bluecellulab 2.6.65__tar.gz → 2.6.66__tar.gz

{bluecellulab-2.6.65 → bluecellulab-2.6.66}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bluecellulab
-Version: 2.6.65
+Version: 2.6.66
 Summary: Biologically detailed neural network simulations and analysis.
 Author: Blue Brain Project, EPFL
 License: Apache2.0

{bluecellulab-2.6.65 → bluecellulab-2.6.66}/bluecellulab/analysis/analysis.py

@@ -20,6 +20,7 @@ from bluecellulab.analysis.inject_sequence import run_stimulus
 from bluecellulab.analysis.plotting import plot_iv_curve, plot_fi_curve
 from bluecellulab.analysis.utils import exp_decay
 from bluecellulab.simulation import Simulation
+from bluecellulab.simulation.neuron_globals import set_neuron_globals
 from bluecellulab.stimulus import StimulusFactory
 from bluecellulab.stimulus.circuit_stimulus_definitions import Hyperpolarizing
 from bluecellulab.tools import calculate_rheobase
@@ -43,7 +44,9 @@ def compute_plot_iv_curve(cell,
                           save_figure=False,
                           output_dir="./",
                           output_fname="iv_curve.pdf",
-                          n_processes=None):
+                          n_processes=None,
+                          celsius=None,
+                          v_init=None):
     """Compute and plot the Current-Voltage (I-V) curve for a given cell by
     injecting a range of currents.
 
@@ -78,6 +81,8 @@ def compute_plot_iv_curve(cell,
         n_processes (int, optional): The number of processes to use for parallel execution.
             If None or if it is higher than the number of steps,
             it will use the number of steps as the number of processes.
+        celsius (float, optional): Temperature in Celsius.
+        v_init (float, optional): Initial membrane potential.
 
     Returns:
         tuple: A tuple containing:
@@ -103,7 +108,7 @@ def compute_plot_iv_curve(cell,
 
     if n_processes is None or n_processes > len(steps):
         n_processes = len(steps)
-    with Pool(n_processes) as p:
+    with Pool(n_processes, initializer=set_neuron_globals, initargs=(celsius, v_init)) as p:
         recordings = p.starmap(
             run_stimulus,
             zip(
@@ -162,7 +167,9 @@ def compute_plot_fi_curve(cell,
                           save_figure=False,
                           output_dir="./",
                           output_fname="fi_curve.pdf",
-                          n_processes=None):
+                          n_processes=None,
+                          celsius=None,
+                          v_init=None):
     """Compute and plot the Frequency-Current (F-I) curve for a given cell by
     injecting a range of currents.
 
@@ -199,6 +206,8 @@ def compute_plot_fi_curve(cell,
         n_processes (int, optional): The number of processes to use for parallel execution.
             If None or if it is higher than the number of steps,
             it will use the number of steps as the number of processes.
+        celsius (float, optional): Temperature in Celsius.
+        v_init (float, optional): Initial membrane potential.
 
     Returns:
         tuple: A tuple containing:
@@ -220,7 +229,7 @@ def compute_plot_fi_curve(cell,
 
     if n_processes is None or n_processes > len(steps):
         n_processes = len(steps)
-    with Pool(n_processes) as p:
+    with Pool(n_processes, initializer=set_neuron_globals, initargs=(celsius, v_init)) as p:
         recordings = p.starmap(
             run_stimulus,
             zip(
@@ -365,43 +374,55 @@ class BPAP:
         except RuntimeError:
             return None, True
 
-    def validate(self, soma_amp, dend_amps, dend_dist, apic_amps, apic_dist):
+    def validate(self, soma_amp, dend_amps, dend_dist, apic_amps, apic_dist, validate_with_fit=True):
         """Check that the exponential fit is decaying."""
         validated = True
         notes = ""
-        popt_dend, dend_fit_error = self.fit(soma_amp, dend_amps, dend_dist)
-        popt_apic, apic_fit_error = self.fit(soma_amp, apic_amps, apic_dist)
-        if dend_fit_error or apic_fit_error:
-            logger.debug("Fitting error occurred.")
-            validated = False
-            notes += "Validation failed: Fitting error occurred.\n"
-            return validated, notes
-
-        if dend_amps is not None:
-            plt.cla()
-            plt.plot([0], soma_amp, '.')
-            plt.plot(dend_dist, dend_amps, '.')
-            x = np.linspace(0, max(dend_dist), 100)
-            plt.plot(x, exp_decay(x, *popt_dend), color='darkgreen', linestyle='--', label='Basal Dendritic Fit')
-            plt.savefig("bad_dendritic_fit.png")
-        if popt_dend is None:
-            logger.debug("No dendritic recordings found.")
-            notes += "No dendritic recordings found.\n"
-        elif popt_dend[1] <= 0 or popt_dend[0] <= 0:
-            logger.debug("Dendritic fit is not decaying.")
-            validated = False
-            notes += "Dendritic fit is not decaying.\n"
+        if validate_with_fit:
+            popt_dend, dend_fit_error = self.fit(soma_amp, dend_amps, dend_dist)
+            popt_apic, apic_fit_error = self.fit(soma_amp, apic_amps, apic_dist)
+            if dend_fit_error or apic_fit_error:
+                logger.debug("Fitting error occurred.")
+                validated = False
+                notes += "Validation failed: Fitting error occurred.\n"
+                return validated, notes
+            if popt_dend is None:
+                logger.debug("No dendritic recordings found.")
+                notes += "No dendritic recordings found.\n"
+            elif popt_dend[1] <= 0 or popt_dend[0] <= 0:
+                logger.debug("Dendritic fit is not decaying.")
+                validated = False
+                notes += "Dendritic fit is not decaying.\n"
+            else:
+                notes += "Dendritic validation passed: dendritic amplitude is decaying with distance relative to soma.\n"
+            if popt_apic is None:
+                logger.debug("No apical recordings found.")
+                notes += "No apical recordings found.\n"
+            elif popt_apic[1] <= 0 or popt_apic[0] <= 0:
+                logger.debug("Apical fit is not decaying.")
+                validated = False
+                notes += "Apical fit is not decaying.\n"
+            else:
+                notes += "Apical validation passed: apical amplitude is decaying with distance relative to soma.\n"
         else:
-            notes += "Dendritic validation passed: dendritic amplitude is decaying with distance relative to soma.\n"
-        if popt_apic is None:
-            logger.debug("No apical recordings found.")
-            notes += "No apical recordings found.\n"
-        elif popt_apic[1] <= 0 or popt_apic[0] <= 0:
-            logger.debug("Apical fit is not decaying.")
-            validated = False
-            notes += "Apical fit is not decaying.\n"
-        else:
-            notes += "Apical validation passed: apical amplitude is decaying with distance relative to soma.\n"
+            if dend_amps and dend_dist:
+                furthest_dend_idx = np.argmax(dend_dist)
+                if dend_amps[furthest_dend_idx] < soma_amp[0]:
+                    notes += "Dendritic validation passed: dendritic amplitude is decaying with distance relative to soma.\n"
+                else:
+                    validated = False
+                    notes += "Dendritic validation failed: dendritic amplitude is not decaying with distance relative to soma.\n"
+            else:
+                notes += "No dendritic recordings found.\n"
+            if apic_amps and apic_dist:
+                furthest_apic_idx = np.argmax(apic_dist)
+                if apic_amps[furthest_apic_idx] < soma_amp[0]:
+                    notes += "Apical validation passed: apical amplitude is decaying with distance relative to soma.\n"
+                else:
+                    validated = False
+                    notes += "Apical validation failed: apical amplitude is not decaying with distance relative to soma.\n"
+            else:
+                notes += "No apical recordings found.\n"
 
         return validated, notes
 
@@ -416,10 +437,14 @@ class BPAP:
         save_figure=False,
         output_dir="./",
         output_fname="bpap.pdf",
+        do_fit=True,
     ):
         """Plot the results of the BPAP analysis."""
-        popt_dend, _ = self.fit(soma_amp, dend_amps, dend_dist)
-        popt_apic, _ = self.fit(soma_amp, apic_amps, apic_dist)
+        popt_dend = None
+        popt_apic = None
+        if do_fit:
+            popt_dend, _ = self.fit(soma_amp, dend_amps, dend_dist)
+            popt_apic, _ = self.fit(soma_amp, apic_amps, apic_dist)
 
         outpath = pathlib.Path(output_dir) / output_fname
         fig, ax1 = plt.subplots(figsize=(10, 6))

{bluecellulab-2.6.65 → bluecellulab-2.6.66}/bluecellulab/simulation/neuron_globals.py

@@ -13,6 +13,7 @@
 # limitations under the License.
 """Module that handles the global NEURON parameters."""
 
+from typing import Optional
 from typing import NamedTuple
 import neuron
 from bluecellulab.circuit.config.sections import Conditions, MechanismConditions
@@ -109,3 +110,14 @@ class NeuronGlobals:
     def load_params(self, params: NeuronGlobalParams) -> None:
         self.temperature = params.temperature
         self.v_init = params.v_init
+
+
+def set_neuron_globals(temperature: Optional[float] = 34.0, v_init: Optional[float] = -80.0) -> None:
+    """Set the global NEURON parameters."""
+    if temperature is None and v_init is None:
+        return
+    neuron_globals = NeuronGlobals.get_instance()
+    if temperature is not None:
+        neuron_globals.temperature = temperature
+    if v_init is not None:
+        neuron_globals.v_init = v_init

{bluecellulab-2.6.65 → bluecellulab-2.6.66}/bluecellulab/tools.py

@@ -26,7 +26,7 @@ import bluecellulab
 from bluecellulab.cell import Cell
 from bluecellulab.circuit.circuit_access import EmodelProperties
 from bluecellulab.exceptions import UnsteadyCellError
-from bluecellulab.simulation.neuron_globals import NeuronGlobals
+from bluecellulab.simulation.neuron_globals import set_neuron_globals
 from bluecellulab.simulation.parallel import IsolatedProcess
 from bluecellulab.utils import CaptureOutput
 from bluecellulab.type_aliases import NeuronSection
@@ -394,6 +394,15 @@ def check_empty_topology() -> bool:
     return stdout == ['', '']
 
 
+def section_exists(name: str) -> bool:
+    """Check if a section exists in the NEURON simulator.
+
+    Args:
+        name (str): The name of the section to check.
+    """
+    return bool(neuron.h.section_exists(name))
+
+
 def calculate_max_thresh_current(cell: Cell,
                                  threshold_voltage: float = -20.0,
                                  section: str = "soma[0]",
@@ -608,9 +617,7 @@ def compute_memodel_properties(
         celsius (float, optional): Temperature in Celsius. Default is 34.0 C.
     """
     # set initial voltage and temperature
-    neuron_globals = NeuronGlobals.get_instance()
-    neuron_globals.temperature = celsius
-    neuron_globals.v_init = v_init
+    set_neuron_globals(temperature=celsius, v_init=v_init)
 
     # get me-model properties
     holding_current = cell.hypamp if cell.hypamp else 0.0

{bluecellulab-2.6.65 → bluecellulab-2.6.66}/bluecellulab/validation/validation.py

@@ -25,11 +25,13 @@ from bluecellulab.analysis.analysis import compute_plot_iv_curve
 from bluecellulab.analysis.inject_sequence import run_multirecordings_stimulus
 from bluecellulab.analysis.inject_sequence import run_stimulus
 from bluecellulab.cell.core import Cell
-from bluecellulab.simulation.neuron_globals import NeuronGlobals
+from bluecellulab.simulation.neuron_globals import set_neuron_globals
 from bluecellulab.stimulus.factory import IDRestTimings
 from bluecellulab.stimulus.factory import StimulusFactory
 from bluecellulab.tools import calculate_input_resistance
 from bluecellulab.tools import calculate_rheobase
+from bluecellulab.tools import section_exists
+from bluecellulab.utils import NestedPool
 
 logger = logging.getLogger(__name__)
 
@@ -83,10 +85,10 @@ def plot_traces(recordings, out_dir, fname, title, labels=None, xlim=None):
     return outpath
 
 
-def spiking_test(template_params, rheobase, out_dir, spike_threshold_voltage=-20.):
+def spiking_test(template_params, rheobase, out_dir, spike_threshold_voltage=-40.):
     """Spiking test: cell should spike."""
     stim_factory = StimulusFactory(dt=1.0)
-    step_stimulus = stim_factory.idrest(threshold_current=rheobase, threshold_percentage=200)
+    step_stimulus = stim_factory.idrest(threshold_current=rheobase, threshold_percentage=130)
     recording = run_stimulus(
         template_params,
         step_stimulus,
@@ -103,7 +105,7 @@ def spiking_test(template_params, rheobase, out_dir, spike_threshold_voltage=-20
         recording,
         out_dir,
         fname="spiking_test.pdf",
-        title="Spiking Test - Step at 200% of Rheobase",
+        title="Spiking Test - Step at 130% of Rheobase",
     )
 
     notes = "Validation passed: Spikes detected." if passed else "Validation failed: No spikes detected."
@@ -135,6 +137,7 @@ def depolarization_block_test(template_params, rheobase, out_dir):
         "stim_start": [IDRestTimings.PRE_DELAY.value],
         "stim_end": [IDRestTimings.PRE_DELAY.value + IDRestTimings.DURATION.value],
     }
+    efel.set_setting("depol_block_min_duration", 150)
     features_results = efel.get_feature_values([trace], ["depol_block_bool"])
     depol_block = bool(features_results[0]["depol_block_bool"][0])
 
@@ -167,7 +170,14 @@ def bpap_test(template_params, rheobase, out_dir="./"):
     bpap = BPAP(Cell.from_template_parameters(template_params))
     bpap.run(duration=1500, amplitude=amplitude)
     soma_amp, dend_amps, dend_dist, apic_amps, apic_dist = bpap.get_amplitudes_and_distances()
-    validated, notes = bpap.validate(soma_amp, dend_amps, dend_dist, apic_amps, apic_dist)
+    validated, notes = bpap.validate(
+        soma_amp,
+        dend_amps,
+        dend_dist,
+        apic_amps,
+        apic_dist,
+        validate_with_fit=False
+    )
     outpath_amp_dist = bpap.plot_amp_vs_dist(
         soma_amp,
         dend_amps,
@@ -177,7 +187,8 @@ def bpap_test(template_params, rheobase, out_dir="./"):
         show_figure=False,
         save_figure=True,
         output_dir=out_dir,
-        output_fname="bpap.pdf"
+        output_fname="bpap.pdf",
+        do_fit=False,
     )
     outpath_recordings = bpap.plot_recordings(
         show_figure=False,
@@ -194,11 +205,11 @@ def bpap_test(template_params, rheobase, out_dir="./"):
     }
 
 
-def ais_spiking_test(template_params, rheobase, out_dir, spike_threshold_voltage=-20.):
+def ais_spiking_test(template_params, rheobase, out_dir, spike_threshold_voltage=-40.):
     """AIS spiking test: axon should spike before soma."""
     name = "Simulatable Neuron AIS Spiking Validation"
     # Check that the cell has an axon
-    if len(Cell.from_template_parameters(template_params).axonal) == 0:
+    if len(Cell.from_template_parameters(template_params).axonal) == 0 or not section_exists("axon[0]"):
         return {
             "name": name,
             "passed": True,
@@ -216,8 +227,7 @@ def ais_spiking_test(template_params, rheobase, out_dir, spike_threshold_voltage
         0.5,
         add_hypamp=True,
         recording_locations=[("axon[0]", 0.5), ("soma[0]", 0.5)],
-        enable_spike_detection=True,
-        threshold_spike_detection=spike_threshold_voltage,
+        enable_spike_detection=False,
     )
     axon_recording, soma_recording = recordings
 
@@ -238,23 +248,37 @@ def ais_spiking_test(template_params, rheobase, out_dir, spike_threshold_voltage
         xlim=(IDRestTimings.PRE_DELAY.value, IDRestTimings.PRE_DELAY.value + 100),
     )
 
-    # Check for spiking
-    for recording in recordings:
-        if recording.spike is None or len(recording.spike) == 0:
-            return {
-                "name": name,
-                "passed": False,
-                "validation_details": "Validation failed: No spikes detected in one or both recordings.",
-                "figures": [outpath1, outpath2],
-            }
+    # Extract spike times using efel
+    traces = [
+        {
+            "T": axon_recording.time,
+            "V": axon_recording.voltage,
+            "stim_start": [IDRestTimings.PRE_DELAY.value],
+            "stim_end": [IDRestTimings.PRE_DELAY.value + IDRestTimings.DURATION.value],
+        },
+        {
+            "T": soma_recording.time,
+            "V": soma_recording.voltage,
+            "stim_start": [IDRestTimings.PRE_DELAY.value],
+            "stim_end": [IDRestTimings.PRE_DELAY.value + IDRestTimings.DURATION.value],
+        }
+    ]
+    efel.set_setting("Threshold", spike_threshold_voltage)
+    features_results = efel.get_feature_values(traces, ["peak_time"])
+    axon_spike_time = features_results[0]["peak_time"]
+    soma_spike_time = features_results[1]["peak_time"]
 
     # Check if axon spike happens before soma spike
-    passed = bool(axon_recording.spike[0] < soma_recording.spike[0])
-    notes = (
-        "Validation passed: Axon spikes before soma."
-        if passed
-        else "Validation failed: Axon does not spike before soma."
-    )
+    if axon_spike_time is None or soma_spike_time is None or len(axon_spike_time) == 0 or len(soma_spike_time) == 0:
+        passed = False
+        notes = "Validation failed: Could not determine spike times for axon or soma."
+    else:
+        passed = bool(axon_spike_time[0] <= soma_spike_time[0])
+        notes = (
+            "Validation passed: Axon spikes before soma."
+            if passed
+            else "Validation failed: Axon does not spike before soma."
+        )
     return {
         "name": name,
         "passed": passed,
@@ -337,7 +361,15 @@ def rin_test(rin):
     }
 
 
-def iv_test(template_params, rheobase, out_dir, spike_threshold_voltage=-20., n_processes=None):
+def iv_test(
+    template_params,
+    rheobase,
+    out_dir,
+    spike_threshold_voltage=-40.,
+    n_processes=None,
+    celsius=None,
+    v_init=None
+):
     """IV curve should have a positive slope."""
     name = "Simulatable Neuron IV Curve Validation"
     amps, steady_states = compute_plot_iv_curve(
@@ -350,6 +382,8 @@ def iv_test(template_params, rheobase, out_dir, spike_threshold_voltage=-20., n_
         output_dir=out_dir,
         output_fname="iv_curve.pdf",
         n_processes=n_processes,
+        celsius=celsius,
+        v_init=v_init,
     )
 
     outpath = pathlib.Path(out_dir) / "iv_curve.pdf"
@@ -377,12 +411,21 @@ def iv_test(template_params, rheobase, out_dir, spike_threshold_voltage=-20., n_
     }
 
 
-def fi_test(template_params, rheobase, out_dir, spike_threshold_voltage=-20., n_processes=None):
+def fi_test(
+    template_params,
+    rheobase,
+    out_dir,
+    spike_threshold_voltage=-40.,
+    n_processes=None,
+    celsius=None,
+    v_init=None,
+):
     """FI curve should have a positive slope."""
     name = "Simulatable Neuron FI Curve Validation"
     amps, spike_counts = compute_plot_fi_curve(
         Cell.from_template_parameters(template_params),
         rheobase=rheobase,
+        max_current=3. * rheobase,
         threshold_voltage=spike_threshold_voltage,
         nb_bins=5,
         show_figure=False,
@@ -390,6 +433,8 @@ def fi_test(template_params, rheobase, out_dir, spike_threshold_voltage=-20., n_
         output_dir=out_dir,
         output_fname="fi_curve.pdf",
         n_processes=n_processes,
+        celsius=celsius,
+        v_init=v_init,
     )
 
     outpath = pathlib.Path(out_dir) / "fi_curve.pdf"
@@ -449,7 +494,7 @@ def thumbnail_test(template_params, rheobase, out_dir):
 def run_validations(
     cell,
     cell_name,
-    spike_threshold_voltage=-20,
+    spike_threshold_voltage=-40,
     v_init=-80.0,
     celsius=34.0,
     output_dir="./memodel_validation_figures",
@@ -461,6 +506,7 @@ def run_validations(
         cell (Cell): The cell to validate.
         cell_name (str): The name of the cell, used in the output directory.
         spike_threshold_voltage (float): The voltage threshold for spike detection.
+            Default value in this module is -40 mV because some cells do not reach -20 mv.
         v_init: Initial membrane potential. Default is -80.0 mV.
         celsius: Temperature in Celsius. Default is 34.0.
         output_dir (str): The directory to save the validation figures.
@@ -472,9 +518,7 @@ def run_validations(
     out_dir.mkdir(parents=True, exist_ok=True)
 
     # set initial voltage and temperature
-    neuron_globals = NeuronGlobals.get_instance()
-    neuron_globals.temperature = celsius
-    neuron_globals.v_init = v_init
+    set_neuron_globals(temperature=celsius, v_init=v_init)
 
     # get me-model properties
     holding_current = cell.hypamp if cell.hypamp else 0.0
@@ -493,9 +537,10 @@ def run_validations(
     )
 
     logger.debug("Running validations...")
-    from bluecellulab.utils import NestedPool
     val_n_processes = n_processes if n_processes is not None else 7
-    with NestedPool(processes=val_n_processes) as pool:
+    with NestedPool(
+        processes=val_n_processes, initializer=set_neuron_globals, initargs=(celsius, v_init)
+    ) as pool:
         # Validation 1: Spiking Test
         spiking_test_result_future = pool.apply_async(
             spiking_test,
@@ -551,10 +596,14 @@ def run_validations(
 
     # IV and FI tests are outside of nestedpool, because they use multiprocessing internaly
     # Validation 8: IV Test
-    iv_test_result = iv_test(cell.template_params, rheobase, out_dir, spike_threshold_voltage, n_processes)
+    iv_test_result = iv_test(
+        cell.template_params, rheobase, out_dir, spike_threshold_voltage, n_processes, celsius, v_init
+    )
 
     # Validation 9: FI Test
-    fi_test_result = fi_test(cell.template_params, rheobase, out_dir, spike_threshold_voltage, n_processes)
+    fi_test_result = fi_test(
+        cell.template_params, rheobase, out_dir, spike_threshold_voltage, n_processes, celsius, v_init
+    )
 
     return {
         "memodel_properties": {

{bluecellulab-2.6.65 → bluecellulab-2.6.66}/bluecellulab.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bluecellulab
-Version: 2.6.65
+Version: 2.6.66
 Summary: Biologically detailed neural network simulations and analysis.
 Author: Blue Brain Project, EPFL
 License: Apache2.0