Merge pull request #1023 from JuliaSprenger/fix/neuralynx_args

Add `filename` keyword argument to NeuralynxIO

Author: samuelgarcia

neo/io/neuralynxio.py

@@ -26,7 +26,7 @@ class NeuralynxIO(NeuralynxRawIO, BaseFromRaw):
     _prefered_signal_group_mode = 'group-by-same-units'
     mode = 'dir'
 
-    def __init__(self, dirname, use_cache=False, cache_path='same_as_resource',
+    def __init__(self, dirname='', filename='', use_cache=False, cache_path='same_as_resource',
                  keep_original_times=False):
         """
         Initialise IO instance
@@ -46,6 +46,9 @@ def __init__(self, dirname, use_cache=False, cache_path='same_as_resource',
             shifted to begin at t_start = 0*pq.second.
             Default: False
         """
-        NeuralynxRawIO.__init__(self, dirname=dirname, use_cache=use_cache,
+        NeuralynxRawIO.__init__(self, dirname=dirname, filename=filename, use_cache=use_cache,
                                 cache_path=cache_path, keep_original_times=keep_original_times)
-        BaseFromRaw.__init__(self, dirname)
+        if self.rawmode == 'one-file':
+            BaseFromRaw.__init__(self, filename)
+        elif self.rawmode == 'one-dir':
+            BaseFromRaw.__init__(self, dirname)

neo/test/iotest/test_neuralynxio.py

@@ -178,6 +178,17 @@ def test_read_block(self):
         block = nio.read_block(signal_group_mode='group-by-same-units')
         self.assertEqual(len(block.groups), 1)
 
+    def test_read_single_file(self):
+        filename = self.get_local_path(
+            'neuralynx/Cheetah_v5.7.4/original_data/CSC1.ncs'
+        )
+        nio = NeuralynxIO(filename=filename, use_cache=False)
+        block = nio.read_block()
+        self.assertTrue(len(block.segments[0].analogsignals) > 0)
+        self.assertTrue((len(block.segments[0].spiketrains)) == 0)
+        self.assertTrue((len(block.segments[0].events)) == 0)
+        self.assertTrue((len(block.segments[0].epochs)) == 0)
+
 
 class TestPegasus_v211(CommonNeuralynxIOTest, unittest.TestCase):
     pegasus_version = '2.1.1'