bluecellulab 2.6.37__py3-none-any.whl → 2.6.39__py3-none-any.whl

bluecellulab/analysis/analysis.py

@@ -0,0 +1,63 @@
+"""Module for analyzing cell simulation results."""
+try:
+    import efel
+except ImportError:
+    efel = None
+import numpy as np
+
+from bluecellulab.stimulus import StimulusFactory
+from bluecellulab.tools import calculate_rheobase
+from bluecellulab.analysis.inject_sequence import run_stimulus
+from bluecellulab.analysis.plotting import plot_iv_curve
+
+
+def compute_plot_iv_curve(cell, stim_start=100.0, duration=500.0, post_delay=100.0, threshold_voltage=-30, nb_bins=11):
+    """Compute and plot the IV curve from a given cell by injecting a
+    predefined range of currents.
+
+    Args:
+        cell (bluecellulab.cell.Cell): The initialized cell model.
+        stim_start (float): Start time for current injection (in ms). Default is 100.0 ms.
+        duration (float): Duration of current injection (in ms). Default is 500.0 ms.
+        post_delay (float): Delay after the stimulation ends (in ms). Default is 100.0 ms.
+        nb_bins (int): Number of current injection levels. Default is 11.
+
+    Returns:
+        tuple: A tuple containing:
+            - list_amp (np.ndarray): The predefined injected step current levels (nA).
+            - steady_states (np.ndarray): The corresponding steady-state voltages (mV).
+    """
+    rheobase = calculate_rheobase(cell)
+
+    list_amp = np.linspace(rheobase - 2, rheobase - 0.1, nb_bins)  # [nA]
+
+    steps = []
+    times = []
+    voltages = []
+    # inject step current and record voltage response
+    for amp in list_amp:
+        stim_factory = StimulusFactory(dt=0.1)
+        step_stimulus = stim_factory.step(pre_delay=stim_start, duration=duration, post_delay=post_delay, amplitude=amp)
+        recording = run_stimulus(cell.template_params, step_stimulus, section="soma[0]", segment=0.5)
+        steps.append(step_stimulus)
+        times.append(recording.time)
+        voltages.append(recording.voltage)
+
+    steady_states = []
+    # compute steady state response
+    efel.set_setting('Threshold', threshold_voltage)
+    for voltage, t in zip(voltages, times):
+        trace = {
+            'T': t,
+            'V': voltage,
+            'stim_start': [stim_start],
+            'stim_end': [stim_start + duration]
+        }
+        features_results = efel.get_feature_values([trace], ['steady_state_voltage_stimend'])
+        steady_state = features_results[0]['steady_state_voltage_stimend']
+        steady_states.append(steady_state)
+
+    # plot I-V curve
+    plot_iv_curve(list_amp, steady_states)
+
+    return np.array(list_amp), np.array(steady_states)

bluecellulab/analysis/plotting.py

@@ -0,0 +1,25 @@
+"""Module for plotting analysis results of cell simulations."""
+
+import matplotlib.pyplot as plt
+
+
+def plot_iv_curve(currents, voltages):
+    """Plots the IV curve.
+
+    Args:
+        currents (iterable): The injected current levels (nA).
+        voltages (iterable): The corresponding steady-state voltages (mV).
+    Raises:
+        ValueError: If the lengths of currents and voltages do not match.
+    """
+    if len(currents) != len(voltages):
+        raise ValueError("currents and voltages must have the same length")
+
+    # Plotting
+    plt.figure(figsize=(10, 6))
+    plt.plot(voltages, currents, marker='o', linestyle='-', color='b')
+    plt.title("I-V Curve")
+    plt.ylabel("Injected current [nA]")
+    plt.xlabel("Steady state voltage [mV]")
+    plt.tight_layout()
+    plt.show()

bluecellulab/tools.py

@@ -23,6 +23,7 @@ import neuron
 import numpy as np
 
 import bluecellulab
+from bluecellulab.cell import Cell
 from bluecellulab.circuit.circuit_access import EmodelProperties
 from bluecellulab.exceptions import UnsteadyCellError
 from bluecellulab.simulation.parallel import IsolatedProcess
@@ -351,3 +352,76 @@ def check_empty_topology() -> bool:
         neuron.h.topology()
 
     return stdout == ['', '']
+
+
+def calculate_max_thresh_current(cell: Cell, threshold_voltage: float = -30.0) -> float:
+    """Calculate the upper bound threshold current.
+
+    Args:
+        cell (bluecellulab.cell.Cell): The initialized cell model.
+        threshold_voltage (float, optional): Voltage threshold for spike detection. Default is -30.0 mV.
+
+    Returns:
+        float: The upper bound threshold current.
+    """
+    # Calculate resting membrane potential (rmp)
+    rmp = calculate_SS_voltage(
+        template_path=cell.template_params.template_filepath,
+        morphology_path=cell.template_params.morph_filepath,
+        template_format=cell.template_params.template_format,
+        emodel_properties=cell.template_params.emodel_properties,
+        step_level=0.0,
+    )
+
+    # Calculate input resistance (rin)
+    rin = calculate_input_resistance(
+        template_path=cell.template_params.template_filepath,
+        morphology_path=cell.template_params.morph_filepath,
+        template_format=cell.template_params.template_format,
+        emodel_properties=cell.template_params.emodel_properties,
+    )
+
+    # Calculate upperbound threshold current
+    upperbound_threshold_current = (threshold_voltage - rmp) / rin
+    upperbound_threshold_current = np.min([upperbound_threshold_current, 2.0])
+
+    return upperbound_threshold_current
+
+
+def calculate_rheobase(cell: Cell,
+                       threshold_voltage: float = -30.0,
+                       threshold_search_stim_start: float = 300.0,
+                       threshold_search_stim_stop: float = 1000.0) -> float:
+    """Calculate the rheobase by first computing the upper bound threshold
+    current.
+
+    Args:
+        cell (bluecellulab.cell.Cell): The initialized cell model.
+        threshold_voltage (float, optional): Voltage threshold for spike detection. Default is -30.0 mV.
+        threshold_search_stim_start (float, optional): Start time for threshold search stimulation (in ms). Default is 300.0 ms.
+        threshold_search_stim_stop (float, optional): Stop time for threshold search stimulation (in ms). Default is 1000.0 ms.
+
+    Returns:
+        float: The rheobase current.
+    """
+    if cell.template_params.emodel_properties is None:
+        raise ValueError("emodel_properties cannot be None")
+
+    # Calculate upper bound threshold current
+    upperbound_threshold_current = calculate_max_thresh_current(cell, threshold_voltage)
+
+    # Compute rheobase
+    rheobase = search_threshold_current(
+        template_name=cell.template_params.template_filepath,
+        morphology_path=cell.template_params.morph_filepath,
+        template_format=cell.template_params.template_format,
+        emodel_properties=cell.template_params.emodel_properties,
+        hyp_level=cell.template_params.emodel_properties.holding_current,
+        inj_start=threshold_search_stim_start,
+        inj_stop=threshold_search_stim_stop,
+        min_current=cell.template_params.emodel_properties.holding_current,
+        max_current=upperbound_threshold_current,
+        current_precision=0.005,
+    )
+
+    return rheobase

{bluecellulab-2.6.37.dist-info → bluecellulab-2.6.39.dist-info}/METADATA

@@ -1,10 +1,10 @@
 Metadata-Version: 2.2
 Name: bluecellulab
-Version: 2.6.37
+Version: 2.6.39
 Summary: Biologically detailed neural network simulations and analysis.
 Author: Blue Brain Project, EPFL
 License: Apache2.0
-Project-URL: Homepage, https://github.com/BlueBrain/BlueCelluLab
+Project-URL: Homepage, https://github.com/openbraininstitute/BlueCelluLab
 Project-URL: Documentation, https://bluecellulab.readthedocs.io/
 Keywords: computational neuroscience,simulation,analysis,SONATA,neural networks,neuron,Blue Brain Project
 Classifier: Development Status :: 5 - Production/Stable
@@ -14,7 +14,7 @@ Classifier: Operating System :: POSIX
 Classifier: Topic :: Scientific/Engineering
 Classifier: Programming Language :: Python :: 3
 Classifier: Topic :: Utilities
-Requires-Python: >=3.8
+Requires-Python: >=3.9
 Description-Content-Type: text/x-rst
 License-File: LICENSE
 License-File: AUTHORS.txt
@@ -91,12 +91,12 @@ If you need to cite a specific version, please use the DOI provided by `Zenodo <
 Support
 =======
 
-We are providing support on `Gitter <https://gitter.im/BlueBrain/BlueCelluLab>`_. We suggest you create tickets on the `Github issue tracker <https://github.com/BlueBrain/BlueCelluLab/issues>`_ in case you encounter problems while using the software or if you have some suggestions.
+We are providing support on `Gitter <https://gitter.im/openbraininstitute/BlueCelluLab>`_. We suggest you create tickets on the `Github issue tracker <https://github.com/openbraininstitute/BlueCelluLab/issues>`_ in case you encounter problems while using the software or if you have some suggestions.
 
 Main dependencies
 =================
 
-* `Python 3.8+ <https://www.python.org/downloads/release/python-380/>`_
+* `Python 3.9+ <https://www.python.org/downloads/release/python-390/>`_
 * `Neuron 8.0.2+ <https://pypi.org/project/NEURON/>`_
 
 Installation
@@ -127,13 +127,13 @@ The following example shows how to create a cell, add a stimulus and run a simul
     time, voltage = cell.get_time(), cell.get_soma_voltage()
     # plotting time and voltage ...
 
-.. image:: https://raw.githubusercontent.com/BlueBrain/BlueCelluLab/main/docs/images/voltage-readme.png
+.. image:: https://raw.githubusercontent.com/openbraininstitute/BlueCelluLab/main/docs/images/voltage-readme.png
    :alt: Voltage plot
 
 Tutorial
 ========
 
-A more detailed explanation on how to use BlueCelluLab, as well as other examples can be found on the `examples page <https://github.com/BlueBrain/BlueCelluLab/blob/main/examples/README.rst>`_.
+A more detailed explanation on how to use BlueCelluLab, as well as other examples can be found on the `examples page <https://github.com/openbraininstitute/BlueCelluLab/blob/main/examples/README.rst>`_.
 
 API Documentation
 =================
@@ -155,7 +155,7 @@ Testing is set up using `tox`:
 Contributing
 ============
 
-We welcome contributions to BlueCelluLab! Please see the `CONTRIBUTING.rst <https://github.com/BlueBrain/BlueCelluLab/blob/main/CONTRIBUTING.rst>`_ for guidelines on how to contribute.
+We welcome contributions to BlueCelluLab! Please see the `CONTRIBUTING.rst <https://github.com/openbraininstitute/BlueCelluLab/blob/main/CONTRIBUTING.rst>`_ for guidelines on how to contribute.
 
 Funding & Acknowledgements
 ==========================
@@ -166,6 +166,7 @@ Copyright
 =========
 
 Copyright (c) 2023-2024 Blue Brain Project/EPFL
+Copyright (c) 2025 Open Brain Institute
 
 This work is licensed under `Apache 2.0 <https://www.apache.org/licenses/LICENSE-2.0.html>`_
 
@@ -175,10 +176,10 @@ The licenses of the morphology files used in this repository are available on: h
 
 
 .. |license| image:: https://img.shields.io/badge/License-Apache%202.0-blue.svg
-                :target: https://github.com/BlueBrain/BlueCelluLab/blob/main/LICENSE
+                :target: https://github.com/openbraininstitute/BlueCelluLab/blob/main/LICENSE
 
-.. |tests| image:: https://github.com/BlueBrain/BlueCelluLab/actions/workflows/test.yml/badge.svg?branch=main
-   :target: https://github.com/BlueBrain/BlueCelluLab/actions/workflows/test.yml
+.. |tests| image:: https://github.com/openbraininstitute/BlueCelluLab/actions/workflows/test.yml/badge.svg?branch=main
+   :target: https://github.com/openbraininstitute/BlueCelluLab/actions/workflows/test.yml
    :alt: CI
 
 .. |pypi| image:: https://img.shields.io/pypi/v/bluecellulab.svg
@@ -189,13 +190,13 @@ The licenses of the morphology files used in this repository are available on: h
                :target: https://bluecellulab.readthedocs.io/
                :alt: latest documentation
 
-.. |coverage| image:: https://codecov.io/github/BlueBrain/BlueCelluLab/coverage.svg?branch=main
-                   :target: https://codecov.io/gh/BlueBrain/bluecellulab
+.. |coverage| image:: https://codecov.io/github/openbraininstitute/BlueCelluLab/coverage.svg?branch=main
+                   :target: https://codecov.io/gh/openbraininstitute/bluecellulab
                    :alt: coverage
 
 .. |gitter| image:: https://badges.gitter.im/Join%20Chat.svg
-                 :target: https://gitter.im/BlueBrain/BlueCelluLab
-                 :alt: Join the chat at https://gitter.im/BlueBrain/BlueCelluLab
+                 :target: https://gitter.im/openbraininstitute/BlueCelluLab
+                 :alt: Join the chat at https://gitter.im/openbraininstitute/BlueCelluLab
 
 .. |joss| image:: https://joss.theoj.org/papers/effd553ca48734a2966d9d7ace3b05ff/status.svg
                 :target: https://joss.theoj.org/papers/effd553ca48734a2966d9d7ace3b05ff
@@ -212,4 +213,4 @@ The licenses of the morphology files used in this repository are available on: h
     to skip content after the marker 'substitutions'.
 
 .. substitutions
-.. |banner| image:: https://raw.githubusercontent.com/BlueBrain/BlueCelluLab/main/docs/source/logo/BlueCelluLabBanner.jpg
+.. |banner| image:: https://raw.githubusercontent.com/openbraininstitute/BlueCelluLab/main/docs/source/logo/BlueCelluLabBanner.jpg

{bluecellulab-2.6.37.dist-info → bluecellulab-2.6.39.dist-info}/RECORD

@@ -10,12 +10,14 @@ bluecellulab/plotwindow.py,sha256=ePU-EegZ1Sqk0SoYYiQ6k24ZO4s3Hgfpx10uePiJ5xM,27
 bluecellulab/psection.py,sha256=FSOwRNuOTyB469BM-jPEf9l1J59FamXmzrQgBI6cnP4,6174
 bluecellulab/psegment.py,sha256=PTgoGLqM4oFIdF_8QHFQCU59j-8TQmtq6PakiGUQhIo,3138
 bluecellulab/rngsettings.py,sha256=2Ykb4Ylk3XTs58x1UIxjg8XJqjSpnCgKRZ8avXCDpxk,4237
-bluecellulab/tools.py,sha256=ytziurCwhp2iuiwhYrr4yk7PywikDL8Hk-Knx5CYFK8,11213
+bluecellulab/tools.py,sha256=LgfP2NNm7dVbig2NFx3FFJXCbVpvK8BkighUoyKVPp8,14321
 bluecellulab/type_aliases.py,sha256=DvgjERv2Ztdw_sW63JrZTQGpJ0x5uMTFB5hcBHDb0WA,441
 bluecellulab/utils.py,sha256=SbOOkzw1YGjCKV3qOw0zpabNEy7V9BRtgMLsQJiFRq4,1526
 bluecellulab/verbosity.py,sha256=T0IgX7DrRo19faxrT4Xzb27gqxzoILQ8FzYKxvUeaPM,1342
 bluecellulab/analysis/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+bluecellulab/analysis/analysis.py,sha256=i64iVNF7-0cCneKP4OjdyNHdhxtixjTFiJiSXK4FHLs,2508
 bluecellulab/analysis/inject_sequence.py,sha256=Ih3wdNRn0-lM-NW8agrMUGS862CEgzn_hl54DFDXyjM,6325
+bluecellulab/analysis/plotting.py,sha256=X2llERRPB9aDMbtw96RzMFfUQFXTKVMwmQ5lEkGWLlQ,791
 bluecellulab/cell/__init__.py,sha256=Sbc0QOsJ8E7tSwf3q7fsXuE_SevBN6ZmoCVyyU5zfII,208
 bluecellulab/cell/cell_dict.py,sha256=VE7pi-NsMVRSmo-PSdbiLYmolDOu0Gc6JxFBkuQpFdk,1346
 bluecellulab/cell/core.py,sha256=QzCC2uVj1yOSLi3-dGN3Iib9POTNRGNJSnjvJue1T5g,31315
@@ -62,9 +64,9 @@ bluecellulab/stimulus/factory.py,sha256=L85RN-lImkyCEM87Pp1X5rpGNIHLNSMwx1b9dZxO
 bluecellulab/synapse/__init__.py,sha256=RW8XoAMXOvK7OG1nHl_q8jSEKLj9ZN4oWf2nY9HAwuk,192
 bluecellulab/synapse/synapse_factory.py,sha256=NHwRMYMrnRVm_sHmyKTJ1bdoNmWZNU4UPOGu7FCi-PE,6987
 bluecellulab/synapse/synapse_types.py,sha256=zs_yBvGTH4QrbQF3nEViidyq1WM_ZcTSFdjUxB3khW0,16871
-bluecellulab-2.6.37.dist-info/AUTHORS.txt,sha256=EDs3H-2HXBojbma10psixk3C2rFiOCTIREi2ZAbXYNQ,179
-bluecellulab-2.6.37.dist-info/LICENSE,sha256=dAMAR2Sud4Nead1wGFleKiwTZfkTNZbzmuGfcTKb3kg,11335
-bluecellulab-2.6.37.dist-info/METADATA,sha256=WjdGXa3ealMZkID135lo2fl2gcDNyHz5TBpUJlAoQ3I,8059
-bluecellulab-2.6.37.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-bluecellulab-2.6.37.dist-info/top_level.txt,sha256=VSyEP8w9l3pXdRkyP_goeMwiNA8KWwitfAqUkveJkdQ,13
-bluecellulab-2.6.37.dist-info/RECORD,,
+bluecellulab-2.6.39.dist-info/AUTHORS.txt,sha256=EDs3H-2HXBojbma10psixk3C2rFiOCTIREi2ZAbXYNQ,179
+bluecellulab-2.6.39.dist-info/LICENSE,sha256=dAMAR2Sud4Nead1wGFleKiwTZfkTNZbzmuGfcTKb3kg,11335
+bluecellulab-2.6.39.dist-info/METADATA,sha256=hkRo4sSq0ypIDM0HXvM8gn8MlomPoCqhy66-Se40IWM,8225
+bluecellulab-2.6.39.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+bluecellulab-2.6.39.dist-info/top_level.txt,sha256=VSyEP8w9l3pXdRkyP_goeMwiNA8KWwitfAqUkveJkdQ,13
+bluecellulab-2.6.39.dist-info/RECORD,,