bluecellulab 2.6.45__tar.gz → 2.6.46__tar.gz

{bluecellulab-2.6.45 → bluecellulab-2.6.46}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: bluecellulab
-Version: 2.6.45
+Version: 2.6.46
 Summary: Biologically detailed neural network simulations and analysis.
 Author: Blue Brain Project, EPFL
 License: Apache2.0

{bluecellulab-2.6.45 → bluecellulab-2.6.46}/bluecellulab/stimulus/factory.py

@@ -16,8 +16,7 @@
 from __future__ import annotations
 from typing import Optional
 import logging
-from bluecellulab.stimulus.stimulus import DelayedZap, Empty, Ramp, Slope, Step, StepNoise, Stimulus, OrnsteinUhlenbeck, ShotNoise, Sinusoidal
-from bluecellulab.stimulus.circuit_stimulus_definitions import Stimulus as CircuitStimulus
+from bluecellulab.stimulus.stimulus import DelayedZap, Empty, Ramp, Slope, Step, StepNoise, Stimulus, OrnsteinUhlenbeck, ShotNoise, Sinusoidal, Pulse
 
 logger = logging.getLogger(__name__)
 
@@ -678,6 +677,38 @@ class StimulusFactory:
 
         raise TypeError("You must provide either `mean` and `sigma`, or `threshold_current` and `mean_percent` and `sigma_percent`  with percentage values.")
 
-    def from_sonata(cls, circuit_stimulus: CircuitStimulus):
-        """Convert a SONATA stimulus into a factory-based stimulus."""
-        raise ValueError(f"Unsupported circuit stimulus type: {type(circuit_stimulus)}")
+    def pulse(
+        self,
+        pre_delay: float,
+        duration: float,
+        post_delay: float,
+        frequency: float,
+        width: float,
+        threshold_current: Optional[float] = None,
+        threshold_percentage: Optional[float] = None,
+        amplitude: Optional[float] = None,
+    ) -> Stimulus:
+        """Creates a pulse stimulus.
+
+        Args:
+            threshold_current: The threshold current of the Cell.
+            threshold_percentage: Percentage of desired threshold_current amplification.
+            amplitude: Raw amplitude of input current.
+            pre_delay: Delay before the first pulse (ms).
+            duration: Duration of the pulse train (ms).
+            post_delay: Delay after the last pulse (ms).
+            frequency: Frequency of the pulses (Hz).
+            width: Width of each pulse (ms).
+        """
+        if amplitude is not None:
+            if threshold_current is not None and threshold_current != 0 and threshold_percentage is not None:
+                logger.info(
+                    "amplitude, threshold_current and threshold_percentage are all set in pulse."
+                    " Will only keep amplitude value."
+                )
+            return Pulse.amplitude_based(self.dt, pre_delay, duration, post_delay, amplitude, frequency, width)
+
+        if threshold_current is not None and threshold_current != 0 and threshold_percentage is not None:
+            return Pulse.threshold_based(self.dt, pre_delay, duration, post_delay, threshold_current, threshold_percentage, frequency, width)
+
+        raise TypeError("You have to give either threshold_current or amplitude")

{bluecellulab-2.6.45 → bluecellulab-2.6.46}/bluecellulab/stimulus/stimulus.py

@@ -369,6 +369,41 @@ class SinusoidalWave(Stimulus):
         return np.array(tvec.to_python()), np.array(stim.to_python())
 
 
+class PulseTrain(Stimulus):
+    """Generates a pulse train signal."""
+
+    def __init__(self, dt: float, duration: float, amplitude: float, frequency: float, width: float):
+        super().__init__(dt)
+        self.duration = duration
+        self.amplitude = amplitude
+        self.frequency = frequency
+        self.width = width
+
+        self._time, self._current = self._generate_pulse_train()
+
+    @property
+    def time(self) -> np.ndarray:
+        return self._time
+
+    @property
+    def current(self) -> np.ndarray:
+        return self._current
+
+    def _generate_pulse_train(self):
+        total_duration = self.duration
+        time_steps = int(total_duration / self.dt)
+        time = np.linspace(0, total_duration, time_steps)
+        current = np.zeros_like(time)
+
+        start_time = 0
+        while start_time + self.width < self.duration:
+            pulse_indices = (time >= start_time) & (time < start_time + self.width)
+            current[pulse_indices] = self.amplitude
+            start_time += 1000.0 / self.frequency
+
+        return time, current
+
+
 class Step(Stimulus):
 
     def __init__(self):
@@ -878,3 +913,34 @@ class Sinusoidal(Stimulus):
             amplitude=amplitude,
             frequency=frequency,
         )
+
+
+class Pulse(Stimulus):
+    """Factory-compatible Pulse Stimulus."""
+
+    def __init__(self):
+        """Prevents direct instantiation of the class."""
+        raise NotImplementedError(
+            "This class cannot be instantiated directly. "
+            "Please use 'amplitude_based' or 'threshold_based' methods."
+        )
+
+    @classmethod
+    def amplitude_based(
+        cls, dt: float, pre_delay: float, duration: float, post_delay: float, amplitude: float, frequency: float, width: float
+    ) -> CombinedStimulus:
+        """Creates a Pulse stimulus from given time events and amplitude."""
+        return (
+            Empty(dt, duration=pre_delay)
+            + PulseTrain(dt, duration, amplitude, frequency, width)
+            + Empty(dt, duration=post_delay)
+        )
+
+    @classmethod
+    def threshold_based(
+        cls, dt: float, pre_delay: float, duration: float, post_delay: float, threshold_current: float, threshold_percentage: float,
+        frequency: float, width: float
+    ) -> CombinedStimulus:
+        """Creates a Pulse stimulus with respect to the threshold current."""
+        amplitude = threshold_current * (threshold_percentage / 100)
+        return cls.amplitude_based(dt, pre_delay, duration, post_delay, amplitude, frequency, width)

{bluecellulab-2.6.45 → bluecellulab-2.6.46}/bluecellulab.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: bluecellulab
-Version: 2.6.45
+Version: 2.6.46
 Summary: Biologically detailed neural network simulations and analysis.
 Author: Blue Brain Project, EPFL
 License: Apache2.0