bluecellulab 2.6.15__tar.gz → 2.6.17__tar.gz

{bluecellulab-2.6.15 → bluecellulab-2.6.17}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bluecellulab
-Version: 2.6.15
+Version: 2.6.17
 Summary: Biologically detailed neural network simulations and analysis.
 Author: Blue Brain Project, EPFL
 License: Apache2.0

{bluecellulab-2.6.15 → bluecellulab-2.6.17}/bluecellulab/analysis/inject_sequence.py

@@ -37,6 +37,7 @@ def run_stimulus(
     stimulus: Stimulus,
     section: str,
     segment: float,
+    cvode: bool = True,
 ) -> Recording:
     """Creates a cell and stimulates it with a given stimulus.
 
@@ -45,6 +46,7 @@ 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.
+        cvode: True to use variable time-steps. False for fixed time-steps.
 
     Returns:
         The voltage-time recording at the specified location.
@@ -61,7 +63,7 @@ def run_stimulus(
     current_vector = neuron.h.Vector()
     current_vector.record(iclamp._ref_i)
     simulation = Simulation(cell)
-    simulation.run(stimulus.stimulus_time)
+    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()
@@ -78,6 +80,7 @@ def apply_multiple_stimuli(
     section_name: str | None = None,
     segment: float = 0.5,
     n_processes: int | None = None,
+    cvode: bool = True,
 ) -> StimulusRecordings:
     """Apply multiple stimuli to the cell on isolated processes.
 
@@ -91,6 +94,7 @@ def apply_multiple_stimuli(
           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.
 
     Returns:
         A dictionary where the keys are the names of the stimuli and the values
@@ -140,7 +144,7 @@ def apply_multiple_stimuli(
         else:
             raise ValueError("Unknown stimulus name.")
 
-        task_args.append((cell.template_params, stimulus, section_name, segment))
+        task_args.append((cell.template_params, stimulus, section_name, segment, cvode))
 
     with IsolatedProcess(processes=n_processes) as pool:
         # Map expects a function and a list of argument tuples

{bluecellulab-2.6.15 → bluecellulab-2.6.17}/bluecellulab/cell/core.py

@@ -719,27 +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-2.6.15 → bluecellulab-2.6.17}/bluecellulab/circuit/simulation_access.py

@@ -172,7 +172,7 @@ class SonataSimulationAccess:
 
 
 def get_synapse_replay_spikes(f_name: str) -> dict:
-    """Read the .dat file containing the spike replays."""
+    """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'][:]

{bluecellulab-2.6.15 → bluecellulab-2.6.17}/bluecellulab/stimulus/circuit_stimulus_definitions.py

@@ -243,7 +243,6 @@ class Stimulus:
                 delay=stimulus_entry["delay"],
                 duration=stimulus_entry["duration"],
                 spike_file=stimulus_entry["spike_file"],
-                source=stimulus_entry["source"],
             )
         elif pattern == Pattern.SHOT_NOISE:
             return ShotNoise(
@@ -331,7 +330,6 @@ class RelativeLinear(Stimulus):
 @dataclass(frozen=True, config=dict(extra="forbid"))
 class SynapseReplay(Stimulus):
     spike_file: str
-    source: str
 
     @field_validator("spike_file")
     @classmethod

{bluecellulab-2.6.15 → bluecellulab-2.6.17}/bluecellulab.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bluecellulab
-Version: 2.6.15
+Version: 2.6.17
 Summary: Biologically detailed neural network simulations and analysis.
 Author: Blue Brain Project, EPFL
 License: Apache2.0