[Insight-users] SimpleITK testing in Python

[David Welch]

Hi Matt,

That's not really an option for me.  I am working on a local machine, but the build is for a network cluster of Macs.  I could have my sysadmin push an update out to the cluster, but I'd prefer to install Numpy on /opt (network drive) and not tamper with the Apple default frameworks.  Should this be made an option in the CMake files, or is there some reason the system default is always chosen?

-Dave

--
David Welch
david.m.welch at gmail.com



On 8Dec, 2011, at 12:13 PM, Matt McCormick wrote:

> Hi David,
> 
> If SimpleITK is using your system Python, then you will need to
> install numpy into your system Python -- it will not use the other
> version.
> 
> Thanks,
> Matt
> 
> On Thu, Dec 8, 2011 at 12:20 PM, David Welch <david.m.welch at gmail.com> wrote:
>> Matt,
>> 
>> Works like a charm.  I have all but three tests passing now: Python.OtsuThreshold, Registration.Simple and Python.Test.Numpy.
>> 
>> I believe the last is caused b/c the submodule SimpleITK.numpy points to my out-of-date OSX Python framework version as opposed to my /Library/Python/site-packages version.  Is there a CMake flag to control that or is this intended?
>> 
>> -Dave
>> 
>> ----
>> David Welch
>> david.m.welch at gmail.com
>> 
>> Something you entered
>> transcended parameters.
>> So much is unknown.
>> 
>> -Salon Magazine, Error Haiku Challenge
>> 
>> 
>> On 30Nov, 2011, at 5:22 PM, Matt McCormick wrote:
>> 
>>> Hi Dave,
>>> 
>>> Please try
>>> 
>>>  git submodule update --init
>>> 
>>> at the top of the source tree.
>>> 
>>> Thanks,
>>> Matt
>>> 
>>> On Wed, Nov 30, 2011 at 6:10 PM, David Welch <david.m.welch at gmail.com> wrote:
>>>> Thanks, Bill.  The tests run, but almost all fail.  Using the -VV flag, I see the first ~10 are looking for the Input/ directory from the SimpleITKData repository.  How do I point CTest (or SITK) to this directory?
>>>> 
>>>> -Dave
>>>> 
>>>> --
>>>> David Welch
>>>> david.m.welch at gmail.com
>>>> 
>>>> 
>>>> 
>>>> On 30Nov, 2011, at 1:53 PM, Bill Lorensen wrote:
>>>> 
>>>>> Try typing ctest at the top[ of your build tree.
>>>>> 
>>>>> 
>>>>> On Wed, Nov 30, 2011 at 2:41 PM, David Welch <david.m.welch at gmail.com> wrote:
>>>>>> Hello all,
>>>>>> I've installed SimpleITK with Python wrapping and testing ON, but now that
>>>>>> I've finished my build, I cannot see how to test it.  After building with
>>>>>> CMake, I did the following:
>>>>>> *******************************************
>>>>>> $ cd Wrapping/
>>>>>> $ python PythonPackage/setup.py install
>>>>>> $ python
>>>>>>>>> import SimpleITK as sitk
>>>>>>>>> sitk.test("1")
>>>>>> Traceback (most recent call last):
>>>>>>   File "<stdin>", line 1, in <module>
>>>>>> AttributeError: 'module' object has no attribute 'test'
>>>>>> *******************************************
>>>>>> Looking at the SimpleITK Jira site, there is a Python virtualenv to test the
>>>>>> python install ( https://issues.itk.org/jira/browse/SIMPLEITK-163 ) but it
>>>>>> doesn't seem to address testing SimpleITK itself.
>>>>>> In the build folder, there is a Testing/Unit/PythonTests folder with many
>>>>>> test files, but running them from the command line gives an error "Usage:
>>>>>> FooBar tag <input(s)> output".  I can't find any documentation to help me,
>>>>>> either.
>>>>>> Cheers,
>>>>>> Dave
>>>>>> ----
>>>>>> David Welch
>>>>>> david.m.welch at gmail.com
>>>>>> 
>>>>>> Something you entered
>>>>>> transcended parameters.
>>>>>> So much is unknown.
>>>>>> -Salon Magazine, Error Haiku Challenge
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> _____________________________________
>>>>>> Powered by www.kitware.com
>>>>>> 
>>>>>> Visit other Kitware open-source projects at
>>>>>> http://www.kitware.com/opensource/opensource.html
>>>>>> 
>>>>>> Kitware offers ITK Training Courses, for more information visit:
>>>>>> http://www.kitware.com/products/protraining.html
>>>>>> 
>>>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>>>> 
>>>>>> Follow this link to subscribe/unsubscribe:
>>>>>> http://www.itk.org/mailman/listinfo/insight-users
>>>>>> 
>>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> --
>>>>> Unpaid intern in BillsBasement at noware dot com
>>>> 
>>>> _____________________________________
>>>> Powered by www.kitware.com
>>>> 
>>>> Visit other Kitware open-source projects at
>>>> http://www.kitware.com/opensource/opensource.html
>>>> 
>>>> Kitware offers ITK Training Courses, for more information visit:
>>>> http://www.kitware.com/products/protraining.html
>>>> 
>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>> 
>>>> Follow this link to subscribe/unsubscribe:
>>>> http://www.itk.org/mailman/listinfo/insight-users
>>