bluecellulab 2.6.13__tar.gz → 2.6.15__tar.gz

{bluecellulab-2.6.13 → bluecellulab-2.6.15}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bluecellulab
-Version: 2.6.13
+Version: 2.6.15
 Summary: Biologically detailed neural network simulations and analysis.
 Author: Blue Brain Project, EPFL
 License: Apache2.0

{bluecellulab-2.6.13 → bluecellulab-2.6.15}/bluecellulab/analysis/inject_sequence.py

@@ -74,6 +74,7 @@ def apply_multiple_stimuli(
     cell: Cell,
     stimulus_name: StimulusName,
     amplitudes: Sequence[float],
+    threshold_based: bool = True,
     section_name: str | None = None,
     segment: float = 0.5,
     n_processes: int | None = None,
@@ -84,6 +85,8 @@ def apply_multiple_stimuli(
         cell: The cell to which the stimuli are applied.
         stimulus_name: The name of the stimulus to apply.
         amplitudes: The amplitudes of the stimuli to apply.
+        threshold_based: Whether to consider amplitudes to be
+            threshold percentages or to be raw amplitudes.
         section_name: Section name of the cell where the stimuli are applied.
           If None, the stimuli are applied at the soma[0] of the cell.
         segment: The segment of the section where the stimuli are applied.
@@ -103,18 +106,37 @@ def apply_multiple_stimuli(
 
     # Prepare arguments for each stimulus
     for amplitude in amplitudes:
+        if threshold_based:
+            thres_perc = amplitude
+            amp = None
+        else:
+            thres_perc = None
+            amp = amplitude
+
         if stimulus_name == StimulusName.AP_WAVEFORM:
-            stimulus = stim_factory.ap_waveform(threshold_current=cell.threshold, threshold_percentage=amplitude)
+            stimulus = stim_factory.ap_waveform(
+                threshold_current=cell.threshold, threshold_percentage=thres_perc, amplitude=amp
+            )
         elif stimulus_name == StimulusName.IDREST:
-            stimulus = stim_factory.idrest(threshold_current=cell.threshold, threshold_percentage=amplitude)
+            stimulus = stim_factory.idrest(
+                threshold_current=cell.threshold, threshold_percentage=thres_perc, amplitude=amp
+            )
         elif stimulus_name == StimulusName.IV:
-            stimulus = stim_factory.iv(threshold_current=cell.threshold, threshold_percentage=amplitude)
+            stimulus = stim_factory.iv(
+                threshold_current=cell.threshold, threshold_percentage=thres_perc, amplitude=amp
+            )
         elif stimulus_name == StimulusName.FIRE_PATTERN:
-            stimulus = stim_factory.fire_pattern(threshold_current=cell.threshold, threshold_percentage=amplitude)
+            stimulus = stim_factory.fire_pattern(
+                threshold_current=cell.threshold, threshold_percentage=thres_perc, amplitude=amp
+            )
         elif stimulus_name == StimulusName.POS_CHEOPS:
-            stimulus = stim_factory.pos_cheops(threshold_current=cell.threshold, threshold_percentage=amplitude)
+            stimulus = stim_factory.pos_cheops(
+                threshold_current=cell.threshold, threshold_percentage=thres_perc, amplitude=amp
+            )
         elif stimulus_name == StimulusName.NEG_CHEOPS:
-            stimulus = stim_factory.neg_cheops(threshold_current=cell.threshold, threshold_percentage=amplitude)
+            stimulus = stim_factory.neg_cheops(
+                threshold_current=cell.threshold, threshold_percentage=thres_perc, amplitude=amp
+            )
         else:
             raise ValueError("Unknown stimulus name.")
 

{bluecellulab-2.6.13 → bluecellulab-2.6.15}/bluecellulab/psegment.py

@@ -25,7 +25,7 @@ class PSegment:
 
     def __init__(self, hsegment, parentsection):
         # import matplotlib as plt
-        from matplotlib import cm
+        from matplotlib import colormaps
 
         self.hsegment = hsegment
         self.parentsection = parentsection
@@ -35,7 +35,7 @@ class PSegment:
         self.figure = None
         self.figX = None
         self.figY = None
-        self.color_map = cm.get_cmap("hot")
+        self.color_map = colormaps["hot"]
         self.ax = None
         self.patch = None
         self.plotvariable = None

{bluecellulab-2.6.13 → bluecellulab-2.6.15}/bluecellulab/stimulus/factory.py

@@ -1,8 +1,12 @@
 from __future__ import annotations
 from abc import ABC, abstractmethod
+from typing import Optional
+import logging
 import matplotlib.pyplot as plt
 import numpy as np
 
+logger = logging.getLogger(__name__)
+
 
 class Stimulus(ABC):
     def __init__(self, dt: float) -> None:
@@ -299,99 +303,182 @@ class StimulusFactory:
         )
 
     def ap_waveform(
-        self, threshold_current: float, threshold_percentage: float = 220.0
+        self,
+        threshold_current: Optional[float] = None,
+        threshold_percentage: Optional[float] = 220.0,
+        amplitude: Optional[float] = None,
     ) -> Stimulus:
         """Returns the APWaveform Stimulus object, a type of Step 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 = 250.0
         duration = 50.0
         post_delay = 250.0
-        return Step.threshold_based(
-            self.dt,
-            pre_delay=pre_delay,
-            duration=duration,
-            post_delay=post_delay,
-            threshold_current=threshold_current,
-            threshold_percentage=threshold_percentage,
-        )
+
+        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 ap_waveform."
+                    " Will only keep amplitude value."
+                )
+            return Step.amplitude_based(
+                self.dt,
+                pre_delay=pre_delay,
+                duration=duration,
+                post_delay=post_delay,
+                amplitude=amplitude,
+            )
+
+        if threshold_current is not None and threshold_current != 0 and threshold_percentage is not None:
+            return Step.threshold_based(
+                self.dt,
+                pre_delay=pre_delay,
+                duration=duration,
+                post_delay=post_delay,
+                threshold_current=threshold_current,
+                threshold_percentage=threshold_percentage,
+            )
+
+        raise TypeError("You have to give either threshold_current or amplitude")
 
     def idrest(
         self,
-        threshold_current: float,
-        threshold_percentage: float = 200.0,
+        threshold_current: Optional[float] = None,
+        threshold_percentage: Optional[float] = 200.0,
+        amplitude: Optional[float] = None,
     ) -> Stimulus:
         """Returns the IDRest Stimulus object, a type of Step 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 = 250.0
         duration = 1350.0
         post_delay = 250.0
-        return Step.threshold_based(
-            self.dt,
-            pre_delay=pre_delay,
-            duration=duration,
-            post_delay=post_delay,
-            threshold_current=threshold_current,
-            threshold_percentage=threshold_percentage,
-        )
+
+        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 idrest."
+                    " Will only keep amplitude value."
+                )
+            return Step.amplitude_based(
+                self.dt,
+                pre_delay=pre_delay,
+                duration=duration,
+                post_delay=post_delay,
+                amplitude=amplitude,
+            )
+
+        if threshold_current is not None and threshold_current != 0 and threshold_percentage is not None:
+            return Step.threshold_based(
+                self.dt,
+                pre_delay=pre_delay,
+                duration=duration,
+                post_delay=post_delay,
+                threshold_current=threshold_current,
+                threshold_percentage=threshold_percentage,
+            )
+
+        raise TypeError("You have to give either threshold_current or amplitude")
 
     def iv(
         self,
-        threshold_current: float,
-        threshold_percentage: float = -40.0,
+        threshold_current: Optional[float] = None,
+        threshold_percentage: Optional[float] = -40.0,
+        amplitude: Optional[float] = None,
     ) -> Stimulus:
         """Returns the IV Stimulus object, a type of Step 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 = 250.0
         duration = 3000.0
         post_delay = 250.0
-        return Step.threshold_based(
-            self.dt,
-            pre_delay=pre_delay,
-            duration=duration,
-            post_delay=post_delay,
-            threshold_current=threshold_current,
-            threshold_percentage=threshold_percentage,
-        )
+
+        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 iv."
+                    " Will only keep amplitude value."
+                )
+            return Step.amplitude_based(
+                self.dt,
+                pre_delay=pre_delay,
+                duration=duration,
+                post_delay=post_delay,
+                amplitude=amplitude,
+            )
+
+        if threshold_current is not None and threshold_current != 0 and threshold_percentage is not None:
+            return Step.threshold_based(
+                self.dt,
+                pre_delay=pre_delay,
+                duration=duration,
+                post_delay=post_delay,
+                threshold_current=threshold_current,
+                threshold_percentage=threshold_percentage,
+            )
+
+        raise TypeError("You have to give either threshold_current or amplitude")
 
     def fire_pattern(
         self,
-        threshold_current: float,
-        threshold_percentage: float = 200.0,
+        threshold_current: Optional[float] = None,
+        threshold_percentage: Optional[float] = 200.0,
+        amplitude: Optional[float] = None,
     ) -> Stimulus:
         """Returns the FirePattern Stimulus object, a type of Step 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 = 250.0
         duration = 3600.0
         post_delay = 250.0
-        return Step.threshold_based(
-            self.dt,
-            pre_delay=pre_delay,
-            duration=duration,
-            post_delay=post_delay,
-            threshold_current=threshold_current,
-            threshold_percentage=threshold_percentage,
-        )
+
+        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 fire_pattern."
+                    " Will only keep amplitude value."
+                )
+            return Step.amplitude_based(
+                self.dt,
+                pre_delay=pre_delay,
+                duration=duration,
+                post_delay=post_delay,
+                amplitude=amplitude,
+            )
+
+        if threshold_current is not None and threshold_current != 0 and threshold_percentage is not None:
+            return Step.threshold_based(
+                self.dt,
+                pre_delay=pre_delay,
+                duration=duration,
+                post_delay=post_delay,
+                threshold_current=threshold_current,
+                threshold_percentage=threshold_percentage,
+            )
+
+        raise TypeError("You have to give either threshold_current or amplitude")
 
     def pos_cheops(
         self,
-        threshold_current: float,
-        threshold_percentage: float = 300.0,
+        threshold_current: Optional[float] = None,
+        threshold_percentage: Optional[float] = 300.0,
+        amplitude: Optional[float] = None,
     ) -> Stimulus:
         """A combination of pyramid shaped Ramp stimuli with a positive
         amplitude.
@@ -399,6 +486,7 @@ class StimulusFactory:
         Args:
             threshold_current: The threshold current of the Cell.
             threshold_percentage: Percentage of desired threshold_current amplification.
+            amplitude: Raw amplitude of input current.
         """
         delay = 250.0
         ramp1_duration = 4000.0
@@ -407,7 +495,15 @@ class StimulusFactory:
         inter_delay = 2000.0
         post_delay = 250.0
 
-        amplitude = threshold_current * threshold_percentage / 100
+        if amplitude is None:
+            if threshold_current is None or threshold_current == 0 or threshold_percentage is None:
+                raise TypeError("You have to give either threshold_current or amplitude")
+            amplitude = threshold_current * threshold_percentage / 100
+        elif 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 pos_cheops."
+                " Will only keep amplitude value."
+            )
         result = (
             Empty(self.dt, duration=delay)
             + Slope(self.dt, duration=ramp1_duration, amplitude_start=0.0, amplitude_end=amplitude)
@@ -424,8 +520,9 @@ class StimulusFactory:
 
     def neg_cheops(
         self,
-        threshold_current: float,
-        threshold_percentage: float = 300.0,
+        threshold_current: Optional[float] = None,
+        threshold_percentage: Optional[float] = 300.0,
+        amplitude: Optional[float] = None,
     ) -> Stimulus:
         """A combination of pyramid shaped Ramp stimuli with a negative
         amplitude.
@@ -433,6 +530,7 @@ class StimulusFactory:
         Args:
             threshold_current: The threshold current of the Cell.
             threshold_percentage: Percentage of desired threshold_current amplification.
+            amplitude: Raw amplitude of input current.
         """
         delay = 1750.0
         ramp1_duration = 3333.0
@@ -441,7 +539,15 @@ class StimulusFactory:
         inter_delay = 2000.0
         post_delay = 250.0
 
-        amplitude = - threshold_current * threshold_percentage / 100
+        if amplitude is None:
+            if threshold_current is None or threshold_current == 0 or threshold_percentage is None:
+                raise TypeError("You have to give either threshold_current or amplitude")
+            amplitude = - threshold_current * threshold_percentage / 100
+        elif 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 neg_cheops."
+                " Will only keep amplitude value."
+            )
         result = (
             Empty(self.dt, duration=delay)
             + Slope(self.dt, duration=ramp1_duration, amplitude_start=0.0, amplitude_end=amplitude)

{bluecellulab-2.6.13 → bluecellulab-2.6.15}/bluecellulab/synapse/synapse_factory.py

@@ -118,6 +118,10 @@ class SynapseFactory:
                 not np.isnan(syn_description[SynapseProperty.AFFERENT_SECTION_POS])):
             # position is pre computed in SONATA
             location = syn_description[SynapseProperty.AFFERENT_SECTION_POS]
+            if location == 0.0:
+                location = 0.0000001
+            elif location >= 1.0:
+                location = 0.9999999
         else:
             ipt = syn_description[SynapseProperty.POST_SEGMENT_ID]
             syn_offset = syn_description[SynapseProperty.POST_SEGMENT_OFFSET]

{bluecellulab-2.6.13 → bluecellulab-2.6.15}/bluecellulab.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bluecellulab
-Version: 2.6.13
+Version: 2.6.15
 Summary: Biologically detailed neural network simulations and analysis.
 Author: Blue Brain Project, EPFL
 License: Apache2.0