Merge branch 'master' into fix/DockerTags

Author: oesteban

CHANGES

@@ -2,6 +2,7 @@ Upcoming release 0.13
 =====================
 
 * TST: reduce the size of docker images & use tags for images (https://github.com/nipy/nipype/pull/1564)
+* ENH: Implement missing inputs/outputs in FSL AvScale (https://github.com/nipy/nipype/pull/1563)
 
 
 Release 0.12.1 (August 3, 2016)

nipype/interfaces/base.py

@@ -1660,7 +1660,7 @@ def _run_wrapper(self, runtime):
         runtime = self._run_interface(runtime)
         return runtime
 
-    def _run_interface(self, runtime, correct_return_codes=[0]):
+    def _run_interface(self, runtime, correct_return_codes=(0,)):
         """Execute command via subprocess
 
         Parameters

nipype/interfaces/fsl/__init__.py

@@ -12,7 +12,7 @@
 from .model import (Level1Design, FEAT, FEATModel, FILMGLS, FEATRegister,
                     FLAMEO, ContrastMgr, MultipleRegressDesign, L2Model, SMM,
                     MELODIC, SmoothEstimate, Cluster, Randomise, GLM)
-from .utils import (Smooth, Merge, ExtractROI, Split, ImageMaths, ImageMeants,
+from .utils import (AvScale, Smooth, Merge, ExtractROI, Split, ImageMaths, ImageMeants,
                     ImageStats, FilterRegressor, Overlay, Slicer,
                     PlotTimeSeries, PlotMotionParams, ConvertXFM,
                     SwapDimensions, PowerSpectrum, Reorient2Std,

nipype/interfaces/fsl/tests/test_auto_AvScale.py

@@ -4,7 +4,9 @@
 
 
 def test_AvScale_inputs():
-    input_map = dict(args=dict(argstr='%s',
+    input_map = dict(all_param=dict(argstr='--allparams',
+    ),
+    args=dict(argstr='%s',
     ),
     environ=dict(nohash=True,
     usedefault=True,
@@ -13,9 +15,12 @@ def test_AvScale_inputs():
     usedefault=True,
     ),
     mat_file=dict(argstr='%s',
-    position=0,
+    position=-2,
     ),
     output_type=dict(),
+    ref_file=dict(argstr='%s',
+    position=-1,
+    ),
     terminal_output=dict(nohash=True,
     ),
     )
@@ -32,9 +37,11 @@ def test_AvScale_outputs():
     determinant=dict(),
     forward_half_transform=dict(),
     left_right_orientation_preserved=dict(),
+    rot_angles=dict(),
     rotation_translation_matrix=dict(),
     scales=dict(),
     skews=dict(),
+    translations=dict(),
     )
     outputs = AvScale.output_spec()
 

nipype/interfaces/fsl/utils.py

@@ -22,6 +22,7 @@
 
 import os
 import os.path as op
+import re
 from glob import glob
 import warnings
 import tempfile
@@ -608,25 +609,32 @@ def aggregate_outputs(self, runtime=None, needed_outputs=None):
         return outputs
 
 
-class AvScaleInputSpec(FSLCommandInputSpec):
-    mat_file = File(exists=True, argstr="%s",
-                    desc='mat file to read', position=0)
+class AvScaleInputSpec(CommandLineInputSpec):
+    all_param = traits.Bool(False, argstr='--allparams')
+    mat_file = File(exists=True, argstr='%s',
+                    desc='mat file to read', position=-2)
+    ref_file = File(exists=True, argstr='%s', position=-1,
+                    desc='reference file to get center of rotation')
 
 
 class AvScaleOutputSpec(TraitedSpec):
-    rotation_translation_matrix = traits.Any(
-        desc='Rotation and Translation Matrix')
-    scales = traits.Any(desc='Scales (x,y,z)')
-    skews = traits.Any(desc='Skews')
-    average_scaling = traits.Any(desc='Average Scaling')
-    determinant = traits.Any(desc='Determinant')
-    forward_half_transform = traits.Any(desc='Forward Half Transform')
-    backward_half_transform = traits.Any(desc='Backwards Half Transform')
+    rotation_translation_matrix = traits.List(
+        traits.List(traits.Float), desc='Rotation and Translation Matrix')
+    scales = traits.List(traits.Float, desc='Scales (x,y,z)')
+    skews = traits.List(traits.Float, desc='Skews')
+    average_scaling = traits.Float(desc='Average Scaling')
+    determinant = traits.Float(desc='Determinant')
+    forward_half_transform = traits.List(
+        traits.List(traits.Float), desc='Forward Half Transform')
+    backward_half_transform = traits.List(
+        traits.List(traits.Float), desc='Backwards Half Transform')
     left_right_orientation_preserved = traits.Bool(
         desc='True if LR orientation preserved')
+    rot_angles = traits.List(traits.Float, desc='rotation angles')
+    translations = traits.List(traits.Float, desc='translations')
 
 
-class AvScale(FSLCommand):
+class AvScale(CommandLine):
     """Use FSL avscale command to extract info from mat file output of FLIRT
 
     Examples
@@ -643,34 +651,47 @@ class AvScale(FSLCommand):
 
     _cmd = 'avscale'
 
-    def _format_arg(self, name, trait_spec, value):
-        return super(AvScale, self)._format_arg(name, trait_spec, value)
-
-    def aggregate_outputs(self, runtime=None, needed_outputs=None):
-        outputs = self._outputs()
-
-        def lines_to_float(lines):
-            out = []
-            for line in lines:
-                values = line.split()
-                out.append([float(val) for val in values])
-            return out
-
-        out = runtime.stdout.split('\n')
-
-        outputs.rotation_translation_matrix = lines_to_float(out[1:5])
-        outputs.scales = lines_to_float([out[6].split(" = ")[1]])
-        outputs.skews = lines_to_float([out[8].split(" = ")[1]])
-        outputs.average_scaling = lines_to_float([out[10].split(" = ")[1]])
-        outputs.determinant = lines_to_float([out[12].split(" = ")[1]])
-        if out[13].split(": ")[1] == 'preserved':
-            outputs.left_right_orientation_preserved = True
-        else:
-            outputs.left_right_orientation_preserved = False
-        outputs.forward_half_transform = lines_to_float(out[16:20])
-        outputs.backward_half_transform = lines_to_float(out[22:-1])
+    def _run_interface(self, runtime):
+        runtime = super(AvScale, self)._run_interface(runtime)
+
+
+        expr = re.compile(
+            'Rotation\ &\ Translation\ Matrix:\n(?P<rot_tran_mat>[0-9\.\ \n-]+)[\s\n]*'
+            '(Rotation\ Angles\ \(x,y,z\)\ \[rads\]\ =\ (?P<rot_angles>[0-9\.\ -]+))?[\s\n]*'
+            '(Translations\ \(x,y,z\)\ \[mm\]\ =\ (?P<translations>[0-9\.\ -]+))?[\s\n]*'
+            'Scales\ \(x,y,z\)\ =\ (?P<scales>[0-9\.\ -]+)[\s\n]*'
+            'Skews\ \(xy,xz,yz\)\ =\ (?P<skews>[0-9\.\ -]+)[\s\n]*'
+            'Average\ scaling\ =\ (?P<avg_scaling>[0-9\.-]+)[\s\n]*'
+            'Determinant\ =\ (?P<determinant>[0-9\.-]+)[\s\n]*'
+            'Left-Right\ orientation:\ (?P<lr_orientation>[A-Za-z]+)[\s\n]*'
+            'Forward\ half\ transform\ =[\s]*\n'
+            '(?P<fwd_half_xfm>[0-9\.\ \n-]+)[\s\n]*'
+            'Backward\ half\ transform\ =[\s]*\n'
+            '(?P<bwd_half_xfm>[0-9\.\ \n-]+)[\s\n]*')
+        out = expr.search(runtime.stdout).groupdict()
+        outputs = {}
+        outputs['rotation_translation_matrix'] = [[
+            float(v) for v in r.strip().split(' ')] for r in out['rot_tran_mat'].strip().split('\n')]
+        outputs['scales'] = [float(s) for s in out['scales'].strip().split(' ')]
+        outputs['skews'] = [float(s) for s in out['skews'].strip().split(' ')]
+        outputs['average_scaling'] = float(out['avg_scaling'].strip())
+        outputs['determinant'] = float(out['determinant'].strip())
+        outputs['left_right_orientation_preserved'] = out['lr_orientation'].strip() == 'preserved'
+        outputs['forward_half_transform'] = [[
+            float(v) for v in r.strip().split(' ')] for r in out['fwd_half_xfm'].strip().split('\n')]
+        outputs['backward_half_transform'] = [[
+            float(v) for v in r.strip().split(' ')] for r in out['bwd_half_xfm'].strip().split('\n')]
+
+        if self.inputs.all_param:
+            outputs['rot_angles'] = [float(r) for r in out['rot_angles'].strip().split(' ')]
+            outputs['translations'] = [float(r) for r in out['translations'].strip().split(' ')]
+
+
+        setattr(self, '_results', outputs)
+        return runtime
 
-        return outputs
+    def _list_outputs(self):
+        return self._results
 
 
 class OverlayInputSpec(FSLCommandInputSpec):