bluecellulab 2.6.43__py3-none-any.whl → 2.6.44__py3-none-any.whl

bluecellulab/cell/injector.py

@@ -30,6 +30,8 @@ from bluecellulab.exceptions import BluecellulabError
 from bluecellulab.rngsettings import RNGSettings
 from bluecellulab.stimulus.circuit_stimulus_definitions import (
     ClampMode,
+    Linear,
+    RelativeLinear,
     Hyperpolarizing,
     Noise,
     OrnsteinUhlenbeck,
@@ -259,12 +261,32 @@ class InjectableMixin:
         self.persistent.append(tstim)  # type: ignore
         return tstim
 
-    def add_replay_relativelinear(self, stimulus):
+    def add_replay_linear(self, stimulus: Linear):
+        """Add a linear stimulus."""
+
+        return self.add_ramp(
+            stimulus.delay,
+            stimulus.delay + stimulus.duration,
+            stimulus.amp_start,
+            stimulus.amp_end
+        )
+
+    def add_replay_relativelinear(self, stimulus: RelativeLinear):
         """Add a relative linear stimulus."""
-        tstim = neuron.h.TStim(0.5, sec=self.soma)
-        amp = stimulus.percent_start / 100.0 * self.threshold
-        tstim.pulse(stimulus.delay, stimulus.duration, amp)
-        self.persistent.append(tstim)
+        tstim = neuron.h.TStim(0.5, sec=self.soma)  # type: ignore
+        amp_start = stimulus.percent_start / 100.0 * self.threshold  # type: ignore
+        amp_end = stimulus.percent_end / 100.0 * self.threshold  # type: ignore
+
+        tstim.ramp(
+            0.0,
+            stimulus.delay,       # Time when the ramp starts
+            amp_start,      # Initial amplitude (amp_start)
+            amp_end,       # Final amplitude (amp_end)
+            stimulus.duration,    # Duration of the ramp
+            0.0,
+            0.0
+        )
+        self.persistent.append(tstim)  # type: ignore
 
         return tstim
 

bluecellulab/circuit/circuit_access/sonata_circuit_access.py

@@ -152,8 +152,9 @@ class SonataCircuitAccess:
 
                 # make multiindex
                 synapses = synapses.reset_index(drop=True)
+                synapse_ids = list(synapses.index)
                 synapses.index = pd.MultiIndex.from_tuples(
-                    zip([edge_population_name] * len(synapses), synapses.index),
+                    [(edge_population_name, syn_id) for syn_id in synapse_ids],
                     names=["edge_name", "synapse_id"],
                 )
 

bluecellulab/circuit_simulation.py

@@ -139,6 +139,7 @@ class CircuitSimulation:
         pre_spike_trains: None | dict[tuple[str, int], Iterable] | dict[int, Iterable] = None,
         add_shotnoise_stimuli: bool = False,
         add_ornstein_uhlenbeck_stimuli: bool = False,
+        add_linear_stimuli: bool = False,
     ):
         """Instantiate a list of cells.
 
@@ -209,6 +210,11 @@ class CircuitSimulation:
                             of the simulation config,
                             Setting add_stimuli=True,
                             will automatically set this option to True.
+        add_linear_stimuli : Process the 'linear' stimuli
+                                blocks of the simulation config.
+                                Setting add_stimuli=True,
+                                will automatically set this option to
+                                True.
         """
         if not isinstance(cells, Iterable) or isinstance(cells, tuple):
             cells = [cells]
@@ -267,20 +273,23 @@ class CircuitSimulation:
             add_pulse_stimuli = True
             add_shotnoise_stimuli = True
             add_ornstein_uhlenbeck_stimuli = True
+            add_linear_stimuli = True
 
         if add_noise_stimuli or \
                 add_hyperpolarizing_stimuli or \
                 add_pulse_stimuli or \
                 add_relativelinear_stimuli or \
                 add_shotnoise_stimuli or \
-                add_ornstein_uhlenbeck_stimuli:
+                add_ornstein_uhlenbeck_stimuli or \
+                add_linear_stimuli:
             self._add_stimuli(
                 add_noise_stimuli=add_noise_stimuli,
                 add_hyperpolarizing_stimuli=add_hyperpolarizing_stimuli,
                 add_relativelinear_stimuli=add_relativelinear_stimuli,
                 add_pulse_stimuli=add_pulse_stimuli,
                 add_shotnoise_stimuli=add_shotnoise_stimuli,
-                add_ornstein_uhlenbeck_stimuli=add_ornstein_uhlenbeck_stimuli
+                add_ornstein_uhlenbeck_stimuli=add_ornstein_uhlenbeck_stimuli,
+                add_linear_stimuli=add_linear_stimuli
             )
 
     def _add_stimuli(self, add_noise_stimuli=False,
@@ -288,7 +297,8 @@ class CircuitSimulation:
                      add_relativelinear_stimuli=False,
                      add_pulse_stimuli=False,
                      add_shotnoise_stimuli=False,
-                     add_ornstein_uhlenbeck_stimuli=False
+                     add_ornstein_uhlenbeck_stimuli=False,
+                     add_linear_stimuli=False
                      ):
         """Instantiate all the stimuli."""
         stimuli_entries = self.circuit_access.config.get_all_stimuli_entries()
@@ -316,6 +326,9 @@ class CircuitSimulation:
                 elif isinstance(stimulus, circuit_stimulus_definitions.Pulse):
                     if add_pulse_stimuli:
                         self.cells[cell_id].add_pulse(stimulus)
+                elif isinstance(stimulus, circuit_stimulus_definitions.Linear):
+                    if add_linear_stimuli:
+                        self.cells[cell_id].add_replay_linear(stimulus)
                 elif isinstance(stimulus, circuit_stimulus_definitions.RelativeLinear):
                     if add_relativelinear_stimuli:
                         self.cells[cell_id].add_replay_relativelinear(stimulus)

bluecellulab/stimulus/circuit_stimulus_definitions.py

@@ -42,6 +42,7 @@ class Pattern(Enum):
     NOISE = "noise"
     HYPERPOLARIZING = "hyperpolarizing"
     PULSE = "pulse"
+    LINEAR = "linear"
     RELATIVE_LINEAR = "relative_linear"
     SYNAPSE_REPLAY = "synapse_replay"
     SHOT_NOISE = "shot_noise"
@@ -80,6 +81,8 @@ class Pattern(Enum):
             return Pattern.HYPERPOLARIZING
         elif pattern == "pulse":
             return Pattern.PULSE
+        elif pattern == "linear":
+            return Pattern.LINEAR
         elif pattern == "relative_linear":
             return Pattern.RELATIVE_LINEAR
         elif pattern == "synapse_replay":
@@ -141,6 +144,7 @@ class Stimulus:
                 delay=stimulus_entry["Delay"],
                 duration=stimulus_entry["Duration"],
                 percent_start=stimulus_entry["PercentStart"],
+                percent_end=stimulus_entry["PercentEnd"],
             )
         elif pattern == Pattern.SYNAPSE_REPLAY:
             warnings.warn("Ignoring syanpse replay stimulus as it is not supported")
@@ -230,12 +234,21 @@ class Stimulus:
                 width=stimulus_entry["width"],
                 frequency=stimulus_entry["frequency"],
             )
+        elif pattern == Pattern.LINEAR:
+            return Linear(
+                target=stimulus_entry["node_set"],
+                delay=stimulus_entry["delay"],
+                duration=stimulus_entry["duration"],
+                amp_start=stimulus_entry["amp_start"],
+                amp_end=stimulus_entry["amp_end"],
+            )
         elif pattern == Pattern.RELATIVE_LINEAR:
             return RelativeLinear(
                 target=stimulus_entry["node_set"],
                 delay=stimulus_entry["delay"],
                 duration=stimulus_entry["duration"],
                 percent_start=stimulus_entry["percent_start"],
+                percent_end=stimulus_entry["percent_end"],
             )
         elif pattern == Pattern.SYNAPSE_REPLAY:
             return SynapseReplay(
@@ -322,9 +335,16 @@ class Pulse(Stimulus):
     frequency: float
 
 
+@dataclass(frozen=True, config=dict(extra="forbid"))
+class Linear(Stimulus):
+    amp_start: float
+    amp_end: float
+
+
 @dataclass(frozen=True, config=dict(extra="forbid"))
 class RelativeLinear(Stimulus):
     percent_start: float
+    percent_end: float
 
 
 @dataclass(frozen=True, config=dict(extra="forbid"))

{bluecellulab-2.6.43.dist-info → bluecellulab-2.6.44.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: bluecellulab
-Version: 2.6.43
+Version: 2.6.44
 Summary: Biologically detailed neural network simulations and analysis.
 Author: Blue Brain Project, EPFL
 License: Apache2.0

{bluecellulab-2.6.43.dist-info → bluecellulab-2.6.44.dist-info}/RECORD

@@ -1,5 +1,5 @@
 bluecellulab/__init__.py,sha256=1d_CKIJLIpon7o13h3lBnV_-33obZEPwa9KDTjlFPD8,880
-bluecellulab/circuit_simulation.py,sha256=zzVCGP-SP8pdzSt03_FSvSCAeigaBfSb4A-mFfw2AwI,33587
+bluecellulab/circuit_simulation.py,sha256=JVGAsrnyuIG_oY39Bcm8QBxAh004jEHCTxiOiEU8Btk,34293
 bluecellulab/connection.py,sha256=-xT0mU7ppeHI_qjCKj17TtxXVVcUDgBsaMKt9ODmcEU,4640
 bluecellulab/dendrogram.py,sha256=FjS6RZ6xcp5zJoY5d5qv_edqPM13tL2-UANgbZuDBjY,6427
 bluecellulab/exceptions.py,sha256=1lKD92VIyD8cUggAI1SLxeKzj_09Ik_TlHCzPLCvDHg,2379
@@ -21,7 +21,7 @@ bluecellulab/analysis/plotting.py,sha256=-ArjWHZsAlUoNSu_t0HQjQmFhGI1tCQtdAoICgw
 bluecellulab/cell/__init__.py,sha256=Sbc0QOsJ8E7tSwf3q7fsXuE_SevBN6ZmoCVyyU5zfII,208
 bluecellulab/cell/cell_dict.py,sha256=VE7pi-NsMVRSmo-PSdbiLYmolDOu0Gc6JxFBkuQpFdk,1346
 bluecellulab/cell/core.py,sha256=BualY0WOtC0arKmvKzQ3sQ0fhc2jrtd6wqSd9M-e25E,33797
-bluecellulab/cell/injector.py,sha256=O2G3ahMzjP3QNS9q_xIXB54NIkiM3DISv-6uFCk9Ono,18056
+bluecellulab/cell/injector.py,sha256=Mq1XU_dfp7F5JPx5t1oYdJQVez3rZDkCEEZUE7-wWT4,18760
 bluecellulab/cell/plotting.py,sha256=t2qDUabFtsBb-nJMkDh5UfsgW-wvQ2wfDwAVZ8-hWPo,4032
 bluecellulab/cell/random.py,sha256=pemekc11geRBKD8Ghb82tvKOZLfFWkUz1IKLc_NWg-A,1773
 bluecellulab/cell/recording.py,sha256=dekJspPb_5yrS6WR3aXtvZ6KWwMNbyhe5aIOVtNDHpY,342
@@ -43,7 +43,7 @@ bluecellulab/circuit/validate.py,sha256=wntnr7oIDyasqD1nM-kqz1NpfWDxBGhx0Ep3e5hH
 bluecellulab/circuit/circuit_access/__init__.py,sha256=sgp6m5kP-pq60V1IFGUiSUR1OW01zdxXNNUJmPA8anI,201
 bluecellulab/circuit/circuit_access/bluepy_circuit_access.py,sha256=aXvtZR8EwpVEkB4KAupjC4DX_1xYC4OrHwMUQcQIWrQ,14273
 bluecellulab/circuit/circuit_access/definition.py,sha256=_sUU0DkesGOFW82kS1G9vki0o0aQP76z3Ltk7Vo9KK4,4435
-bluecellulab/circuit/circuit_access/sonata_circuit_access.py,sha256=oxMHFG4IBZXhr0mAQpgTNueLaagKbm-7f8VgDDJIg0E,10361
+bluecellulab/circuit/circuit_access/sonata_circuit_access.py,sha256=tADHxVZw4VgZAz2z4NKMUwc0rd_EO40EZggw5fDhnF4,10411
 bluecellulab/circuit/config/__init__.py,sha256=aaoJXRKBJzpxxREo9NxKc-_CCPmVeuR1mcViRXcLrC4,215
 bluecellulab/circuit/config/bluepy_simulation_config.py,sha256=V3eqOzskX7VrMDpl-nMQVEhDg8QWgRmRduyJBii5sgI,6974
 bluecellulab/circuit/config/definition.py,sha256=I1jd4KUX21mw03FEv1aYNsT0UFbDANY3YEPwwKXqe4k,2774
@@ -59,15 +59,15 @@ bluecellulab/simulation/neuron_globals.py,sha256=iBjhg0-1YMP5LsVdtUDt24PEypkCL6m
 bluecellulab/simulation/parallel.py,sha256=oQ_oV2EKr8gP4yF2Dq8q9MiblDyi89_wBgLzQkLV_U0,1514
 bluecellulab/simulation/simulation.py,sha256=VhftOMYU1Rfrphvud6f0U4kvbUivSviQ5TlVljuTb88,6486
 bluecellulab/stimulus/__init__.py,sha256=DgIgVaSyR-URf3JZzvO6j-tjCerzvktuK-ep8pjMRPQ,37
-bluecellulab/stimulus/circuit_stimulus_definitions.py,sha256=WdjxoPL4_T1yn3mEhxH-TvU7d441Kf4v5QwFfH30UNI,15890
+bluecellulab/stimulus/circuit_stimulus_definitions.py,sha256=SApXtVs5zXT2JimbG2JImDLvUVhMe82hjfRGYhp6Jyc,16577
 bluecellulab/stimulus/factory.py,sha256=mjbI8JqujXzc_SuxuUGx2zU_T41RDwYsn9IAtA39T1M,25412
 bluecellulab/stimulus/stimulus.py,sha256=da8XEP5Kw2s73fVhJJgu6kJ7DyLhQcdB4VQB9F63mL4,24842
 bluecellulab/synapse/__init__.py,sha256=RW8XoAMXOvK7OG1nHl_q8jSEKLj9ZN4oWf2nY9HAwuk,192
 bluecellulab/synapse/synapse_factory.py,sha256=NHwRMYMrnRVm_sHmyKTJ1bdoNmWZNU4UPOGu7FCi-PE,6987
 bluecellulab/synapse/synapse_types.py,sha256=zs_yBvGTH4QrbQF3nEViidyq1WM_ZcTSFdjUxB3khW0,16871
-bluecellulab-2.6.43.dist-info/AUTHORS.txt,sha256=EDs3H-2HXBojbma10psixk3C2rFiOCTIREi2ZAbXYNQ,179
-bluecellulab-2.6.43.dist-info/LICENSE,sha256=dAMAR2Sud4Nead1wGFleKiwTZfkTNZbzmuGfcTKb3kg,11335
-bluecellulab-2.6.43.dist-info/METADATA,sha256=Ufce79d7u5kWAg5fwcbJgWgpEhvpc_D-GFW1c-ZY4L4,8214
-bluecellulab-2.6.43.dist-info/WHEEL,sha256=jB7zZ3N9hIM9adW7qlTAyycLYW9npaWKLRzaoVcLKcM,91
-bluecellulab-2.6.43.dist-info/top_level.txt,sha256=VSyEP8w9l3pXdRkyP_goeMwiNA8KWwitfAqUkveJkdQ,13
-bluecellulab-2.6.43.dist-info/RECORD,,
+bluecellulab-2.6.44.dist-info/AUTHORS.txt,sha256=EDs3H-2HXBojbma10psixk3C2rFiOCTIREi2ZAbXYNQ,179
+bluecellulab-2.6.44.dist-info/LICENSE,sha256=dAMAR2Sud4Nead1wGFleKiwTZfkTNZbzmuGfcTKb3kg,11335
+bluecellulab-2.6.44.dist-info/METADATA,sha256=A83Dnkygey8TxQr5zHXGabNKylbpzRYTWEAnQReVeUo,8214
+bluecellulab-2.6.44.dist-info/WHEEL,sha256=52BFRY2Up02UkjOa29eZOS2VxUrpPORXg1pkohGGUS8,91
+bluecellulab-2.6.44.dist-info/top_level.txt,sha256=VSyEP8w9l3pXdRkyP_goeMwiNA8KWwitfAqUkveJkdQ,13
+bluecellulab-2.6.44.dist-info/RECORD,,

{bluecellulab-2.6.43.dist-info → bluecellulab-2.6.44.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.8.2)
+Generator: setuptools (76.0.0)
 Root-Is-Purelib: true
 Tag: py3-none-any