bluecellulab 2.6.18__py3-none-any.whl → 2.6.20__py3-none-any.whl

bluecellulab/analysis/inject_sequence.py

@@ -9,6 +9,7 @@ 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
 
 
@@ -38,6 +39,7 @@ def run_stimulus(
     section: str,
     segment: float,
     cvode: bool = True,
+    add_hypamp: bool = True,
 ) -> Recording:
     """Creates a cell and stimulates it with a given stimulus.
 
@@ -56,6 +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
@@ -81,6 +86,7 @@ def apply_multiple_stimuli(
     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.
 
@@ -95,6 +101,7 @@ def apply_multiple_stimuli(
         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
@@ -144,7 +151,7 @@ def apply_multiple_stimuli(
         else:
             raise ValueError("Unknown stimulus name.")
 
-        task_args.append((cell.template_params, stimulus, section_name, segment, cvode))
+        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/circuit_simulation.py

@@ -26,6 +26,7 @@ import numpy as np
 import pandas as pd
 from pydantic.types import NonNegativeInt
 from typing_extensions import deprecated
+from typing import Optional
 
 import bluecellulab
 from bluecellulab.cell import CellDict
@@ -116,6 +117,8 @@ class CircuitSimulation:
         self.spike_threshold = self.circuit_access.config.spike_threshold
         self.spike_location = self.circuit_access.config.spike_location
 
+        self.projections: list[str] = []
+
         condition_parameters = self.circuit_access.config.condition_parameters()
         set_global_condition_parameters(condition_parameters)
 
@@ -239,18 +242,17 @@ class CircuitSimulation:
                                         "pre_spike_trains")
 
         if add_projections is True:
-            projections = self.circuit_access.config.get_all_projection_names()
+            self.projections = self.circuit_access.config.get_all_projection_names()
         elif add_projections is False:
-            projections = []
+            self.projections = []
         else:
-            projections = add_projections
+            self.projections = add_projections
 
         self._add_cells(cell_ids)
         if add_synapses:
             self._add_synapses(
                 pre_gids=pre_gids,
-                add_minis=add_minis,
-                projections=projections)
+                add_minis=add_minis)
         if add_replay or interconnect_cells or pre_spike_trains:
             if add_replay and not add_synapses:
                 raise BluecellulabError("add_replay option can not be used if "
@@ -357,18 +359,17 @@ class CircuitSimulation:
                 ornstein_uhlenbeck_stim_count += 1
 
     def _add_synapses(
-            self, pre_gids=None, add_minis=False, projections=None):
+            self, pre_gids=None, add_minis=False):
         """Instantiate all the synapses."""
         for cell_id in self.cells:
             self._add_cell_synapses(
                 cell_id, pre_gids=pre_gids,
-                add_minis=add_minis,
-                projections=projections)
+                add_minis=add_minis)
 
     def _add_cell_synapses(
-        self, cell_id: CellId, pre_gids=None, add_minis=False, projections=None
+        self, cell_id: CellId, pre_gids=None, add_minis=False
     ) -> None:
-        syn_descriptions = self.get_syn_descriptions(cell_id, projections=projections)
+        syn_descriptions = self.get_syn_descriptions(cell_id)
 
         if pre_gids is not None:
             if self.circuit_format == CircuitFormat.SONATA:
@@ -423,12 +424,10 @@ class CircuitSimulation:
         )
         return syn_descriptions[filtered_rows]
 
-    def get_syn_descriptions(
-        self, cell_id: int | tuple[str, int], projections=None
-    ) -> pd.DataFrame:
+    def get_syn_descriptions(self, cell_id: int | tuple[str, int]) -> pd.DataFrame:
         """Get synapse descriptions dataframe."""
         cell_id = create_cell_id(cell_id)
-        return self.circuit_access.extract_synapses(cell_id, projections=projections)
+        return self.circuit_access.extract_synapses(cell_id, projections=self.projections)
 
     @staticmethod
     def merge_pre_spike_trains(*train_dicts) -> dict[CellId, np.ndarray]:

{bluecellulab-2.6.18.dist-info → bluecellulab-2.6.20.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bluecellulab
-Version: 2.6.18
+Version: 2.6.20
 Summary: Biologically detailed neural network simulations and analysis.
 Author: Blue Brain Project, EPFL
 License: Apache2.0

{bluecellulab-2.6.18.dist-info → bluecellulab-2.6.20.dist-info}/RECORD

@@ -1,5 +1,5 @@
 bluecellulab/__init__.py,sha256=JvigOm_7WDjVAodm4R_TyRzj7vd9hmEbvLJDUVtgeqo,899
-bluecellulab/circuit_simulation.py,sha256=GLy_O5onhiSa-RajorDHlgP1rkFxjUONB4G6B4upyg0,33672
+bluecellulab/circuit_simulation.py,sha256=cLCA97WKjhlEitD4CUad9n4pH4KF7Iw68w1bZH512yw,33587
 bluecellulab/connection.py,sha256=volV2YKtmqAF7MOEJar5ldF1ARAo7k2vF9MB1NXybUY,4640
 bluecellulab/dendrogram.py,sha256=w0vvv0Q169DolTX1j9dAZIvHIl4H258gAjQ1xQaNiGk,6427
 bluecellulab/exceptions.py,sha256=KIxF7s_7gPVJ07TiQ-Z1D8de7ylV74gNMhzl0339CVM,2379
@@ -15,7 +15,7 @@ bluecellulab/type_aliases.py,sha256=DvgjERv2Ztdw_sW63JrZTQGpJ0x5uMTFB5hcBHDb0WA,
 bluecellulab/utils.py,sha256=SbOOkzw1YGjCKV3qOw0zpabNEy7V9BRtgMLsQJiFRq4,1526
 bluecellulab/verbosity.py,sha256=T0IgX7DrRo19faxrT4Xzb27gqxzoILQ8FzYKxvUeaPM,1342
 bluecellulab/analysis/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-bluecellulab/analysis/inject_sequence.py,sha256=6_OuUtUjmSvhCj5_mX-8ZnUpv5jXUHHYDYPUcV2m0eE,5958
+bluecellulab/analysis/inject_sequence.py,sha256=Ih3wdNRn0-lM-NW8agrMUGS862CEgzn_hl54DFDXyjM,6325
 bluecellulab/cell/__init__.py,sha256=Sbc0QOsJ8E7tSwf3q7fsXuE_SevBN6ZmoCVyyU5zfII,208
 bluecellulab/cell/cell_dict.py,sha256=PVmZsjhZ9jp3HC-8QmdFqp-crAcVMSVeLWujcOPLlpo,1346
 bluecellulab/cell/core.py,sha256=2UtXXd4FA2X5A_7ljjbN4yobpMWD2FWfux67ZFND2rI,31315
@@ -62,9 +62,9 @@ bluecellulab/stimulus/factory.py,sha256=XDbnqCuMCh1RdZLKvlRucMj3wkXDqy6mEda_Oh6Y
 bluecellulab/synapse/__init__.py,sha256=RW8XoAMXOvK7OG1nHl_q8jSEKLj9ZN4oWf2nY9HAwuk,192
 bluecellulab/synapse/synapse_factory.py,sha256=3y15LlaBoNJiU2KUeTkh70pyU5OYf6xQIMSBmmMPMak,6987
 bluecellulab/synapse/synapse_types.py,sha256=4gne-hve2vq1Lau-LAVPsfLjffVYqAYBW3kCfC7_600,16871
-bluecellulab-2.6.18.dist-info/AUTHORS.txt,sha256=EDs3H-2HXBojbma10psixk3C2rFiOCTIREi2ZAbXYNQ,179
-bluecellulab-2.6.18.dist-info/LICENSE,sha256=xOouu1gC1GGklDxkITlaVl60I9Ab860O-nZsFbWydvU,11749
-bluecellulab-2.6.18.dist-info/METADATA,sha256=qRtydITfTVimJQmOLizHxMlxNIteEBD1-W9FWWXMr74,7054
-bluecellulab-2.6.18.dist-info/WHEEL,sha256=y4mX-SOX4fYIkonsAGA5N0Oy-8_gI4FXw5HNI1xqvWg,91
-bluecellulab-2.6.18.dist-info/top_level.txt,sha256=VSyEP8w9l3pXdRkyP_goeMwiNA8KWwitfAqUkveJkdQ,13
-bluecellulab-2.6.18.dist-info/RECORD,,
+bluecellulab-2.6.20.dist-info/AUTHORS.txt,sha256=EDs3H-2HXBojbma10psixk3C2rFiOCTIREi2ZAbXYNQ,179
+bluecellulab-2.6.20.dist-info/LICENSE,sha256=xOouu1gC1GGklDxkITlaVl60I9Ab860O-nZsFbWydvU,11749
+bluecellulab-2.6.20.dist-info/METADATA,sha256=yTXxAI-720NEswCTw_VFn6SZ-MAVtsprxRaM-ZdwSsE,7054
+bluecellulab-2.6.20.dist-info/WHEEL,sha256=y4mX-SOX4fYIkonsAGA5N0Oy-8_gI4FXw5HNI1xqvWg,91
+bluecellulab-2.6.20.dist-info/top_level.txt,sha256=VSyEP8w9l3pXdRkyP_goeMwiNA8KWwitfAqUkveJkdQ,13
+bluecellulab-2.6.20.dist-info/RECORD,,