dendrotweaks 0.4.0__py3-none-any.whl → 0.4.2__py3-none-any.whl

dendrotweaks/__init__.py

@@ -1,7 +1,7 @@
-__version__ = "0.4.0"
+__version__ = "0.4.2"
 
 from dendrotweaks.model import Model
-from dendrotweaks.simulators import NEURONSimulator
+from dendrotweaks.simulators import NeuronSimulator
 from dendrotweaks.biophys.distributions import Distribution
 from dendrotweaks.path_manager import PathManager
 from dendrotweaks.stimuli import Synapse, Population, IClamp

dendrotweaks/biophys/groups.py

@@ -1,10 +1,5 @@
 from typing import List, Callable, Dict
 
-from dendrotweaks.morphology.trees import Node
-from dendrotweaks.morphology.sec_trees import Section
-from dendrotweaks.morphology.seg_trees import Segment
-from dendrotweaks.biophys.mechanisms import Mechanism
-from dendrotweaks.biophys.distributions import Distribution
 from dendrotweaks.utils import timeit
 from dataclasses import dataclass, field, asdict
 from typing import List, Tuple, Dict, Optional

dendrotweaks/biophys/io/code_generators.py

@@ -134,7 +134,8 @@ class PythonCodeGenerator(CodeGenerator):
             # Generate the signature
             signature_str = self._generate_signature(procedure.signature, 
                                                      is_method=True,
-                                                     extra_params=['celsius'])
+                                                     extra_params=['celsius'],
+                                                     default_params=True)
 
             # Generate the body
             body_str = self._generate_body(procedure.statements)
@@ -160,7 +161,7 @@ class PythonCodeGenerator(CodeGenerator):
         
         return procedures
 
-    def _generate_signature(self, signature, is_method=True, extra_params=None):
+    def _generate_signature(self, signature, is_method=True, extra_params=None, default_params=False):
         """
         Generate the signature string for a function using a Jinja2 template.
         The function AST representation is used to retrieve the function name
@@ -180,6 +181,9 @@ class PythonCodeGenerator(CodeGenerator):
         template = Template(signature_template)
         name = signature['name']
         params = [param['name'] for param in signature.get('params', [])]
+        if params == [] and default_params:
+            print(f"Warning: Procedure {name} has no parameters! Expected 'v' or 'cai'. Defaulting to 'v'.")
+            params = ['v']
         if is_method:
             params = ['self'] + params
 

dendrotweaks/model.py

@@ -6,9 +6,9 @@ import numpy as np
 import quantities as pq
 
 from dendrotweaks.morphology.point_trees import PointTree
-from dendrotweaks.morphology.sec_trees import Section, SectionTree, Domain
-from dendrotweaks.morphology.seg_trees import Segment, SegmentTree
-from dendrotweaks.simulators import NEURONSimulator
+from dendrotweaks.morphology.sec_trees import NeuronSection, Section, SectionTree, Domain
+from dendrotweaks.morphology.seg_trees import NeuronSegment, Segment, SegmentTree
+from dendrotweaks.simulators import NeuronSimulator
 from dendrotweaks.biophys.groups import SegmentGroup
 from dendrotweaks.biophys.mechanisms import Mechanism, LeakChannel, CaDynamics
 from dendrotweaks.biophys.io import create_channel, standardize_channel, create_standard_channel
@@ -149,7 +149,7 @@ class Model():
 
         # Simulator
         if simulator_name == 'NEURON':
-            self.simulator = NEURONSimulator()
+            self.simulator = NeuronSimulator()
         elif simulator_name == 'Jaxley':
             self.simulator = JaxleySimulator()
         else:
@@ -231,9 +231,9 @@ class Model():
         The dictionary mapping mechanisms to domains where they are inserted.
         """
         mechs_to_domains = defaultdict(set)
-        for domain, mechs in self.domains_to_mechs.items():
-            for mech in mechs:
-                mechs_to_domains[mech].add(domain)
+        for domain_name, mech_names in self.domains_to_mechs.items():
+            for mech_name in mech_names:
+                mechs_to_domains[mech_name].add(domain_name)
         return dict(mechs_to_domains)
 
 
@@ -418,7 +418,7 @@ class Model():
         """
         if self.verbose: print(f'Building sections in {self.simulator_name}...')
         for sec in self.sec_tree.sections:
-            sec.create_and_reference(self.simulator_name)
+            sec.create_and_reference()
         n_sec = len([sec._ref for sec in self.sec_tree.sections 
                     if sec._ref is not None])
         if self.verbose: print(f'{n_sec} sections created.')
@@ -439,9 +439,10 @@ class Model():
             # TODO: Check that domains match
             if not domain_name in self.domains_to_mechs: 
                 self.domains_to_mechs[domain_name] = set()
-        for domain_name, mechs in self.domains_to_mechs.items():
-            for mech_name in mechs:
-                self.insert_mechanism(mech_name, domain_name)
+        for domain_name, mech_names in self.domains_to_mechs.items():
+            for mech_name in mech_names:
+                mech = self.mechanisms[mech_name]
+                self.insert_mechanism(mech, domain_name)
 
 
     def get_sections(self, filter_function):
@@ -493,7 +494,8 @@ class Model():
         for sec in self.sec_tree.sections:
             lambda_f = calculate_lambda_f(sec.distances, sec.diameters, sec.Ra, sec.cm, f)
             nseg = int((sec.L / (d_lambda * lambda_f) + 0.9) / 2) * 2 + 1
-            # TODO: Set sec._nseg instead
+            # TODO: Set sec.nseg instead
+            sec._nseg = nseg
             sec._ref.nseg = nseg
         # Rebuild the segment tree
         self.seg_tree = create_segment_tree(self.sec_tree)
@@ -631,8 +633,8 @@ class Model():
 
         # Get data to transfer
         channel = self.mechanisms[channel_name]
-        channel_domain_names = [domain_name for domain_name, mechs 
-            in self.domains_to_mechs.items() if channel_name in mechs]
+        channel_domain_names = [domain_name for domain_name, mech_names 
+            in self.domains_to_mechs.items() if channel_name in mech_names]
         gbar_name = f'gbar_{channel_name}'
         gbar_distributions = self.params[gbar_name]
         # Kinetic variables cannot be transferred
@@ -709,13 +711,15 @@ class Model():
             for mech_name in self.domains_to_mechs[old_domain.name]:
                 # TODO: What if section is already in domain? Can't be as
                 # we use a filtered list of sections.
-                sec.uninsert_mechanism(mech_name)
+                mech = self.mechanisms[mech_name]
+                sec.uninsert_mechanism(mech)
             
 
         for sec in sections_to_move:
             domain.add_section(sec)
             for mech_name in self.domains_to_mechs.get(domain.name, set()):
-                sec.insert_mechanism(mech_name, distribute=distribute)
+                mech = self.mechanisms[mech_name]
+                sec.insert_mechanism(mech, distribute=distribute)
 
         self._remove_empty()
 
@@ -797,7 +801,7 @@ class Model():
         # domain.insert_mechanism(mech)
         self.domains_to_mechs[domain_name].add(mech.name)
         for sec in domain.sections:
-            sec.insert_mechanism(mech.name)
+            sec.insert_mechanism(mech)
         self._add_mechanism_params(mech)
 
         # TODO: Redistribute parameters if any group contains this domain
@@ -847,7 +851,7 @@ class Model():
 
         # domain.uninsert_mechanism(mech)
         for sec in domain.sections:
-            sec.uninsert_mechanism(mech.name)
+            sec.uninsert_mechanism(mech)
         self.domains_to_mechs[domain_name].remove(mech.name)
 
         if not self.mechs_to_domains.get(mech.name):
@@ -1402,7 +1406,8 @@ class Model():
             if mech_name == 'Leak':
                 continue
             for sec in root.subtree:
-                sec.uninsert_mechanism(mech_name)
+                mech = self.mechanisms[mech_name]
+                sec.uninsert_mechanism(mech)
 
         # Disconnect
         root.disconnect_from_parent()
@@ -1434,7 +1439,8 @@ class Model():
             if mech_name == 'Leak':
                 continue
             for sec in root.subtree:
-                sec.insert_mechanism(mech_name)
+                mech = self.mechanisms[mech_name]
+                sec.insert_mechanism(mech)
         
         # Replace locs with corresponding segs
         
@@ -1466,7 +1472,8 @@ class Model():
 
         # Reinsert active mechanisms after creating the new domain
         for mech_name in inserted_mechs:
-            root.insert_mechanism(mech_name)
+            mech = self.mechanisms[mech_name]
+            root.insert_mechanism(mech)
         self.domains_to_mechs[new_reduced_domain_name] = set(inserted_mechs.keys())
         
                

dendrotweaks/morphology/__init__.py

@@ -1,5 +1,5 @@
 from dendrotweaks.morphology.trees import Node, Tree
 from dendrotweaks.morphology.point_trees import Point, PointTree
-from dendrotweaks.morphology.sec_trees import Section, SectionTree, Domain
-from dendrotweaks.morphology.seg_trees import Segment, SegmentTree
+from dendrotweaks.morphology.sec_trees import NeuronSection, Section, SectionTree, Domain
+from dendrotweaks.morphology.seg_trees import NeuronSegment, Segment, SegmentTree
 from dendrotweaks.morphology.io.validation import validate_tree

dendrotweaks/morphology/io/factories.py

@@ -1,7 +1,7 @@
 from dendrotweaks.morphology.trees import Node, Tree
 from dendrotweaks.morphology.point_trees import Point, PointTree
-from dendrotweaks.morphology.sec_trees import Section, SectionTree
-from dendrotweaks.morphology.seg_trees import Segment, SegmentTree
+from dendrotweaks.morphology.sec_trees import NeuronSection, Section, SectionTree
+from dendrotweaks.morphology.seg_trees import NeuronSegment, Segment, SegmentTree
 
 from dendrotweaks.morphology.io.reader import SWCReader
 
@@ -86,7 +86,7 @@ def _split_to_sections(point_tree: PointTree) -> List[Section]:
 
     # Assign a section to each bifurcation child
     for i, child in enumerate(bifurcation_children):
-        section = Section(idx=i, parent_idx=-1, points=[child])
+        section = NeuronSection(idx=i, parent_idx=-1, points=[child])
         sections.append(section)
         child._section = section
         # Propagate the section to the children until the next 
@@ -181,8 +181,8 @@ def _create_segments(sec_tree) -> List[Segment]:
         segs = {seg: idx + idx_counter for idx, seg in enumerate(sec._ref)}
         sec.segments = []
         for seg, idx in segs.items():
-            segment = Segment(
-                idx=idx, parent_idx=parent_idx, neuron_seg=seg, section=sec)
+            segment = NeuronSegment(
+                idx=idx, parent_idx=parent_idx, sim_seg=seg, section=sec)
             segments.append(segment)
             sec.segments.append(segment)
 

dendrotweaks/morphology/sec_trees.py

@@ -54,7 +54,9 @@ class Section(Node):
         self.points = points
         self.segments = []
         self._ref = None
+        self._nseg = None
         self._domain = self.points[0].domain
+        self._cell = None
 
         if not all(pt.domain == self._domain for pt in points):
             raise ValueError('All points in a section must belong to the same domain.')
@@ -125,105 +127,6 @@ class Section(Node):
                             'parent_idx': [self.parent_idx]})
 
 
-    # TODO: Figure out why this is different from NEURON's diam
-    # Update: In NEURON, sec.diam returns the diameter of the segment at the center of the section
-    # In this implementation, sec.diam returns the average diameter of the section
-    # @property
-    # def diam(self):
-    #     """
-    #     Average diameter of the section calculated from
-    #     the radii and distances of the points.
-    #     """
-    #     distances = self.distances  # Cumulative distances
-    #     radii = self.radii  # Corresponding radii
-    #     total_length = distances[-1]  # Total section length
-        
-    #     if total_length == 0:
-    #         return 0  # Avoid division by zero for zero-length sections
-
-    #     segment_lengths = np.diff(distances)  # Lengths of frusta segments
-    #     segment_diameters = 2 * (np.array(radii[:-1]) + np.array(radii[1:])) / 2  # Mean diameter per segment
-
-    #     # Length-weighted average
-    #     avg_diameter = np.sum(segment_diameters * segment_lengths) / total_length
-
-    #     return avg_diameter
-
-    @property
-    def diam(self):
-        """
-        Diameter of the central segment of the section (from NEURON).
-        """
-        return self._ref.diam
-        
-
-    @property
-    def L(self):
-        """
-        Length of the section (from NEURON).
-        """
-        return self._ref.L
-
-
-    @property
-    def cm(self):
-        """
-        Specific membrane capacitance of the section (from NEURON).
-        """
-        return self._ref.cm
-
-
-    @property
-    def Ra(self):
-        """
-        Axial resistance of the section (from NEURON).
-        """
-        return self._ref.Ra
-
-
-    @property
-    def nseg(self):
-        """
-        Number of segments in the section (from NEURON).
-        """
-        return self._ref.nseg
-
-    @nseg.setter
-    def nseg(self, value):
-        if value < 1:
-            raise ValueError('Number of segments must be at least 1.')
-        if value % 2 == 0:
-            raise ValueError('Number of segments must be odd.')
-        # Set the number in NEURON
-        self._ref.nseg = value
-        # Get the new NEURON segments
-        nrnsegs = [seg for seg in self._ref]
-
-        # Create new DendroTweaks segments
-        from dendrotweaks.morphology.seg_trees import Segment
-        old_segments = self.segments
-        new_segments = [Segment(idx=0, parent_idx=0, neuron_seg=seg, section=self)
-                            for seg in nrnsegs]
-        
-        seg_tree = self._tree._seg_tree
-        first_segment = self.segments[0]
-        parent = first_segment.parent
-
-        for i, seg in enumerate(new_segments[:]):
-            if i == 0:
-                seg_tree.insert_node_before(seg, first_segment)
-            else:
-                seg_tree.insert_node_before(seg, new_segments[i-1])
-
-        for seg in old_segments:
-            seg_tree.remove_node(seg)
-        
-        # Sort the tree
-        self._tree._seg_tree.sort()
-        # Update the section's segments
-        self.segments = new_segments
-
-
     @property
     def radii(self):
         """
@@ -271,8 +174,8 @@ class Section(Node):
         """
         if self._ref is None:
             raise ValueError('Section is not referenced in NEURON.')
-        return (np.array([(2*i - 1) / (2 * self._ref.nseg)
-                for i in range(1, self._ref.nseg + 1)]) * self._ref.L).tolist()
+        return (np.array([(2*i - 1) / (2 * self.nseg)
+                for i in range(1, self.nseg + 1)]) * self.L).tolist()
 
 
     @property
@@ -282,7 +185,7 @@ class Section(Node):
         """
         if self._ref is None:
             raise ValueError('Section is not referenced in NEURON.')
-        nseg = int(self._ref.nseg)
+        nseg = int(self.nseg)
         return [i / nseg for i in range(nseg + 1)]
 
 
@@ -322,80 +225,27 @@ class Section(Node):
         areas = [np.pi * (r1 + r2) * np.sqrt((r1 - r2)**2 + h**2) for r1, r2, h in zip(self.radii[:-1], self.radii[1:], np.diff(self.distances))]
         return sum(areas)
 
-    def has_mechanism(mech_name):
-        """
-        Check if the section has a mechanism inserted.
-
-        Parameters
-        ----------
-        mech_name : str
-            The name of the mechanism to check.
-        """
-        return self._ref.has_membrane(mech_name)
-
-
-    # REFERENCING METHODS
-
-    def create_and_reference(self, simulator_name='NEURON'):
-        """
-        Add a reference to the section in the simulator.
-
-        Parameters
-        ----------
-        simulator_name : str
-            The name of the simulator to create the section in.
-        """
-        if simulator_name == 'NEURON':
-            self.create_NEURON_section()
-        elif simulator_name == 'JAXLEY':
-            self.create_JAXLEY_section()
-
-
-    def create_NEURON_section(self):
-        """
-        Create a NEURON section.
-        """
-        self._ref = h.Section() # name=f'Sec_{self.idx}'
-        if self.parent is not None:
-            # TODO: Attaching basal to soma 0
-            if self.parent.parent is None: # if parent is soma
-                self._ref.connect(self.parent._ref(0.5))
-            else:
-                self._ref.connect(self.parent._ref(1))
-        # Add 3D points to the section
-        self._ref.pt3dclear()
-        for pt in self.points:
-            diam = 2*pt.r
-            diam = round(diam, 16)
-            self._ref.pt3dadd(pt.x, pt.y, pt.z, diam)
-
-    def create_JAXLEY_section(self):
-        """
-        Create a JAXLEY section.
-        """
-        raise NotImplementedError
-
 
     # MECHANISM METHODS
 
-    def insert_mechanism(self, name: str):
+    def insert_mechanism(self, mech):
         """
         Inserts a mechanism in the section if 
         it is not already inserted.
         """
-        if self._ref.has_membrane(name):
+        if self._ref.has_membrane(mech.name):
             return
-        self._ref.insert(name)
+        self._ref.insert(mech.name)
 
 
-    def uninsert_mechanism(self, name: str):
+    def uninsert_mechanism(self, mech):
         """
         Uninserts a mechanism in the section if
         it was inserted.
         """
-        if not self._ref.has_membrane(name):
+        if not self._ref.has_membrane(mech.name):
             return
-        self._ref.uninsert(name)
+        self._ref.uninsert(mech.name)
 
 
     # PARAMETER METHODS
@@ -636,7 +486,7 @@ class Section(Node):
             seg_radii = np.array([seg.diam / 2 for seg in self._ref])
             
             # Use the specified bar width calculation from original code
-            bar_width = [self._ref.L / self._ref.nseg] * self._ref.nseg
+            bar_width = [self.L / self._nseg] * self._nseg
             
             # Plot segment radii as bars
             ax.bar(normalized_seg_centers, seg_radii, width=bar_width, 
@@ -666,7 +516,7 @@ class Section(Node):
                 parent_seg_radii = np.array([seg.diam / 2 for seg in self.parent._ref])
                 
                 # Use the specified bar width calculation for parent
-                parent_bar_width = [self.parent._ref.L / self.parent._ref.nseg] * self.parent._ref.nseg
+                parent_bar_width = [self.parent.L / self.parent._nseg] * self.parent._nseg
                 
                 # Plot parent segment radii as bars
                 ax.bar(normalized_parent_seg_centers, parent_seg_radii, 
@@ -738,6 +588,131 @@ class Section(Node):
         return ax
 
 
+
+ # --------------------------------------------------------------
+ # NEURON SECTION
+ # --------------------------------------------------------------
+ 
+class NeuronSection(Section):
+
+    def __init__(self, idx, parent_idx, points) -> None:
+        super().__init__(idx, parent_idx, points)
+
+    @property
+    def diam(self):
+        """
+        Diameter of the central segment of the section (from NEURON).
+        """
+        return self._ref.diam
+        
+
+    @property
+    def L(self):
+        """
+        Length of the section (from NEURON).
+        """
+        return self._ref.L
+
+
+    @property
+    def cm(self):
+        """
+        Specific membrane capacitance of the section (from NEURON).
+        """
+        return self._ref.cm
+
+
+    @property
+    def Ra(self):
+        """
+        Axial resistance of the section (from NEURON).
+        """
+        return self._ref.Ra
+
+
+    def has_mechanism(mech_name):
+        """
+        Check if the section has a mechanism inserted.
+
+        Parameters
+        ----------
+        mech_name : str
+            The name of the mechanism to check.
+        """
+        return self._ref.has_membrane(mech_name)
+
+    
+    @property
+    def nseg(self):
+        """
+        Number of segments in the section (from NEURON).
+        """
+        return self._nseg
+
+
+    @nseg.setter
+    def nseg(self, value):
+        if value < 1:
+            raise ValueError('Number of segments must be at least 1.')
+        if value % 2 == 0:
+            raise ValueError('Number of segments must be odd.')
+        # Set the number in NEURON
+        self._nseg = self._ref.nseg = value
+        # Get the new NEURON segments
+        nrnsegs = [seg for seg in self._ref]
+
+        # Create new DendroTweaks segments
+        from dendrotweaks.morphology.seg_trees import NeuronSegment
+        old_segments = self.segments
+        new_segments = [NeuronSegment(idx=0, parent_idx=0, sim_seg=seg, section=self)
+                            for seg in nrnsegs]
+        
+        seg_tree = self._tree._seg_tree
+        first_segment = self.segments[0]
+        parent = first_segment.parent
+
+        for i, seg in enumerate(new_segments[:]):
+            if i == 0:
+                seg_tree.insert_node_before(seg, first_segment)
+            else:
+                seg_tree.insert_node_before(seg, new_segments[i-1])
+
+        for seg in old_segments:
+            seg_tree.remove_node(seg)
+        
+        # Sort the tree
+        self._tree._seg_tree.sort()
+        # Update the section's segments
+        self.segments = new_segments
+
+
+    # REFERENCING METHODS
+
+    def create_and_reference(self):
+        """
+        Create a NEURON section.
+        """
+        self._ref = h.Section() # name=f'Sec_{self.idx}'
+        self._nseg = self._ref.nseg
+        if self.parent is not None:
+            # TODO: Attaching basal to soma 0
+            if self.parent.parent is None: # if parent is soma
+                self._ref.connect(self.parent._ref(0.5))
+            else:
+                self._ref.connect(self.parent._ref(1))
+        # Add 3D points to the section
+        self._ref.pt3dclear()
+        for pt in self.points:
+            diam = 2*pt.r
+            diam = round(diam, 16)
+            self._ref.pt3dadd(pt.x, pt.y, pt.z, diam)
+
+
+
+# ========================================================================
+# SECTION TREE
+# ========================================================================
+
 class SectionTree(Tree):
     """
     A class representing a tree graph of sections in a neuron morphology.

dendrotweaks/morphology/seg_trees.py

@@ -14,8 +14,8 @@ class Segment(Node):
         The index of the segment.
     parent_idx : int
         The index of the parent segment.
-    neuron_seg : h.Segment
-        The NEURON segment.
+    sim_seg : h.Segment
+        The segment object from a simulator (e.g. NEURON).
     section : Section
         The section to which the segment belongs.
 
@@ -24,13 +24,13 @@ class Segment(Node):
     _section : Section
         The section to which the segment belongs.
     _ref : h.Segment
-        The NEURON segment.
+        The segment object from a simulator (e.g. NEURON).
     """
 
-    def __init__(self, idx, parent_idx, neuron_seg, section) -> None:
+    def __init__(self, idx, parent_idx, sim_seg, section) -> None:
         super().__init__(idx, parent_idx)
         self._section = section
-        self._ref = neuron_seg
+        self._ref = sim_seg
 
 
     # PROPERTIES
@@ -43,30 +43,6 @@ class Segment(Node):
         return self._section.domain
 
 
-    @property
-    def x(self):
-        """
-        The position of the segment along the normalized section length (from NEURON).
-        """
-        return self._ref.x
-
-
-    @property
-    def area(self):
-        """
-        The area of the segment (from NEURON).
-        """
-        return self._ref.area()
-
-
-    @property
-    def diam(self):
-        """
-        The diameter of the segment (from NEURON).
-        """
-        return self._ref.diam
-
-
     @property
     def subtree_size(self):
         """
@@ -137,6 +113,42 @@ class Segment(Node):
             return np.nan
 
 
+
+# -------------------------------------------------------------------
+# NEURON SEGMENT
+# -------------------------------------------------------------------
+
+class NeuronSegment(Segment):
+    """
+    A class representing a segment for the Jaxley simulator.
+    """
+
+    def __init__(self, idx, parent_idx, sim_seg, section) -> None:
+        super().__init__(idx, parent_idx, sim_seg, section)
+
+    @property
+    def x(self):
+        """
+        The position of the segment along the normalized section length (from NEURON).
+        """
+        return self._ref.x
+
+
+    @property
+    def area(self):
+        """
+        The area of the segment (from NEURON).
+        """
+        return self._ref.area()
+
+
+    @property
+    def diam(self):
+        """
+        The diameter of the segment (from NEURON).
+        """
+        return self._ref.diam
+
 class SegmentTree(Tree):
     """
     A class representing a tree graph of segments.

dendrotweaks/simulators.py

@@ -10,6 +10,7 @@ h.load_file('stdrun.hoc')
 # h.load_file('import3d.hoc')
 # h.load_file('nrngui.hoc')
 # h.load_file('import3d')
+import numpy as np
 
 import contextlib
 
@@ -31,6 +32,10 @@ def reset_neuron():
 
 reset_neuron()            
 
+# -------------------------------------------------------
+# SIMULATOR
+# -------------------------------------------------------
+
 class Simulator:
     """
     A generic simulator class.
@@ -79,7 +84,7 @@ class Simulator:
             
         
 
-class NEURONSimulator(Simulator):
+class NeuronSimulator(Simulator):
     """
     A class to represent the NEURON simulator.
 
@@ -193,18 +198,25 @@ class NEURONSimulator(Simulator):
 
 
     def _init_simulation(self):
-        h.CVode().active(self._cvode)
+
         h.celsius = self.temperature
-        h.dt = self.dt
-        h.stdinit()
-        h.init()
+
+        if self._cvode:
+            h.cvode.active(1)
+        else:
+            h.cvode.active(0)
+            h.dt = self.dt
+
         h.finitialize(self.v_init)
-        if h.cvode.active():
+
+        if self._cvode:
             h.cvode.re_init()
         else:
             h.fcurrent()
+
         h.frecord_init()
 
+
     def run(self, duration=300):
         """
         Run a simulation.

{dendrotweaks-0.4.0.dist-info → dendrotweaks-0.4.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dendrotweaks
-Version: 0.4.0
+Version: 0.4.2
 Summary: A toolbox for exploring dendritic dynamics
 Home-page: https://dendrotweaks.dendrites.gr
 Author: Roman Makarov

{dendrotweaks-0.4.0.dist-info → dendrotweaks-0.4.2.dist-info}/RECORD

@@ -1,15 +1,15 @@
-dendrotweaks/__init__.py,sha256=qmlQDMHQGSD70naZme_cEMgale9T5OH6VqjdxhznouM,384
-dendrotweaks/model.py,sha256=XX4WPaHPYUzm9CF4S6lUCDc_a1mORJaEbwtLexqEKCQ,68796
+dendrotweaks/__init__.py,sha256=9L85_UrXGRtxCoSzemZUlzdq_FWZPX0Hjz7HUtyqepg,384
+dendrotweaks/model.py,sha256=rMvS0BnqQ4ozIbM65t1jgydm5IeFo1QH0FAXEQNM-bs,69141
 dendrotweaks/model_io.py,sha256=xwXKMcUle-Y0HoWFYVZu3G8v4pdQXmeaDfl2Xi65eHw,2137
 dendrotweaks/path_manager.py,sha256=dai5o6UA0nk-ubwKWRu4LFdDBO77zW_SsMf6k0MLBiI,8703
-dendrotweaks/simulators.py,sha256=ADiXPqcWZ7oLQfMMnhgQNpgCW-NE6lBb5hZCQACSIkM,7237
+dendrotweaks/simulators.py,sha256=Vg6ToTkDZ4OGcANYwYtamGnasyLNbyP8pfPHl9PnMnM,7413
 dendrotweaks/utils.py,sha256=jaUJNb39Bsevg3WJByP56bO7CLj1wzlh-uGZl-lxi1I,7131
 dendrotweaks/analysis/__init__.py,sha256=SEYpoQ5iXiQXyHB20-IAdDHYI-7CR5GYFXIwr-O05Ug,858
 dendrotweaks/analysis/ephys_analysis.py,sha256=Caiww27p9dnL5_27OmZ95AZ_OmefvImAPyItsJMSdmA,14320
 dendrotweaks/analysis/morphometric_analysis.py,sha256=5zohjGssyx-wezI-yY3Q-kYM_wzAQLLFBJ9Xk950_JY,3571
 dendrotweaks/biophys/__init__.py,sha256=k0o2xwyoaJUb1lfO9OHtqxheNP6R-Ya5o0g-bJOdCZg,360
 dendrotweaks/biophys/distributions.py,sha256=ADPFPA-CN7AbRJj0Ry4TxFZJhdYXJm87iIGWZSDr5vI,10299
-dendrotweaks/biophys/groups.py,sha256=Kze8ft8EYFXWW6zJhhbpWQUUt82L47g2IbB-5WpsWrY,3481
+dendrotweaks/biophys/groups.py,sha256=Q4kBIqL1-piIgrpsVq6ojinAWHiEJ1GzMjSAQ7Ni_E8,3212
 dendrotweaks/biophys/mechanisms.py,sha256=j9uygcwkK6Z_08hpTHax40Wn-eV4V_k_on_KyPDnO90,18520
 dendrotweaks/biophys/default_mod/AMPA.mod,sha256=HY_pWzYvaSDV-w7qruenG2mnll8v79s40HFHjUCIi4U,980
 dendrotweaks/biophys/default_mod/AMPA_NMDA.mod,sha256=ztv2ePUiEQZ93-23FTkGO2DC91rehQuqo0NUIbHZ368,2318
@@ -25,21 +25,21 @@ dendrotweaks/biophys/default_templates/template_jaxley.py,sha256=t-GsCSUyQ7rDoaL
 dendrotweaks/biophys/default_templates/template_jaxley_new.py,sha256=I62KhnOYNV1bT-nPsDTxjIISYmDcso2X8rnsos28nYs,3631
 dendrotweaks/biophys/io/__init__.py,sha256=kkmQ4L0SatI3lWd3qE8KqOIKd7x3G2OnqAAW93sWWCU,575
 dendrotweaks/biophys/io/ast.py,sha256=7x_Kxz1qoQHZeIjovUNyVuKgUo4vAFKm-bd4hn9n1CI,6078
-dendrotweaks/biophys/io/code_generators.py,sha256=yg0Do1XLM_rIXk4i_FibJGfkWOt-GN0lq5dOCD4D3pk,11702
+dendrotweaks/biophys/io/code_generators.py,sha256=RX0nw5-0CyWR3KOrTZUabKuPAQg2ysQ_nQi2iu9TxiE,11978
 dendrotweaks/biophys/io/converter.py,sha256=5yrPJhyZbuwV7tTGoacnNOvmRdVgXPIyGfiR0PyOVzg,3371
 dendrotweaks/biophys/io/factories.py,sha256=j1Hi2u-NTFFL8ElRYlgGVNHRcfKWH6o5GfKvraMTlwM,5020
 dendrotweaks/biophys/io/grammar.py,sha256=TJLTDlr8Ajp3J9DJ4IvulOCcpUkYr7HnoI0TGnNuEPc,11677
 dendrotweaks/biophys/io/loader.py,sha256=Wv9ZkEDyA3MkCdV0sMeRnBffg2WAI7yTV3r6C412GiY,6378
 dendrotweaks/biophys/io/parser.py,sha256=boT27lFrn5LYrJnkZFs0SwrZZrkSkwO8efqGPJ4Qj0I,17914
 dendrotweaks/biophys/io/reader.py,sha256=JWm5WM9illvSfDkhWEmWBcj8Y7PSi8zeZX9j1ARUHVU,6576
-dendrotweaks/morphology/__init__.py,sha256=aqJTQOpRVOYcbWqZ2q4e-Oy735r9_ubW-uE_5cFZVtI,323
+dendrotweaks/morphology/__init__.py,sha256=JwXmSmdn9e_jqslITEdiU9kWvzxcxT9Aw_kUkXLbm5o,353
 dendrotweaks/morphology/domains.py,sha256=Y4txcGdBdl2aK1DfbTRziNtDyd6bChczwpCWE7lTFzg,2391
 dendrotweaks/morphology/point_trees.py,sha256=5dUPaQXYPdJbWoD3pFI2DV2XnuFRhB5d0wTBlfmmIeI,21600
-dendrotweaks/morphology/sec_trees.py,sha256=4EU8YbYsi1Pr_n7vkFuKQtIIWbJwP-8Q_epmioEXAIw,36902
-dendrotweaks/morphology/seg_trees.py,sha256=uwL1X9qeFNyJVHua1I3rhp0fLSRrS2TAVyb1Fnw4RwQ,3595
+dendrotweaks/morphology/sec_trees.py,sha256=fj-1kBj7InkqB27Ux-jPidGQXts7FAPXa1m2LdzekNY,35816
+dendrotweaks/morphology/seg_trees.py,sha256=-XeSJuD7ZixBJYQDzvmSEiNvOWbVmX_DanyAPkkR-NA,4042
 dendrotweaks/morphology/trees.py,sha256=NrNvPMR-U0clt63eqwVJqU0H8NJgY53QGA_BkdcwkQI,16033
 dendrotweaks/morphology/io/__init__.py,sha256=gAZqZdf5VKPb6ksK8Lwt7MbTAq8TDP8uq3Vs_ebNFEY,324
-dendrotweaks/morphology/io/factories.py,sha256=NngNINw73diGK7fud314JzWVhxv2aYLuA9wUuQA0Diw,6344
+dendrotweaks/morphology/io/factories.py,sha256=DCE37QCloiYVro5HGihJbxPz91BB3y5NNf-oRaQ-M2g,6383
 dendrotweaks/morphology/io/reader.py,sha256=hW3c541WtG1rNag_YreEhvrLzm8-OTtw0fQREeHDthM,1913
 dendrotweaks/morphology/io/validation.py,sha256=lVkYw9y9yG5QpRh_N0YQ3FbZwuSUsQfSqJTMumMcDdc,7872
 dendrotweaks/morphology/reduce/__init__.py,sha256=p6Mg3KDHxTt8S4DtI0m7L7MqV6dS2pdIYAwB7B-toVw,921
@@ -49,8 +49,8 @@ dendrotweaks/stimuli/__init__.py,sha256=bFfSEZhCVpwOVEBgLe65iiY3SdpjKPhyLemC1z5O
 dendrotweaks/stimuli/iclamps.py,sha256=NjkhhwZKJR1f_g3N9BVxMVoO9ubBk5WkQ6h9Bnf9xgA,1681
 dendrotweaks/stimuli/populations.py,sha256=y85v8smiMifINIqXm1O3mOINAlDTz-SPGLS78alhX5A,8325
 dendrotweaks/stimuli/synapses.py,sha256=g4MgWTske2TZ2i9FIIOE8-KXNx_3dWa3zEhB2rcqYig,5470
-dendrotweaks-0.4.0.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-dendrotweaks-0.4.0.dist-info/METADATA,sha256=9AAcxk2ZzIvqUOQg7hNf0Tw1an2EYJLl76gSI21WAKM,2740
-dendrotweaks-0.4.0.dist-info/WHEEL,sha256=lTU6B6eIfYoiQJTZNc-fyaR6BpL6ehTzU3xGYxn2n8k,91
-dendrotweaks-0.4.0.dist-info/top_level.txt,sha256=OzT_2BSI5j5zxC447K6Y-0W-GHbued7iX-_hFGAKMxY,13
-dendrotweaks-0.4.0.dist-info/RECORD,,
+dendrotweaks-0.4.2.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+dendrotweaks-0.4.2.dist-info/METADATA,sha256=RHDsvzirnDTlrF2wl4IqLgSLw-40UOJ8_VfNtoezyYw,2740
+dendrotweaks-0.4.2.dist-info/WHEEL,sha256=Nw36Djuh_5VDukK0H78QzOX-_FQEo6V37m3nkm96gtU,91
+dendrotweaks-0.4.2.dist-info/top_level.txt,sha256=OzT_2BSI5j5zxC447K6Y-0W-GHbued7iX-_hFGAKMxY,13
+dendrotweaks-0.4.2.dist-info/RECORD,,

{dendrotweaks-0.4.0.dist-info → dendrotweaks-0.4.2.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (78.1.1)
+Generator: setuptools (80.7.1)
 Root-Is-Purelib: true
 Tag: py3-none-any