Merge pull request #1043 from JuliaSprenger/add/neuralynx_exclude_files

[Neuralynx] add 'exclude_filename' keyword

Author: samuelgarcia

neo/io/neuralynxio.py

@@ -27,7 +27,7 @@ class NeuralynxIO(NeuralynxRawIO, BaseFromRaw):
     mode = 'dir'
 
     def __init__(self, dirname='', filename='', use_cache=False, cache_path='same_as_resource',
-                 keep_original_times=False):
+                 exclude_filename=None, keep_original_times=False):
         """
         Initialise IO instance
 
@@ -41,13 +41,17 @@ def __init__(self, dirname='', filename='', use_cache=False, cache_path='same_as
         cache_path : str, optional
             Folder path to use for cache files.
             Default: 'same_as_resource'
+        exclude_filename: str or list
+            Filename or list of filenames to be excluded. Expects base filenames without
+            directory path.
         keep_original_times : bool
             Preserve original time stamps as in data files. By default datasets are
             shifted to begin at t_start = 0*pq.second.
             Default: False
         """
         NeuralynxRawIO.__init__(self, dirname=dirname, filename=filename, use_cache=use_cache,
-                                cache_path=cache_path, keep_original_times=keep_original_times)
+                                cache_path=cache_path, exclude_filename=exclude_filename,
+                                keep_original_times=keep_original_times)
         if self.rawmode == 'one-file':
             BaseFromRaw.__init__(self, filename)
         elif self.rawmode == 'one-dir':

neo/rawio/neuralynxrawio/neuralynxrawio.py

@@ -78,7 +78,8 @@ class NeuralynxRawIO(BaseRawIO):
     _ncs_dtype = [('timestamp', 'uint64'), ('channel_id', 'uint32'), ('sample_rate', 'uint32'),
                   ('nb_valid', 'uint32'), ('samples', 'int16', (NcsSection._RECORD_SIZE))]
 
-    def __init__(self, dirname='', filename='', keep_original_times=False, **kargs):
+    def __init__(self, dirname='', filename='', exclude_filename=None, keep_original_times=False,
+                 **kargs):
         """
         Initialize io for either a directory of Ncs files or a single Ncs file.
 
@@ -90,6 +91,9 @@ def __init__(self, dirname='', filename='', keep_original_times=False, **kargs):
         filename: str
             name of a single ncs, nse, nev, or ntt file to include in dataset. If used,
             dirname must not be provided.
+        exclude_filename: str or list
+            name of a single ncs, nse, nev or ntt file or list of such files. Expects plain
+            filenames (without directory path).
         keep_original_times:
             if True, keep original start time as in files,
             otherwise set 0 of time to first time in dataset
@@ -104,6 +108,7 @@ def __init__(self, dirname='', filename='', keep_original_times=False, **kargs):
             raise ValueError("One of dirname or filename must be provided.")
 
         self.keep_original_times = keep_original_times
+        self.exclude_filename = exclude_filename
         BaseRawIO.__init__(self, **kargs)
 
     def _source_name(self):
@@ -152,6 +157,15 @@ def _parse_header(self):
             dirname, fname = os.path.split(self.filename)
             filenames = [fname]
 
+        if not isinstance(self.exclude_filename, (list, set, np.ndarray)):
+            self.exclude_filename = [self.exclude_filename]
+
+        # remove files that were explicitly excluded
+        if self.exclude_filename is not None:
+            for excl_file in self.exclude_filename:
+                if excl_file in filenames:
+                    filenames.remove(excl_file)
+
         for filename in filenames:
             filename = os.path.join(dirname, filename)
 

neo/test/iotest/test_neuralynxio.py

@@ -189,6 +189,29 @@ def test_read_single_file(self):
         self.assertTrue((len(block.segments[0].events)) == 0)
         self.assertTrue((len(block.segments[0].epochs)) == 0)
 
+    def test_exclude_filename(self):
+        dname = self.get_local_path(
+            'neuralynx/Cheetah_v5.7.4/original_data/'
+        )
+
+        # exclude a single file
+        nio = NeuralynxIO(dirname=dname, exclude_filename='CSC1.ncs', 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)
+
+        # exclude all ncs files from session
+        exclude_files = [f'CSC{i}.ncs' for i in range(6)]
+        nio = NeuralynxIO(dirname=dname, exclude_filename=exclude_files,
+                          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'

neo/test/rawiotest/test_neuralynxrawio.py

@@ -120,6 +120,35 @@ def test_single_file_mode(self):
         self.assertEqual(len(rawio.header['signal_channels']), 0)
         self.assertEqual(len(rawio.header['event_channels']), 0)
 
+    def test_exclude_filenames(self):
+        # exclude single ncs file from session
+        dname = self.get_local_path('neuralynx/Cheetah_v5.6.3/original_data/')
+        rawio = NeuralynxRawIO(dirname=dname, exclude_filename='CSC2.ncs')
+        rawio.parse_header()
+
+        self.assertEqual(rawio._nb_segment, 2)
+        self.assertEqual(len(rawio.ncs_filenames), 1)
+        self.assertEqual(len(rawio.nev_filenames), 1)
+        sigHdrs = rawio.header['signal_channels']
+        self.assertEqual(sigHdrs.size, 1)
+        self.assertEqual(sigHdrs[0][0], 'CSC1')
+        self.assertEqual(sigHdrs[0][1], '58')
+        self.assertEqual(len(rawio.header['spike_channels']), 8)
+        self.assertEqual(len(rawio.header['event_channels']), 2)
+
+        # exclude multiple files from session
+        rawio = NeuralynxRawIO(dirname=dname, exclude_filename=['Events.nev', 'CSC2.ncs'])
+        rawio.parse_header()
+
+        self.assertEqual(rawio._nb_segment, 2)
+        self.assertEqual(len(rawio.ncs_filenames), 1)
+        self.assertEqual(len(rawio.nev_filenames), 0)
+        sigHdrs = rawio.header['signal_channels']
+        self.assertEqual(sigHdrs.size, 1)
+        self.assertEqual(sigHdrs[0][0], 'CSC1')
+        self.assertEqual(sigHdrs[0][1], '58')
+        self.assertEqual(len(rawio.header['spike_channels']), 8)
+        self.assertEqual(len(rawio.header['event_channels']), 0)
 
 class TestNcsRecordingType(TestNeuralynxRawIO, unittest.TestCase):
     """