[FIX] Initialization of interfaces with from_files

Improved the way interfaces were initialized to prevent that lists of lists of int
are not set. Fixes #1625

Author: oesteban

nipype/interfaces/base.py

@@ -776,7 +776,10 @@ def __init__(self, from_file=None, **inputs):
         self.num_threads = 1
 
         if from_file is not None:
-            self.load_inputs_from_json(from_file, overwrite=False)
+            self.load_inputs_from_json(from_file, overwrite=True)
+
+            for name, value in list(inputs.items()):
+                setattr(self.inputs, name, value)
 
 
     @classmethod

nipype/interfaces/tests/test_base.py

@@ -503,20 +503,16 @@ def __init__(self, **inputs):
     settings = example_data(example_data('smri_ants_registration_settings.json'))
     with open(settings) as setf:
         data_dict = json.load(setf)
-    tsthash = Registration(from_file=settings)
-    yield assert_all_true, data_dict, tsthash.inputs.get_traitsfree()
-    hashed_inputs, hashvalue = tsthash.inputs.get_hashval(hash_method='timestamp')
-    # yield assert_equal, hashvalue, '9ab944cbccba61475becb9eac65052af'
 
-def assert_not_raises(fn, *args, **kwargs):
-    fn(*args, **kwargs)
-    return True
+    tsthash = Registration()
+    tsthash.load_inputs_from_json(settings)
+    yield assert_equal, {}, check_dict(data_dict, tsthash.inputs.get_traitsfree())
 
-def assert_all_true(ref_dict, tst_dict):
-    for key, value in list(ref_dict.items()):
-        if tst_dict[key] != value:
-            return False
-    return True
+    tsthash2 = Registration(from_file=settings)
+    yield assert_equal, {}, check_dict(data_dict, tsthash2.inputs.get_traitsfree())
+
+    hashed_inputs, hashvalue = tsthash.inputs.get_hashval(hash_method='timestamp')
+    yield assert_equal, hashvalue, '9ab944cbccba61475becb9eac65052af'
 
 def test_input_version():
     class InputSpec(nib.TraitedSpec):
@@ -754,3 +750,27 @@ def test_global_CommandLine_output():
     yield assert_equal, res.runtime.stdout, ''
     os.chdir(pwd)
     teardown_file(tmpd)
+
+def assert_not_raises(fn, *args, **kwargs):
+    fn(*args, **kwargs)
+    return True
+
+def check_dict(ref_dict, tst_dict):
+    """Compare dictionaries of inputs and and those loaded from json files"""
+    def to_list(x):
+        if isinstance(x, tuple):
+            x = list(x)
+
+        if isinstance(x, list):
+            for i, xel in enumerate(x):
+                x[i] = to_list(xel)
+
+        return x
+
+    failed_dict = {}
+    for key, value in list(ref_dict.items()):
+        newval = to_list(tst_dict[key])
+        if newval != value:
+            failed_dict[key] = (value, newval)
+    return failed_dict
+