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Buildbot failures with missing 'nit' key in dipy.core.optimize #461

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matthew-brett opened this issue Nov 13, 2014 · 4 comments
Closed

Buildbot failures with missing 'nit' key in dipy.core.optimize #461

matthew-brett opened this issue Nov 13, 2014 · 4 comments

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@matthew-brett
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See; http://nipy.bic.berkeley.edu/builders/dipy-py2.7-osx-10.6/builds/290/steps/shell_8/logs/stdio

Could this be an incompatibility with earlier scipy? This machine has numpy 1.7 and scipy 0.11.

======================================================================
ERROR: dipy.align.tests.test_streamlinear.test_rigid_parallel_lines
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/buildslave/osx-10.6/dipy-py2_7-osx-10_6/build/venv/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/Users/buildslave/osx-10.6/dipy-py2_7-osx-10_6/build/venv/lib/python2.7/site-packages/dipy/align/tests/test_streamlinear.py", line 74, in test_rigid_parallel_lines
    new_bundle2 = srr.optimize(bundle, bundle2).transform(bundle2)
  File "/Users/buildslave/osx-10.6/dipy-py2_7-osx-10_6/build/venv/lib/python2.7/site-packages/dipy/align/streamlinear.py", line 344, in optimize
    mat_history, opt.nfev, opt.nit)
  File "/Users/buildslave/osx-10.6/dipy-py2_7-osx-10_6/build/venv/lib/python2.7/site-packages/dipy/core/optimize.py", line 215, in nit
    return self.res['nit']
KeyError: 'nit'

======================================================================
ERROR: dipy.align.tests.test_streamlinear.test_rigid_partial_real_bundles
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/buildslave/osx-10.6/dipy-py2_7-osx-10_6/build/venv/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/Users/buildslave/osx-10.6/dipy-py2_7-osx-10_6/build/venv/lib/python2.7/site-packages/dipy/align/tests/test_streamlinear.py", line 123, in test_rigid_partial_real_bundles
    srm = srr.optimize(static_center, moved)
  File "/Users/buildslave/osx-10.6/dipy-py2_7-osx-10_6/build/venv/lib/python2.7/site-packages/dipy/align/streamlinear.py", line 344, in optimize
    mat_history, opt.nfev, opt.nit)
  File "/Users/buildslave/osx-10.6/dipy-py2_7-osx-10_6/build/venv/lib/python2.7/site-packages/dipy/core/optimize.py", line 215, in nit
    return self.res['nit']
KeyError: 'nit'
-------------------- >> begin captured stdout << ---------------------
[  88.12210846  109.13088989   81.60664368]

--------------------- >> end captured stdout << ----------------------

======================================================================
ERROR: dipy.align.tests.test_streamlinear.test_stream_rigid
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/buildslave/osx-10.6/dipy-py2_7-osx-10_6/build/venv/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/Users/buildslave/osx-10.6/dipy-py2_7-osx-10_6/build/venv/lib/python2.7/site-packages/dipy/align/tests/test_streamlinear.py", line 172, in test_stream_rigid
    sr_params = srr.optimize(static, moving)
  File "/Users/buildslave/osx-10.6/dipy-py2_7-osx-10_6/build/venv/lib/python2.7/site-packages/dipy/align/streamlinear.py", line 344, in optimize
    mat_history, opt.nfev, opt.nit)
  File "/Users/buildslave/osx-10.6/dipy-py2_7-osx-10_6/build/venv/lib/python2.7/site-packages/dipy/core/optimize.py", line 215, in nit
    return self.res['nit']
KeyError: 'nit'

======================================================================
ERROR: dipy.align.tests.test_streamlinear.test_evolution_of_previous_iterations
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/buildslave/osx-10.6/dipy-py2_7-osx-10_6/build/venv/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/Users/buildslave/osx-10.6/dipy-py2_7-osx-10_6/build/venv/lib/python2.7/site-packages/dipy/align/tests/test_streamlinear.py", line 343, in test_evolution_of_previous_iterations
    slm = slr.optimize(static, moving)
  File "/Users/buildslave/osx-10.6/dipy-py2_7-osx-10_6/build/venv/lib/python2.7/site-packages/dipy/align/streamlinear.py", line 337, in optimize
    if opt.evolution is not None:
  File "/Users/buildslave/osx-10.6/dipy-py2_7-osx-10_6/build/venv/lib/python2.7/site-packages/dipy/core/optimize.py", line 237, in evolution
    history = np.loadtxt(f).reshape((self.res['nit'], self.size_of_x))
KeyError: 'nit'

======================================================================
ERROR: dipy.align.tests.test_streamlinear.test_affine_real_bundles
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/buildslave/osx-10.6/dipy-py2_7-osx-10_6/build/venv/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/Users/buildslave/osx-10.6/dipy-py2_7-osx-10_6/build/venv/lib/python2.7/site-packages/dipy/align/tests/test_streamlinear.py", line 399, in test_affine_real_bundles
    slm = slr.optimize(bundle, bundle2)
  File "/Users/buildslave/osx-10.6/dipy-py2_7-osx-10_6/build/venv/lib/python2.7/site-packages/dipy/align/streamlinear.py", line 344, in optimize
    mat_history, opt.nfev, opt.nit)
  File "/Users/buildslave/osx-10.6/dipy-py2_7-osx-10_6/build/venv/lib/python2.7/site-packages/dipy/core/optimize.py", line 215, in nit
    return self.res['nit']
KeyError: 'nit'
-------------------- >> begin captured stdout << ---------------------
  status: 0
    nfev: 224
 success: True
     fun: 3.4462746890369411e-07
       x: array([ -3.30742409e-05,   2.70839952e-05,  -4.50638642e-04,
         2.43647501e+00,  -1.21251485e+01,  -1.14489623e+01,
         8.13637822e-01,   9.05562696e-01,   1.02810357e+00,
        -3.94146063e-02,  -8.66503992e-02,  -1.71090548e-02])
 message: 'CONVERGENCE: REL_REDUCTION_OF_F_<=_FACTR*EPSMCH'
     jac: array([  4.19777333e-05,   2.05871223e-04,  -6.98220187e-04,
        -2.40374934e-06,   7.22981419e-06,  -2.13818548e-05,
        -1.37464873e-03,   5.59955634e-04,  -2.13373593e-03,
         5.50705915e-05,  -1.42710778e-03,   1.89767024e-03])

--------------------- >> end captured stdout << ----------------------

======================================================================
ERROR: dipy.core.tests.test_optimize.test_optimize
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/buildslave/osx-10.6/dipy-py2_7-osx-10_6/build/venv/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/Users/buildslave/osx-10.6/dipy-py2_7-osx-10_6/build/venv/lib/python2.7/site-packages/dipy/core/tests/test_optimize.py", line 54, in test_optimize
    print(opt.nit)
  File "/Users/buildslave/osx-10.6/dipy-py2_7-osx-10_6/build/venv/lib/python2.7/site-packages/dipy/core/optimize.py", line 215, in nit
    return self.res['nit']
KeyError: 'nit'
-------------------- >> begin captured stdout << ---------------------
  status: 0
    nfev: 3
 success: True
     fun: 1.1908915926500003e-16
       x: array([ -6.30050684e-09,  -6.30050684e-09,  -6.30050684e-09])
 message: 'CONVERGENCE: NORM_OF_PROJECTED_GRADIENT_<=_PGTOL'
     jac: array([ -2.60101368e-09,  -2.60101368e-09,  -2.60101368e-09])

--------------------- >> end captured stdout << ----------------------
@matthew-brett matthew-brett changed the title Buildbot failures with missing 'nit' key in scipy.optimize Buildbot failures with missing 'nit' key in dipy.core.optimize Nov 13, 2014
@matthew-brett
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Same failures here : http://nipy.bic.berkeley.edu/builders/dipy-py2.7-osx-10.7/builds/170/steps/shell_8/logs/stdio

@Garyfallidis
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Hi @matthew-brett, according to
http://docs.scipy.org/doc/scipy-0.14.0/reference/generated/scipy.optimize.minimize.html

the minimize function was introduced in 0.11.0 so it should be called here. Minimize returns a dictionary which should have a key called 'nit' (number of iterations). Could it be that the key was added after 0.11?

Ooops! Yes! Look here:
In 0.11 no 'nit' !
https://github.com/scipy/scipy/blob/maintenance/0.11.x/scipy/optimize/lbfgsb.py#L175
And in 0.12 'nit' is there
https://github.com/scipy/scipy/blob/maintenance/0.12.x/scipy/optimize/lbfgsb.py#L189

Okay will make a fix asap! Thanx for reporting. Hmm.. this is a serious bug for 0.11 actually. You cannot even set the number of maximum iterations.... Grrr....!

@Garyfallidis Garyfallidis mentioned this issue Nov 13, 2014
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@Garyfallidis
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Hopefully the issue is addressed here #465

matthew-brett added a commit that referenced this issue Nov 14, 2014
@matthew-brett
Merge pull request #465 from Garyfallidis/fix_optimize_scipy_version
c781789 
MRG: increased SCIPY version definition flag to 0.12

Change scipy dependency rules; should fix issue #461
@matthew-brett
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Fixed by #465 - thanks

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@matthew-brett @Garyfallidis