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==========================
Auto-generated filenames
==========================
In refactoring the inputs in the traitlets branch I'm working through
the different ways that filenames are generated and want to make sure
the interface is consistent. The notes below are all using fsl.Bet as
that's the first class we're Traiting. Other interface classes may
handle this differently, but should agree on a convention and apply it
across all Interfaces (if possible).
Current Rules
-------------
These rules are for fsl.Bet, but it appears they are the same for all
fsl and spm Interfaces.
Bet has two mandatory parameters, ``infile`` and ``outfile``. These
are the rules for how they are handled in different use cases.
1. If ``infile`` or ``outfile`` are absolute paths, they are used
as-is and never changed. This allows users to override any
filename/path generation.
2. If ``outfile`` is not specified, a filename is generated.
3. Generated filenames (at least for ``outfile``) are based on:
* ``infile``, the filename minus the extensions.
* A suffix specified by the Interface. For example Bet uses
*_brain* suffix.
* The current working directory, os.getcwd(). Example:
If ``infile`` == 'foo.nii' and the cwd is ``/home/cburns`` then
generated ``outfile`` for Bet will be
``/home/cburns/foo_brain.nii.gz``
4. If ``outfile`` is not an absolute path, for instance just a
filename, the absolute path is generated using
``os.path.realpath``. This absolute path is needed to make sure the
packages (Bet in this case) write the output file to a location of
our choosing. The generated absolute path is only used in the
``cmdline`` at runtime and does __not__ overwrite the class attr
``self.inputs.outfile``. It is generated only when the ``cmdline``
is invoked.
Walking through some examples
-----------------------------
In this example we assign ``infile`` directly but ``outfile`` is
generated in ``Bet._parse_inputs`` based on ``infile``. The generated
``outfile`` is only used in the cmdline at runtime and not stored in
``self.inputs.outfile``. This seems correct.
.. sourcecode:: ipython
In [15]: from nipype.interfaces import fsl
In [16]: mybet = fsl.Bet()
In [17]: mybet.inputs.infile = 'foo.nii'
In [18]: res = mybet.run()
In [19]: res.runtime.cmdline
Out[19]: 'bet foo.nii /Users/cburns/src/nipy-sf/nipype/trunk/nipype/interfaces/tests/foo_brain.nii.gz'
In [21]: mybet.inputs
Out[21]: Bunch(center=None, flags=None, frac=None, functional=None,
infile='foo.nii', mask=None, mesh=None, nooutput=None, outfile=None,
outline=None, radius=None, reduce_bias=None, skull=None, threshold=None,
verbose=None, vertical_gradient=None)
In [24]: mybet.cmdline
Out[24]: 'bet foo.nii /Users/cburns/src/nipy-sf/nipype/trunk/nipype/interfaces/tests/foo_brain.nii.gz'
In [25]: mybet.inputs.outfile
In [26]: mybet.inputs.infile
Out[26]: 'foo.nii'
We get the same behavior here when we assign ``infile`` at initialization:
.. sourcecode:: ipython
In [28]: mybet = fsl.Bet(infile='foo.nii')
In [29]: mybet.cmdline
Out[29]: 'bet foo.nii /Users/cburns/src/nipy-sf/nipype/trunk/nipype/interfaces/tests/foo_brain.nii.gz'
In [30]: mybet.inputs
Out[30]: Bunch(center=None, flags=None, frac=None, functional=None,
infile='foo.nii', mask=None, mesh=None, nooutput=None, outfile=None,
outline=None, radius=None, reduce_bias=None, skull=None, threshold=None,
verbose=None, vertical_gradient=None)
In [31]: res = mybet.run()
In [32]: res.runtime.cmdline
Out[32]: 'bet foo.nii /Users/cburns/src/nipy-sf/nipype/trunk/nipype/interfaces/tests/foo_brain.nii.gz'
Here we specify absolute paths for both ``infile`` and
``outfile``. The command line's look as expected:
.. sourcecode:: ipython
In [53]: import os
In [54]: mybet = fsl.Bet()
In [55]: mybet.inputs.infile = os.path.join('/Users/cburns/tmp/junk', 'foo.nii')
In [56]: mybet.inputs.outfile = os.path.join('/Users/cburns/tmp/junk', 'bar.nii')
In [57]: mybet.cmdline
Out[57]: 'bet /Users/cburns/tmp/junk/foo.nii /Users/cburns/tmp/junk/bar.nii'
In [58]: res = mybet.run()
In [59]: res.runtime.cmdline
Out[59]: 'bet /Users/cburns/tmp/junk/foo.nii /Users/cburns/tmp/junk/bar.nii'
Here passing in a new ``outfile`` in the ``run`` method will update
``mybet.inputs.outfile`` to the passed in value. Should this be the
case?
.. sourcecode:: ipython
In [110]: mybet = fsl.Bet(infile='foo.nii', outfile='bar.nii')
In [111]: mybet.inputs.outfile
Out[111]: 'bar.nii'
In [112]: mybet.cmdline
Out[112]: 'bet foo.nii /Users/cburns/src/nipy-sf/nipype/trunk/nipype/interfaces/tests/bar.nii'
In [113]: res = mybet.run(outfile = os.path.join('/Users/cburns/tmp/junk', 'not_bar.nii'))
In [114]: mybet.inputs.outfile
Out[114]: '/Users/cburns/tmp/junk/not_bar.nii'
In [115]: mybet.cmdline
Out[115]: 'bet foo.nii /Users/cburns/tmp/junk/not_bar.nii'
In this case we provide ``outfile`` but not as an absolue path, so the
absolue path is generated and used for the ``cmdline`` when run, but
``mybet.inputs.outfile`` is not updated with the absolute path.
.. sourcecode:: ipython
In [74]: mybet = fsl.Bet(infile='foo.nii', outfile='bar.nii')
In [75]: mybet.inputs.outfile
Out[75]: 'bar.nii'
In [76]: mybet.cmdline
Out[76]: 'bet foo.nii /Users/cburns/src/nipy-sf/nipype/trunk/nipype/interfaces/tests/bar.nii'
In [77]: res = mybet.run()
In [78]: res.runtime.cmdline
Out[78]: 'bet foo.nii /Users/cburns/src/nipy-sf/nipype/trunk/nipype/interfaces/tests/bar.nii'
In [80]: res.interface.inputs.outfile
Out[80]: 'bar.nii'
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