Add default timing values for PosCheops, NegCheops and HyperDepol stim

bluepyefe/ecode/HyperDePol.py

@@ -26,6 +26,13 @@
 
 logger = logging.getLogger(__name__)
 
+DEFAULT_TIMING_MS = {
+    "ton": 250.0,
+    "tmid": 700.0,
+    "toff": 970.0,
+    "totduration": 1220.0,
+}
+
 
 class HyperDePol(Recording):
 
@@ -113,7 +120,14 @@ def interpret(self, t, current, config_data, reader_data):
         # Smooth the current
         smooth_current = scipy_signal2d(current, 85)
 
-        self.set_timing_ecode(["ton", "tmid", "toff"], config_data)
+        timing_keys = ["ton", "tmid", "toff"]
+        if any(config_data.get(key) is None for key in timing_keys):
+            logger.warning(
+                f"Missing timing key(s) for {self.protocol_name}, using defaults: {DEFAULT_TIMING_MS}"
+            )
+            for key in timing_keys:
+                config_data[key] = DEFAULT_TIMING_MS[key]
+        self.set_timing_ecode(timing_keys, config_data)
 
         hypamp_value = numpy.median(
             numpy.concatenate(

bluepyefe/ecode/negCheops.py

@@ -26,12 +26,21 @@
 
 logger = logging.getLogger(__name__)
 
+DEFAULT_TIMING_MS = {
+    "ton": 1750.0,
+    "t1": 8416.0,
+    "t2": 10416.0,
+    "t3": 13748.0,
+    "t4": 15748.0,
+    "toff": 17970.0,
+}
+
 
 class NegCheops(Recording):
 
     # pylint: disable=line-too-long,anomalous-backslash-in-string
 
-    """NegCheops current stimulus
+    r"""NegCheops current stimulus
 
     .. code-block:: none
 
@@ -117,8 +126,15 @@ def interpret(self, t, current, config_data, reader_data):
         # Smooth the current
         smooth_current = scipy_signal2d(current, 85)
 
-        self.set_timing_ecode(
-            ["ton", "t1", "t2", "t3", "t4", "toff"], config_data)
+        timing_keys = ["ton", "t1", "t2", "t3", "t4", "toff"]
+        if any(config_data.get(k) is None for k in timing_keys):
+            logger.warning(
+                f"Missing timing key(s) for {self.protocol_name}, using defaults: {DEFAULT_TIMING_MS}"
+            )
+            for k in timing_keys:
+                config_data[k] = DEFAULT_TIMING_MS[k]
+
+        self.set_timing_ecode(timing_keys, config_data)
 
         hypamp_value = numpy.median(smooth_current[: self.ton])
         self.set_amplitudes_ecode("hypamp", config_data, reader_data, hypamp_value)

bluepyefe/ecode/posCheops.py

@@ -26,12 +26,21 @@
 
 logger = logging.getLogger(__name__)
 
+DEFAULT_TIMING_MS = {
+    "ton": 250.0,
+    "t1": 8250.0,
+    "t2": 10250.0,
+    "t3": 14250.0,
+    "t4": 16250.0,
+    "toff": 18916.0,
+}
+
 
 class PosCheops(Recording):
 
     # pylint: disable=line-too-long,anomalous-backslash-in-string
 
-    """PosCheops current stimulus
+    r"""PosCheops current stimulus
 
     .. code-block:: none
 
@@ -117,8 +126,15 @@ def interpret(self, t, current, config_data, reader_data):
         # Smooth the current
         smooth_current = scipy_signal2d(current, 85)
 
-        self.set_timing_ecode(
-            ["ton", "t1", "t2", "t3", "t4", "toff"], config_data)
+        timing_keys = ["ton", "t1", "t2", "t3", "t4", "toff"]
+        if any(config_data.get(k) is None for k in timing_keys):
+            logger.warning(
+                f"Missing timing key(s) for {self.protocol_name}, using defaults: {DEFAULT_TIMING_MS}"
+            )
+            for k in timing_keys:
+                config_data[k] = DEFAULT_TIMING_MS[k]
+
+        self.set_timing_ecode(timing_keys, config_data)
 
         hypamp_value = numpy.median(smooth_current[: self.ton])
         self.set_amplitudes_ecode("hypamp", config_data, reader_data, hypamp_value)