[SciPy-Dev] Enhancements to scipy.spatial.cKDTree

Sturla Molden sturla@molden...
Sat Jul 14 13:03:01 CDT 2012


Raph, do you mind testing again on your Mac?

(I am suspecting another integer problem related to Windows 64...)

Sturla




Den 14.07.2012 19:36, skrev Sturla Molden:
> I have traced down the bug, it was related to an array being altered 
> inplace instead of copied.
>
> I have also taken out two other bugs related to C long (and Python 
> int) being 32 bit on Windows 64.
>
> I still get four fails on Win 64. They are there in Patrick's code as 
> well, so they are related to his coding.
>
> An update is commited here:
>
> https://github.com/sturlamolden/scipy/blob/master/scipy/spatial/ckdtree.pyx
>
>
> Sturla
>
>
>
> D:\kd-tree\20120714-cKDTree>python test.py
> ..............................................................................................................................FFFF...
> ======================================================================
> FAIL: test.test_onetree_query_compiled(<ckdtree.cKDTree object at 
> 0x000000000583AE18>, 0.1)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "C:\Python27\lib\site-packages\nose\case.py", line 197, in runTest
>     self.test(*self.arg)
>   File "D:\kd-tree\20120714-cKDTree\test.py", line 570, in 
> check_onetree_query
>     assert_(s == T.query_pairs(d))
>   File "C:\Python27\lib\site-packages\numpy\testing\utils.py", line 
> 34, in assert_
>     raise AssertionError(msg)
> AssertionError
>
> ======================================================================
> FAIL: test.test_onetree_query_compiled(<ckdtree.cKDTree object at 
> 0x000000000583AE18>, 0.001)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "C:\Python27\lib\site-packages\nose\case.py", line 197, in runTest
>     self.test(*self.arg)
>   File "D:\kd-tree\20120714-cKDTree\test.py", line 570, in 
> check_onetree_query
>     assert_(s == T.query_pairs(d))
>   File "C:\Python27\lib\site-packages\numpy\testing\utils.py", line 
> 34, in assert_
>     raise AssertionError(msg)
> AssertionError
>
> ======================================================================
> FAIL: test.test_onetree_query_compiled(<ckdtree.cKDTree object at 
> 0x000000000583AE18>, 1e-05)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "C:\Python27\lib\site-packages\nose\case.py", line 197, in runTest
>     self.test(*self.arg)
>   File "D:\kd-tree\20120714-cKDTree\test.py", line 570, in 
> check_onetree_query
>     assert_(s == T.query_pairs(d))
>   File "C:\Python27\lib\site-packages\numpy\testing\utils.py", line 
> 34, in assert_
>     raise AssertionError(msg)
> AssertionError
>
> ======================================================================
> FAIL: test.test_onetree_query_compiled(<ckdtree.cKDTree object at 
> 0x000000000583AE18>, 1e-06)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "C:\Python27\lib\site-packages\nose\case.py", line 197, in runTest
>     self.test(*self.arg)
>   File "D:\kd-tree\20120714-cKDTree\test.py", line 570, in 
> check_onetree_query
>     assert_(s == T.query_pairs(d))
>   File "C:\Python27\lib\site-packages\numpy\testing\utils.py", line 
> 34, in assert_
>     raise AssertionError(msg)
> AssertionError
>
> ----------------------------------------------------------------------
> Ran 133 tests in 4.351s
>
> FAILED (failures=4)
>
>
>
> Den 14.07.2012 13:17, skrev Ralf Gommers:
>>
>> I took your edits and committed them as a diff to Patricks last 
>> commit. Then I added a few style fixes: 
>> https://github.com/rgommers/scipy/tree/fixes-sturla. The best way to 
>> get this in would be for Patrick to add these commits to his branch 
>> so they show up in his PR (after finding a bug, see below).
>>
>> I did some testing (python 2.6, 32-bit, OS X 10.6), I get one test 
>> failure with Sturla's edits. Patrick's branch given me no failures.
>>
>>  ======================================================================
>> FAIL: test_kdtree.test_count_neighbors_compiled.test_multiple_radius
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>>   File 
>> "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/nose-1.1.2-py2.6.egg/nose/case.py", 
>> line 197, in runTest
>>     self.test(*self.arg)
>>   File 
>> "/Users/rgommers/Code/scipy/scipy/spatial/tests/test_kdtree.py", line 
>> 496, in test_multiple_radius
>>     assert_equal(self.T1.count_neighbors(self.T2, r), result)
>>   File "/Users/rgommers/Code/numpy/numpy/testing/utils.py", line 313, 
>> in assert_equal
>>     raise AssertionError(msg)
>> AssertionError:
>> Items are not equal:
>>  ACTUAL: 6
>>  DESIRED: 54
>>
>> The actual and desired numbers change due to random numbers without a 
>> seed being used, but it fails consistently. The missing seed is no 
>> real problem here, because the code simply does the same twice; it 
>> only tests if the "r" input to count_neighbors is correctly vectorized.
>>
>> Ralf
>>
>>
>>
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>
>
>
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