bluecellulab 2.5.0__py3-none-any.whl → 2.6.38__py3-none-any.whl

bluecellulab/__init__.py

@@ -7,7 +7,7 @@ try:
 except ImportError:
     BLUEPY_AVAILABLE = False
 
-from .importer import *  # NOQA
+from bluecellulab.importer import import_hoc
 from .verbosity import *
 from .cell import Cell, create_ball_stick  # NOQA
 from .circuit import EmodelProperties
@@ -18,8 +18,8 @@ from .psection import PSection  # NOQA
 from .psegment import PSegment  # NOQA
 from .simulation import Simulation  # NOQA
 from .rngsettings import RNGSettings  # NOQA
-from .ssim import SSim  # NOQA
-
+from .circuit_simulation import CircuitSimulation  # NOQA
+import neuron
 
 from .simulation.neuron_globals import NeuronGlobals
 

bluecellulab/analysis/inject_sequence.py

@@ -7,9 +7,10 @@ import neuron
 import numpy as np
 from bluecellulab.cell.core import Cell
 from bluecellulab.cell.template import TemplateParams
+from bluecellulab.simulation.parallel import IsolatedProcess
 from bluecellulab.simulation.simulation import Simulation
+from bluecellulab.stimulus.circuit_stimulus_definitions import Hyperpolarizing
 from bluecellulab.stimulus.factory import Stimulus, StimulusFactory
-from bluecellulab.utils import IsolatedProcess
 
 
 class StimulusName(Enum):
@@ -18,6 +19,8 @@ class StimulusName(Enum):
     IDREST = auto()
     IV = auto()
     FIRE_PATTERN = auto()
+    POS_CHEOPS = auto()
+    NEG_CHEOPS = auto()
 
 
 class Recording(NamedTuple):
@@ -35,7 +38,8 @@ def run_stimulus(
     stimulus: Stimulus,
     section: str,
     segment: float,
-    duration: float,
+    cvode: bool = True,
+    add_hypamp: bool = True,
 ) -> Recording:
     """Creates a cell and stimulates it with a given stimulus.
 
@@ -44,7 +48,7 @@ def run_stimulus(
         stimulus: The input stimulus to inject into the cell.
         section: Name of the section of cell where the stimulus is to be injected.
         segment: The segment of the section where the stimulus is to be injected.
-        duration: The duration for which the simulation is to be run.
+        cvode: True to use variable time-steps. False for fixed time-steps.
 
     Returns:
         The voltage-time recording at the specified location.
@@ -54,6 +58,9 @@ def run_stimulus(
     """
     cell = Cell.from_template_parameters(template_params)
     neuron_section = cell.sections[section]
+    if add_hypamp:
+        hyp_stim = Hyperpolarizing(target="", delay=0.0, duration=stimulus.stimulus_time)
+        cell.add_replay_hypamp(hyp_stim)
     cell.add_voltage_recording(neuron_section, segment)
     iclamp, _ = cell.inject_current_waveform(
         stimulus.time, stimulus.current, section=neuron_section, segx=segment
@@ -61,7 +68,7 @@ def run_stimulus(
     current_vector = neuron.h.Vector()
     current_vector.record(iclamp._ref_i)
     simulation = Simulation(cell)
-    simulation.run(duration)
+    simulation.run(stimulus.stimulus_time, cvode=cvode)
     current = np.array(current_vector.to_python())
     voltage = cell.get_voltage_recording(neuron_section, segment)
     time = cell.get_time()
@@ -70,14 +77,16 @@ def run_stimulus(
     return Recording(current, voltage, time)
 
 
-def apply_multiple_step_stimuli(
+def apply_multiple_stimuli(
     cell: Cell,
     stimulus_name: StimulusName,
     amplitudes: Sequence[float],
-    duration: float,
+    threshold_based: bool = True,
     section_name: str | None = None,
     segment: float = 0.5,
     n_processes: int | None = None,
+    cvode: bool = True,
+    add_hypamp: bool = True,
 ) -> StimulusRecordings:
     """Apply multiple stimuli to the cell on isolated processes.
 
@@ -85,11 +94,14 @@ def apply_multiple_step_stimuli(
         cell: The cell to which the stimuli are applied.
         stimulus_name: The name of the stimulus to apply.
         amplitudes: The amplitudes of the stimuli to apply.
-        duration: The duration for which each stimulus is applied.
+        threshold_based: Whether to consider amplitudes to be
+            threshold percentages or to be raw amplitudes.
         section_name: Section name of the cell where the stimuli are applied.
           If None, the stimuli are applied at the soma[0] of the cell.
         segment: The segment of the section where the stimuli are applied.
         n_processes: The number of processes to use for running the stimuli.
+        cvode: True to use variable time-steps. False for fixed time-steps.
+        add_hypamp: True to add the cell's holding current stimulus
 
     Returns:
         A dictionary where the keys are the names of the stimuli and the values
@@ -105,18 +117,41 @@ def apply_multiple_step_stimuli(
 
     # Prepare arguments for each stimulus
     for amplitude in amplitudes:
+        if threshold_based:
+            thres_perc = amplitude
+            amp = None
+        else:
+            thres_perc = None
+            amp = amplitude
+
         if stimulus_name == StimulusName.AP_WAVEFORM:
-            stimulus = stim_factory.ap_waveform(threshold_current=cell.threshold, threshold_percentage=amplitude)
+            stimulus = stim_factory.ap_waveform(
+                threshold_current=cell.threshold, threshold_percentage=thres_perc, amplitude=amp
+            )
         elif stimulus_name == StimulusName.IDREST:
-            stimulus = stim_factory.idrest(threshold_current=cell.threshold, threshold_percentage=amplitude)
+            stimulus = stim_factory.idrest(
+                threshold_current=cell.threshold, threshold_percentage=thres_perc, amplitude=amp
+            )
         elif stimulus_name == StimulusName.IV:
-            stimulus = stim_factory.iv(threshold_current=cell.threshold, threshold_percentage=amplitude)
+            stimulus = stim_factory.iv(
+                threshold_current=cell.threshold, threshold_percentage=thres_perc, amplitude=amp
+            )
         elif stimulus_name == StimulusName.FIRE_PATTERN:
-            stimulus = stim_factory.fire_pattern(threshold_current=cell.threshold, threshold_percentage=amplitude)
+            stimulus = stim_factory.fire_pattern(
+                threshold_current=cell.threshold, threshold_percentage=thres_perc, amplitude=amp
+            )
+        elif stimulus_name == StimulusName.POS_CHEOPS:
+            stimulus = stim_factory.pos_cheops(
+                threshold_current=cell.threshold, threshold_percentage=thres_perc, amplitude=amp
+            )
+        elif stimulus_name == StimulusName.NEG_CHEOPS:
+            stimulus = stim_factory.neg_cheops(
+                threshold_current=cell.threshold, threshold_percentage=thres_perc, amplitude=amp
+            )
         else:
             raise ValueError("Unknown stimulus name.")
 
-        task_args.append((cell.template_params, stimulus, section_name, segment, duration))
+        task_args.append((cell.template_params, stimulus, section_name, segment, cvode, add_hypamp))
 
     with IsolatedProcess(processes=n_processes) as pool:
         # Map expects a function and a list of argument tuples

bluecellulab/cell/cell_dict.py

@@ -1,4 +1,4 @@
-# Copyright 2012-2024 Blue Brain Project / EPFL
+# Copyright 2023-2024 Blue Brain Project / EPFL
 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

bluecellulab/cell/core.py

@@ -1,4 +1,4 @@
-# Copyright 2012-2024 Blue Brain Project / EPFL
+# Copyright 2023-2024 Blue Brain Project / EPFL
 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -142,7 +142,8 @@ class Cell(InjectableMixin, PlottableMixin):
                             dt=self.record_dt)
 
         self.delayed_weights = queue.PriorityQueue()  # type: ignore
-        self.psections, self.secname_to_psection = init_psections(public_hoc_cell(self.cell))
+        self.psections: dict[int, PSection] = {}
+        self.secname_to_psection: dict[str, PSection] = {}
 
         # Keep track of when a cell is made passive by make_passive()
         # Used to know when re_init_rng() can be executed
@@ -155,6 +156,11 @@ class Cell(InjectableMixin, PlottableMixin):
         # as the object exists
         self.persistent: list[HocObjectType] = []
 
+    def _init_psections(self) -> None:
+        """Initialize the psections of the cell."""
+        if not self.psections:
+            self.psections, self.secname_to_psection = init_psections(public_hoc_cell(self.cell))
+
     def _extract_sections(self, sections) -> SectionMapping:
         res: SectionMapping = {}
         for section in sections:
@@ -198,6 +204,7 @@ class Cell(InjectableMixin, PlottableMixin):
 
     def get_psection(self, section_id: int | str) -> PSection:
         """Return a python section with the specified section id."""
+        self._init_psections()
         if isinstance(section_id, int):
             return self.psections[section_id]
         elif isinstance(section_id, str):
@@ -490,10 +497,6 @@ class Cell(InjectableMixin, PlottableMixin):
         # numpy int to int
         post_sec_id = int(syn_description[SynapseProperty.POST_SECTION_ID])
 
-        location = SynapseFactory.determine_synapse_location(
-            syn_description, self
-        )
-
         weight_scalar = connection_modifiers.get('Weight', 1.0)
         exc_mini_frequency, inh_mini_frequency = mini_frequencies \
             if mini_frequencies is not None else (None, None)
@@ -509,13 +512,15 @@ class Cell(InjectableMixin, PlottableMixin):
             spont_minis_rate = inh_mini_frequency
 
         if spont_minis_rate is not None and spont_minis_rate > 0:
-            sec = self.get_psection(post_sec_id).hsection
+            synapse_hoc_args = SynapseFactory.determine_synapse_location(
+                syn_description, self
+            )
             # add the *minis*: spontaneous synaptic events
             self.ips[synapse_id] = neuron.h.\
-                InhPoissonStim(location, sec=sec)
+                InhPoissonStim(synapse_hoc_args.location, sec=synapse_hoc_args.section)
 
             self.syn_mini_netcons[synapse_id] = neuron.h.\
-                NetCon(self.ips[synapse_id], synapse.hsynapse, sec=sec)
+                NetCon(self.ips[synapse_id], synapse.hsynapse, sec=synapse_hoc_args.section)
             self.syn_mini_netcons[synapse_id].delay = 0.1
             self.syn_mini_netcons[synapse_id].weight[0] = weight * weight_scalar
             # set netcon type
@@ -714,27 +719,26 @@ class Cell(InjectableMixin, PlottableMixin):
             pre_gid = CellId(
                 source_population, int(synapse.syn_description[SynapseProperty.PRE_GID])
             )
-            if self.sonata_proxy.circuit_access.target_contains_cell(stimulus.source, pre_gid):
-                if pre_gid.id in synapse_spikes:
-                    spikes_of_interest = synapse_spikes[pre_gid.id]
-                    # filter spikes of interest >=stimulus.delay, <=stimulus.duration
-                    spikes_of_interest = spikes_of_interest[
-                        (spikes_of_interest >= stimulus.delay)
-                        & (spikes_of_interest <= stimulus.duration)
-                    ]
-                    connection = bluecellulab.Connection(
-                        synapse,
-                        pre_spiketrain=spikes_of_interest,
-                        pre_cell=None,
-                        stim_dt=self.record_dt,
-                        spike_threshold=spike_threshold,
-                        spike_location=spike_location,
-                    )
-                    logger.debug(
-                        f"Added synapse replay from {pre_gid} to {self.cell_id.id}, {synapse_id}"
-                    )
-
-                    self.connections[synapse_id] = connection
+            if pre_gid.id in synapse_spikes:
+                spikes_of_interest = synapse_spikes[pre_gid.id]
+                # filter spikes of interest >=stimulus.delay, <=stimulus.duration
+                spikes_of_interest = spikes_of_interest[
+                    (spikes_of_interest >= stimulus.delay)
+                    & (spikes_of_interest <= stimulus.duration)
+                ]
+                connection = bluecellulab.Connection(
+                    synapse,
+                    pre_spiketrain=spikes_of_interest,
+                    pre_cell=None,
+                    stim_dt=self.record_dt,
+                    spike_threshold=spike_threshold,
+                    spike_location=spike_location,
+                )
+                logger.debug(
+                    f"Added synapse replay from {pre_gid} to {self.cell_id.id}, {synapse_id}"
+                )
+
+                self.connections[synapse_id] = connection
 
     @property
     def info_dict(self):

bluecellulab/cell/injector.py

@@ -1,4 +1,4 @@
-# Copyright 2012-2024 Blue Brain Project / EPFL
+# Copyright 2023-2024 Blue Brain Project / EPFL
 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -360,17 +360,15 @@ class InjectableMixin:
             stimulus: RelativeShotNoise,
             shotnoise_stim_count=0):
         """Add a replay relative shot noise stimulus."""
-        cv_square = stimulus.amp_cv**2
 
         stim_mode = stimulus.mode
         rel_prop = self.relativity_proportion(stim_mode)
 
         mean = stimulus.mean_percent / 100 * rel_prop
         sd = stimulus.sd_percent / 100 * rel_prop
-        var = sd * sd
 
         rate, amp_mean, amp_var = get_relative_shotnoise_params(
-            mean, var, stimulus.decay_time, stimulus.rise_time, cv_square)
+            mean, sd, stimulus.decay_time, stimulus.rise_time, stimulus.relative_skew)
 
         rng = self._get_shotnoise_step_rand(shotnoise_stim_count, stimulus.seed)
         tvec, svec = gen_shotnoise_signal(stimulus.decay_time, stimulus.rise_time, rate, amp_mean,

bluecellulab/cell/plotting.py

@@ -1,4 +1,4 @@
-# Copyright 2012-2024 Blue Brain Project / EPFL
+# Copyright 2023-2024 Blue Brain Project / EPFL
 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -60,6 +60,7 @@ class PlottableMixin:
             scale_bar_size=10.0,
             fig_title=None):
         """Show a dendrogram of the cell."""
+        self._init_psections()
         cell_dendrogram = bluecellulab.Dendrogram(
             self.psections,
             variable=variable,

bluecellulab/cell/random.py

@@ -1,4 +1,4 @@
-# Copyright 2012-2024 Blue Brain Project / EPFL
+# Copyright 2023-2024 Blue Brain Project / EPFL
 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

bluecellulab/cell/section_distance.py

@@ -1,4 +1,4 @@
-# Copyright 2012-2024 Blue Brain Project / EPFL
+# Copyright 2023-2024 Blue Brain Project / EPFL
 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

bluecellulab/cell/serialized_sections.py

@@ -1,4 +1,4 @@
-# Copyright 2012-2024 Blue Brain Project / EPFL
+# Copyright 2023-2024 Blue Brain Project / EPFL
 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -15,17 +15,14 @@
 index."""
 from __future__ import annotations
 import logging
-import warnings
 import neuron
 from bluecellulab.type_aliases import HocObjectType, NeuronSection
 
 
 logger = logging.getLogger(__name__)
-warnings.filterwarnings("once", category=UserWarning, module=__name__)
 
 
 class SerializedSections:
-
     def __init__(self, cell: HocObjectType) -> None:
         self.isec2sec: dict[int, NeuronSection] = {}
         n = cell.nSecAll
@@ -37,7 +34,8 @@ class SerializedSections:
                 raise ValueError("Error: failure in mk2_isec2sec()")
 
             if v_value < 0:
-                warnings.warn(
-                    f"[Warning] SerializedSections: v(0.0001) < 0. index={index} v()={v_value}")
+                logging.debug(
+                    f"[Warning] SerializedSections: v(0.0001) < 0. index={index} v()={v_value}"
+                )
             else:
                 self.isec2sec[int(v_value)] = neuron.h.SectionRef(sec=sec)

bluecellulab/cell/sonata_proxy.py

@@ -1,4 +1,4 @@
-# Copyright 2012-2024 Blue Brain Project / EPFL
+# Copyright 2023-2024 Blue Brain Project / EPFL
 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

bluecellulab/cell/stimuli_generator.py

@@ -1,4 +1,4 @@
-# Copyright 2012-2024 Blue Brain Project / EPFL
+# Copyright 2023-2024 Blue Brain Project / EPFL
 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -114,17 +114,35 @@ def gen_shotnoise_signal(tau_D, tau_R, rate, amp_mean, amp_var,
     return tvec, P
 
 
-def get_relative_shotnoise_params(mean, var, tau_D, tau_R, cv_square):
+def get_relative_shotnoise_params(mean, sd, tau_D, tau_R, relative_skew):
     """Returns Rate, amp_mean and amp_var parameters."""
     # bi-exponential time to peak [ms]
     t_peak = math.log(tau_D / tau_R) / (1 / tau_R - 1 / tau_D)
     # bi-exponential peak height [1]
-    x_peak = math.exp(-t_peak / tau_D) - math.exp(-t_peak / tau_R)
-
-    rate_ms = (1 + cv_square) / 2 * (mean ** 2 / var) / (tau_D + tau_R)
-    rate = rate_ms * 1000  # rate in 1 / s [Hz]
-    amp_mean = mean * x_peak / rate_ms / (tau_D - tau_R)
-    amp_var = cv_square * amp_mean ** 2
+    F_peak = math.exp(-t_peak / tau_D) - math.exp(-t_peak / tau_R)
+
+    # utility constants
+    Xi = (tau_D - tau_R) / F_peak
+    A = 1 / (tau_D + tau_R)
+    B = 1 / ((tau_D + 2 * tau_R) * (2 * tau_D + tau_R))
+
+    # skewness
+    skew_bnd_min = (8 / 3) * (B / A ** 2) * (sd / mean)
+    skew = (1 + relative_skew) * skew_bnd_min
+    if skew < skew_bnd_min or skew > 2 * skew_bnd_min:
+        raise ValueError("skewness out of bounds")
+
+    # cumulants
+    lambda2_1 = sd ** 2 / mean                     # lambda2 over lambda1
+    lambda3_2 = sd * skew                          # lambda3 over lambda2
+    theta1pk = 2 / (A * Xi) * lambda2_1            # = (1 + k) * theta
+    theta2pk = (3 * A) / (4 * B * Xi) * lambda3_2  # = (2 + k) * theta
+
+    # derived parameters
+    amp_mean = 2 * theta1pk - theta2pk               # mean amplitude [nA or uS]
+    amp_var = amp_mean * (theta2pk - theta1pk)  # variance of amplitude [nA^2 or uS^2]
+    rate_ms = mean / (amp_mean * Xi)                 # event rate in 1 / ms
+    rate = rate_ms * 1000                            # event rate in 1 / s [Hz]
 
     return rate, amp_mean, amp_var
 

bluecellulab/cell/template.py

@@ -1,4 +1,4 @@
-# Copyright 2012-2024 Blue Brain Project / EPFL
+# Copyright 2023-2024 Blue Brain Project / EPFL
 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -21,6 +21,7 @@ from pathlib import Path
 import re
 import string
 from typing import NamedTuple, Optional
+import uuid
 
 import neuron
 
@@ -126,8 +127,8 @@ class NeuronTemplate:
         # templates load outside of bluecellulab
         template_name = "%s_bluecellulab" % template_name
         template_name = get_neuron_compliant_template_name(template_name)
-        obj_address = hex(id(self))
-        template_name = f"{template_name}_{obj_address}"
+        unique_id = uuid.uuid4().hex
+        template_name = f"{template_name}_{unique_id}"
 
         template_content = re.sub(
             r"begintemplate\s*(\S*)",

bluecellulab/circuit/circuit_access/bluepy_circuit_access.py

@@ -1,4 +1,4 @@
-# Copyright 2012-2024 Blue Brain Project / EPFL
+# Copyright 2023-2024 Blue Brain Project / EPFL
 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -19,8 +19,9 @@ import os
 from pathlib import Path
 from typing import Optional
 
+import neuron
 import pandas as pd
-from bluecellulab import circuit, neuron
+from bluecellulab import circuit
 from bluecellulab.circuit.circuit_access import EmodelProperties
 from bluecellulab.circuit.config import BluepySimulationConfig
 from bluecellulab.circuit.config.definition import SimulationConfig
@@ -57,7 +58,6 @@ class BluepyCircuitAccess:
             raise FileNotFoundError(
                 f"Circuit config file {simulation_config} not found.")
 
-        # to allow the usage of SimulationConfig outside of Ssim
         if isinstance(simulation_config, BluepySimulationConfig):
             simulation_config = simulation_config.impl
 
@@ -191,23 +191,15 @@ class BluepyCircuitAccess:
 
             if isinstance(connectome._impl, SonataConnectome):
                 logger.debug('Using sonata style synapse file, not nrn.h5')
-                # load 'afferent_section_pos' instead of '_POST_DISTANCE'
-                if 'afferent_section_pos' in connectome.available_properties:
-                    connectome_properties[
-                        connectome_properties.index(SynapseProperty.POST_SEGMENT_OFFSET)
-                    ] = 'afferent_section_pos'
-
-                connectome_properties = properties_to_bluepy(connectome_properties)
-                synapses = connectome.afferent_synapses(
-                    gid, properties=connectome_properties
-                )
-                synapses.columns = properties_from_bluepy(synapses.columns)
-            else:
-                connectome_properties = properties_to_bluepy(connectome_properties)
-                synapses = connectome.afferent_synapses(
-                    gid, properties=connectome_properties
-                )
-                synapses.columns = properties_from_bluepy(synapses.columns)
+                connectome_properties.remove(SynapseProperty.POST_SEGMENT_OFFSET)
+            else:  # afferent section_pos will be computed via post_segment_offset
+                connectome_properties.remove(SynapseProperty.AFFERENT_SECTION_POS)
+
+            connectome_properties = properties_to_bluepy(connectome_properties)
+            synapses = connectome.afferent_synapses(
+                gid, properties=connectome_properties
+            )
+            synapses.columns = properties_from_bluepy(synapses.columns)
 
             synapses = synapses.reset_index(drop=True)
             synapses.index = pd.MultiIndex.from_tuples(

bluecellulab/circuit/circuit_access/definition.py

@@ -1,4 +1,4 @@
-# Copyright 2012-2024 Blue Brain Project / EPFL
+# Copyright 2023-2024 Blue Brain Project / EPFL
 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

bluecellulab/circuit/circuit_access/sonata_circuit_access.py

@@ -1,4 +1,4 @@
-# Copyright 2012-2024 Blue Brain Project / EPFL
+# Copyright 2023-2024 Blue Brain Project / EPFL
 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -22,8 +22,9 @@ from bluepysnap.bbp import Cell as SnapCell
 from bluepysnap.circuit_ids import CircuitNodeId, CircuitEdgeIds
 from bluepysnap.exceptions import BluepySnapError
 from bluepysnap import Circuit as SnapCircuit
+import neuron
 import pandas as pd
-from bluecellulab import circuit, neuron
+from bluecellulab import circuit
 from bluecellulab.circuit.circuit_access.definition import EmodelProperties
 from bluecellulab.circuit import CellId, SynapseProperty
 from bluecellulab.circuit.config import SimulationConfig
@@ -46,7 +47,7 @@ class SonataCircuitAccess:
             raise FileNotFoundError(f"Circuit config file {simulation_config} not found.")
 
         if isinstance(simulation_config, SonataSimulationConfig):
-            self.config: SimulationConfig = simulation_config
+            self.config = simulation_config
         else:
             self.config = SonataSimulationConfig(simulation_config)
         circuit_config = self.config.impl.config["network"]
@@ -190,7 +191,7 @@ class SonataCircuitAccess:
 
     @lru_cache(maxsize=16)
     def get_target_cell_ids(self, target: str) -> set[CellId]:
-        ids = self._circuit.nodes.ids(target)
+        ids = self._circuit.nodes.ids(self.config.impl.node_sets[target])
         return {CellId(x.population, x.id) for x in ids}
 
     @lru_cache(maxsize=100)

bluecellulab/circuit/config/bluepy_simulation_config.py

@@ -1,4 +1,4 @@
-# Copyright 2012-2024 Blue Brain Project / EPFL
+# Copyright 2023-2024 Blue Brain Project / EPFL
 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

bluecellulab/circuit/config/definition.py

@@ -1,4 +1,4 @@
-# Copyright 2012-2024 Blue Brain Project / EPFL
+# Copyright 2023-2024 Blue Brain Project / EPFL
 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

bluecellulab/circuit/config/sections.py

@@ -1,4 +1,4 @@
-# Copyright 2012-2024 Blue Brain Project / EPFL
+# Copyright 2023-2024 Blue Brain Project / EPFL
 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

bluecellulab/circuit/config/sonata_simulation_config.py

@@ -1,4 +1,4 @@
-# Copyright 2012-2024 Blue Brain Project / EPFL
+# Copyright 2023-2024 Blue Brain Project / EPFL
 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

bluecellulab/circuit/format.py

@@ -1,4 +1,4 @@
-# Copyright 2012-2024 Blue Brain Project / EPFL
+# Copyright 2023-2024 Blue Brain Project / EPFL
 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

bluecellulab/circuit/iotools.py

@@ -1,4 +1,4 @@
-# Copyright 2012-2024 Blue Brain Project / EPFL
+# Copyright 2023-2024 Blue Brain Project / EPFL
 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -32,7 +32,7 @@ def parse_outdat(path: str | Path) -> dict[CellId, np.ndarray]:
     # convert Series to DataFrame with 2 columns for `groupby` operation
     spike_df = spikes.to_frame().reset_index()
     if (spike_df["t"] < 0).any():
-        logger.warning('SSim: Found negative spike times in out.dat ! '
+        logger.warning('Found negative spike times in out.dat ! '
                        'Clipping them to 0')
         spike_df["t"].clip(lower=0., inplace=True)
 

bluecellulab/circuit/node_id.py

@@ -1,4 +1,4 @@
-# Copyright 2012-2024 Blue Brain Project / EPFL
+# Copyright 2023-2024 Blue Brain Project / EPFL
 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

bluecellulab/circuit/simulation_access.py

@@ -1,4 +1,4 @@
-# Copyright 2012-2024 Blue Brain Project / EPFL
+# Copyright 2023-2024 Blue Brain Project / EPFL
 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -18,6 +18,7 @@ import logging
 from pathlib import Path
 from typing import Optional, Protocol
 
+import h5py
 import pandas as pd
 
 from bluecellulab.circuit.config import SimulationConfig, SonataSimulationConfig
@@ -171,13 +172,15 @@ class SonataSimulationAccess:
 
 
 def get_synapse_replay_spikes(f_name: str) -> dict:
-    """Read the .dat file containing the spike replays."""
-    data = np.genfromtxt(f_name, skip_header=1)
-    spikes = pd.DataFrame(data=data, columns=["t", "node_id"]).astype({"node_id": int})
-    # subtract 1 from all node_ids to make them 0-based
-    # source: https://sonata-extension.readthedocs.io/
-    # en/latest/blueconfig-projection-example.html#dat-spike-files
-    spikes["node_id"] -= 1
+    """Read the .h5 file containing the spike replays."""
+    with h5py.File(f_name, 'r') as f:
+        # Access the timestamps and node_ids datasets
+        timestamps = f['/spikes/All/timestamps'][:]
+        node_ids = f['/spikes/All/node_ids'][:]
+
+        spikes = pd.DataFrame(data={'t': timestamps, 'node_id': node_ids})
+        spikes = spikes.astype({"node_id": int})
+
     if (spikes["t"] < 0).any():
         logger.warning("Found negative spike times... Clipping them to 0")
         spikes["t"].clip(lower=0., inplace=True)