ENH: AFNI (3d)LocalBistat interface #2590
Conversation
nipype/interfaces/afni/utils.py
Outdated
| @@ -1338,6 +1338,124 @@ def _list_outputs(self): | |||
| return outputs | |||
|
|
|||
|
|
|||
| class LocalBistatInputSpec(AFNICommandInputSpec): | |||
| in_files = InputMultiPath( | |||
There was a problem hiding this comment.
This should just be traits.List, not InputMultiPath.
And out of curiosity, is it more likely that people will want to pass in a list of two files or want separate names for each file (e.g. in_file1, in_file2)?
There was a problem hiding this comment.
may be separate names are more suitable, you are right
There was a problem hiding this comment.
Is the plan to split this into two traits, or leave it as one?
There was a problem hiding this comment.
sorry I forgot this, I am doing it
nipype/interfaces/afni/utils.py
Outdated
| 'jointent', 'hellinger', 'crU', 'crM', 'crA', 'L2slope', | ||
| 'L1slope', 'num', 'ALL'] | ||
| stat = traits.Either( | ||
| traits.Enum(*_stat_names), traits.List(traits.Enum(_stat_names)), |
There was a problem hiding this comment.
Does this not work?
stat = traits.MultiPath(traits.Enum(_stat_names), ...)There was a problem hiding this comment.
I am not sure I understand: traits does not seem to have a `MultiPath
AttributeError: 'module' object has no attribute 'MultiPath'`
There was a problem hiding this comment.
Oh, sorry. I meant InputMultiPath, not traits.MultiPath. I don't know if I copy-pasted or actually wrote that out.
nipype/interfaces/afni/utils.py
Outdated
| '\'SPHERE\', \'RHDD\' (rhombic dodecahedron), \'TOHD\' ' | ||
| '(truncated octahedron) with a given radius in mm or ' | ||
| '\'RECT\' (rectangular block) with dimensions to specify in mm.', | ||
| argstr='-nbhd %s') |
There was a problem hiding this comment.
How about:
argstr='-nbhd %s(%s)'Related to a comment below.
nipype/interfaces/afni/utils.py
Outdated
| "'{0}({1})'".format(region_name, ','.join(region_size))) | ||
| else: | ||
| return spec.argstr % ( | ||
| "'{0}({1})'".format(region_name, region_size)) |
There was a problem hiding this comment.
With the argstr='-nbhd %s(%s)' as suggested above, you could make this whole block:
if name == 'neighborhood' and value[0] == 'RECT':
value = ('RECT', '%s,%s,%s' % value[1])(Letting value fall through into the super call.)
| desc='File name of an image to use as a weight. Only applies to ' | ||
| '\'pearson\' statistics.', | ||
| argstr='-weight %s', | ||
| xor=['automask']) |
There was a problem hiding this comment.
You have two mask_file traits.
nipype/interfaces/afni/utils.py
Outdated
| 'will have its statistic(s) computed as zero (0).', | ||
| argstr='-mask %s') | ||
| automask = traits.Bool( | ||
| desc='Compute the mask as in program 3dAutomask.') |
There was a problem hiding this comment.
Should there be an argstr here?
nipype/interfaces/afni/utils.py
Outdated
| if isinstance(value, (str, bytes)): | ||
| return spec.argstr % value | ||
| else: | ||
| return ' '.join([spec.argstr % v for v in value]) |
There was a problem hiding this comment.
I'm pretty sure you can drop this if name == 'stat' block and get the same behavior.
There was a problem hiding this comment.
I'm pretty sure you can drop this if name == 'stat' block and get the same behavior.
this doesn't seem to work: it doesn't repeat the option '-stat' before each value
bistat.inputs.stat = ['pearson', 'ALL']gives -stat pearson ALL instead of -stat pearson -stat ALL
There was a problem hiding this comment.
@salma1601 - if you change the argstr above to '-stat %s...' it will do what you are looking for.
Codecov Report
@@ Coverage Diff @@
## master #2590 +/- ##
=========================================
+ Coverage 67.57% 67.6% +0.02%
=========================================
Files 335 336 +1
Lines 42630 42699 +69
Branches 5270 5278 +8
=========================================
+ Hits 28807 28865 +58
- Misses 13150 13157 +7
- Partials 673 677 +4
Continue to review full report at Codecov.
|
|
Hi @salma1601, not to rush you, but just a heads up that we should try to get this in by Friday (EDT) if we want it in 1.0.4. |
nipype/interfaces/afni/utils.py
Outdated
| ' map that size.' | ||
| ' * ALL = all of the above, in that order' | ||
| 'More than one option can be used.', | ||
| argstr='-stat %s') |
There was a problem hiding this comment.
yes it works, thanks !
effigies
changed the title
try add interface for
3dLocalBistat