patches: fix Spiking.t_samp_ms and IOProc sample skipping (#47)

* fix Spiking.t_samp_ms

* fix sample time test bug

cleo/ephys/spiking.py

@@ -65,7 +65,8 @@ def _update_saved_vars(self, t_ms, i, t_samp_ms):
         if self.probe.save_history:
             self.i = np.concatenate([self.i, i])
             self.t_ms = np.concatenate([self.t_ms, t_ms])
-            self.t_samp_ms = np.concatenate([self.t_samp_ms, [t_samp_ms]])
+            t_samp_ms_rep = np.full_like(t_ms, t_samp_ms)
+            self.t_samp_ms = np.concatenate([self.t_samp_ms, t_samp_ms_rep])
 
     def connect_to_neuron_group(
         self, neuron_group: NeuronGroup, **kwparams

cleo/ioproc/base.py

@@ -193,7 +193,8 @@ def _is_currently_idle(self, query_time_ms):
 
     def is_sampling_now(self, query_time_ms):
         if self.sampling == "fixed":
-            if np.isclose(query_time_ms % self.sample_period_ms, 0):
+            resid = query_time_ms % self.sample_period_ms
+            if np.isclose(resid, 0) or np.isclose(resid, self.sample_period_ms):
                 return True
         elif self.sampling == "when idle":
             if np.isclose(query_time_ms % self.sample_period_ms, 0):

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "cleosim"
-version = "0.14.1"
+version = "0.14.2"
 description = "Cleo: the Closed-Loop, Electrophysiology, and Optogenetics experiment simulation testbed"
 authors = [
     "Kyle Johnsen <kyle@kjohnsen.org>",

tests/ephys/test_spiking.py

@@ -1,12 +1,10 @@
 """Tests for ephys.spiking module"""
-import pytest
 import numpy as np
-from brian2 import SpikeGeneratorGroup, ms, mm, Network
-import neo
 import quantities as pq
+from brian2 import Network, SpikeGeneratorGroup, mm, ms
 
 from cleo import CLSimulator
-from cleo.ephys import *
+from cleo.ephys import MultiUnitSpiking, Probe, SortedSpiking
 from cleo.ioproc import RecordOnlyProcessor
 
 
@@ -81,7 +79,7 @@ def test_MUS_multiple_contacts():
     assert np.sum(mus.i == 0) < len(indices)
     assert np.sum(mus.i == 1) < len(indices)
 
-    assert len(mus.i) == len(mus.t_ms)
+    assert len(mus.i) == len(mus.t_ms) == len(mus.t_samp_ms)
 
 
 def test_MUS_multiple_groups():
@@ -106,6 +104,8 @@ def test_MUS_multiple_groups():
     assert 20 < np.sum(mus.i == 0) < 60
     # second channel would have caught all spikes from sgg1 and sgg2
     assert np.sum(mus.i == 1) == 60
+    assert len(mus.t_ms) == len(mus.t_samp_ms)
+    assert np.all(mus.t_samp_ms == 10)
 
 
 def test_MUS_reset():
@@ -156,7 +156,10 @@ def test_SortedSpiking():
     assert all(i == [2, 3, 5])
 
     for i in (0, 1, 4):
-        assert not i in ss.i
+        assert i not in ss.i
+
+    assert ss.t_ms.shape == ss.i.shape == ss.t_samp_ms.shape
+    assert np.all(np.in1d(ss.t_samp_ms, [3, 4, 5, 6]))
 
 
 def _test_reset(spike_signal_class):

tests/ioproc/test_processing.py

@@ -52,13 +52,18 @@ def __init__(self, sample_period_ms, **kwargs):
         super().__init__(sample_period_ms, **kwargs)
         self.delay = 1.199
         self.component = MyProcessingBlock(delay=ConstantDelay(self.delay))
+        self.count = 0
 
     def process(self, state_dict: dict, sample_time_ms: float) -> Tuple[dict, float]:
-        input = state_dict["in"]
-        out, out_t = self.component.process(
-            input, sample_time_ms, measurement_time=sample_time_ms
-        )
-        return {"out": out}, out_t
+        try:
+            input = state_dict["in"]
+            out, out_t = self.component.process(
+                input, sample_time_ms, measurement_time=sample_time_ms
+            )
+            return {"out": out}, out_t
+        except KeyError:
+            self.count += 1
+            return {}, sample_time_ms
 
 
 def _test_LatencyIOProcessor(myLIOP, t, sampling, inputs, outputs):
@@ -117,14 +122,13 @@ class SampleCounter(cleo.IOProcessor):
     def is_sampling_now(self, t_query_ms) -> np.bool:
         return t_query_ms % self.sample_period_ms == 0
 
-    def __init__(self):
+    def __init__(self, sample_period_ms=1):
         self.count = 0
-        self.sample_period_ms = 1
+        self.sample_period_ms = sample_period_ms
         self.latest_ctrl_signal = {}
 
     def put_state(self, state_dict: dict, sample_time_ms: float):
         self.count += 1
-        print(sample_time_ms)
         return ({}, sample_time_ms)
 
     def get_ctrl_signals(self, query_time_ms: np.float) -> dict:
@@ -141,6 +145,17 @@ def test_no_skip_sampling():
     assert sc.count == nsamp
 
 
+def test_no_skip_sampling_short():
+    net = Network()
+    sim = cleo.CLSimulator(net)
+    Tsamp = 0.2 * ms
+    liop = MyLIOP(Tsamp / ms)
+    sim.set_io_processor(liop)
+    nsamp = 20
+    sim.run(nsamp * Tsamp)
+    assert liop.count == nsamp
+
+
 class WaveformController(LatencyIOProcessor):
     def process(self, state_dict, t_ms):
         return {"steady": t_ms, "time-varying": t_ms + 1}, t_ms + 3