bluecellulab 2.6.4__py3-none-any.whl → 2.6.6__py3-none-any.whl

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/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/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.dist-info → bluecellulab-2.6.6.dist-info}/METADATA

@@ -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.dist-info → bluecellulab-2.6.6.dist-info}/RECORD

@@ -15,7 +15,7 @@ bluecellulab/type_aliases.py,sha256=DvgjERv2Ztdw_sW63JrZTQGpJ0x5uMTFB5hcBHDb0WA,
 bluecellulab/utils.py,sha256=SbOOkzw1YGjCKV3qOw0zpabNEy7V9BRtgMLsQJiFRq4,1526
 bluecellulab/verbosity.py,sha256=T0IgX7DrRo19faxrT4Xzb27gqxzoILQ8FzYKxvUeaPM,1342
 bluecellulab/analysis/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-bluecellulab/analysis/inject_sequence.py,sha256=qr3N1tQX4avvKzFBT0L7W6LnSgk2y_P_7Yhy0UjlGmk,4769
+bluecellulab/analysis/inject_sequence.py,sha256=Kgs-Be6CtRc9LI1qsM7mC4oGfpW6VrqGPHSuoa7XFYs,5148
 bluecellulab/cell/__init__.py,sha256=Sbc0QOsJ8E7tSwf3q7fsXuE_SevBN6ZmoCVyyU5zfII,208
 bluecellulab/cell/cell_dict.py,sha256=PVmZsjhZ9jp3HC-8QmdFqp-crAcVMSVeLWujcOPLlpo,1346
 bluecellulab/cell/core.py,sha256=ZVzy3tsA5X7OyCmnHQn0d6AlNg9rOG2ojKuojvKdsFw,31487
@@ -35,7 +35,7 @@ bluecellulab/circuit/__init__.py,sha256=Khpa13nzNvDlDS2JduyoFTukEduEkWCc5ML_JwGp
 bluecellulab/circuit/format.py,sha256=eYhiBIQnPnnVBmaSDymFjQprXN9QjEYKmFhb2mIS86o,1674
 bluecellulab/circuit/iotools.py,sha256=KVE7x5LNQ4RgjNh05Q-h3Swpbs3nRFtrcWNHj62aiRI,1585
 bluecellulab/circuit/node_id.py,sha256=gaRAW3UhbPOPsoXMHLjo3qH9iNod7YB8ZOcguWprrU4,1265
-bluecellulab/circuit/simulation_access.py,sha256=QHVEN-sEZbCCvblhBHEShGX0-NEXCD1AYpavpVGCgAE,7073
+bluecellulab/circuit/simulation_access.py,sha256=jrVz6pFNAuwvuvsTq9OqeDfjIZ5akE98RBMBNDwuDVQ,7062
 bluecellulab/circuit/synapse_properties.py,sha256=a4-Yw_f8JIR6i2YG8qhCW97TMSd_Z-aF6lp_a1wBwnM,6374
 bluecellulab/circuit/validate.py,sha256=7EUN15u0JFFlLf389jUBqLwDOHyZdfKtoidI-xLUVYA,3593
 bluecellulab/circuit/circuit_access/__init__.py,sha256=sgp6m5kP-pq60V1IFGUiSUR1OW01zdxXNNUJmPA8anI,201
@@ -58,13 +58,13 @@ bluecellulab/simulation/parallel.py,sha256=xmlIelxYNct-vGhPip7_vF9gwyehdpomYB8kf
 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=uij_s44uNdmMwMLGmTHSRgmp9K9B_vvHHshX6YPJNJU,15686
-bluecellulab/stimulus/factory.py,sha256=cjnMqFx-Y31kV1XHvkSbGI2f1OpEawU3Wg_cLqcIyRc,11883
+bluecellulab/stimulus/factory.py,sha256=hoq5JA69eX4bAdtOJNErhBn_p0uQh8QPoFvCqqeGBN4,14874
 bluecellulab/synapse/__init__.py,sha256=RW8XoAMXOvK7OG1nHl_q8jSEKLj9ZN4oWf2nY9HAwuk,192
 bluecellulab/synapse/synapse_factory.py,sha256=MjUorWoMl4lFSBgQw4QS09Dzh0-LYWlCHJKYy8N-d3w,6847
 bluecellulab/synapse/synapse_types.py,sha256=4gne-hve2vq1Lau-LAVPsfLjffVYqAYBW3kCfC7_600,16871
-bluecellulab-2.6.4.dist-info/AUTHORS.txt,sha256=EDs3H-2HXBojbma10psixk3C2rFiOCTIREi2ZAbXYNQ,179
-bluecellulab-2.6.4.dist-info/LICENSE,sha256=xOouu1gC1GGklDxkITlaVl60I9Ab860O-nZsFbWydvU,11749
-bluecellulab-2.6.4.dist-info/METADATA,sha256=0d2std48SNCpQmGlEd8Hr7YJWKIPoKpNqDNA8aIts8U,7025
-bluecellulab-2.6.4.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-bluecellulab-2.6.4.dist-info/top_level.txt,sha256=VSyEP8w9l3pXdRkyP_goeMwiNA8KWwitfAqUkveJkdQ,13
-bluecellulab-2.6.4.dist-info/RECORD,,
+bluecellulab-2.6.6.dist-info/AUTHORS.txt,sha256=EDs3H-2HXBojbma10psixk3C2rFiOCTIREi2ZAbXYNQ,179
+bluecellulab-2.6.6.dist-info/LICENSE,sha256=xOouu1gC1GGklDxkITlaVl60I9Ab860O-nZsFbWydvU,11749
+bluecellulab-2.6.6.dist-info/METADATA,sha256=4_xecVXsjYRMbTw9HJXdgWR4o5S-uiv3UVuXotp0gD4,7054
+bluecellulab-2.6.6.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+bluecellulab-2.6.6.dist-info/top_level.txt,sha256=VSyEP8w9l3pXdRkyP_goeMwiNA8KWwitfAqUkveJkdQ,13
+bluecellulab-2.6.6.dist-info/RECORD,,