bluecellulab 2.6.21__py3-none-any.whl → 2.6.23__py3-none-any.whl

bluecellulab/__init__.py

@@ -18,7 +18,7 @@ from .psection import PSection  # NOQA
 from .psegment import PSegment  # NOQA
 from .simulation import Simulation  # NOQA
 from .rngsettings import RNGSettings  # NOQA
-from .circuit_simulation import CircuitSimulation, CircuitSimulation  # NOQA
+from .circuit_simulation import CircuitSimulation  # NOQA
 import neuron
 
 from .simulation.neuron_globals import NeuronGlobals

bluecellulab/cell/injector.py

@@ -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/stimuli_generator.py

@@ -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/stimulus/circuit_stimulus_definitions.py

@@ -170,7 +170,7 @@ class Stimulus:
                 decay_time=stimulus_entry["DecayTime"],
                 mean_percent=stimulus_entry["MeanPercent"],
                 sd_percent=stimulus_entry["SDPercent"],
-                amp_cv=stimulus_entry["AmpCV"],
+                relative_skew=stimulus_entry.get("RelativeSkew", 0.5),
                 seed=stimulus_entry.get("Seed", None),
                 mode=mode,
                 reversal=stimulus_entry.get("Reversal", 0.0)
@@ -269,7 +269,7 @@ class Stimulus:
                 decay_time=stimulus_entry["decay_time"],
                 mean_percent=stimulus_entry["mean_percent"],
                 sd_percent=stimulus_entry["sd_percent"],
-                amp_cv=stimulus_entry["amp_cv"],
+                relative_skew=stimulus_entry.get("RelativeSkew", 0.5),
                 seed=stimulus_entry.get("random_seed", None),
                 mode=ClampMode(stimulus_entry.get("input_type", "current_clamp").lower()),
                 reversal=stimulus_entry.get("reversal", 0.0)
@@ -365,7 +365,7 @@ class RelativeShotNoise(Stimulus):
     decay_time: float
     mean_percent: float
     sd_percent: float
-    amp_cv: float
+    relative_skew: float = 0.5
     dt: float = 0.25
     seed: Optional[int] = None
     mode: ClampMode = ClampMode.CURRENT
@@ -378,6 +378,13 @@ class RelativeShotNoise(Stimulus):
             raise ValueError("decay_time must be greater than rise_time")
         return v
 
+    @field_validator("relative_skew")
+    @classmethod
+    def relative_skew_in_range(cls, v):
+        if v < 0.0 or v > 1.0:
+            raise ValueError("relative skewness must be in [0,1]")
+        return v
+
 
 @dataclass(frozen=True, config=dict(extra="forbid"))
 class OrnsteinUhlenbeck(Stimulus):

{bluecellulab-2.6.21.dist-info → bluecellulab-2.6.23.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bluecellulab
-Version: 2.6.21
+Version: 2.6.23
 Summary: Biologically detailed neural network simulations and analysis.
 Author: Blue Brain Project, EPFL
 License: Apache2.0

{bluecellulab-2.6.21.dist-info → bluecellulab-2.6.23.dist-info}/RECORD

@@ -1,4 +1,4 @@
-bluecellulab/__init__.py,sha256=JvigOm_7WDjVAodm4R_TyRzj7vd9hmEbvLJDUVtgeqo,899
+bluecellulab/__init__.py,sha256=1d_CKIJLIpon7o13h3lBnV_-33obZEPwa9KDTjlFPD8,880
 bluecellulab/circuit_simulation.py,sha256=cLCA97WKjhlEitD4CUad9n4pH4KF7Iw68w1bZH512yw,33587
 bluecellulab/connection.py,sha256=volV2YKtmqAF7MOEJar5ldF1ARAo7k2vF9MB1NXybUY,4640
 bluecellulab/dendrogram.py,sha256=w0vvv0Q169DolTX1j9dAZIvHIl4H258gAjQ1xQaNiGk,6427
@@ -19,14 +19,14 @@ bluecellulab/analysis/inject_sequence.py,sha256=Ih3wdNRn0-lM-NW8agrMUGS862CEgzn_
 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
-bluecellulab/cell/injector.py,sha256=XC49VSHw78xCHzLJKO_-unnnVZAZXsYg5qbmZPx01AA,18091
+bluecellulab/cell/injector.py,sha256=u6Jvf_14rNOy5azK_mIUU8C2WioiGZd-7YGKoSnbR6Y,18042
 bluecellulab/cell/plotting.py,sha256=hW5KAmaSonJ1tgR6xRrnfVe33I5mBsBUrKJQwGvAbUc,4032
 bluecellulab/cell/random.py,sha256=FDby9BN4eJT27COwHP59bhDE2v-c6rdOKNFj3cYZTVY,1773
 bluecellulab/cell/recording.py,sha256=dekJspPb_5yrS6WR3aXtvZ6KWwMNbyhe5aIOVtNDHpY,342
 bluecellulab/cell/section_distance.py,sha256=J8-oqgCHzRaJkpfjPUR6NFtXDhwbrXad9nDaTCKNkTU,3908
 bluecellulab/cell/serialized_sections.py,sha256=sH9mV2CJU_DlhfJhwtuMs1gGnNEnKUvB_Bxx3AEmLHQ,1543
 bluecellulab/cell/sonata_proxy.py,sha256=dLT9mLlGVpXxj2O2lXN0g7Sq4BwroPLVdPikR2yNMv4,1529
-bluecellulab/cell/stimuli_generator.py,sha256=cJwjNwsQeEBHLjuJIFv6VBSqd9IpmbR7CuSMyotCiWc,6320
+bluecellulab/cell/stimuli_generator.py,sha256=01CjXToBYtz24QP_h_LkZnSKhmEpDFIQOk4TU-ueeXg,7129
 bluecellulab/cell/template.py,sha256=K8Vp1-yE6-9wxjmhkLBhnjBhgciUixoMk8LU-GioTgM,7562
 bluecellulab/cell/ballstick/__init__.py,sha256=v1Z8tHFfbpWShxOBdShCUaE0utoz-7rZumuNBQtNOFI,439
 bluecellulab/cell/ballstick/emodel.hoc,sha256=7WcuepK-wB9bASRvNdCwO9Woc9-SpBCFqBqCXKgjsV8,1517
@@ -57,14 +57,14 @@ bluecellulab/simulation/neuron_globals.py,sha256=_8xmJPQMfCyhVn6KppK7i3jaUZaALML
 bluecellulab/simulation/parallel.py,sha256=oQ_oV2EKr8gP4yF2Dq8q9MiblDyi89_wBgLzQkLV_U0,1514
 bluecellulab/simulation/simulation.py,sha256=I__cZwV_A8I7XSefn6aJDBA_jXCI3E35-pCNCLUsnvo,6206
 bluecellulab/stimulus/__init__.py,sha256=DgIgVaSyR-URf3JZzvO6j-tjCerzvktuK-ep8pjMRPQ,37
-bluecellulab/stimulus/circuit_stimulus_definitions.py,sha256=QztVteUUeMZolPMVjx-S-KgpahnQlbfTziJsJ_wCmaw,15621
+bluecellulab/stimulus/circuit_stimulus_definitions.py,sha256=Vt95dfvkSFAKl53wSv7CEECgYUVbkVAh1uZrD5ial1Y,15890
 bluecellulab/stimulus/factory.py,sha256=XDbnqCuMCh1RdZLKvlRucMj3wkXDqy6mEda_Oh6Yqo4,19955
 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-2.6.21.dist-info/AUTHORS.txt,sha256=EDs3H-2HXBojbma10psixk3C2rFiOCTIREi2ZAbXYNQ,179
-bluecellulab-2.6.21.dist-info/LICENSE,sha256=xOouu1gC1GGklDxkITlaVl60I9Ab860O-nZsFbWydvU,11749
-bluecellulab-2.6.21.dist-info/METADATA,sha256=LKVNoBDRhEGl3HqRRq3YDgfkJ3nFDzoP6I5mZ0A2yo8,7267
-bluecellulab-2.6.21.dist-info/WHEEL,sha256=Z4pYXqR_rTB7OWNDYFOm1qRk0RX6GFP2o8LgvP453Hk,91
-bluecellulab-2.6.21.dist-info/top_level.txt,sha256=VSyEP8w9l3pXdRkyP_goeMwiNA8KWwitfAqUkveJkdQ,13
-bluecellulab-2.6.21.dist-info/RECORD,,
+bluecellulab-2.6.23.dist-info/AUTHORS.txt,sha256=EDs3H-2HXBojbma10psixk3C2rFiOCTIREi2ZAbXYNQ,179
+bluecellulab-2.6.23.dist-info/LICENSE,sha256=xOouu1gC1GGklDxkITlaVl60I9Ab860O-nZsFbWydvU,11749
+bluecellulab-2.6.23.dist-info/METADATA,sha256=Yizrto13DoMEm7O3ac9WrtHo_JuTOgNdmetsmNN42c0,7267
+bluecellulab-2.6.23.dist-info/WHEEL,sha256=Z4pYXqR_rTB7OWNDYFOm1qRk0RX6GFP2o8LgvP453Hk,91
+bluecellulab-2.6.23.dist-info/top_level.txt,sha256=VSyEP8w9l3pXdRkyP_goeMwiNA8KWwitfAqUkveJkdQ,13
+bluecellulab-2.6.23.dist-info/RECORD,,