Merge pull request #2233 from jdkent/enh-create_susan_smooth

[ENH]: add list_fwhm option to create_susan_smooth

Author: effigies

nipype/workflows/fmri/fsl/preprocess.py

@@ -4,7 +4,6 @@
 from __future__ import division
 
 import os
-
 from ....interfaces import fsl as fsl # fsl
 from ....interfaces import utility as util # utility
 from ....pipeline import engine as pe # pypeline engine
@@ -771,7 +770,7 @@ def create_susan_smooth(name="susan_smooth", separate_masks=True):
  Inputs::
 
  inputnode.in_files : functional runs (filename or list of filenames)
- inputnode.fwhm : fwhm for smoothing with SUSAN
+ inputnode.fwhm : fwhm for smoothing with SUSAN (float or list of floats)
  inputnode.mask_file : mask used for estimating SUSAN thresholds (but not for smoothing)
 
  Outputs::
@@ -788,6 +787,19 @@ def create_susan_smooth(name="susan_smooth", separate_masks=True):
  >>> smooth.run() # doctest: +SKIP
 
  """
+ # replaces the functionality of a "for loop"
+ def cartesian_product(fwhms, in_files, usans, btthresh):
+ from nipype.utils.filemanip import filename_to_list
+ # ensure all inputs are lists
+ in_files = filename_to_list(in_files)
+ fwhms = [fwhms] if isinstance(fwhms, (int, float)) else fwhms
+ # create cartesian product lists (s_<name> = single element of list)
+ cart_in_file = [s_in_file for s_in_file in in_files for s_fwhm in fwhms]
+ cart_fwhm = [s_fwhm for s_in_file in in_files for s_fwhm in fwhms]
+ cart_usans = [s_usans for s_usans in usans for s_fwhm in fwhms]
+ cart_btthresh = [s_btthresh for s_btthresh in btthresh for s_fwhm in fwhms]
+
+ return cart_in_file, cart_fwhm, cart_usans, cart_btthresh
 
  susan_smooth = pe.Workflow(name=name)
 
@@ -807,8 +819,15 @@ def create_susan_smooth(name="susan_smooth", separate_masks=True):
  functional
  """
 
+ multi_inputs = pe.Node(util.Function(function=cartesian_product,
+ output_names=['cart_in_file',
+ 'cart_fwhm',
+ 'cart_usans',
+ 'cart_btthresh']),
+ name='multi_inputs')
+
  smooth = pe.MapNode(interface=fsl.SUSAN(),
- iterfield=['in_file', 'brightness_threshold', 'usans'],
+ iterfield=['in_file', 'brightness_threshold', 'usans', 'fwhm'],
  name='smooth')
 
  """
@@ -865,10 +884,17 @@ def create_susan_smooth(name="susan_smooth", separate_masks=True):
  """
  Define a function to get the brightness threshold for SUSAN
  """
- susan_smooth.connect(inputnode, 'fwhm', smooth, 'fwhm')
- susan_smooth.connect(inputnode, 'in_files', smooth, 'in_file')
- susan_smooth.connect(median, ('out_stat', getbtthresh), smooth, 'brightness_threshold')
- susan_smooth.connect(merge, ('out', getusans), smooth, 'usans')
+
+ susan_smooth.connect([
+ (inputnode, multi_inputs, [('in_files', 'in_files'),
+ ('fwhm', 'fwhms')]),
+ (median, multi_inputs, [(('out_stat', getbtthresh), 'btthresh')]),
+ (merge, multi_inputs, [(('out', getusans), 'usans')]),
+ (multi_inputs, smooth, [('cart_in_file', 'in_file'),
+ ('cart_fwhm', 'fwhm'),
+ ('cart_btthresh', 'brightness_threshold'),
+ ('cart_usans', 'usans')]),
+ ])
 
  outputnode = pe.Node(interface=util.IdentityInterface(fields=['smoothed_files']),
  name='outputnode')