bluecellulab 2.6.45__tar.gz → 2.6.47__tar.gz

{bluecellulab-2.6.45 → bluecellulab-2.6.47}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: bluecellulab
-Version: 2.6.45
+Version: 2.6.47
 Summary: Biologically detailed neural network simulations and analysis.
 Author: Blue Brain Project, EPFL
 License: Apache2.0
@@ -27,6 +27,7 @@ Requires-Dist: pydantic<3.0.0,>=2.5.2
 Requires-Dist: typing-extensions>=4.8.0
 Requires-Dist: networkx>=3.1
 Requires-Dist: h5py>=3.8.0
+Dynamic: license-file
 
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{bluecellulab-2.6.45 → bluecellulab-2.6.47}/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-2.6.47}/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-2.6.47}/bluecellulab/tools.py

@@ -268,7 +268,8 @@ def detect_spike_step(
     inj_stop: float,
     step_level: float,
     section: str = "soma[0]",
-    segx: float = 0.5
+    segx: float = 0.5,
+    step_thresh: float = -20.
 ) -> bool:
     """Detect if there is a spike at a certain step level."""
     with IsolatedProcess() as runner:
@@ -284,7 +285,8 @@ def detect_spike_step(
                 inj_stop,
                 step_level,
                 section,
-                segx
+                segx,
+                step_thresh
             ],
         )
     return spike_detected
@@ -300,7 +302,8 @@ def detect_spike_step_subprocess(
     inj_stop: float,
     step_level: float,
     section: str = "soma[0]",
-    segx: float = 0.5
+    segx: float = 0.5,
+    step_thresh: float = -20.
 ) -> bool:
     """Detect if there is a spike at a certain step level."""
     cell = bluecellulab.Cell(
@@ -321,19 +324,19 @@ def detect_spike_step_subprocess(
     time = cell.get_time()
     voltage = cell.get_voltage_recording(section=neuron_section, segx=segx)
     voltage_step = voltage[np.where((time > inj_start) & (time < inj_stop))]
-    spike_detected = detect_spike(voltage_step)
+    spike_detected = detect_spike(voltage_step, step_thresh)
 
     cell.delete()
 
     return spike_detected
 
 
-def detect_spike(voltage: np.ndarray) -> bool:
+def detect_spike(voltage: np.ndarray, step_thresh: float = -20.) -> bool:
     """Detect if there is a spike in the voltage trace."""
     if len(voltage) == 0:
         return False
     else:
-        return bool(np.max(voltage) > -20)  # bool not np.bool_
+        return bool(np.max(voltage) > step_thresh)  # bool not np.bool_
 
 
 def search_threshold_current(
@@ -348,7 +351,8 @@ def search_threshold_current(
     max_current: float,
     current_precision: float = 0.01,
     section: str = "soma[0]",
-    segx: float = 0.5
+    segx: float = 0.5,
+    step_thresh: float = -20.
 ):
     """Search current necessary to reach threshold."""
     if abs(max_current - min_current) < current_precision:
@@ -359,7 +363,7 @@ def search_threshold_current(
     spike_detected = detect_spike_step(
         template_name, morphology_path, template_format, emodel_properties,
         hyp_level, inj_start, inj_stop, med_current,
-        section=section, segx=segx
+        section=section, segx=segx, step_thresh=step_thresh
     )
     logger.info("Spike threshold detection at: %f nA" % med_current)
 
@@ -369,14 +373,16 @@ def search_threshold_current(
                                         hyp_level, inj_start, inj_stop,
                                         min_current, med_current,
                                         current_precision,
-                                        section=section, segx=segx)
+                                        section=section, segx=segx,
+                                        step_thresh=step_thresh)
     else:
         return search_threshold_current(template_name, morphology_path,
                                         template_format, emodel_properties,
                                         hyp_level, inj_start, inj_stop,
                                         med_current, max_current,
                                         current_precision,
-                                        section=section, segx=segx)
+                                        section=section, segx=segx,
+                                        step_thresh=step_thresh)
 
 
 def check_empty_topology() -> bool:
@@ -435,7 +441,8 @@ def calculate_rheobase(cell: Cell,
                        threshold_search_stim_start: float = 300.0,
                        threshold_search_stim_stop: float = 1000.0,
                        section: str = "soma[0]",
-                       segx: float = 0.5) -> float:
+                       segx: float = 0.5,
+                       step_thresh: float = -20.) -> float:
     """Calculate the rheobase by first computing the upper bound threshold
     current.
 
@@ -474,7 +481,8 @@ def calculate_rheobase(cell: Cell,
         max_current=upperbound_threshold_current,
         current_precision=0.005,
         section=section,
-        segx=segx
+        segx=segx,
+        step_thresh=threshold_voltage
     )
 
     return rheobase

{bluecellulab-2.6.45 → bluecellulab-2.6.47}/bluecellulab.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: bluecellulab
-Version: 2.6.45
+Version: 2.6.47
 Summary: Biologically detailed neural network simulations and analysis.
 Author: Blue Brain Project, EPFL
 License: Apache2.0
@@ -27,6 +27,7 @@ Requires-Dist: pydantic<3.0.0,>=2.5.2
 Requires-Dist: typing-extensions>=4.8.0
 Requires-Dist: networkx>=3.1
 Requires-Dist: h5py>=3.8.0
+Dynamic: license-file
 
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