bluecellulab 2.6.4__tar.gz → 2.6.6__tar.gz

{bluecellulab-2.6.4 → bluecellulab-2.6.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bluecellulab
-Version: 2.6.4
+Version: 2.6.6
 Summary: Biologically detailed neural network simulations and analysis.
 Author: Blue Brain Project, EPFL
 License: Apache2.0
@@ -26,6 +26,7 @@ Requires-Dist: bluepysnap<4.0.0,>=3.0.0
 Requires-Dist: pydantic<3.0.0,>=2.5.2
 Requires-Dist: typing-extensions>=4.8.0
 Requires-Dist: networkx>=3.1
+Requires-Dist: h5py>=3.11.0
 
 |banner|
 

{bluecellulab-2.6.4 → bluecellulab-2.6.6}/bluecellulab/analysis/inject_sequence.py

@@ -18,6 +18,8 @@ class StimulusName(Enum):
     IDREST = auto()
     IV = auto()
     FIRE_PATTERN = auto()
+    POS_CHEOPS = auto()
+    NEG_CHEOPS = auto()
 
 
 class Recording(NamedTuple):
@@ -68,7 +70,7 @@ def run_stimulus(
     return Recording(current, voltage, time)
 
 
-def apply_multiple_step_stimuli(
+def apply_multiple_stimuli(
     cell: Cell,
     stimulus_name: StimulusName,
     amplitudes: Sequence[float],
@@ -109,6 +111,10 @@ def apply_multiple_step_stimuli(
             stimulus = stim_factory.iv(threshold_current=cell.threshold, threshold_percentage=amplitude)
         elif stimulus_name == StimulusName.FIRE_PATTERN:
             stimulus = stim_factory.fire_pattern(threshold_current=cell.threshold, threshold_percentage=amplitude)
+        elif stimulus_name == StimulusName.POS_CHEOPS:
+            stimulus = stim_factory.pos_cheops(threshold_current=cell.threshold, threshold_percentage=amplitude)
+        elif stimulus_name == StimulusName.NEG_CHEOPS:
+            stimulus = stim_factory.neg_cheops(threshold_current=cell.threshold, threshold_percentage=amplitude)
         else:
             raise ValueError("Unknown stimulus name.")
 

{bluecellulab-2.6.4 → bluecellulab-2.6.6}/bluecellulab/circuit/simulation_access.py

@@ -18,6 +18,7 @@ import logging
 from pathlib import Path
 from typing import Optional, Protocol
 
+import h5py
 import pandas as pd
 
 from bluecellulab.circuit.config import SimulationConfig, SonataSimulationConfig
@@ -172,12 +173,14 @@ class SonataSimulationAccess:
 
 def get_synapse_replay_spikes(f_name: str) -> dict:
     """Read the .dat file containing the spike replays."""
-    data = np.genfromtxt(f_name, skip_header=1)
-    spikes = pd.DataFrame(data=data, columns=["t", "node_id"]).astype({"node_id": int})
-    # subtract 1 from all node_ids to make them 0-based
-    # source: https://sonata-extension.readthedocs.io/
-    # en/latest/blueconfig-projection-example.html#dat-spike-files
-    spikes["node_id"] -= 1
+    with h5py.File(f_name, 'r') as f:
+        # Access the timestamps and node_ids datasets
+        timestamps = f['/spikes/All/timestamps'][:]
+        node_ids = f['/spikes/All/node_ids'][:]
+
+        spikes = pd.DataFrame(data={'t': timestamps, 'node_id': node_ids})
+        spikes = spikes.astype({"node_id": int})
+
     if (spikes["t"] < 0).any():
         logger.warning("Found negative spike times... Clipping them to 0")
         spikes["t"].clip(lower=0., inplace=True)

{bluecellulab-2.6.4 → bluecellulab-2.6.6}/bluecellulab/stimulus/factory.py

@@ -387,3 +387,71 @@ class StimulusFactory:
             threshold_current=threshold_current,
             threshold_percentage=threshold_percentage,
         )
+
+    def pos_cheops(
+        self,
+        threshold_current: float,
+        threshold_percentage: float = 300.0,
+    ) -> Stimulus:
+        """A combination of pyramid shaped Ramp stimuli with a positive
+        amplitude.
+
+        Args:
+            threshold_current: The threshold current of the Cell.
+            threshold_percentage: Percentage of desired threshold_current amplification.
+        """
+        delay = 250.0
+        ramp1_duration = 4000.0
+        ramp2_duration = 2000.0
+        ramp3_duration = 1333.0
+        inter_delay = 2000.0
+        post_delay = 250.0
+
+        amplitude = threshold_current * threshold_percentage / 100
+        result = (
+            Empty(self.dt, duration=delay)
+            + Slope(self.dt, duration=ramp1_duration, amplitude_start=0.0, amplitude_end=amplitude)
+            + Slope(self.dt, duration=ramp1_duration, amplitude_start=amplitude, amplitude_end=0.0)
+            + Empty(self.dt, duration=inter_delay)
+            + Slope(self.dt, duration=ramp2_duration, amplitude_start=0.0, amplitude_end=amplitude)
+            + Slope(self.dt, duration=ramp2_duration, amplitude_start=amplitude, amplitude_end=0.0)
+            + Empty(self.dt, duration=inter_delay)
+            + Slope(self.dt, duration=ramp3_duration, amplitude_start=0.0, amplitude_end=amplitude)
+            + Slope(self.dt, duration=ramp3_duration, amplitude_start=amplitude, amplitude_end=0.0)
+            + Empty(self.dt, duration=post_delay)
+        )
+        return result
+
+    def neg_cheops(
+        self,
+        threshold_current: float,
+        threshold_percentage: float = 300.0,
+    ) -> Stimulus:
+        """A combination of pyramid shaped Ramp stimuli with a negative
+        amplitude.
+
+        Args:
+            threshold_current: The threshold current of the Cell.
+            threshold_percentage: Percentage of desired threshold_current amplification.
+        """
+        delay = 1750.0
+        ramp1_duration = 3333.0
+        ramp2_duration = 1666.0
+        ramp3_duration = 1111.0
+        inter_delay = 2000.0
+        post_delay = 250.0
+
+        amplitude = - threshold_current * threshold_percentage / 100
+        result = (
+            Empty(self.dt, duration=delay)
+            + Slope(self.dt, duration=ramp1_duration, amplitude_start=0.0, amplitude_end=amplitude)
+            + Slope(self.dt, duration=ramp1_duration, amplitude_start=amplitude, amplitude_end=0.0)
+            + Empty(self.dt, duration=inter_delay)
+            + Slope(self.dt, duration=ramp2_duration, amplitude_start=0.0, amplitude_end=amplitude)
+            + Slope(self.dt, duration=ramp2_duration, amplitude_start=amplitude, amplitude_end=0.0)
+            + Empty(self.dt, duration=inter_delay)
+            + Slope(self.dt, duration=ramp3_duration, amplitude_start=0.0, amplitude_end=amplitude)
+            + Slope(self.dt, duration=ramp3_duration, amplitude_start=amplitude, amplitude_end=0.0)
+            + Empty(self.dt, duration=post_delay)
+        )
+        return result

{bluecellulab-2.6.4 → bluecellulab-2.6.6}/bluecellulab.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bluecellulab
-Version: 2.6.4
+Version: 2.6.6
 Summary: Biologically detailed neural network simulations and analysis.
 Author: Blue Brain Project, EPFL
 License: Apache2.0
@@ -26,6 +26,7 @@ Requires-Dist: bluepysnap<4.0.0,>=3.0.0
 Requires-Dist: pydantic<3.0.0,>=2.5.2
 Requires-Dist: typing-extensions>=4.8.0
 Requires-Dist: networkx>=3.1
+Requires-Dist: h5py>=3.11.0
 
 |banner|
 

{bluecellulab-2.6.4 → bluecellulab-2.6.6}/bluecellulab.egg-info/SOURCES.txt

@@ -210,7 +210,7 @@ tests/test_tools.py
 tests/test_ttx.py
 tests/test_utils.py
 tests/test_verbosity.py
-tests/data/synapse_replay_file/spikes.dat
+tests/data/synapse_replay_file/spikes.h5
 tests/examples/ballstick_cell/analytic_expsyn.txt
 tests/examples/ballstick_cell/ballstick.asc
 tests/examples/ballstick_cell/ballstick.hoc
@@ -345,7 +345,7 @@ tests/examples/sonata_unit_test_sims/projections/output_sonata/soma.h5
 tests/examples/sonata_unit_test_sims/synapse_replay/circuit_config.json
 tests/examples/sonata_unit_test_sims/synapse_replay/node_sets.json
 tests/examples/sonata_unit_test_sims/synapse_replay/simulation_config.json
-tests/examples/sonata_unit_test_sims/synapse_replay/synapse_replay.dat
+tests/examples/sonata_unit_test_sims/synapse_replay/synapse_replay.h5
 tests/examples/tapertest_cells/notaper_cell.hoc
 tests/examples/tapertest_cells/taper_cell.hoc
 tests/examples/tapertest_cells/test_cell.asc

{bluecellulab-2.6.4 → bluecellulab-2.6.6}/bluecellulab.egg-info/requires.txt

@@ -6,3 +6,4 @@ bluepysnap<4.0.0,>=3.0.0
 pydantic<3.0.0,>=2.5.2
 typing-extensions>=4.8.0
 networkx>=3.1
+h5py>=3.11.0