Merge pull request #128 from BlueBrain/square_ecode

Square ecode

bluepyemodel/ecode/__init__.py

@@ -36,6 +36,7 @@
 from .sahp import sAHP
 from .sinespec import SineSpec
 from .spikerec import SpikeRecMultiSpikes
+from .square import BPOSquarePulse
 from .subwhitenoise import SubWhiteNoise
 from .thresholdaddition import ThresholdAddition
 from .whitenoise import WhiteNoise
@@ -44,10 +45,10 @@
 # define duplicates.
 eCodes = {
     "spontaneous": IDrest,
+    "step": IDrest,
     "idrest": IDrest,
     "idthres": IDrest,
     "idthresh": IDrest,
-    "step": IDrest,
     "spontaps": IDrest,
     "sponnohold30": IDrest,
     "sponhold30": IDrest,
@@ -83,6 +84,7 @@
     "startnohold": IDrest,
     "thresholdaddition": ThresholdAddition,
     "probampanmda_ems": ProbAMPANMDA_EMS,
+    "bposquarepulse": BPOSquarePulse,
 }
 
 fixed_timestep_eCodes = ["probampanmda_ems"]

bluepyemodel/ecode/square.py

@@ -0,0 +1,118 @@
+"""BPEM_stimulus class"""
+
+"""
+Copyright 2023, EPFL/Blue Brain Project
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+"""
+
+import logging
+
+import numpy
+from bluepyopt.ephys.stimuli import NrnSquarePulse
+
+logger = logging.getLogger(__name__)
+
+
+class BPOSquarePulse(NrnSquarePulse):
+    """Abstract current stimulus based on BluePyOpt square stimulus.
+
+    Can be used to reproduce results using BluePyOpt's NrnSquarePulse.
+
+    .. code-block:: none
+
+              holdi               holdi+amp                holdi
+                :                     :                      :
+                :                     :                      :
+                :           ______________________           :
+                :          |                      |          :
+                :          |                      |          :
+                :          |                      |          :
+                :          |                      |          :
+        |__________________|                      |______________________
+        ^                  ^                      ^                      ^
+        :                  :                      :                      :
+        :                  :                      :                      :
+        t=0                delay                  delay+duration         totduration
+    """
+
+    name = ""
+
+    def __init__(self, location, **kwargs):
+        """Constructor
+        Args:
+            location(Location): location of stimulus
+        """
+
+        super().__init__(
+            step_amplitude=kwargs.get("amp", None),
+            step_delay=kwargs.get("delay", 250.0),
+            step_duration=kwargs.get("duration", 1350.0),
+            total_duration=kwargs.get("totduration", 1850.0),
+            location=location,
+        )
+
+        self.holding_current = kwargs.get("holding_current", None)
+        self.holding_iclamp = None
+
+    @property
+    def stim_start(self):
+        return self.step_delay
+
+    @property
+    def stim_end(self):
+        return self.step_delay + self.step_duration
+
+    @property
+    def amplitude(self):
+        return self.step_amplitude
+
+    def instantiate(self, sim=None, icell=None):
+        """Run stimulus"""
+
+        icomp = self.location.instantiate(sim=sim, icell=icell)
+
+        self.iclamp = sim.neuron.h.IClamp(icomp.x, sec=icomp.sec)
+        self.iclamp.dur = self.step_duration
+
+        self.iclamp.delay = self.step_delay
+        self.iclamp.amp = self.step_amplitude
+
+        if self.holding_current is not None:
+            self.holding_iclamp = sim.neuron.h.IClamp(icomp.x, sec=icomp.sec)
+            self.holding_iclamp.dur = self.total_duration
+            self.holding_iclamp.delay = 0
+            self.holding_iclamp.amp = self.holding_current
+
+    def destroy(self, sim=None):  # pylint:disable=W0613
+        """Destroy stimulus"""
+        self.iclamp = None
+        self.holding_iclamp = None
+
+    def generate(self, dt=0.1):
+        """Return current time series"""
+        holding_current = self.holding_current if self.holding_current is not None else 0
+
+        t = numpy.arange(0.0, self.total_duration, dt)
+        current = numpy.full(t.shape, holding_current, dtype="float64")
+
+        ton_idx = int(self.stim_start / dt)
+        toff_idx = int(self.stim_end / dt)
+
+        current[ton_idx:toff_idx] += self.amplitude
+
+        return t, current
+
+    def __str__(self):
+        """String representation"""
+        return f"{self.name} current played at {self.location}"

bluepyemodel/efeatures_extraction/targets_configuration.py

@@ -330,7 +330,8 @@ def is_configuration_valid(self):
 
     def check_presence_RMP_Rin_efeatures(self, name_rmp_protocol, name_Rin_protocol):
         """Check that the protocols supposed to be used for RMP and Rin are present in the target
-        and that they have the correct efeatures. If some features are missing, add them."""
+        and that they have the correct efeatures. If some features are missing, add them.
+        """
 
         if self.targets:
             efeatures_rmp = [

bluepyemodel/emodel_pipeline/emodel.py

@@ -179,7 +179,10 @@ def get_related_nexus_ids(self):
                 "type": "Generation",
                 "activity": {
                     "type": "Activity",
-                    "followedWorkflow": {"type": "EModelWorkflow", "id": self.workflow_id},
+                    "followedWorkflow": {
+                        "type": "EModelWorkflow",
+                        "id": self.workflow_id,
+                    },
                 },
             }
         }

bluepyemodel/emodel_pipeline/emodel_metadata.py

@@ -201,7 +201,15 @@ def as_dict(self):
     def as_string(self, seed=None, use_allen_notation=True):
         s = ""
 
-        for k in ["emodel", "etype", "ttype", "mtype", "species", "brain_region", "iteration"]:
+        for k in [
+            "emodel",
+            "etype",
+            "ttype",
+            "mtype",
+            "species",
+            "brain_region",
+            "iteration",
+        ]:
             v = getattr(self, k)
             if use_allen_notation and k == "brain_region" and self.allen_notation:
                 v = self.allen_notation
@@ -220,7 +228,8 @@ def as_string(self, seed=None, use_allen_notation=True):
 
     def check_emodel_name(self):
         """Check if name complies with requirements:
-        https://nrn.readthedocs.io/en/8.2.3/guide/hoc_chapter_11_old_reference.html#names"""
+        https://nrn.readthedocs.io/en/8.2.3/guide/hoc_chapter_11_old_reference.html#names
+        """
 
         allowed_chars = string.ascii_letters + string.digits + "_"
         translate_args = str.maketrans("", "", allowed_chars)

bluepyemodel/emodel_pipeline/emodel_pipeline.py

@@ -148,7 +148,11 @@ def __init__(
         )
 
     def configure_model(
-        self, morphology_name, morphology_path=None, morphology_format=None, use_gene_data=False
+        self,
+        morphology_name,
+        morphology_path=None,
+        morphology_format=None,
+        use_gene_data=False,
     ):
         """To be deprecated"""
 
@@ -335,7 +339,14 @@ def sanitize_gitignore():
 
     lines = " ".join(line for line in lines)
 
-    to_add = ["run/", "checkpoints/", "figures/", "logs/", ".ipython/", ".ipynb_checkpoints/"]
+    to_add = [
+        "run/",
+        "checkpoints/",
+        "figures/",
+        "logs/",
+        ".ipython/",
+        ".ipynb_checkpoints/",
+    ]
 
     with open(str(path_gitignore), "a") as f:
         for a in to_add:

bluepyemodel/emodel_pipeline/emodel_script.py

@@ -38,7 +38,10 @@ def get_related_nexus_ids(self):
                 "type": "Generation",
                 "activity": {
                     "type": "Activity",
-                    "followedWorkflow": {"type": "EModelWorkflow", "id": self.workflow_id},
+                    "followedWorkflow": {
+                        "type": "EModelWorkflow",
+                        "id": self.workflow_id,
+                    },
                 },
             }
         }

bluepyemodel/emodel_pipeline/emodel_workflow.py

@@ -78,13 +78,19 @@ def get_related_nexus_ids(self):
         generates = emodels_ids + emodel_scripts_ids
         if self.fitness_configuration_id:
             generates.append(
-                {"id": self.fitness_configuration_id, "type": "FitnessCalculatorConfiguration"}
+                {
+                    "id": self.fitness_configuration_id,
+                    "type": "FitnessCalculatorConfiguration",
+                }
             )
 
         has_part = []
         if self.targets_configuration_id:
             has_part.append(
-                {"id": self.targets_configuration_id, "type": "ExtractionTargetsConfiguration"}
+                {
+                    "id": self.targets_configuration_id,
+                    "type": "ExtractionTargetsConfiguration",
+                }
             )
         if self.pipeline_settings_id:
             has_part.append({"id": self.pipeline_settings_id, "type": "EModelPipelineSettings"})