bluecellulab 2.6.3__py3-none-any.whl → 2.6.5__py3-none-any.whl

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Files changed (7) hide show
  1. bluecellulab/circuit/simulation_access.py +9 -6
  2. {bluecellulab-2.6.3.dist-info → bluecellulab-2.6.5.dist-info}/METADATA +2 -1
  3. {bluecellulab-2.6.3.dist-info → bluecellulab-2.6.5.dist-info}/RECORD +7 -7
  4. {bluecellulab-2.6.3.dist-info → bluecellulab-2.6.5.dist-info}/AUTHORS.txt +0 -0
  5. {bluecellulab-2.6.3.dist-info → bluecellulab-2.6.5.dist-info}/LICENSE +0 -0
  6. {bluecellulab-2.6.3.dist-info → bluecellulab-2.6.5.dist-info}/WHEEL +0 -0
  7. {bluecellulab-2.6.3.dist-info → bluecellulab-2.6.5.dist-info}/top_level.txt +0 -0
bluecellulab/circuit/simulation_access.py CHANGED
@@ -18,6 +18,7 @@ import logging
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  from pathlib import Path
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  from typing import Optional, Protocol
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+ import h5py
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  import pandas as pd
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  from bluecellulab.circuit.config import SimulationConfig, SonataSimulationConfig
@@ -172,12 +173,14 @@ class SonataSimulationAccess:
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  def get_synapse_replay_spikes(f_name: str) -> dict:
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  """Read the .dat file containing the spike replays."""
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- data = np.genfromtxt(f_name, skip_header=1)
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- spikes = pd.DataFrame(data=data, columns=["t", "node_id"]).astype({"node_id": int})
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- # subtract 1 from all node_ids to make them 0-based
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- # source: https://sonata-extension.readthedocs.io/
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- # en/latest/blueconfig-projection-example.html#dat-spike-files
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- spikes["node_id"] -= 1
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+ with h5py.File(f_name, 'r') as f:
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+ # Access the timestamps and node_ids datasets
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+ timestamps = f['/spikes/All/timestamps'][:]
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+ node_ids = f['/spikes/All/node_ids'][:]
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+
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+ spikes = pd.DataFrame(data={'t': timestamps, 'node_id': node_ids})
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+ spikes = spikes.astype({"node_id": int})
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+
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  if (spikes["t"] < 0).any():
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  logger.warning("Found negative spike times... Clipping them to 0")
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  spikes["t"].clip(lower=0., inplace=True)
{bluecellulab-2.6.3.dist-info → bluecellulab-2.6.5.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: bluecellulab
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- Version: 2.6.3
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+ Version: 2.6.5
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  Summary: Biologically detailed neural network simulations and analysis.
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  Author: Blue Brain Project, EPFL
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  License: Apache2.0
@@ -26,6 +26,7 @@ Requires-Dist: bluepysnap <4.0.0,>=3.0.0
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  Requires-Dist: pydantic <3.0.0,>=2.5.2
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  Requires-Dist: typing-extensions >=4.8.0
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  Requires-Dist: networkx >=3.1
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+ Requires-Dist: h5py >=3.11.0
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  |banner|
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{bluecellulab-2.6.3.dist-info → bluecellulab-2.6.5.dist-info}/RECORD RENAMED
@@ -35,7 +35,7 @@ bluecellulab/circuit/__init__.py,sha256=Khpa13nzNvDlDS2JduyoFTukEduEkWCc5ML_JwGp
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  bluecellulab/circuit/format.py,sha256=eYhiBIQnPnnVBmaSDymFjQprXN9QjEYKmFhb2mIS86o,1674
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  bluecellulab/circuit/iotools.py,sha256=KVE7x5LNQ4RgjNh05Q-h3Swpbs3nRFtrcWNHj62aiRI,1585
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  bluecellulab/circuit/node_id.py,sha256=gaRAW3UhbPOPsoXMHLjo3qH9iNod7YB8ZOcguWprrU4,1265
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- bluecellulab/circuit/simulation_access.py,sha256=QHVEN-sEZbCCvblhBHEShGX0-NEXCD1AYpavpVGCgAE,7073
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+ bluecellulab/circuit/simulation_access.py,sha256=jrVz6pFNAuwvuvsTq9OqeDfjIZ5akE98RBMBNDwuDVQ,7062
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  bluecellulab/circuit/synapse_properties.py,sha256=a4-Yw_f8JIR6i2YG8qhCW97TMSd_Z-aF6lp_a1wBwnM,6374
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  bluecellulab/circuit/validate.py,sha256=7EUN15u0JFFlLf389jUBqLwDOHyZdfKtoidI-xLUVYA,3593
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  bluecellulab/circuit/circuit_access/__init__.py,sha256=sgp6m5kP-pq60V1IFGUiSUR1OW01zdxXNNUJmPA8anI,201
@@ -62,9 +62,9 @@ bluecellulab/stimulus/factory.py,sha256=cjnMqFx-Y31kV1XHvkSbGI2f1OpEawU3Wg_cLqcI
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  bluecellulab/synapse/__init__.py,sha256=RW8XoAMXOvK7OG1nHl_q8jSEKLj9ZN4oWf2nY9HAwuk,192
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  bluecellulab/synapse/synapse_factory.py,sha256=MjUorWoMl4lFSBgQw4QS09Dzh0-LYWlCHJKYy8N-d3w,6847
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  bluecellulab/synapse/synapse_types.py,sha256=4gne-hve2vq1Lau-LAVPsfLjffVYqAYBW3kCfC7_600,16871
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- bluecellulab-2.6.3.dist-info/AUTHORS.txt,sha256=EDs3H-2HXBojbma10psixk3C2rFiOCTIREi2ZAbXYNQ,179
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- bluecellulab-2.6.3.dist-info/LICENSE,sha256=xOouu1gC1GGklDxkITlaVl60I9Ab860O-nZsFbWydvU,11749
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- bluecellulab-2.6.3.dist-info/METADATA,sha256=yg81T-fh1WY_SIy1BaGDTXzBe2_b7kmtUJie9gPIIqM,7025
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- bluecellulab-2.6.3.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
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- bluecellulab-2.6.3.dist-info/top_level.txt,sha256=VSyEP8w9l3pXdRkyP_goeMwiNA8KWwitfAqUkveJkdQ,13
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- bluecellulab-2.6.3.dist-info/RECORD,,
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+ bluecellulab-2.6.5.dist-info/AUTHORS.txt,sha256=EDs3H-2HXBojbma10psixk3C2rFiOCTIREi2ZAbXYNQ,179
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+ bluecellulab-2.6.5.dist-info/LICENSE,sha256=xOouu1gC1GGklDxkITlaVl60I9Ab860O-nZsFbWydvU,11749
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+ bluecellulab-2.6.5.dist-info/METADATA,sha256=N9CDlJekDBY0lDhztlnlbbQGcMXYsMQqn6W4VbHu104,7054
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+ bluecellulab-2.6.5.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
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+ bluecellulab-2.6.5.dist-info/top_level.txt,sha256=VSyEP8w9l3pXdRkyP_goeMwiNA8KWwitfAqUkveJkdQ,13
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+ bluecellulab-2.6.5.dist-info/RECORD,,