[ENH] Convenient load/save of interface inputs

CHANGES

@@ -1,6 +1,7 @@
 Upcoming release 0.13
 =====================
 
+* ENH: Convenient load/save of interface inputs (https://github.com/nipy/nipype/pull/1591)
 * 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)
 * FIX: Fix symlink test in copyfile (https://github.com/nipy/nipype/pull/1570, https://github.com/nipy/nipype/pull/1586)

nipype/interfaces/base.py

@@ -35,7 +35,7 @@
 from datetime import datetime as dt
 from dateutil.parser import parse as parseutc
 from warnings import warn
-
+import simplejson as json
 
 from .traits_extension import (traits, Undefined, TraitDictObject,
                                TraitListObject, TraitError,
@@ -56,6 +56,8 @@
 
 iflogger = logging.getLogger('interface')
 
+PY35 = sys.version_info >= (3, 5)
+
 if runtime_profile:
     try:
         import psutil
@@ -758,14 +760,19 @@ class BaseInterface(Interface):
     _additional_metadata = []
     _redirect_x = False
 
-    def __init__(self, **inputs):
+    def __init__(self, from_file=None, **inputs):
         if not self.input_spec:
             raise Exception('No input_spec in class: %s' %
                             self.__class__.__name__)
+
         self.inputs = self.input_spec(**inputs)
         self.estimated_memory_gb = 1
         self.num_threads = 1
 
+        if from_file is not None:
+            self.load_inputs_from_json(from_file, overwrite=False)
+
+
     @classmethod
     def help(cls, returnhelp=False):
         """ Prints class help
@@ -1148,6 +1155,34 @@ def version(self):
                                  self.__class__.__name__)
         return self._version
 
+    def load_inputs_from_json(self, json_file, overwrite=True):
+        """
+        A convenient way to load pre-set inputs from a JSON file.
+        """
+
+        with open(json_file) as fhandle:
+            inputs_dict = json.load(fhandle)
+
+        for key, newval in list(inputs_dict.items()):
+            if not hasattr(self.inputs, key):
+                continue
+            val = getattr(self.inputs, key)
+            if overwrite or not isdefined(val):
+                setattr(self.inputs, key, newval)
+
+    def save_inputs_to_json(self, json_file):
+        """
+        A convenient way to save current inputs to a JSON file.
+        """
+        inputs = self.inputs.get()
+        for key, val in list(inputs.items()):
+            if not isdefined(val):
+                inputs.pop(key, None)
+
+        iflogger.debug('saving inputs {}', inputs)
+        with open(json_file, 'w') as fhandle:
+            json.dump(inputs, fhandle, indent=4)
+
 
 class Stream(object):
     """Function to capture stdout and stderr streams with timestamps

nipype/interfaces/tests/test_base.py

@@ -455,6 +455,42 @@ def _run_interface(self, runtime):
     nib.BaseInterface.input_spec = None
     yield assert_raises, Exception, nib.BaseInterface
 
+def test_BaseInterface_load_save_inputs():
+    tmp_dir = tempfile.mkdtemp()
+    tmp_json = os.path.join(tmp_dir, 'settings.json')
+
+    def _rem_undefined(indict):
+        for key, val in list(indict.items()):
+            if not nib.isdefined(val):
+                indict.pop(key, None)
+        return indict
+
+    class InputSpec(nib.TraitedSpec):
+        input1 = nib.traits.Int()
+        input2 = nib.traits.Float()
+        input3 = nib.traits.Bool()
+        input4 = nib.traits.Str()
+
+    class DerivedInterface(nib.BaseInterface):
+        input_spec = InputSpec
+
+        def __init__(self, **inputs):
+            super(DerivedInterface, self).__init__(**inputs)
+
+    inputs_dict = {'input1': 12, 'input3': True,
+                   'input4': 'some string'}
+    bif = DerivedInterface(**inputs_dict)
+    bif.save_inputs_to_json(tmp_json)
+    bif2 = DerivedInterface()
+    bif2.load_inputs_from_json(tmp_json)
+    yield assert_equal, _rem_undefined(bif2.inputs.get()), inputs_dict
+
+    bif3 = DerivedInterface(from_file=tmp_json)
+    yield assert_equal, _rem_undefined(bif3.inputs.get()), inputs_dict
+
+    inputs_dict.update({'input4': 'some other string'})
+    bif4 = DerivedInterface(from_file=tmp_json, input4='some other string')
+    yield assert_equal, _rem_undefined(bif4.inputs.get()), inputs_dict
 
 def assert_not_raises(fn, *args, **kwargs):
     fn(*args, **kwargs)