Merge pull request #1390 from effigies/merge_all

ENH: Make interfaces.utility.Merge(1) merge a list of lists

Author: oesteban

nipype/interfaces/utility/base.py

@@ -109,6 +109,8 @@ class MergeOutputSpec(TraitedSpec):
 class Merge(IOBase):
     """Basic interface class to merge inputs into a single list
 
+    ``Merge(1)`` will merge a list of lists
+
     Examples
     --------
 
@@ -121,33 +123,50 @@ class Merge(IOBase):
     >>> out.outputs.out
     [1, 2, 5, 3]
 
+    >>> merge = Merge()   # Or Merge(1)
+    >>> merge.inputs.in_lists = [1, [2, 5], 3]
+    >>> out = merge.run()
+    >>> out.outputs.out
+    [1, 2, 5, 3]
+
     """
     input_spec = MergeInputSpec
     output_spec = MergeOutputSpec
 
-    def __init__(self, numinputs=0, **inputs):
+    def __init__(self, numinputs=1, **inputs):
         super(Merge, self).__init__(**inputs)
         self._numinputs = numinputs
-        add_traits(self.inputs, ['in%d' % (i + 1) for i in range(numinputs)])
+        if numinputs > 1:
+            input_names = ['in%d' % (i + 1) for i in range(numinputs)]
+        elif numinputs == 1:
+            input_names = ['in_lists']
+        else:
+            input_names = []
+        add_traits(self.inputs, input_names)
 
     def _list_outputs(self):
         outputs = self._outputs().get()
         out = []
+
+        if self._numinputs < 1:
+            return outputs
+        elif self._numinputs == 1:
+            values = self.inputs.in_lists
+        else:
+            getval = lambda idx: getattr(self.inputs, 'in%d' % (idx + 1))
+            values = [getval(idx) for idx in range(self._numinputs)
+                      if isdefined(getval(idx))]
+
         if self.inputs.axis == 'vstack':
-            for idx in range(self._numinputs):
-                value = getattr(self.inputs, 'in%d' % (idx + 1))
-                if isdefined(value):
-                    if isinstance(value, list) and not self.inputs.no_flatten:
-                        out.extend(value)
-                    else:
-                        out.append(value)
+            for value in values:
+                if isinstance(value, list) and not self.inputs.no_flatten:
+                    out.extend(value)
+                else:
+                    out.append(value)
         else:
-            for i in range(len(filename_to_list(self.inputs.in1))):
-                out.insert(i, [])
-                for j in range(self._numinputs):
-                    out[i].append(filename_to_list(getattr(self.inputs, 'in%d' % (j + 1)))[i])
-        if out:
-            outputs['out'] = out
+            lists = [filename_to_list(val) for val in values]
+            out = [[val[i] for val in lists] for i in range(len(lists[0]))]
+        outputs['out'] = out
         return outputs
 
 

nipype/interfaces/utility/tests/test_base.py

@@ -6,6 +6,7 @@
 import pytest
 
 from nipype.interfaces import utility
+from nipype.interfaces.base import isdefined
 import nipype.pipeline.engine as pe
 
 
@@ -49,3 +50,36 @@ def test_split(tmpdir, args, expected):
     res = node.run()
     assert res.outputs.out1 == expected[0]
     assert res.outputs.out2 == expected[1]
+
+
+@pytest.mark.parametrize("args, kwargs, in_lists, expected", [
+        ([3], {}, [0, [1, 2], [3, 4, 5]], [0, 1, 2, 3, 4, 5]),
+        ([0], {}, None, None),
+        ([], {}, [], []),
+        ([], {}, [0, [1, 2], [3, 4, 5]], [0, 1, 2, 3, 4, 5]),
+        ([3], {'axis': 'hstack'}, [[0], [1, 2], [3, 4, 5]], [[0, 1, 3]]),
+        ([3], {'axis': 'hstack'}, [[0, 1], [2, 3], [4, 5]],
+         [[0, 2, 4], [1, 3, 5]]),
+        ([3], {'axis': 'hstack'}, [[0, 1], [2, 3], [4, 5]],
+         [[0, 2, 4], [1, 3, 5]]),
+        ([1], {'axis': 'hstack'}, [[0], [1, 2], [3, 4, 5]], [[0, 1, 3]]),
+        ([1], {'axis': 'hstack'}, [[0, 1], [2, 3], [4, 5]],
+         [[0, 2, 4], [1, 3, 5]]),
+        ])
+def test_merge(tmpdir, args, kwargs, in_lists, expected):
+    os.chdir(str(tmpdir))
+
+    node = pe.Node(utility.Merge(*args, **kwargs), name='merge')
+
+    numinputs = args[0] if args else 1
+    if numinputs == 1:
+        node.inputs.in_lists = in_lists
+    elif numinputs > 1:
+        for i in range(1, numinputs + 1):
+            setattr(node.inputs, 'in{:d}'.format(i), in_lists[i - 1])
+
+    res = node.run()
+    if numinputs < 1:
+        assert not isdefined(res.outputs.out)
+    else:
+        assert res.outputs.out == expected