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doc/devel/interface_specs.rst

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@@ -7,19 +7,18 @@ Interface Specifications
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Before you start
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----------------
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Nipype is a young project maintained by an enthusiastic group of developers.
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Even though the documentation might be sparse or cryptic at times we strongly
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encourage you to contact us on the official nipype developers mailing list in
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case of any troubles: nipy-devel@neuroimaging.scipy.org (we are sharing a
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mailing list with the nipy community therefore please add ``[nipype]`` to the
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messsage title).
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Nipype is maintained by an enthusiastic group of developers, and we're excited to have you join!
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In case of trouble, we encourage you to post on `NeuroStars <https://neurostars.org>`_ with the `nipype` tag.
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NeuroStars.org is a platform similar to StackOverflow but dedicated to neuroinformatics.
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You can also post on the nipype developers mailing list: http://mail.python.org/mailman/listinfo/neuroimaging.
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We are sharing a mailing list with the nipy community therefore please add ``[nipype]`` to the message title.
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Overview
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--------
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We're using the `Enthought Traits
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<http://code.enthought.com/projects/traits/>`_ package for all of our
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We're using the `Traits, formerly known as Enthought Traits
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<http://docs.enthought.com/traits/traits_user_manual/intro.html>`_ package for all of our
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inputs and outputs. Traits allows us to validate user inputs and
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provides a mechanism to handle all the *special cases* in a simple and
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concise way though metadata. With the metadata, each input/output can
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Here are a few starting points in the documentation:
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* What are Traits? The `Introduction in the User Manual
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<http://code.enthought.com/projects/traits/docs/html/traits_user_manual/intro.html>`_
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<http://docs.enthought.com/traits/traits_user_manual/intro.html>`_
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gives a brief description of the functionality traits provides.
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* Traits and metadata. The `second section of the User Manual
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<http://code.enthought.com/projects/traits/docs/html/traits_user_manual/defining.html>`_
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<http://docs.enthought.com/traits/traits_user_manual/defining.html>`_
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gives more details on traits and how to use them. Plus there a
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section describing metadata, including the metadata all traits have.
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* If your interested in more of a *big picture* overview, `Gael wrote
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a good tutorial
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<http://code.enthought.com/projects/traits/docs/html/tutorials/traits_ui_scientific_app.html>`_
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<http://docs.enthought.com/traitsui/tutorials/traits_ui_scientific_app.html>`_
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that shows how to write a scientific application using traits for
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the benefit of the generated UI components. (For now, Nipype is not
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taking advantage of the generated UI feature of traits.)
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Traits version
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^^^^^^^^^^^^^^
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We're using Traits version 3.x which can be install as part of `EPD
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<http://enthought.com/products/epd.php>`_ or from `pypi
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<http://pypi.python.org/pypi/Traits/3.3.0>`_
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We're using Traits version 4.x which can be installed from `pypi
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<https://pypi.python.org/pypi/traits>`_
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More documentation
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^^^^^^^^^^^^^^^^^^
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Not everything is documented in the User Manual, in those cases the
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`enthought-dev mailing list
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<https://mail.enthought.com/mailman/listinfo/enthought-dev>`_ or the
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`API docs
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<http://code.enthought.com/projects/files/ETS32_API/enthought.traits.html>`_
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the `API docs
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<http://docs.enthought.com/traits/traits_api_reference/index.html>`_
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is your next place to look.
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Nipype Interface Specifications
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- BETOutputSpec
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Each of these Specs are classes, derived from a base TraitedSpec class
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(more on these below). The InputSpec consists of attributes which
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(more on these below). The InputSpec consists of attributes which
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correspond to different parameters for the tool they wrap/interface.
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In the case of a command-line tool like Bet, the InputSpec attributes
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correspond to the different command-line parameters that can be passed
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to Bet. If you are familiar with the Nipype 0.2 code-base, these
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attributes are the same as the keys in the opt_map dictionaries. When
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an interfaces class is instantiated, the InputSpec is bound to the
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to Bet.
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When an interfaces class is instantiated, the InputSpec is bound to the
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``inputs`` attribute of that object. Below is an example of how the
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``inputs`` appear to a user for Bet::
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