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Some PSA module components don't behave as expected #1507

sseyler opened this Issue Jul 18, 2017 · 0 comments


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sseyler commented Jul 18, 2017

NOTE: The issues described below are fixed in the context of #1006 (increase code coverage in PSA)

Expected behaviour

  1. MDAnalysis.analysis.psa.dist_mat_to_vec() should return an integer index between 0 and N*(N-1)/2 - 1, regardless of input type; e.g.,
>>> MDAnalysis.analysis.psa.dist_mat_to_vec(3, 0, 1)
<type 'int'>
>>> MDAnalysis.analysis.psa.dist_mat_to_vec(3.0, 0, 1)
<type 'int'>
  1. MDAnalysis.analysis.psa.PSAnalysis.run_pairs_analysis() should store (Hausdorff) distances in an all-pairs matrix as does. (The distances are computed anyway, so it is trivial to store them in a 2D NumPy array as usual.)

Actual behaviour

  1. MDAnalysis.analysis.psa.dist_mat_to_vec() returns a float if one or more arguments are of type float.
  2. MDAnalysis.analysis.psa.PSAnalysis.run_pairs_analysis() doesn't store (Hausdorff) distances in an all-pairs matrix like does; the user must utilize dist_mat_to_vec() to extract distances from MDAnalysis.analysis.psa.PSAnalysis.hausdorff_pairs[idx]['distance'], where idx would be an integer index of a pair of compared paths (e.g., calculated from dist_mat_to_vec()).

Note: The problem with dist_mat_to_vec(), where a float was returned for float argument(s) provided as input, became apparent in attempting to extract Hausdorff distances from the list of {frames, distance} dictionaries in stored as psa.PSAnalysis.hausdorff_pairs after running run_pairs_analysis().

Code to reproduce the behaviour

>>> import MDAnalysis
>>> MDAnalysis.analysis.psa.dist_mat_to_vec(3.0, 0, 1)
<type 'float'>
In [1]: import MDAnalysis as mda
In [2]: import MDAnalysis.analysis.psa as PSA
In [3]: from MDAnalysisTests.datafiles import PSF, DCD
In [4]: u1 = mda.Universe(PSF, DCD)
In [5]: u2 = mda.Universe(PSF, DCD)
In [6]: u3 = mda.Universe(PSF, DCD)
In [7]: mypsa = PSA.PSAnalysis([u1, u2, u3],  path_select='name CA')
In [8]: mypsa.generate_paths(align=True)
Fitted frame    98/98  [100.0%]
Fitted frame    98/98  [100.0%]
Fitted frame    98/98  [100.0%]

In [9]: mypsa.paths[-1] = mypsa.paths[-1][::-1,:,:]  # reverse third path
In [10]: idx = PSA.dist_mat_to_vec(3.0, 0, 1)
In [11]: mypsa.run_pairs_analysis(neighbors=True, hausdorff_pairs=True)
In [12]: mypsa.hausdorff_pairs[idx]['distance']
TypeError                                 Traceback (most recent call last)
<ipython-input-13-b6132d74b16e> in <module>()
----> 1 mypsa.hausdorff_pairs[idx]['distance']

TypeError: list indices must be integers, not float

Applicable versions of MDAnalysis: 0.15.0 (up through 0.16.2)

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