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Merged
merged 4 commits into from
Jul 24, 2015
Merged

New interface for fslcpgeom #1152

merged 4 commits into from
Jul 24, 2015

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mick-d
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@mick-d mick-d commented Jul 22, 2015

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mick-d commented Jul 22, 2015

@satra I had to spend quite some time cleaning everything up as I coulnd't get rid of all the test files. Everything is good now.

To ensure that no input files are overwritten (more precisely dest_file) I had to copy dest_file locally (to the cwd) and then modify it there. I am not sure this the most elegant implementation so don't hesitate to let me know if there is a better solution. In any case I tested it and it works fine.

satra
satra reviewed Jul 22, 2015
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nipype/interfaces/fsl/utils.py
class CopyGeomInputSpec(FSLCommandInputSpec):
in_file = File(exists=True, mandatory=True, argstr="%s", position=0,
desc="source image")
dest_file = File(exists=True, mandatory=True, argstr="%s", position=1,
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you could add another two pieces of metadata to this:
output_name='out_file', name_template='%s_newhd'

and then remove all three functions (run_interface, gen_filename, list_outputs) from interface

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oops. this may not work for this scenario where dest_file is an existing file.

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I see. So the current implementation is ok?

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mick-d commented Jul 24, 2015

@satra Done

satra added a commit that referenced this pull request Jul 24, 2015
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Merge pull request #1152 from mick-d/FSLgeom
b77b4bc 
New interface for fslcpgeom
@satra satra merged commit b77b4bc into nipy:master Jul 24, 2015
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@mick-d @satra