Merge branch 'master' into develop

McsPyDataTools/MANIFEST.in

@@ -1,6 +1,6 @@
-include README AUTHORS CHANGES LICENSE
+include README.rst AUTHORS.rst HISTORY.rst LICENSE.txt
 recursive-include docs *
-recursive-include docs-html *
 recursive-include docs-pdf *
+recursive-exclude docs-html *
 prune docs/_build
 global-exclude *.pyc *~ *__pycache__* *.pyo

McsPyDataTools/McsPy/McsData.py

@@ -948,8 +948,6 @@ class SegmentStream(Stream):
     """
     def __init__(self, stream_grp):
         Stream.__init__(self, stream_grp, "SegmentStreamInfoVersion")
-        self.segment_entity = {}
-        self.data_subtype = None
         self.__read_segment_entities()
 
     def  __read_segment_entities(self):

McsPyDataTools/McsPy/tests/TestCmosMeaDataStructures.py

@@ -8,7 +8,7 @@
 
 from McsPy import *
 
-test_data_file_path             = os.path.join(os.path.dirname(__file__), 'TestData', '2017.12.14-18.38.15-GFP8ms_470nm_100pc_10rep_nofilter(AnalysisSet1).cmtr')
+test_data_file_path             = os.path.join(os.path.dirname(__file__), 'TestData', 'CMOS_MEA_Results.cmtr')
 test_rawdata_file_path          = os.path.join(os.path.dirname(__file__), 'TestData', '2017.12.14-18.38.15-GFP8ms_470nm_100pc_10rep_nofilter.cmcr')
 test_multiple_roi_file_path     = os.path.join(os.path.dirname(__file__), 'TestData', 'Rec_1-2-3_1s.cmcr')
 test_multiple_streams_file_path = os.path.join(os.path.dirname(__file__), 'TestData', 'V200-SensorRoi-3Aux-Dig-Stim2-DiginEvts-5kHz.cmcr')
@@ -118,13 +118,38 @@ def test_acquisition(self):
 
 
         #Test 
-        def test_sta_explorer(self):
-            sta_explorer = self.data.STA_Explorer
-            print(sta_explorer)
-            print(sta_explorer.sta_entity[0])
-            print(sta_explorer.sta_entity[10])
+        def test_network_explorer(self):
+            network_explorer = self.data.Network_Explorer
+            print(network_explorer)
+            print(network_explorer.sta_entity[0])
+            print(network_explorer.sta_entity[10])
+
+        test_network_explorer(self)
+
+        def test_spike_sorter(self):
+            spike_sorter = self.data.Spike_Sorter
+            print(spike_sorter)
+            units = spike_sorter.get_units_by_id()
+            self.assertEqual(len(units), 90, "The number of units is {} and not {} as expected!".format(len(units), 90))
+            ordered = spike_sorter.get_units_by_measure(measure='Separability', descending=False)
+            self.assertEqual(len(ordered), 90, "The number of ordered units is {} and not {} as expected!".format(len(ordered), 90))
+            ordered_sep = [u.get_measure('Separability') for u in ordered]
+            s = sorted(ordered_sep)
+            self.assertEqual(ordered_sep, s, "The units are not ordered correctly!")
+            unit = spike_sorter.get_unit(14)
+            print(unit)
+            pks = unit.get_peaks()
+            for p in pks:
+                self.assertEqual(p['IncludePeak'], 1, "IncludePeak is not set!")
+            ts = unit.get_peaks_timestamps()
+            self.assertEqual(len(pks), len(ts), "The number of timestamps is {} and not {} as expected!".format(len(pks), len(ts)))
+            cutouts = unit.get_peaks_cutouts()
+            self.assertEqual(len(pks), len(cutouts), "The number of cutouts is {} and not {} as expected!".format(len(pks), len(cutouts)))
+            amplitudes = unit.get_peaks_amplitudes()
+            self.assertEqual(len(pks), len(amplitudes), "The number of amplitudes is {} and not {} as expected!".format(len(pks), len(amplitudes)))
+
+        test_spike_sorter(self)
 
-        test_sta_explorer(self)
 
      #Test access to streams if multiple streams of one type exists: example multiple analog streams
     def test_analog_streams(self):

McsPyDataTools/McsPy/tests/TestRawDataStructures.py

@@ -117,7 +117,7 @@ def test_analog_stream_data_timestamps(self):
         analog_stream = self.data.recordings[0].analog_streams[0]
         signal_ts = analog_stream.get_channel_sample_timestamps(6, 1996, 2000)
         sig_ts = signal_ts[0]
-        expected_ts = [3992000, 3994000, 3996000, 3998000, 4000000]
+        expected_ts = [3992000, 3994000, 3996000, 3998000, 4000000, 4002000]
         np.testing.assert_array_equal(sig_ts, expected_ts, "Selected timestamps were '%s' and not as expected '%s'" % (sig_ts, expected_ts))
         self.assertEqual(str(signal_ts[1]), 'microsecond', "Unit of timestamps was expected to be 'microsecond' but was '%s'!" % str(signal_ts[1]))