sqrt of the detective quantum efficiency.
    
        Parameters
        ----------
        i0_f : numpy.ndarray, shape (N,N)
            Image with ctf applied.
        dqe : numpy.ndarray, shape (N,N)
            Detective quantum efficiency (in 2D).
    
        Returns
        -------
        i0_dqe : numpy.ndarray, shape (N,N)
            Exit wave with dqe applied (in real space).
        """
>       i0_dqe = fourier.do_ifft(i0_f * np.sqrt(dqe), dim=2)
E       ValueError: operands could not be broadcast together with shapes (98,98) (99,99)

simSPI/multislice.py:47: ValueError
=============================== warnings summary ===============================
../../../../../usr/share/miniconda/lib/python3.9/site-packages/raster_geometry/raster.py:2447
  /usr/share/miniconda/lib/python3.9/site-packages/raster_geometry/raster.py:2447: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    dtype=np.float):

-- Docs: https://docs.pytest.org/en/stable/warnings.html

----------- coverage: platform linux, python 3.9.5-final-0 -----------
Name                   Stmts   Miss  Cover   Missing
----------------------------------------------------
simSPI/__init__.py         1      0   100%
simSPI/multislice.py      21      0   100%
simSPI/transfer.py        50      3    94%   90, 97, 167
----------------------------------------------------
TOTAL                     72      3    96%
Coverage XML written to file coverage.xml

Required test coverage of 90.0% reached. Total coverage: 95.83%
=========================== short test summary info ============================
FAILED tests/test_multislice.py::test_apply_dqe - ValueError: operands could ...
=================== 1 failed, 7 passed, 1 warning in 10.13s ====================
Error: Process completed with exit code 1.

[codecov]

Codecov Report

Merging #12 (ecca33d) into master (9f392bd) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master      #12   +/-   ##
=======================================
  Coverage   95.84%   95.84%           
=======================================
  Files           3        3           
  Lines          72       72           
=======================================
  Hits           69       69           
  Misses          3        3           

Impacted Files	Coverage Δ
simSPI/transfer.py	94.00% <ø> (ø)

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[geoffwoollard]

Passing all tests consistently.