Implemented test_phyio.py

Author: rjurkus

neo/test/iotest/test_phyio.py

@@ -0,0 +1,96 @@
+"""
+Tests of neo.io.exampleio
+"""
+
+import unittest
+
+from neo.io.phyio import PhyIO  # , HAVE_SCIPY
+from neo.test.iotest.common_io_test import BaseTestIO
+from neo.io.proxyobjects import (AnalogSignalProxy,
+                                 SpikeTrainProxy, EventProxy, EpochProxy)
+from neo import (AnalogSignal, SpikeTrain)
+
+import quantities as pq
+import numpy as np
+
+import tempfile
+from pathlib import Path
+
+# This run standart tests, this is mandatory for all IO
+
+
+class TestPhyIO(BaseTestIO, unittest.TestCase):
+    ioclass = PhyIO
+    files_to_test = ['phy_example_0']
+    files_to_download = [
+        'phy_example_0/spike_times.npy',
+        'phy_example_0/spike_templates.npy',
+        'phy_example_0/spike_clusters.npy',
+        'phy_example_0/params.py',
+        'phy_example_0/cluster_KSLabel.tsv',
+        'phy_example_0/cluster_ContamPct.tsv',
+        'phy_example_0/cluster_Amplitude.tsv',
+        'phy_example_0/cluster_group.tsv'
+    ]
+
+
+class SpecificTestPhyIO(unittest.TestCase):
+    def setUp(self):
+        temp_directory = Path(tempfile.gettempdir())
+        self.temp_folder = temp_directory.joinpath(
+            'files_for_testing_neo/phy/phy_example_0')
+
+    def test_read_segment_lazy(self):
+        r = PhyIO(dirname=self.temp_folder)
+        seg = r.read_segment(lazy=True)
+        for ana in seg.analogsignals:
+            assert isinstance(ana, AnalogSignalProxy)
+            ana = ana.load()
+            assert isinstance(ana, AnalogSignal)
+        for st in seg.spiketrains:
+            assert isinstance(st, SpikeTrainProxy)
+            st = st.load()
+            assert isinstance(st, SpikeTrain)
+
+        seg = r.read_segment(lazy=False)
+        for anasig in seg.analogsignals:
+            assert isinstance(ana, AnalogSignal)
+            self.assertNotEqual(anasig.size, 0)
+        for st in seg.spiketrains:
+            assert isinstance(st, SpikeTrain)
+            self.assertNotEqual(st.size, 0)
+
+        # annotations
+        assert 'seg_extra_info' in seg.annotations
+        assert seg.name == 'Seg #0 Block #0'
+        for anasig in seg.analogsignals:
+            assert anasig.name is not None
+        for st in seg.spiketrains:
+            assert st.name is not None
+        for ev in seg.events:
+            assert ev.name is not None
+        for ep in seg.epochs:
+            assert ep.name is not None
+
+    def test_read_block(self):
+        r = PhyIO(dirname=self.temp_folder)
+        bl = r.read_block(lazy=True)
+
+    def test_read_segment_with_time_slice(self):
+        r = PhyIO(dirname=self.temp_folder)
+        seg = r.read_segment(time_slice=None)
+        spikes_full = seg.spiketrains[0]
+
+        t_start, t_stop = 260 * pq.ms, 1.854 * pq.s
+        seg = r.read_segment(time_slice=(t_start, t_stop))
+        spikes_slice = seg.spiketrains[0]
+
+        assert spikes_full.size > spikes_slice.size
+        assert np.all(spikes_slice >= t_start)
+        assert np.all(spikes_slice <= t_stop)
+        assert spikes_slice.t_start == t_start
+        assert spikes_slice.t_stop == t_stop
+
+
+if __name__ == "__main__":
+    unittest.main()