Merge pull request #765 from chrisfilo/enh/datafinder_test

Test and sorting for DataFinder

Author: satra

CHANGES

@@ -1,3 +1,9 @@
+Release 0.9.2 (January 8, 2014)
+============
+
+* FIX: DataFinder was broken due to a typo
+* FIX: Order of DataFinder outputs was not guaranteed, it's human sorted now
+
 Release 0.9.1 (December 25, 2013)
 ============
 

nipype/interfaces/io.py

@@ -827,8 +827,19 @@ def _run_interface(self, runtime):
             ):
             for key, vals in self.result.iteritems():
                 self.result[key] = vals[0]
+        else:
+            #sort all keys acording to out_paths
+            for key in self.result.keys():
+                if key == "out_paths":
+                    continue
+                sort_tuples = human_order_sorted(zip(self.result["out_paths"],
+                                                     self.result[key]))
+                self.result[key] = [x for (_, x) in sort_tuples]
+            self.result["out_paths"] = human_order_sorted(self.result["out_paths"])
+
         if not self.result:
             raise RuntimeError("Regular expression did not match any files!")
+
         return runtime
 
     def _list_outputs(self):

nipype/interfaces/tests/test_io.py

@@ -172,6 +172,67 @@ def test_datasink_copydir():
     shutil.rmtree(pth)
 
 
+def test_datafinder_copydir():
+    outdir = mkdtemp()
+    open(os.path.join(outdir, "findme.txt"), 'a').close()
+    open(os.path.join(outdir, "dontfindme"), 'a').close()
+    open(os.path.join(outdir, "dontfindmealsotxt"), 'a').close()
+    open(os.path.join(outdir, "findmetoo.txt"), 'a').close()
+    open(os.path.join(outdir, "ignoreme.txt"), 'a').close()
+    open(os.path.join(outdir, "alsoignore.txt"), 'a').close()
+
+    from nipype.interfaces.io import DataFinder
+    df = DataFinder()
+    df.inputs.root_paths = outdir
+    df.inputs.match_regex = '.+/(?P<basename>.+)\.txt'
+    df.inputs.ignore_regexes = ['ignore']
+    result = df.run()
+    expected = ["findme.txt", "findmetoo.txt"]
+    for path, expected_fname in zip(result.outputs.out_paths, expected):
+        _, fname = os.path.split(path)
+        yield assert_equal, fname, expected_fname
+
+    yield assert_equal, result.outputs.basename, ["findme", "findmetoo"]
+
+    shutil.rmtree(outdir)
+
+
+def test_datafinder_depth():
+    outdir = mkdtemp()
+    os.makedirs(os.path.join(outdir, '0', '1', '2', '3'))
+
+    from nipype.interfaces.io import DataFinder
+    df = DataFinder()
+    df.inputs.root_paths = os.path.join(outdir, '0')
+    for min_depth in range(4):
+        for max_depth in range(min_depth, 4):
+            df.inputs.min_depth = min_depth
+            df.inputs.max_depth = max_depth
+            result = df.run()
+            expected = [str(x) for x in range(min_depth, max_depth + 1)]
+            for path, exp_fname in zip(result.outputs.out_paths, expected):
+                _, fname = os.path.split(path)
+                yield assert_equal, fname, exp_fname
+
+    shutil.rmtree(outdir)
+
+
+def test_datafinder_unpack():
+    outdir = mkdtemp()
+    single_res = os.path.join(outdir, "findme.txt")
+    open(single_res, 'a').close()
+    open(os.path.join(outdir, "dontfindme"), 'a').close()
+
+    from nipype.interfaces.io import DataFinder
+    df = DataFinder()
+    df.inputs.root_paths = outdir
+    df.inputs.match_regex = '.+/(?P<basename>.+)\.txt'
+    df.inputs.unpack_single = True
+    result = df.run()
+    print result.outputs.out_paths
+    yield assert_equal, result.outputs.out_paths, single_res
+
+
 def test_freesurfersource():
     fss = nio.FreeSurferSource()
     yield assert_equal, fss.inputs.hemi, 'both'

nipype/utils/misc.py

@@ -17,6 +17,8 @@ def atoi(text):
         return int(text) if text.isdigit() else text
 
     def natural_keys(text):
+        if isinstance(text, tuple):
+            text = text[0]
         return [ atoi(c) for c in re.split('(\d+)', text) ]
 
     return sorted(l, key=natural_keys)