dendrotweaks 0.4.5__py3-none-any.whl → 0.4.6__py3-none-any.whl

dendrotweaks/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.4.5"
+__version__ = "0.4.6"
 
 from dendrotweaks.model import Model
 from dendrotweaks.simulators import NeuronSimulator

dendrotweaks/analysis/ephys_analysis.py

@@ -257,7 +257,7 @@ def plot_somatic_spikes(data, ax=None, show_metrics=False):
             ax.plot([t - 10*w/2, t + 10*w/2], [v - a/2, v - a/2], color='lawngreen', linestyle='--')
 
 
-def calculate_fI_curve(model, duration=1000, min_amp=0, max_amp=1, n=5, **kwargs):
+def calculate_fI_curve(model, duration=1000, prerun_time=0, min_amp=0, max_amp=1, n=5, **kwargs):
     """
     Calculate the frequency-current (f-I) curve of the neuron model.
 
@@ -289,7 +289,7 @@ def calculate_fI_curve(model, duration=1000, min_amp=0, max_amp=1, n=5, **kwargs
     vs = {}
     for amp in amps:
         iclamp.amp = amp
-        model.simulator.run(duration)
+        model.run(duration=duration, prerun_time=prerun_time)
         spike_data = detect_somatic_spikes(model, **kwargs)
         n_spikes = len(spike_data['spike_times'])
         rate = n_spikes / iclamp.dur * 1000
@@ -304,7 +304,22 @@ def calculate_fI_curve(model, duration=1000, min_amp=0, max_amp=1, n=5, **kwargs
     }
 
 
-def plot_fI_curve(data, ax=None, **kwargs):
+def plot_fI_curve(data, ax=None, vshift=200, **kwargs):
+    """
+    Plot the f-I curve and somatic voltage traces.
+
+    Parameters
+    ----------
+    data : dict
+        A dictionary containing the current amplitudes, firing rates, and voltages.
+        Can be obtained from `calculate_fI_curve`.
+    ax : matplotlib.axes.Axes, optional
+        The axes to plot on. If two axes are provided, the first will show the somatic voltage traces and the second will show the f-I curve.
+        If a single axis is provided, it will show the f-I curve only.
+        If None, a new figure will be created.
+    vshift : int, optional
+        The vertical shift for the somatic voltage traces. Default is 200.
+    """
 
     if ax is None:
         _, ax = plt.subplots(1, 2, figsize=(5, 5))
@@ -314,25 +329,20 @@ def plot_fI_curve(data, ax=None, **kwargs):
     vs = data['voltages']
     t = data['time']
 
-    for i, (amp, v) in enumerate(vs.items()):
-        ax[0].plot(t, np.array(v) - i*200, label=f'{amp} nA')
-    # ax[0].set_xlabel('Time (ms)')
-    # ax[0].set_ylabel('Voltage (mV)')
-    ax[0].set_title('Somatic spikes')
-    ax[0].legend()
-    ax[0].spines['top'].set_visible(False)
-    ax[0].spines['right'].set_visible(False)
-    ax[0].spines['bottom'].set_visible(False)
-    ax[0].spines['left'].set_visible(False)
-    ax[0].set_xticks([])
-    ax[0].set_yticks([])
+    if isinstance(ax, (list, np.ndarray)):        
+        for i, (amp, v) in enumerate(vs.items()):
+            ax[0].plot(t, np.array(v) - i*vshift, label=f'{amp} nA')
+        ax[0].set_title('Somatic spikes')
+        ax[0].legend()
+        ax[0].axis('off')
+        ax = ax[1]
     
-    ax[1].plot(amps, rates, color='gray', zorder=0)
+    ax.plot(amps, rates, color='gray', zorder=0)
     for a, r in zip(amps, rates):
-        ax[1].scatter(a, r, s=50, edgecolor='white')
-    ax[1].set_xlabel('Current (nA)')
-    ax[1].set_ylabel('Firing rate (Hz)')
-    ax[1].set_title('f-I curve')
+        ax.plot(a, r, 'o', zorder=1)
+    ax.set_xlabel('Current (nA)')
+    ax.set_ylabel('Firing rate (Hz)')
+    ax.set_title('f-I curve')
 
 
 # =============================================================================
@@ -416,7 +426,7 @@ def plot_voltage_attenuation(data, ax=None):
     ax.set_ylabel('Voltage attenuation')
     ax.set_title('Voltage attenuation')
 
-def calculate_dendritic_nonlinearity(model, duration=1000, max_weight=None, n=None):
+def calculate_dendritic_nonlinearity(model, duration=1000, prerun_time=0, max_weight=None, n=None):
     """Calculate the expected and observed voltage changes for a range of synaptic weights.
 
     Parameters
@@ -460,7 +470,7 @@ def calculate_dendritic_nonlinearity(model, duration=1000, max_weight=None, n=No
 
     for w in weights:
         population.update_input_params(weight=w)
-        model.simulator.run(duration)
+        model.run(duration=duration, prerun_time=prerun_time)
         v = np.array(model.simulator.recordings['v'][seg])
         v_start = v[start_ts]
         v_max = np.max(v[start_ts:])
@@ -479,7 +489,22 @@ def calculate_dendritic_nonlinearity(model, duration=1000, max_weight=None, n=No
     }
 
 
-def plot_dendritic_nonlinearity(data, ax=None, **kwargs):
+def plot_dendritic_nonlinearity(data, ax=None, vshift=200, **kwargs):
+    """
+    Plot the dendritic nonlinearity based on expected and observed voltage changes.
+
+    Parameters
+    ----------
+    data : dict
+        A dictionary containing the expected and observed voltage changes.
+        Can be obtained from `calculate_dendritic_nonlinearity`.
+    ax : matplotlib.axes.Axes, optional
+        The axes to plot on. If two axes are provided, the first will show the voltage traces and the second will show the dendritic nonlinearity.
+        If a single axis is provided, it will show the dendritic nonlinearity only.
+        If None, a new figure will be created.
+    vshift : int, optional
+        The vertical shift for the voltage traces.
+    """
     
     if ax is None:
         _, ax = plt.subplots(1, 2, figsize=(10, 5))
@@ -489,22 +514,21 @@ def plot_dendritic_nonlinearity(data, ax=None, **kwargs):
     vs = data['voltages']
     t = data['time']
 
-    for i, (weight, v) in enumerate(vs.items()):
-        ax[0].plot(t, np.array(v) - i*200, label=f'{weight} synapses')
-    ax[0].set_title('Voltage traces')
-    ax[0].legend()
-    ax[0].spines['top'].set_visible(False)
-    ax[0].spines['right'].set_visible(False)
-    ax[0].spines['bottom'].set_visible(False)
-    ax[0].spines['left'].set_visible(False)
-    ax[0].set_xticks([])
-    ax[0].set_yticks([])
-
-    ax[1].plot(expected_delta_vs, delta_vs, 'o-')
-    ax[1].plot(expected_delta_vs, expected_delta_vs, color='gray', linestyle='--')
-    ax[1].set_xlabel('Expected voltage change (mV)')
-    ax[1].set_ylabel('Observed voltage change (mV)')
-    ax[1].set_title('Dendritic nonlinearity')
+    if isinstance(ax, (list, np.ndarray)):        
+        for i, (weight, v) in enumerate(vs.items()):
+            ax[0].plot(t, np.array(v) - i*vshift, label=f'{weight} synapses')
+        ax[0].set_title('Voltage traces')
+        ax[0].legend()
+        ax[0].axis('off')
+        ax = ax[1]
+    
+    ax.plot(expected_delta_vs, delta_vs, zorder=1)
+    ax.plot(expected_delta_vs, expected_delta_vs, color='gray', linestyle='--', zorder=0)
+    for ep, ob in zip(expected_delta_vs, delta_vs):
+        ax.plot(ep, ob, 'o', zorder=2)
+    ax.set_xlabel('Expected voltage change (mV)')
+    ax.set_ylabel('Observed voltage change (mV)')
+    ax.set_title('Dendritic nonlinearity')
     
 
 def calculate_sag_ratio(model):

dendrotweaks/biophys/default_mod/vecstim.mod

@@ -1,6 +1,7 @@
 :  Vector stream of events
 
 NEURON {
+	THREADSAFE
 	ARTIFICIAL_CELL VecStim
 	RANGE delay
 }
@@ -12,13 +13,8 @@ ASSIGNED {
 	delay
 }
 
-PARAMETER { 
-	:delay = 0.0
-} 
-
 INITIAL {
 	index = 0
-	:delay = 0
 	element()
 	if (index > 0) {
 		net_send(delay + etime - t, 1)
@@ -35,12 +31,6 @@ NET_RECEIVE (w) {
 	}
 }
 
-VERBATIM
-extern double* vector_vec();
-extern int vector_capacity();
-extern void* vector_arg();
-ENDVERBATIM
-
 PROCEDURE element() {
 VERBATIM	
   { void* vv; int i, size; double* px;

dendrotweaks/biophys/distributions.py

@@ -131,16 +131,16 @@ def gaussian(distance: float, amplitude: float, mean: float, std: float) -> floa
     return amplitude * exp(-((distance - mean) ** 2) / (2 * std ** 2))
 
 
-def step(distance: float, max_value: float,  min_value: float, start: float, end: float) -> float:
+def step(distance: float, start: float, end: float, min_value: float, max_value: float) -> float:
     """
     Step distribution function.
 
     Args:
         distance (float): The distance parameter.
-        min_value (float): The minimum value parameter.
-        max_value (float): The maximum value parameter.
         start (float): The start parameter.
         end (float): The end parameter.
+        min_value (float): The minimum value parameter.
+        max_value (float): The maximum value parameter.
 
     Returns:
         The result of the step equation: min_value if distance < start, max_value if distance > end, and a linear interpolation between min_value and max_value if start <= distance <= end.

dendrotweaks/biophys/io/converter.py

@@ -94,6 +94,10 @@ class MODFileConverter():
         self.reader.read_file(path_to_mod_file)
         self.reader.preprocess()
         blocks = self.reader.get_blocks(verbose)
+        if blocks.get('KINETIC'):
+            raise NotImplementedError(
+                "Conversion aborted: MOD files containing KINETIC blocks are not supported by DendroTweaks."
+            )
         
         if verbose: print(f"\nPARSING")
         self.parser.parse(blocks, verbose)

dendrotweaks/biophys/mechanisms.py

@@ -575,4 +575,14 @@ class CaDynamics(Mechanism):
             'gamma': 0.05,
             'kt': 0.0,
             'kd': 0.0
-        }
+        }
+
+
+class FallbackChannel(IonChannel):
+    """
+    Fallback channel class in case of import failure.
+    """
+    def __init__(self, name):
+        super().__init__(name=name)
+        self.params = {'gbar': 0.0}
+        self.range_params = {'gbar': 0.0}