Remove 'all-in-one' in last remaining IO and tests

neo/io/asciisignalio.py

@@ -58,8 +58,7 @@ class AsciiSignalIO(BaseIO):
         t_start:
             time of the first sample (Quantity). Ignored if timecolumn is not None
         signal_group_mode:
-            if 'all-in-one', load data as a single, multi-channel AnalogSignal, if 'split-all'
-            (default for backwards compatibility) load data as separate, single-channel
+            'split-all' (default for backwards compatibility) load data as separate, single-channel
             AnalogSignals
         method:
             'genfromtxt', 'csv', 'homemade' or a user-defined function which takes a filename and
@@ -94,7 +93,7 @@ class AsciiSignalIO(BaseIO):
                 "units": "kHz"
             },
             "method": "genfromtxt",
-            "signal_group_mode": 'all-in-one'
+            "signal_group_mode": 'split-all'
         }
     """
 
@@ -285,53 +284,28 @@ def read_segment(self, lazy=False):
                 sampling_rate = None
             t_start = sig[0, self.timecolumn] * self.time_units
 
-        if self.signal_group_mode == "all-in-one":
-            channel_index_annotation = self.usecols or np.arange(sig.shape[1])
-            channel_index_annotation = np.asarray(channel_index_annotation)
-            if self.timecolumn is not None:
-                mask = list(range(sig.shape[1]))
-                if self.timecolumn >= 0:
-                    mask.remove(self.timecolumn)
-                else:  # allow negative column index
-                    mask.remove(sig.shape[1] + self.timecolumn)
-                signal = sig[:, mask]
-                channel_index_annotation = channel_index_annotation[mask]
-            else:
-                signal = sig
+        if self.timecolumn is not None and self.timecolumn < 0:
+            time_col = sig.shape[1] + self.timecolumn
+        else:
+            time_col = self.timecolumn
+        for i in range(sig.shape[1]):
+            if time_col == i:
+                continue
+            signal = sig[:, i] * self.units
             if sampling_rate is None:
                 irr_sig = IrregularlySampledSignal(
-                    signal[:, self.timecolumn] * self.time_units, signal * self.units, name="multichannel"
+                    sig[:, time_col] * self.time_units,
+                    signal,
+                    t_start=t_start,
+                    channel_index=i,
+                    name="Column %d" % i,
                 )
                 seg.irregularlysampledsignals.append(irr_sig)
             else:
                 ana_sig = AnalogSignal(
-                    signal * self.units, sampling_rate=sampling_rate, t_start=t_start, name="multichannel"
+                    signal, sampling_rate=sampling_rate, t_start=t_start, channel_index=i, name="Column %d" % i
                 )
-                ana_sig.array_annotate(channel_index=channel_index_annotation)
                 seg.analogsignals.append(ana_sig)
-        else:
-            if self.timecolumn is not None and self.timecolumn < 0:
-                time_col = sig.shape[1] + self.timecolumn
-            else:
-                time_col = self.timecolumn
-            for i in range(sig.shape[1]):
-                if time_col == i:
-                    continue
-                signal = sig[:, i] * self.units
-                if sampling_rate is None:
-                    irr_sig = IrregularlySampledSignal(
-                        sig[:, time_col] * self.time_units,
-                        signal,
-                        t_start=t_start,
-                        channel_index=i,
-                        name="Column %d" % i,
-                    )
-                    seg.irregularlysampledsignals.append(irr_sig)
-                else:
-                    ana_sig = AnalogSignal(
-                        signal, sampling_rate=sampling_rate, t_start=t_start, channel_index=i, name="Column %d" % i
-                    )
-                    seg.analogsignals.append(ana_sig)
 
         seg.check_relationships()
         return seg

neo/io/nixio_fr.py

@@ -9,7 +9,7 @@ class NixIO(NIXRawIO, BaseFromRaw):
     name = "NIX IO"
 
     _prefered_signal_group_mode = "group-by-same-units"
-    _prefered_units_group_mode = "all-in-one"
+    _prefered_units_group_mode = "split-all"
 
     def __init__(self, filename):
         NIXRawIO.__init__(self, filename)

neo/test/iotest/test_asciisignalio.py

@@ -68,15 +68,14 @@ def test_csv_expect_success(self):
             delimiter=",",
             units="mV",
             method="csv",
-            signal_group_mode="all-in-one",
+            signal_group_mode="split-all",
             t_start=0.5,
         )
 
         block = io.read_block()
         signal = block.segments[0].analogsignals[0]
-        self.assertEqual(signal.shape, (4, 2))  # two columns remaining after usecols
-        # and timecolumn applied
-        assert_array_almost_equal(signal[:, 1].reshape(-1).magnitude, np.array(sample_data)[:, 1], decimal=5)
+        self.assertEqual(signal.shape, (4, 1))  
+        assert_array_almost_equal(signal[:, 0].reshape(-1).magnitude, np.array(sample_data)[:, 0], decimal=5)
         self.assertAlmostEqual(signal.sampling_period, 0.1 * pq.ms)
 
         expected_channel_index = list(usecols)
@@ -110,15 +109,14 @@ def test_homemade_expect_success(self):
             delimiter="\t",
             units="mV",
             method="homemade",
-            signal_group_mode="all-in-one",
+            signal_group_mode="split-all",
             t_start=0.5,
         )
 
         block = io.read_block()
         signal = block.segments[0].analogsignals[0]
-        self.assertEqual(signal.shape, (4, 2))  # two columns remaining after usecols
-        # and timecolumn applied
-        assert_array_almost_equal(signal[:, 1].reshape(-1).magnitude, np.array(sample_data)[:, 1], decimal=5)
+        self.assertEqual(signal.shape, (4, 1))  
+        assert_array_almost_equal(signal[:, 0].reshape(-1).magnitude, np.array(sample_data)[:, 0], decimal=5)
         self.assertAlmostEqual(signal.sampling_period, 0.1 * pq.ms)
 
         os.remove(filename)
@@ -290,12 +288,14 @@ def test_multichannel(self):
             delimiter=" ",
             units="mV",
             method="genfromtxt",
-            signal_group_mode="all-in-one",
+            signal_group_mode="split-all",
         )
         block = io.read_block()
 
         signal = block.segments[0].analogsignals[0]
-        assert_array_almost_equal(signal.magnitude, sample_data, decimal=6)
+        assert_array_almost_equal(signal.magnitude, sample_data[:, 0], decimal=6)
+        signal1 = block.segments[1].analogsignals[1]
+        assert_array_almost_equal(signal1.magnitude, sample_data[:, 1], decimal=6)
         self.assertEqual(len(block.segments[0].analogsignals), 1)
         self.assertEqual(signal.t_stop, sample_data.shape[0] / sampling_rate)
         self.assertEqual(signal.units, pq.mV)
@@ -316,12 +316,14 @@ def test_multichannel_with_timecolumn(self):
             method="genfromtxt",
             timecolumn=0,
             time_units="ms",
-            signal_group_mode="all-in-one",
+            signal_group_mode="split-all",
         )
         block = io.read_block()
 
         signal = block.segments[0].analogsignals[0]
-        assert_array_almost_equal(signal.magnitude, sample_data, decimal=6)
+        assert_array_almost_equal(signal.magnitude, sample_data[:,0], decimal=6)
+        signal1 = block.segments[1].analogsignals[0]
+        assert_array_almost_equal(signal1.magnitude, sample_data[:,1], decimal=6)
         self.assertEqual(signal.sampling_period, sampling_period * pq.ms)
         self.assertEqual(len(block.segments[0].analogsignals), 1)
         self.assertEqual(signal.t_stop, sample_data.shape[0] * sampling_period * pq.ms)
@@ -343,12 +345,14 @@ def test_multichannel_with_negative_timecolumn(self):
             method="genfromtxt",
             timecolumn=-1,
             time_units="ms",
-            signal_group_mode="all-in-one",
+            signal_group_mode="split-all",
         )
         block = io.read_block()
 
         signal = block.segments[0].analogsignals[0]
-        assert_array_almost_equal(signal.magnitude, sample_data, decimal=6)
+        assert_array_almost_equal(signal.magnitude, sample_data[:,0], decimal=6)
+        signal1 = block.segments[1].analogsignals[0]
+        assert_array_almost_equal(signal1.magnitude, sample_data[:,1], decimal=6)
         self.assertEqual(signal.sampling_period, sampling_period * pq.ms)
         self.assertEqual(len(block.segments[0].analogsignals), 1)
         self.assertEqual(signal.t_stop, sample_data.shape[0] * sampling_period * pq.ms)
@@ -371,7 +375,7 @@ def test_write_without_timecolumn(self):
         seg1.analogsignals.append(signal1)
         block1.segments.append(seg1)
 
-        iow = AsciiSignalIO(filename, method="genfromtxt", time_units="ms", signal_group_mode="all-in-one")
+        iow = AsciiSignalIO(filename, method="genfromtxt", time_units="ms", signal_group_mode="split-all")
         iow.write_block(block1)
 
         ior = AsciiSignalIO(filename)
@@ -410,7 +414,7 @@ def test_write_with_timecolumn(self):
         block1.segments.append(seg1)
 
         iow = AsciiSignalIO(
-            filename, method="genfromtxt", timecolumn=0, time_units="ms", signal_group_mode="all-in-one"
+            filename, method="genfromtxt", timecolumn=0, time_units="ms", signal_group_mode="split-all"
         )
         iow.write_block(block1)
 
@@ -448,7 +452,7 @@ def test_write_with_timeunits_different_from_those_of_signal(self):
         block1.segments.append(seg1)
 
         iow = AsciiSignalIO(
-            filename, method="genfromtxt", timecolumn=0, units="mV", time_units="ms", signal_group_mode="all-in-one"
+            filename, method="genfromtxt", timecolumn=0, units="mV", time_units="ms", signal_group_mode="split-all"
         )
         def_units = iow.units
         def_time_units = iow.time_units
@@ -560,7 +564,7 @@ def test_irregular_multichannel(self):
         np.savetxt(filename, sample_data, delimiter=" ")
 
         io = AsciiSignalIO(
-            filename, delimiter=" ", timecolumn=0, units="mV", method="genfromtxt", signal_group_mode="all-in-one"
+            filename, delimiter=" ", timecolumn=0, units="mV", method="genfromtxt", signal_group_mode="split-all"
         )
         block = io.read_block()
 

neo/test/iotest/test_blackrockio.py

@@ -149,7 +149,7 @@ def test_inputs_V21(self):
         block = reader.read_block(
             load_waveforms=True,
             signal_group_mode="split-all",
-        )  # units_group_mode='all-in-one')
+        )
 
         self.assertEqual(len(block.segments[0].analogsignals), 96)
         # self.assertEqual(len(block.channel_indexes[-1].units), 218)

neo/test/iotest/test_neuralynxio.py

@@ -69,9 +69,6 @@ def test_read_block(self):
 
         # self.assertEqual(len(block.channel_indexes[-1].units[0].spiketrains), 2)  # 2 segment
 
-        # block = nio.read_block(load_waveforms=True, units_group_mode='all-in-one')
-        # self.assertEqual(len(block.channel_indexes[-1].units), 2)  # 2 units
-
         # block = nio.read_block(load_waveforms=True, units_group_mode='split-all')
         # self.assertEqual(len(block.channel_indexes[-1].units), 1)  # 1 units by ChannelIndex
 
@@ -125,9 +122,6 @@ def test_read_block(self):
 
         # self.assertEqual(len(block.channel_indexes[-1].units[0].spiketrains), 2)
 
-        # block = nio.read_block(load_waveforms=True, units_group_mode='all-in-one')
-        # self.assertEqual(len(block.channel_indexes[-1].units), 8)
-
         # block = nio.read_block(load_waveforms=True, units_group_mode='split-all')
         # self.assertEqual(len(block.channel_indexes[-1].units), 1)  # 1 units by ChannelIndex