bmtool 0.7.0.6.4__py3-none-any.whl → 0.7.1.1__py3-none-any.whl

bmtool/singlecell.py

@@ -1,38 +1,40 @@
 import glob
-import os
 import json
+import os
 from typing import Tuple
-import numpy as np
+
 import matplotlib.pyplot as plt
-from scipy.optimize import curve_fit
 import neuron
-from neuron import h
+import numpy as np
 import pandas as pd
+from neuron import h
+from scipy.optimize import curve_fit
 
 
 def load_biophys1():
     """
     Load the Biophys1 template from BMTK if it hasn't been loaded yet.
-    
+
     This function checks if the Biophys1 object exists in NEURON's h namespace.
     If not, it loads the necessary HOC files for Allen Cell Types Database models.
-    
+
     Notes:
     ------
     This is primarily used for working with cell models from the Allen Cell Types Database.
     """
-    if not hasattr(h, 'Biophys1'):
+    if not hasattr(h, "Biophys1"):
         from bmtk import utils
+
         module_dir = os.path.dirname(os.path.abspath(utils.__file__))
-        hoc_file = os.path.join(module_dir, 'scripts', 'bionet', 'templates', 'Biophys1.hoc')
+        hoc_file = os.path.join(module_dir, "scripts", "bionet", "templates", "Biophys1.hoc")
         h.load_file("import3d.hoc")
         h.load_file(hoc_file)
 
 
-def load_allen_database_cells(morphology, dynamic_params, model_processing='aibs_perisomatic'):
+def load_allen_database_cells(morphology, dynamic_params, model_processing="aibs_perisomatic"):
     """
     Create a cell model from the Allen Cell Types Database.
-    
+
     Parameters:
     -----------
     morphology : str
@@ -42,34 +44,37 @@ def load_allen_database_cells(morphology, dynamic_params, model_processing='aibs
     model_processing : str, optional
         Model processing type from the AllenCellType database.
         Default is 'aibs_perisomatic'.
-    
+
     Returns:
     --------
     callable
         A function that, when called, creates and returns a NEURON cell object
         with the specified morphology and biophysical properties.
-        
+
     Notes:
     ------
     This function creates a closure that loads and returns a cell when called.
     The cell is created using the Allen Institute's modeling framework.
     """
     from bmtk.simulator.bionet.default_setters import cell_models
+
     load_biophys1()
     model_processing = getattr(cell_models, model_processing)
     with open(dynamic_params) as f:
         dynamics_params = json.load(f)
+
     def create_cell():
         hobj = h.Biophys1(morphology)
         hobj = model_processing(hobj, cell=None, dynamics_params=dynamics_params)
         return hobj
+
     return create_cell
 
 
-def get_target_site(cell, sec=('soma', 0), loc=0.5, site=''):
+def get_target_site(cell, sec=("soma", 0), loc=0.5, site=""):
     """
     Get a segment and its section from a cell model using flexible section specification.
-    
+
     Parameters:
     -----------
     cell : NEURON cell object
@@ -84,12 +89,12 @@ def get_target_site(cell, sec=('soma', 0), loc=0.5, site=''):
         Location along the section (0-1), default is 0.5 (middle of section).
     site : str, optional
         Name of the site for error messages (e.g., 'injection', 'recording').
-    
+
     Returns:
     --------
     tuple
         (segment, section) at the specified location
-        
+
     Raises:
     -------
     ValueError
@@ -98,9 +103,9 @@ def get_target_site(cell, sec=('soma', 0), loc=0.5, site=''):
     if isinstance(sec, str):
         sec = (sec, 0)
     elif isinstance(sec, int):
-        if not hasattr(cell, 'all'):
+        if not hasattr(cell, "all"):
             raise ValueError("Section list named 'all' does not exist in the template.")
-        sec = ('all', sec)
+        sec = ("all", sec)
     loc = float(loc)
     try:
         section = next(s for i, s in enumerate(getattr(cell, sec[0])) if i == sec[1])
@@ -117,11 +122,23 @@ def get_target_site(cell, sec=('soma', 0), loc=0.5, site=''):
 
 
 class CurrentClamp(object):
-    def __init__(self, template_name, post_init_function=None, record_sec='soma', record_loc=0.5, threshold=None,
-                 inj_sec='soma', inj_loc=0.5, inj_amp=100., inj_delay=100., inj_dur=1000., tstop=1000.):
+    def __init__(
+        self,
+        template_name,
+        post_init_function=None,
+        record_sec="soma",
+        record_loc=0.5,
+        threshold=None,
+        inj_sec="soma",
+        inj_loc=0.5,
+        inj_amp=100.0,
+        inj_delay=100.0,
+        inj_dur=1000.0,
+        tstop=1000.0,
+    ):
         """
         Initialize a current clamp simulation environment.
-        
+
         Parameters:
         -----------
         template_name : str or callable
@@ -153,7 +170,9 @@ class CurrentClamp(object):
             Total simulation time (ms). Default is 1000.0.
             Will be extended if necessary to include the full current injection.
         """
-        self.create_cell = getattr(h, template_name) if isinstance(template_name, str) else template_name
+        self.create_cell = (
+            getattr(h, template_name) if isinstance(template_name, str) else template_name
+        )
         self.record_sec = record_sec
         self.record_loc = record_loc
         self.inj_sec = inj_sec
@@ -161,14 +180,14 @@ class CurrentClamp(object):
         self.threshold = threshold
 
         self.tstop = max(tstop, inj_delay + inj_dur)
-        self.inj_delay = inj_delay # use x ms after start of inj to calculate r_in, etc
+        self.inj_delay = inj_delay  # use x ms after start of inj to calculate r_in, etc
         self.inj_dur = inj_dur
-        self.inj_amp = inj_amp * 1e-3 # pA to nA
+        self.inj_amp = inj_amp * 1e-3  # pA to nA
 
-        # sometimes people may put a hoc object in for the template name 
+        # sometimes people may put a hoc object in for the template name
         if callable(template_name):
             self.cell = template_name()
-        else:    
+        else:
             self.cell = self.create_cell()
         if post_init_function:
             eval(f"self.cell.{post_init_function}")
@@ -178,23 +197,23 @@ class CurrentClamp(object):
     def setup(self):
         """
         Set up the simulation environment for current clamp experiments.
-        
+
         This method:
         1. Creates the current clamp stimulus at the specified injection site
         2. Sets up voltage recording at the specified recording site
         3. Creates vectors to store time and voltage data
-        
+
         Notes:
         ------
         Sets self.cell_src as the current clamp object that can be accessed later.
         """
-        inj_seg, _ = get_target_site(self.cell, self.inj_sec, self.inj_loc, 'injection')
+        inj_seg, _ = get_target_site(self.cell, self.inj_sec, self.inj_loc, "injection")
         self.cell_src = h.IClamp(inj_seg)
         self.cell_src.delay = self.inj_delay
         self.cell_src.dur = self.inj_dur
         self.cell_src.amp = self.inj_amp
 
-        rec_seg, rec_sec = get_target_site(self.cell, self.record_sec, self.record_loc, 'recording')
+        rec_seg, rec_sec = get_target_site(self.cell, self.record_sec, self.record_loc, "recording")
         self.v_vec = h.Vector()
         self.v_vec.record(rec_seg._ref_v)
 
@@ -207,18 +226,18 @@ class CurrentClamp(object):
             self.tspk_vec = h.Vector()
             self.nc.record(self.tspk_vec)
 
-        print(f'Injection location: {inj_seg}')
-        print(f'Recording: {rec_seg}._ref_v')
+        print(f"Injection location: {inj_seg}")
+        print(f"Recording: {rec_seg}._ref_v")
 
     def execute(self) -> Tuple[list, list]:
         """
         Run the current clamp simulation and return recorded data.
-        
+
         This method:
         1. Sets up the simulation duration
         2. Initializes and runs the NEURON simulation
         3. Converts recorded vectors to Python lists
-        
+
         Returns:
         --------
         tuple
@@ -234,17 +253,25 @@ class CurrentClamp(object):
         if self.threshold is not None:
             self.nspks = len(self.tspk_vec)
             print()
-            print(f'Number of spikes: {self.nspks:d}')
+            print(f"Number of spikes: {self.nspks:d}")
             print()
         return self.t_vec.to_python(), self.v_vec.to_python()
 
 
 class Passive(CurrentClamp):
-    def __init__(self, template_name, inj_amp=-100., inj_delay=200., inj_dur=1000.,
-                 tstop=1200., method=None, **kwargs):
+    def __init__(
+        self,
+        template_name,
+        inj_amp=-100.0,
+        inj_delay=200.0,
+        inj_dur=1000.0,
+        tstop=1200.0,
+        method=None,
+        **kwargs,
+    ):
         """
         Initialize a passive membrane property simulation environment.
-        
+
         Parameters:
         -----------
         template_name : str or callable
@@ -264,39 +291,49 @@ class Passive(CurrentClamp):
             - 'exp': Fit a single exponential curve
             - 'exp2': Fit a double exponential curve
             Default is None, which uses 'simple' when calculations are performed.
-        **kwargs : 
+        **kwargs :
             Additional keyword arguments to pass to the parent CurrentClamp constructor.
-            
+
         Notes:
         ------
         This class is designed for measuring passive membrane properties including
         input resistance and membrane time constant.
-        
+
         Raises:
         -------
         AssertionError
             If inj_amp is zero (must be non-zero to measure passive properties).
         """
-        assert(inj_amp != 0)
-        super().__init__(template_name=template_name, tstop=tstop,
-                         inj_amp=inj_amp, inj_delay=inj_delay, inj_dur=inj_dur, **kwargs)
+        assert inj_amp != 0
+        super().__init__(
+            template_name=template_name,
+            tstop=tstop,
+            inj_amp=inj_amp,
+            inj_delay=inj_delay,
+            inj_dur=inj_dur,
+            **kwargs,
+        )
         self.inj_stop = inj_delay + inj_dur
         self.method = method
-        self.tau_methods = {'simple': self.tau_simple, 'exp2': self.tau_double_exponential, 'exp': self.tau_single_exponential}
+        self.tau_methods = {
+            "simple": self.tau_simple,
+            "exp2": self.tau_double_exponential,
+            "exp": self.tau_single_exponential,
+        }
 
     def tau_simple(self):
         """
         Calculate membrane time constant using the simple 0.632 criterion method.
-        
+
         This method calculates the membrane time constant by finding the time it takes
-        for the membrane potential to reach 63.2% (1-1/e) of its final value after 
+        for the membrane potential to reach 63.2% (1-1/e) of its final value after
         a step current injection.
-        
+
         Returns:
         --------
         callable
             A function that prints the calculation details when called.
-        
+
         Notes:
         ------
         Sets the following attributes:
@@ -308,19 +345,22 @@ class Passive(CurrentClamp):
 
         def print_calc():
             print()
-            print('Tau Calculation: time until 63.2% of dV')
-            print('v_rest + 0.632*(v_final-v_rest)')
-            print(f'{self.v_rest:.2f} + 0.632*({self.cell_v_final:.2f}-({self.v_rest:.2f})) = {v_t_const:.2f} (mV)')
-            print(f'Time where V = {v_t_const:.2f} (mV) is {self.v_rest_time + self.tau:.2f} (ms)')
-            print(f'{self.v_rest_time + self.tau:.2f} - {self.v_rest_time:g} = {self.tau:.2f} (ms)')
+            print("Tau Calculation: time until 63.2% of dV")
+            print("v_rest + 0.632*(v_final-v_rest)")
+            print(
+                f"{self.v_rest:.2f} + 0.632*({self.cell_v_final:.2f}-({self.v_rest:.2f})) = {v_t_const:.2f} (mV)"
+            )
+            print(f"Time where V = {v_t_const:.2f} (mV) is {self.v_rest_time + self.tau:.2f} (ms)")
+            print(f"{self.v_rest_time + self.tau:.2f} - {self.v_rest_time:g} = {self.tau:.2f} (ms)")
             print()
+
         return print_calc
 
     @staticmethod
     def single_exponential(t, a0, a, tau):
         """
         Single exponential function for fitting membrane potential response.
-        
+
         Parameters:
         -----------
         t : array-like
@@ -331,7 +371,7 @@ class Passive(CurrentClamp):
             Amplitude of the exponential component
         tau : float
             Time constant of the exponential decay
-            
+
         Returns:
         --------
         array-like
@@ -342,18 +382,18 @@ class Passive(CurrentClamp):
     def tau_single_exponential(self):
         """
         Calculate membrane time constant by fitting a single exponential curve.
-        
+
         This method:
         1. Identifies the peak response (for sag characterization)
         2. Falls back to simple method for initial estimate
         3. Fits a single exponential function to the membrane potential response
         4. Sets tau to the exponential time constant
-        
+
         Returns:
         --------
         callable
             A function that prints the calculation details when called.
-            
+
         Notes:
         ------
         Sets the following attributes:
@@ -376,33 +416,44 @@ class Passive(CurrentClamp):
 
         p0 = (self.v_diff, self.tau)  # initial estimate
         v0 = self.v_rest
+
         def fit_func(t, a, tau):
             return self.single_exponential(t, a0=v0 - a, a=a, tau=tau)
+
         bounds = ((-np.inf, 1e-3), np.inf)
-        popt, self.pcov = curve_fit(fit_func, self.t_vec_inj, self.v_vec_inj, p0=p0, bounds=bounds, maxfev=10000)
+        popt, self.pcov = curve_fit(
+            fit_func, self.t_vec_inj, self.v_vec_inj, p0=p0, bounds=bounds, maxfev=10000
+        )
         self.popt = np.insert(popt, 0, v0 - popt[0])
         self.tau = self.popt[2]
 
         def print_calc():
             print()
-            print('Tau Calculation: Fit a single exponential curve to the membrane potential response')
-            print('f(t) = a0 + a*exp(-t/tau)')
-            print(f'Fit parameters: (a0, a, tau) = ({self.popt[0]:.2f}, {self.popt[1]:.2f}, {self.popt[2]:.2f})')
-            print(f'Membrane time constant is determined from the exponential term: {self.tau:.2f} (ms)')
+            print(
+                "Tau Calculation: Fit a single exponential curve to the membrane potential response"
+            )
+            print("f(t) = a0 + a*exp(-t/tau)")
+            print(
+                f"Fit parameters: (a0, a, tau) = ({self.popt[0]:.2f}, {self.popt[1]:.2f}, {self.popt[2]:.2f})"
+            )
+            print(
+                f"Membrane time constant is determined from the exponential term: {self.tau:.2f} (ms)"
+            )
             print()
-            print('Sag potential: v_sag = v_peak - v_final = %.2f (mV)' % self.v_sag)
-            print('Normalized sag potential: v_sag / (v_peak - v_rest) = %.3f' % self.sag_norm)
+            print("Sag potential: v_sag = v_peak - v_final = %.2f (mV)" % self.v_sag)
+            print("Normalized sag potential: v_sag / (v_peak - v_rest) = %.3f" % self.sag_norm)
             print()
+
         return print_calc
 
     @staticmethod
     def double_exponential(t, a0, a1, a2, tau1, tau2):
         """
         Double exponential function for fitting membrane potential response.
-        
+
         This function is particularly useful for modeling cells with sag responses,
         where the membrane potential shows two distinct time constants.
-        
+
         Parameters:
         -----------
         t : array-like
@@ -417,7 +468,7 @@ class Passive(CurrentClamp):
             Time constant of the first exponential component
         tau2 : float
             Time constant of the second exponential component
-            
+
         Returns:
         --------
         array-like
@@ -428,15 +479,15 @@ class Passive(CurrentClamp):
     def tau_double_exponential(self):
         """
         Calculate membrane time constant by fitting a double exponential curve.
-        
+
         This method is useful for cells with sag responses that cannot be
         fitted well with a single exponential.
-        
+
         Returns:
         --------
         callable
             A function that prints the calculation details when called.
-            
+
         Notes:
         ------
         Sets the following attributes:
@@ -458,30 +509,43 @@ class Passive(CurrentClamp):
         self.tau_simple()
         p0 = (self.v_sag, -self.v_max_diff, self.t_peak, self.tau)  # initial estimate
         v0 = self.v_rest
+
         def fit_func(t, a1, a2, tau1, tau2):
             return self.double_exponential(t, v0 - a1 - a2, a1, a2, tau1, tau2)
+
         bounds = ((-np.inf, -np.inf, 1e-3, 1e-3), np.inf)
-        popt, self.pcov = curve_fit(fit_func, self.t_vec_inj, self.v_vec_inj, p0=p0, bounds=bounds, maxfev=10000)
+        popt, self.pcov = curve_fit(
+            fit_func, self.t_vec_inj, self.v_vec_inj, p0=p0, bounds=bounds, maxfev=10000
+        )
         self.popt = np.insert(popt, 0, v0 - sum(popt[:2]))
         self.tau = max(self.popt[-2:])
 
         def print_calc():
             print()
-            print('Tau Calculation: Fit a double exponential curve to the membrane potential response')
-            print('f(t) = a0 + a1*exp(-t/tau1) + a2*exp(-t/tau2)')
-            print('Constrained by initial value: f(0) = a0 + a1 + a2 = v_rest')
-            print('Fit parameters: (a0, a1, a2, tau1, tau2) = (' + ', '.join(f'{x:.2f}' for x in self.popt) + ')')
-            print(f'Membrane time constant is determined from the slowest exponential term: {self.tau:.2f} (ms)')
+            print(
+                "Tau Calculation: Fit a double exponential curve to the membrane potential response"
+            )
+            print("f(t) = a0 + a1*exp(-t/tau1) + a2*exp(-t/tau2)")
+            print("Constrained by initial value: f(0) = a0 + a1 + a2 = v_rest")
+            print(
+                "Fit parameters: (a0, a1, a2, tau1, tau2) = ("
+                + ", ".join(f"{x:.2f}" for x in self.popt)
+                + ")"
+            )
+            print(
+                f"Membrane time constant is determined from the slowest exponential term: {self.tau:.2f} (ms)"
+            )
             print()
-            print('Sag potential: v_sag = v_peak - v_final = %.2f (mV)' % self.v_sag)
-            print('Normalized sag potential: v_sag / (v_peak - v_rest) = %.3f' % self.sag_norm)
+            print("Sag potential: v_sag = v_peak - v_final = %.2f (mV)" % self.v_sag)
+            print("Normalized sag potential: v_sag / (v_peak - v_rest) = %.3f" % self.sag_norm)
             print()
+
         return print_calc
 
     def double_exponential_fit(self):
         """
         Get the double exponential fit values for plotting.
-        
+
         Returns:
         --------
         tuple
@@ -492,11 +556,11 @@ class Passive(CurrentClamp):
         t_vec = self.v_rest_time + self.t_vec_inj
         v_fit = self.double_exponential(self.t_vec_inj, *self.popt)
         return t_vec, v_fit
-    
+
     def single_exponential_fit(self):
         """
         Get the single exponential fit values for plotting.
-        
+
         Returns:
         --------
         tuple
@@ -511,19 +575,19 @@ class Passive(CurrentClamp):
     def execute(self):
         """
         Run the simulation and calculate passive membrane properties.
-        
+
         This method:
         1. Runs the NEURON simulation
         2. Extracts membrane potential at rest and steady-state
         3. Calculates input resistance from the step response
         4. Calculates membrane time constant using the specified method
         5. Prints detailed calculations for educational purposes
-        
+
         Returns:
         --------
         tuple
             (time_vector, voltage_vector) from the simulation
-        
+
         Notes:
         ------
         Sets several attributes including:
@@ -553,28 +617,42 @@ class Passive(CurrentClamp):
         print_calc = self.tau_methods.get(self.method, self.tau_simple)()
 
         print()
-        print(f'V Rest: {self.v_rest:.2f} (mV)')
-        print(f'Resistance: {self.r_in:.2f} (MOhms)')
-        print(f'Membrane time constant: {self.tau:.2f} (ms)')
+        print(f"V Rest: {self.v_rest:.2f} (mV)")
+        print(f"Resistance: {self.r_in:.2f} (MOhms)")
+        print(f"Membrane time constant: {self.tau:.2f} (ms)")
         print()
-        print(f'V_rest Calculation: Voltage taken at time {self.v_rest_time:.1f} (ms) is')
-        print(f'{self.v_rest:.2f} (mV)')
+        print(f"V_rest Calculation: Voltage taken at time {self.v_rest_time:.1f} (ms) is")
+        print(f"{self.v_rest:.2f} (mV)")
         print()
-        print('R_in Calculation: dV/dI = (v_final-v_rest)/(i_final-i_start)')
-        print(f'({self.cell_v_final:.2f} - ({self.v_rest:.2f})) / ({self.inj_amp:g} - 0)')
-        print(f'{np.sign(self.inj_amp) * self.v_diff:.2f} (mV) / {np.abs(self.inj_amp)} (nA) = {self.r_in:.2f} (MOhms)')
+        print("R_in Calculation: dV/dI = (v_final-v_rest)/(i_final-i_start)")
+        print(f"({self.cell_v_final:.2f} - ({self.v_rest:.2f})) / ({self.inj_amp:g} - 0)")
+        print(
+            f"{np.sign(self.inj_amp) * self.v_diff:.2f} (mV) / {np.abs(self.inj_amp)} (nA) = {self.r_in:.2f} (MOhms)"
+        )
         print_calc()
 
         return self.t_vec.to_python(), self.v_vec.to_python()
 
 
 class FI(object):
-    def __init__(self, template_name, post_init_function=None,
-                 i_start=0., i_stop=1050., i_increment=100., tstart=50., tdur=1000., threshold=0.,
-                 record_sec='soma', record_loc=0.5, inj_sec='soma', inj_loc=0.5):
+    def __init__(
+        self,
+        template_name,
+        post_init_function=None,
+        i_start=0.0,
+        i_stop=1050.0,
+        i_increment=100.0,
+        tstart=50.0,
+        tdur=1000.0,
+        threshold=0.0,
+        record_sec="soma",
+        record_loc=0.5,
+        inj_sec="soma",
+        inj_loc=0.5,
+    ):
         """
         Initialize a frequency-current (F-I) curve simulation environment.
-        
+
         Parameters:
         -----------
         template_name : str or callable
@@ -602,16 +680,18 @@ class FI(object):
             Section for current injection. Same format as record_sec. Default is 'soma'.
         inj_loc : float, optional
             Location (0-1) within section for current injection. Default is 0.5.
-            
+
         Notes:
         ------
         This class creates multiple instances of the cell model, one for each
         current amplitude to be tested, allowing all simulations to be run
         in a single call to NEURON's run() function.
         """
-        self.create_cell = getattr(h, template_name) if isinstance(template_name, str) else template_name
+        self.create_cell = (
+            getattr(h, template_name) if isinstance(template_name, str) else template_name
+        )
         self.post_init_function = post_init_function
-        self.i_start = i_start * 1e-3 # pA to nA
+        self.i_start = i_start * 1e-3  # pA to nA
         self.i_stop = i_stop * 1e-3
         self.i_increment = i_increment * 1e-3
         self.tstart = tstart
@@ -644,26 +724,26 @@ class FI(object):
     def setup(self):
         """
         Set up the simulation environment for frequency-current (F-I) analysis.
-        
+
         For each current amplitude to be tested, this method:
         1. Creates a current source at the injection site
         2. Sets up spike detection at the recording site
         3. Creates vectors to record spike times
-        
+
         Notes:
         ------
         This preparation allows multiple simulations to be run with different
         current amplitudes in a single call to h.run().
         """
         for cell, amp in zip(self.cells, self.amps):
-            inj_seg, _ = get_target_site(cell, self.inj_sec, self.inj_loc, 'injection')
+            inj_seg, _ = get_target_site(cell, self.inj_sec, self.inj_loc, "injection")
             src = h.IClamp(inj_seg)
             src.delay = self.tstart
             src.dur = self.tdur
             src.amp = amp
             self.sources.append(src)
 
-            rec_seg, rec_sec = get_target_site(cell, self.record_sec, self.record_loc, 'recording')
+            rec_seg, rec_sec = get_target_site(cell, self.record_sec, self.record_loc, "recording")
             nc = h.NetCon(rec_seg._ref_v, None, sec=rec_sec)
             nc.threshold = self.threshold
             spvec = h.Vector()
@@ -671,18 +751,18 @@ class FI(object):
             self.ncs.append(nc)
             self.tspk_vecs.append(spvec)
 
-        print(f'Injection location: {inj_seg}')
-        print(f'Recording: {rec_seg}._ref_v')
+        print(f"Injection location: {inj_seg}")
+        print(f"Recording: {rec_seg}._ref_v")
 
     def execute(self):
         """
         Run the simulation and count spikes for each current amplitude.
-        
+
         This method:
         1. Initializes and runs a single NEURON simulation that evaluates all current amplitudes
         2. Counts spikes for each current amplitude
         3. Prints a summary of results in tabular format
-        
+
         Returns:
         --------
         tuple
@@ -699,22 +779,32 @@ class FI(object):
         print()
         print("Results")
         # lets make a df so the results line up nice
-        data = {'Injection (nA):':self.amps,'number of spikes':self.nspks}
+        data = {"Injection (nA):": self.amps, "number of spikes": self.nspks}
         df = pd.DataFrame(data)
         print(df)
-        #print(f'Injection (nA): ' + ', '.join(f'{x:g}' for x in self.amps))
-        #print(f'Number of spikes: ' + ', '.join(f'{x:d}' for x in self.nspks))
+        # print(f'Injection (nA): ' + ', '.join(f'{x:g}' for x in self.amps))
+        # print(f'Number of spikes: ' + ', '.join(f'{x:d}' for x in self.nspks))
         print()
 
         return self.amps, self.nspks
 
 
 class ZAP(CurrentClamp):
-    def __init__(self, template_name, inj_amp=100., inj_delay=200., inj_dur=15000.,
-                 tstop=15500., fstart=0., fend=15., chirp_type=None, **kwargs):
+    def __init__(
+        self,
+        template_name,
+        inj_amp=100.0,
+        inj_delay=200.0,
+        inj_dur=15000.0,
+        tstop=15500.0,
+        fstart=0.0,
+        fend=15.0,
+        chirp_type=None,
+        **kwargs,
+    ):
         """
         Initialize a ZAP (impedance amplitude profile) simulation environment.
-        
+
         Parameters:
         -----------
         template_name : str or callable
@@ -736,35 +826,41 @@ class ZAP(CurrentClamp):
             Type of chirp current determining how frequency increases over time:
             - 'linear': Linear increase in frequency (default if None)
             - 'exponential': Exponential increase in frequency
-        **kwargs : 
+        **kwargs :
             Additional keyword arguments to pass to the parent CurrentClamp constructor.
-            
+
         Notes:
         ------
         This class is designed for measuring the frequency-dependent impedance profile
         of a neuron using a chirp current that sweeps through frequencies.
-        
+
         Raises:
         -------
         AssertionError
             - If inj_amp is zero
             - If chirp_type is 'exponential' and either fstart or fend is <= 0
         """
-        assert(inj_amp != 0)
-        super().__init__(template_name=template_name, tstop=tstop,
-                         inj_amp=inj_amp, inj_delay=inj_delay, inj_dur=inj_dur, **kwargs)
+        assert inj_amp != 0
+        super().__init__(
+            template_name=template_name,
+            tstop=tstop,
+            inj_amp=inj_amp,
+            inj_delay=inj_delay,
+            inj_dur=inj_dur,
+            **kwargs,
+        )
         self.inj_stop = inj_delay + inj_dur
         self.fstart = fstart
         self.fend = fend
         self.chirp_type = chirp_type
-        self.chirp_func = {'linear': self.linear_chirp, 'exponential': self.exponential_chirp}
-        if chirp_type=='exponential':
-            assert(fstart > 0 and fend > 0)
+        self.chirp_func = {"linear": self.linear_chirp, "exponential": self.exponential_chirp}
+        if chirp_type == "exponential":
+            assert fstart > 0 and fend > 0
 
     def linear_chirp(self, t, f0, f1):
         """
         Generate a chirp current with linearly increasing frequency.
-        
+
         Parameters:
         -----------
         t : ndarray
@@ -773,11 +869,11 @@ class ZAP(CurrentClamp):
             Start frequency (kHz)
         f1 : float
             End frequency (kHz)
-            
+
         Returns:
         --------
         ndarray
-            Current values with amplitude self.inj_amp and frequency 
+            Current values with amplitude self.inj_amp and frequency
             increasing linearly from f0 to f1 Hz over time t
         """
         return self.inj_amp * np.sin(np.pi * (2 * f0 + (f1 - f0) / t[-1] * t) * t)
@@ -785,7 +881,7 @@ class ZAP(CurrentClamp):
     def exponential_chirp(self, t, f0, f1):
         """
         Generate a chirp current with exponentially increasing frequency.
-        
+
         Parameters:
         -----------
         t : ndarray
@@ -794,13 +890,13 @@ class ZAP(CurrentClamp):
             Start frequency (kHz), must be > 0
         f1 : float
             End frequency (kHz), must be > 0
-            
+
         Returns:
         --------
         ndarray
-            Current values with amplitude self.inj_amp and frequency 
+            Current values with amplitude self.inj_amp and frequency
             increasing exponentially from f0 to f1 Hz over time t
-        
+
         Notes:
         ------
         For exponential chirp, both f0 and f1 must be positive.
@@ -811,12 +907,12 @@ class ZAP(CurrentClamp):
     def zap_current(self):
         """
         Create a frequency-modulated (chirp) current for probing impedance.
-        
+
         This method:
         1. Sets up time vectors for the simulation and current injection
         2. Creates a chirp current based on the specified parameters (linear or exponential)
         3. Prepares the current vector for NEURON playback
-        
+
         Notes:
         ------
         The chirp current increases in frequency from fstart to fend Hz over the duration
@@ -828,13 +924,13 @@ class ZAP(CurrentClamp):
         self.index_v_final = int(self.inj_stop / dt)
 
         t = np.arange(int(self.tstop / dt) + 1) * dt
-        t_inj = t[:self.index_v_final - self.index_v_rest + 1]
-        f0 = self.fstart * 1e-3 # Hz to 1/ms
+        t_inj = t[: self.index_v_final - self.index_v_rest + 1]
+        f0 = self.fstart * 1e-3  # Hz to 1/ms
         f1 = self.fend * 1e-3
         chirp_func = self.chirp_func.get(self.chirp_type, self.linear_chirp)
         self.zap_vec_inj = chirp_func(t_inj, f0, f1)
         i_inj = np.zeros_like(t)
-        i_inj[self.index_v_rest:self.index_v_final + 1] = self.zap_vec_inj
+        i_inj[self.index_v_rest : self.index_v_final + 1] = self.zap_vec_inj
 
         self.zap_vec = h.Vector()
         self.zap_vec.from_python(i_inj)
@@ -843,50 +939,52 @@ class ZAP(CurrentClamp):
     def get_impedance(self, smooth=1):
         """
         Calculate and extract the frequency-dependent impedance profile.
-        
+
         This method:
         1. Filters the impedance to the frequency range of interest
         2. Optionally applies smoothing to reduce noise
         3. Identifies the resonant frequency (peak impedance)
-        
+
         Parameters:
         -----------
         smooth : int, optional
             Window size for smoothing the impedance. Default is 1 (no smoothing).
-            
+
         Returns:
         --------
         tuple
             (frequencies, impedance_values) in the range of interest
-            
+
         Notes:
         ------
         Sets self.peak_freq to the resonant frequency (frequency of maximum impedance).
         """
-        f_idx = (self.freq > min(self.fstart, self.fend)) & (self.freq < max(self.fstart, self.fend))
+        f_idx = (self.freq > min(self.fstart, self.fend)) & (
+            self.freq < max(self.fstart, self.fend)
+        )
         impedance = self.impedance
         if smooth > 1:
-            impedance = np.convolve(impedance, np.ones(smooth) / smooth, mode='same')
+            impedance = np.convolve(impedance, np.ones(smooth) / smooth, mode="same")
         freq, impedance = self.freq[f_idx], impedance[f_idx]
         self.peak_freq = freq[np.argmax(impedance)]
-        print(f'Resonant Peak Frequency: {self.peak_freq:.3g} (Hz)')
+        print(f"Resonant Peak Frequency: {self.peak_freq:.3g} (Hz)")
         return freq, impedance
 
     def execute(self) -> Tuple[list, list]:
         """
         Run the ZAP simulation and calculate the impedance profile.
-        
+
         This method:
         1. Sets up the chirp current
         2. Runs the NEURON simulation
         3. Calculates the impedance using FFT
         4. Prints a summary of the frequency range and analysis method
-        
+
         Returns:
         --------
         tuple
             (time_vector, voltage_vector) from the simulation
-            
+
         Notes:
         ------
         Sets several attributes including:
@@ -909,21 +1007,26 @@ class ZAP(CurrentClamp):
         self.t_vec_inj = np.array(self.t_vec)[t_idx] - self.v_rest_time
 
         self.cell_v_amp_max = np.abs(self.v_vec_inj).max()
-        self.Z = np.fft.rfft(self.v_vec_inj) / np.fft.rfft(self.zap_vec_inj) # MOhms
-        self.freq = np.fft.rfftfreq(self.zap_vec_inj.size, d=self.dt * 1e-3) # ms to sec
+        self.Z = np.fft.rfft(self.v_vec_inj) / np.fft.rfft(self.zap_vec_inj)  # MOhms
+        self.freq = np.fft.rfftfreq(self.zap_vec_inj.size, d=self.dt * 1e-3)  # ms to sec
         self.impedance = np.abs(self.Z)
 
         print()
-        print('Chirp current injection with frequency changing from '
-              f'{self.fstart:g} to {self.fend:g} Hz over {self.inj_dur * 1e-3:g} seconds')
-        print('Impedance is calculated as the ratio of FFT amplitude '
-              'of membrane voltage to FFT amplitude of chirp current')
+        print(
+            "Chirp current injection with frequency changing from "
+            f"{self.fstart:g} to {self.fend:g} Hz over {self.inj_dur * 1e-3:g} seconds"
+        )
+        print(
+            "Impedance is calculated as the ratio of FFT amplitude "
+            "of membrane voltage to FFT amplitude of chirp current"
+        )
         print()
         return self.t_vec.to_python(), self.v_vec.to_python()
 
 
-class Profiler():
+class Profiler:
     """All in one single cell profiler"""
+
     def __init__(self, template_dir: str = None, mechanism_dir: str = None, dt=None):
         self.template_dir = None
         self.mechanism_dir = None
@@ -942,8 +1045,12 @@ class Profiler():
             h.steps_per_ms = 1 / h.dt
 
     def load_templates(self, hoc_template_file=None):
-        if self.templates is None: # Can really only do this once
-            if self.mechanism_dir != './' and self.mechanism_dir != '.' and self.mechanism_dir != '././':
+        if self.templates is None:  # Can really only do this once
+            if (
+                self.mechanism_dir != "./"
+                and self.mechanism_dir != "."
+                and self.mechanism_dir != "././"
+            ):
                 neuron.load_mechanisms(self.mechanism_dir)
             h_base = set(dir(h))
 
@@ -966,9 +1073,16 @@ class Profiler():
 
         return self.templates
 
-    def passive_properties(self, template_name: str, post_init_function: str = None,
-                           record_sec: str = 'soma', inj_sec: str = 'soma', plot: bool = True,
-                           method=None, **kwargs) -> Tuple[list, list]:
+    def passive_properties(
+        self,
+        template_name: str,
+        post_init_function: str = None,
+        record_sec: str = "soma",
+        inj_sec: str = "soma",
+        plot: bool = True,
+        method=None,
+        **kwargs,
+    ) -> Tuple[list, list]:
         """
         Calculates passive properties for the specified cell template_name
 
@@ -991,45 +1105,67 @@ class Profiler():
             extra key word arguments for Passive()
 
         Returns time (ms), membrane voltage (mV)
-    """
-        passive = Passive(template_name, post_init_function=post_init_function,
-                          record_sec=record_sec, inj_sec=inj_sec, method=method, **kwargs)
+        """
+        passive = Passive(
+            template_name,
+            post_init_function=post_init_function,
+            record_sec=record_sec,
+            inj_sec=inj_sec,
+            method=method,
+            **kwargs,
+        )
         time, amp = passive.execute()
 
         if plot:
             plt.figure()
             plt.plot(time, amp)
-            if passive.method == 'exp2':
-                plt.plot(*passive.double_exponential_fit(), 'r:', label='double exponential fit')
+            if passive.method == "exp2":
+                plt.plot(*passive.double_exponential_fit(), "r:", label="double exponential fit")
                 plt.legend()
             plt.title("Passive Cell Current Injection")
-            plt.xlabel('Time (ms)')
-            plt.ylabel('Membrane Potential (mV)')
+            plt.xlabel("Time (ms)")
+            plt.ylabel("Membrane Potential (mV)")
             plt.show()
 
         return time, amp
 
-    def current_injection(self, template_name: str, post_init_function: str = None,
-                          record_sec: str = 'soma', inj_sec: str = 'soma', plot: bool = True,
-                          **kwargs) -> Tuple[list, list]:
-
-        ccl = CurrentClamp(template_name, post_init_function=post_init_function,
-                           record_sec=record_sec, inj_sec=inj_sec, **kwargs)
+    def current_injection(
+        self,
+        template_name: str,
+        post_init_function: str = None,
+        record_sec: str = "soma",
+        inj_sec: str = "soma",
+        plot: bool = True,
+        **kwargs,
+    ) -> Tuple[list, list]:
+        ccl = CurrentClamp(
+            template_name,
+            post_init_function=post_init_function,
+            record_sec=record_sec,
+            inj_sec=inj_sec,
+            **kwargs,
+        )
         time, amp = ccl.execute()
 
         if plot:
             plt.figure()
             plt.plot(time, amp)
             plt.title("Current Injection")
-            plt.xlabel('Time (ms)')
-            plt.ylabel('Membrane Potential (mV)')
+            plt.xlabel("Time (ms)")
+            plt.ylabel("Membrane Potential (mV)")
             plt.show()
 
         return time, amp
 
-    def fi_curve(self, template_name: str, post_init_function: str = None,
-                 record_sec: str = 'soma', inj_sec: str = 'soma', plot: bool = True,
-                 **kwargs) -> Tuple[list, list]:
+    def fi_curve(
+        self,
+        template_name: str,
+        post_init_function: str = None,
+        record_sec: str = "soma",
+        inj_sec: str = "soma",
+        plot: bool = True,
+        **kwargs,
+    ) -> Tuple[list, list]:
         """
         Calculates an FI curve for the specified cell template_name
 
@@ -1050,23 +1186,36 @@ class Profiler():
         Returns the injection amplitudes (nA) used, number of spikes per amplitude supplied
             list(amps), list(# of spikes)
         """
-        fi = FI(template_name, post_init_function=post_init_function,
-                record_sec=record_sec, inj_sec=inj_sec, **kwargs)
+        fi = FI(
+            template_name,
+            post_init_function=post_init_function,
+            record_sec=record_sec,
+            inj_sec=inj_sec,
+            **kwargs,
+        )
         amp, nspk = fi.execute()
 
         if plot:
             plt.figure()
             plt.plot(amp, nspk)
             plt.title("FI Curve")
-            plt.xlabel('Injection (nA)')
-            plt.ylabel('# Spikes')
+            plt.xlabel("Injection (nA)")
+            plt.ylabel("# Spikes")
             plt.show()
 
         return amp, nspk
 
-    def impedance_amplitude_profile(self, template_name: str, post_init_function: str = None,
-                                    record_sec: str = 'soma', inj_sec: str = 'soma', plot: bool = True,
-                                    chirp_type=None, smooth: int = 9, **kwargs) -> Tuple[list, list]:
+    def impedance_amplitude_profile(
+        self,
+        template_name: str,
+        post_init_function: str = None,
+        record_sec: str = "soma",
+        inj_sec: str = "soma",
+        plot: bool = True,
+        chirp_type=None,
+        smooth: int = 9,
+        **kwargs,
+    ) -> Tuple[list, list]:
         """
         chirp_type: str
             Type of chirp current (see ZAP)
@@ -1075,32 +1224,39 @@ class Profiler():
         **kwargs:
             extra key word arguments for ZAP()
         """
-        zap = ZAP(template_name, post_init_function=post_init_function,
-                  record_sec=record_sec, inj_sec=inj_sec, chirp_type=chirp_type, **kwargs)
+        zap = ZAP(
+            template_name,
+            post_init_function=post_init_function,
+            record_sec=record_sec,
+            inj_sec=inj_sec,
+            chirp_type=chirp_type,
+            **kwargs,
+        )
         time, amp = zap.execute()
 
         if plot:
             plt.figure()
             plt.plot(time, amp)
             plt.title("ZAP Response")
-            plt.xlabel('Time (ms)')
-            plt.ylabel('Membrane Potential (mV)')
+            plt.xlabel("Time (ms)")
+            plt.ylabel("Membrane Potential (mV)")
 
             plt.figure()
             plt.plot(time, zap.zap_vec)
-            plt.title('ZAP Current')
-            plt.xlabel('Time (ms)')
-            plt.ylabel('Current Injection (nA)')
+            plt.title("ZAP Current")
+            plt.xlabel("Time (ms)")
+            plt.ylabel("Current Injection (nA)")
 
             plt.figure()
             plt.plot(*zap.get_impedance(smooth=smooth))
-            plt.title('Impedance Amplitude Profile')
-            plt.xlabel('Frequency (Hz)')
-            plt.ylabel('Impedance (MOhms)')
+            plt.title("Impedance Amplitude Profile")
+            plt.xlabel("Frequency (Hz)")
+            plt.ylabel("Impedance (MOhms)")
             plt.show()
 
         return time, amp
 
+
 # Example usage
 # profiler = Profiler('./temp/templates', './temp/mechanisms/modfiles')
 # profiler.passive_properties('Cell_Cf')
@@ -1108,8 +1264,14 @@ class Profiler():
 # profiler.current_injection('Cell_Cf', post_init_function="insert_mechs(123)", inj_amp=300, inj_delay=100)
 
 
-def run_and_plot(sim, title=None, xlabel='Time (ms)', ylabel='Membrane Potential (mV)',
-                 plot=True, plot_injection_only=False):
+def run_and_plot(
+    sim,
+    title=None,
+    xlabel="Time (ms)",
+    ylabel="Membrane Potential (mV)",
+    plot=True,
+    plot_injection_only=False,
+):
     """Helper function for running simulation and plot
     sim: instance of the simulation class in this module
     title, xlabel, ylabel: plot labels