Merge branch 'enh/ImproveJSONInterfaces' into enh/AntsForFMBworkflow

Conflicts:
	CHANGES

Author: oesteban

CHANGES

@@ -3,6 +3,8 @@ Next release
 
 * ENH: Improved FieldMap-Based (FMB) workflow for correction of susceptibility distortions in EPI seqs.
        (https://github.com/nipy/nipype/pull/1019)
+* ENH: Improve JSON interfaces: default settings when reading and consistent output creation
+       when writing (https://github.com/nipy/nipype/pull/1047)
 * ENH: New io interfaces for JSON files reading/writing (https://github.com/nipy/nipype/pull/1020)
 * ENH: Enhanced openfmri script to support freesurfer linkage (https://github.com/nipy/nipype/pull/1037)
 * BUG: matplotlib is supposed to be optional (https://github.com/nipy/nipype/pull/1003)

nipype/interfaces/io.py

@@ -1804,8 +1804,9 @@ def _get_ssh_client(self):
 
 
 class JSONFileGrabberInputSpec(DynamicTraitedSpec, BaseInterfaceInputSpec):
-    in_file = File(exists=True, mandatory=True,
-                   desc='JSON source file')
+    in_file = File(exists=True, desc='JSON source file')
+    defaults = traits.Dict(desc=('JSON dictionary that sets default output'
+                                'values, overridden by values found in in_file'))
 
 
 class JSONFileGrabber(IOBase):
@@ -1819,12 +1820,15 @@ class JSONFileGrabber(IOBase):
 
     >>> from nipype.interfaces.io import JSONFileGrabber
     >>> jsonSource = JSONFileGrabber()
+    >>> jsonSource.inputs.defaults = {'param1': u'overrideMe', 'param3': 1.0}
+    >>> res = jsonSource.run()
+    >>> res.outputs.get()
+    {'param3': 1.0, 'param1': u'overrideMe'}
     >>> jsonSource.inputs.in_file = 'jsongrabber.txt'
     >>> res = jsonSource.run()
-    >>> print res.outputs.param1
-    exampleStr
-    >>> print res.outputs.param2
-    4
+    >>> res.outputs.get()
+    {'param3': 1.0, 'param2': 4, 'param1': u'exampleStr'}
+
 
     """
     input_spec = JSONFileGrabberInputSpec
@@ -1834,15 +1838,22 @@ class JSONFileGrabber(IOBase):
     def _list_outputs(self):
         import json
 
-        with open(self.inputs.in_file, 'r') as f:
-            data = json.load(f)
+        outputs = {}
+        if isdefined(self.inputs.in_file):
+            with open(self.inputs.in_file, 'r') as f:
+                data = json.load(f)
 
-        if not isinstance(data, dict):
-            raise RuntimeError('JSON input has no dictionary structure')
+            if not isinstance(data, dict):
+                raise RuntimeError('JSON input has no dictionary structure')
 
-        outputs = {}
-        for key, value in data.iteritems():
-            outputs[key] = value
+            for key, value in data.iteritems():
+                outputs[key] = value
+
+        if isdefined(self.inputs.defaults):
+            defaults = self.inputs.defaults
+            for key, value in defaults.iteritems():
+                if key not in outputs.keys():
+                    outputs[key] = value
 
         return outputs
 

nipype/interfaces/tests/test_auto_JSONFileGrabber.py

@@ -3,11 +3,11 @@
 from nipype.interfaces.io import JSONFileGrabber
 
 def test_JSONFileGrabber_inputs():
-    input_map = dict(ignore_exception=dict(nohash=True,
+    input_map = dict(defaults=dict(),
+    ignore_exception=dict(nohash=True,
     usedefault=True,
     ),
-    in_file=dict(mandatory=True,
-    ),
+    in_file=dict(),
     )
     inputs = JSONFileGrabber.input_spec()
 

nipype/workflows/dmri/fsl/artifacts.py

@@ -554,10 +554,8 @@ def sdc_fmb(name='fmb_correction',
 
     """
 
-    defaults = dict(delta_te=2.46e-3, echospacing=0.77e-3, acc_factor=3,
-                    enc_dir='AP')
-
-    delta_te = epi_params['echospacing'] / (1.0 * epi_params['acc_factor'])
+    epi_defaults = {'delta_te': 2.46e-3, 'echospacing': 0.77e-3,
+                    'acc_factor': 3, 'enc_dir': u'AP'}
 
     def _fix_enc_dir(enc_dir):
         enc_dir = enc_dir.lower()
@@ -579,7 +577,8 @@ def _fix_enc_dir(enc_dir):
     outputnode = pe.Node(niu.IdentityInterface(
         fields=['out_file', 'out_vsm', 'out_warp']), name='outputnode')
 
-    r_params = pe.Node(JSONFileGrabber(), name='SettingsGrabber')
+    r_params = pe.Node(JSONFileGrabber(defaults=epi_defaults),
+                       name='SettingsGrabber')
     eff_echo = pe.Node(niu.Function(function=_eff_t_echo,
                                     input_names=['echospacing', 'acc_factor'],
                                     output_names=['eff_echo']), name='EffEcho')