dendrotweaks 0.4.1__py3-none-any.whl → 0.4.3__py3-none-any.whl

dendrotweaks/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.4.1"
+__version__ = "0.4.3"
 
 from dendrotweaks.model import Model
 from dendrotweaks.simulators import NeuronSimulator

dendrotweaks/analysis/ephys_analysis.py

@@ -24,7 +24,8 @@ def get_somatic_data(model):
     tuple
         A tuple containing the voltage, time, time step, and injected current.
     """
-    seg = model.seg_tree.root
+    soma = model.sec_tree.root
+    seg = soma(0.5)
     iclamp = model.iclamps[seg]
 
     v = np.array(model.simulator.recordings['v'][seg])
@@ -163,7 +164,8 @@ def detect_somatic_spikes(model, **kwargs):
     Returns:
         dict: A dictionary containing spike metrics.
     """
-    seg = model.seg_tree.root
+    soma = model.sec_tree.root
+    seg = soma(0.5)
             
     v = np.array(model.simulator.recordings['v'][seg])
     t = np.array(model.simulator.t)

dendrotweaks/biophys/distributions.py

@@ -20,7 +20,7 @@ def constant(position, value=0):
         The value of the constant function at the given position.
     """
     if isinstance(position, ndarray):
-        return full_like(position, value)
+        return full_like(position, value, dtype=float)
     else:
         return value
 
@@ -42,7 +42,7 @@ def uniform(position, value=0):
         The value of the constant function at the given position.
     """
     if isinstance(position, ndarray):
-        return full_like(position, value)
+        return full_like(position, value, dtype=float)
     else:
         return value
 

dendrotweaks/biophys/mechanisms.py

@@ -71,7 +71,7 @@ class Mechanism():
         }
 
     def __repr__(self):
-        return f"<Mechnaism({self.name})>"
+        return f"<Mechanism({self.name})>"
 
 
 

dendrotweaks/model.py

@@ -473,6 +473,25 @@ class Model():
     # SEGMENTATION
     # ========================================================================
 
+    # TODO Make a context manager for this
+    def _temp_clear_stimuli(self):
+        """
+        Temporarily save and clear stimuli.
+        """
+        self.export_stimuli(file_name='_temp_stimuli')
+        self.remove_all_stimuli()
+        self.remove_all_recordings()
+
+    def _temp_reload_stimuli(self):
+        """
+        Load stimuli from a temporary file and clean up.
+        """
+        self.load_stimuli(file_name='_temp_stimuli')
+        for ext in ['json', 'csv']:
+            temp_path = self.path_manager.get_file_path('stimuli', '_temp_stimuli', extension=ext)
+            if os.path.exists(temp_path):
+                os.remove(temp_path)
+
     def set_segmentation(self, d_lambda=0.1, f=100):
         """
         Set the number of segments in each section based on the geometry.
@@ -486,22 +505,26 @@ class Model():
         """
         self.d_lambda = d_lambda
 
+        # Temporarily save and clear stimuli
+        self._temp_clear_stimuli()
+
         # Pre-distribute parameters needed for lambda_f calculation
         for param_name in ['cm', 'Ra']:
             self.distribute(param_name)
 
-        # Calculate lambda_f for each section and set nseg
+        # Calculate lambda_f and set nseg for each section
         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
-            sec._ref.nseg = nseg
-        # Rebuild the segment tree
-        self.seg_tree = create_segment_tree(self.sec_tree)
+            nseg = max(1, int((sec.L / (d_lambda * lambda_f) + 0.9) / 2) * 2 + 1)
+            sec._nseg = sec._ref.nseg = nseg
 
-        # Redistribute parameters
+        # Rebuild the segment tree and redistribute parameters
+        self.seg_tree = create_segment_tree(self.sec_tree)
         self.distribute_all()
 
+        # Reload stimuli and clean up temporary files
+        self._temp_reload_stimuli()
+
 
     # ========================================================================
     # MECHANISMS
@@ -674,17 +697,26 @@ class Model():
 
     def define_domain(self, domain_name: str, sections, distribute=True):
         """
-        Adds a new domain to the tree and ensures correct partitioning of
-        the section tree graph.
+        Adds a new domain to the cell and ensures proper partitioning 
+        of the section tree graph.
+
+        This method does not automatically insert mechanisms into the newly 
+        created domain. It is the user's responsibility to insert mechanisms 
+        into the domain after its creation. However, if the domain already 
+        exists and is being extended, mechanisms will be inserted automatically 
+        into the newly added sections.
 
         Parameters
         ----------
         domain_name : str
-            The name of the domain.
+            The name of the domain to be added or extended.
         sections : list[Section] or Callable
-            The sections to include in the domain. If a callable is provided,
-            it should be a filter function applied to the list of all sections
-            of the cell.
+            The sections to include in the domain. If a callable is provided, 
+            it should be a filter function applied to the list of all sections 
+            in the model.
+        distribute : bool, optional
+            Whether to re-distribute the parameters after defining the domain. 
+            Default is True.
         """
         if isinstance(sections, Callable):
             sections = self.get_sections(sections)
@@ -714,14 +746,22 @@ class Model():
                 sec.uninsert_mechanism(mech)
             
 
+        # Add sections to the new domain
         for sec in sections_to_move:
             domain.add_section(sec)
+            # Important: here we insert mechanisms only if we extend the domain,
+            # i.e. the domain already exists and has mechanisms.
+            # If the domain is new, we DO NOT insert mechanisms automatically
+            # and leave it to the user to do so.
             for mech_name in self.domains_to_mechs.get(domain.name, set()):
                 mech = self.mechanisms[mech_name]
-                sec.insert_mechanism(mech, distribute=distribute)
+                sec.insert_mechanism(mech)
 
         self._remove_empty()
 
+        if distribute:
+            self.distribute_all()
+
 
     def _add_domain_groups(self, domain_name):
         """
@@ -1023,7 +1063,6 @@ class Model():
             distribution = Distribution(distr_type, **distr_params)
         self.params[param_name][group_name] = distribution
 
-    
     def distribute_all(self):
         """
         Distribute all parameters to the segments.
@@ -1065,8 +1104,9 @@ class Model():
                     value = seg.parent.get_param_value(param_name)
                     seg.set_param_value(param_name, value)
             else:
-                for seg in filtered_segments:
-                    value = distribution(seg.path_distance())
+                dists = np.array([seg.path_distance() for seg in filtered_segments])
+                values = distribution(dists)
+                for seg, value in zip(filtered_segments, values):
                     seg.set_param_value(param_name, value)
 
 
@@ -1470,6 +1510,8 @@ class Model():
         
 
         # Reinsert active mechanisms after creating the new domain
+        # The new domain by default has no mechanisms. Here we re-insert the
+        # exact same mechanisms as in the original domain of the root section.
         for mech_name in inserted_mechs:
             mech = self.mechanisms[mech_name]
             root.insert_mechanism(mech)
@@ -1888,10 +1930,10 @@ class Model():
                 segments = [self.sec_tree.sections[sec_idx](loc) 
                             for sec_idx, loc in zip(df_pop['sec_idx'], df_pop['loc'])]
                 
-                pop = Population(i, 
-                                segments, 
-                                pop_data['N'], 
-                                'AMPA')
+                pop = Population(idx=i, 
+                                segments=segments, 
+                                N=pop_data['N'], 
+                                syn_type=syn_type)
                 
                 syn_locs = [(self.sec_tree.sections[sec_idx], loc) for sec_idx, loc in zip(df_pop['sec_idx'].tolist(), df_pop['loc'].tolist())]
                 

dendrotweaks/morphology/domains.py

@@ -85,6 +85,9 @@ class Domain:
             return
         sec.domain = None
         sec.domain_idx = None
+        if hasattr(sec, 'path_distance_within_domain'):
+            # Remove cached property if it exists
+            del sec.path_distance_within_domain
         self._sections.remove(sec)
 
 

dendrotweaks/morphology/sec_trees.py

@@ -11,6 +11,7 @@ from dendrotweaks.morphology.trees import Node, Tree
 from dendrotweaks.morphology.domains import Domain
 from dataclasses import dataclass, field
 from bisect import bisect_left
+from functools import cached_property
 
 import warnings
 
@@ -271,11 +272,55 @@ class Section(Node):
         seg_values = [seg.get_param_value(param_name) for seg in self.segments]
         return round(np.mean(seg_values), 16)
 
+    @cached_property
+    def path_distance_to_root(self) -> float:
+        """
+        Calculate the total distance from the section start to the root.
+
+        Returns
+        -------
+        float
+            The distance from the section start to the root.
+        """
+        distance = 0
+        node = self.parent  # Start from the parent node
+
+        if node is None:
+            return 0
+
+        while node.parent:
+            distance += node.length
+            node = node.parent
+            
+        return distance
+
+    @cached_property
+    def path_distance_within_domain(self) -> float:
+        """
+        Calculate the distance from the section start to the root within the same domain.
+
+        Returns
+        -------
+        float
+            The distance from the section start to the root within the same domain.
+        """
+        distance = 0
+        node = self.parent  # Start from the parent node
+
+        if node is None:
+            return 0
 
-    def path_distance(self, relative_position: float = 0, 
-                        within_domain: bool = False) -> float:
+        while node.parent:
+            if node.domain != self.domain:
+                break
+            distance += node.length
+            node = node.parent
+            
+        return distance
+
+    def path_distance(self, relative_position: float = 0, within_domain: bool = False) -> float:
         """
-        Calculate the distance from the section to the root at a given relative position.
+        Get the distance from the section to the root at a given relative position.
 
         Parameters
         ----------
@@ -288,29 +333,16 @@ class Section(Node):
         -------
         float
             The distance from the section to the root.
-
-        Important
-        ---------
-        Assumes that we always attach the 0 end of the child.
         """
         if not (0 <= relative_position <= 1):
             raise ValueError('Relative position must be between 0 and 1.')
 
-        distance = 0
-        factor = relative_position
-        node = self
-
-        while node.parent:
+        if self.parent is None: # Soma section
+            # relative_position = abs(relative_position - 0.5)
+            return 0
 
-            distance += factor * node.length
-
-            if within_domain and node.parent.domain != node.domain:
-                break
-
-            node = node.parent
-            factor = 1
-            
-        return distance       
+        base_distance = self.path_distance_within_domain if within_domain else self.path_distance_to_root
+        return base_distance + relative_position * self.length
 
     
     def disconnect_from_parent(self):
@@ -671,11 +703,13 @@ class NeuronSection(Section):
         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 new_segments:
+            seg_tree.insert_node_before(seg, first_segment)
+        # for i, seg in enumerate(new_segments[:]):
+        #     if i == 0:
+        #         seg_tree.insert_node_before(seg, first_segment)
+        #     else:
+        #         seg_tree.insert_node_after(seg, new_segments[i-1])
 
         for seg in old_segments:
             seg_tree.remove_node(seg)

dendrotweaks/simulators.py

@@ -178,7 +178,7 @@ class NeuronSimulator(Simulator):
             The location along the normalized section length to remove the recording from.
         """
         seg = sec(loc)
-        if self._recordings[var].get(seg):
+        if seg in self._recordings[var]:
             self._recordings[var][seg] = None
             self._recordings[var].pop(seg)
             if not self._recordings[var]:

dendrotweaks/stimuli/populations.py

@@ -255,7 +255,7 @@ class Population():
             'syn_type': [self.syn_type] * len(flat_synapses),
             'name': [self.name] * len(flat_synapses),
             'sec_idx': [syn.sec.idx for syn in flat_synapses],
-            'loc': [syn.loc for syn in flat_synapses],
+            'loc': [round(syn.loc, 8) for syn in flat_synapses],
         }
         
 

{dendrotweaks-0.4.1.dist-info → dendrotweaks-0.4.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dendrotweaks
-Version: 0.4.1
+Version: 0.4.3
 Summary: A toolbox for exploring dendritic dynamics
 Home-page: https://dendrotweaks.dendrites.gr
 Author: Roman Makarov

{dendrotweaks-0.4.1.dist-info → dendrotweaks-0.4.3.dist-info}/RECORD

@@ -1,16 +1,16 @@
-dendrotweaks/__init__.py,sha256=t5t6BzFqY45ePdil4bFlkEaQZiKS-KKthacbRUkwDhc,384
-dendrotweaks/model.py,sha256=Y6m9U0FOoMYG3qCLZczxYfl1-nXeL-4uZNuAqrDlwPQ,69113
+dendrotweaks/__init__.py,sha256=qo6haBW1LRSOhXRjByeruiXSnrnjxrUxqRbDymWSLaQ,384
+dendrotweaks/model.py,sha256=Dm_KJ8KbvHLCFKB3LwBHhgSrdiQteamqgda1J0p898w,71053
 dendrotweaks/model_io.py,sha256=xwXKMcUle-Y0HoWFYVZu3G8v4pdQXmeaDfl2Xi65eHw,2137
 dendrotweaks/path_manager.py,sha256=dai5o6UA0nk-ubwKWRu4LFdDBO77zW_SsMf6k0MLBiI,8703
-dendrotweaks/simulators.py,sha256=Vg6ToTkDZ4OGcANYwYtamGnasyLNbyP8pfPHl9PnMnM,7413
+dendrotweaks/simulators.py,sha256=OscZ4H6z9YiNloDtMAgpPx9n2e-9WJyLEWtcSD1YZR8,7411
 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/ephys_analysis.py,sha256=PqT3aBCuxQbvdm9jnXjlTJ3R5n7_Vwp4fLrHGgtfoWw,14362
 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/distributions.py,sha256=XGczxBYJ0-vkIfXbfzvlIqlH9OpBuT9J95Kzyd2zL5A,10325
 dendrotweaks/biophys/groups.py,sha256=Q4kBIqL1-piIgrpsVq6ojinAWHiEJ1GzMjSAQ7Ni_E8,3212
-dendrotweaks/biophys/mechanisms.py,sha256=j9uygcwkK6Z_08hpTHax40Wn-eV4V_k_on_KyPDnO90,18520
+dendrotweaks/biophys/mechanisms.py,sha256=IxKcyYftEbupJWPqGAV20Ox5a3uPbnXs3gYSlC3z-E0,18520
 dendrotweaks/biophys/default_mod/AMPA.mod,sha256=HY_pWzYvaSDV-w7qruenG2mnll8v79s40HFHjUCIi4U,980
 dendrotweaks/biophys/default_mod/AMPA_NMDA.mod,sha256=ztv2ePUiEQZ93-23FTkGO2DC91rehQuqo0NUIbHZ368,2318
 dendrotweaks/biophys/default_mod/CaDyn.mod,sha256=gwc69K_rxu2w_mV7CnOSOnVaCMc8Z-MfdBFf6lAj4kg,1298
@@ -33,9 +33,9 @@ dendrotweaks/biophys/io/loader.py,sha256=Wv9ZkEDyA3MkCdV0sMeRnBffg2WAI7yTV3r6C41
 dendrotweaks/biophys/io/parser.py,sha256=boT27lFrn5LYrJnkZFs0SwrZZrkSkwO8efqGPJ4Qj0I,17914
 dendrotweaks/biophys/io/reader.py,sha256=JWm5WM9illvSfDkhWEmWBcj8Y7PSi8zeZX9j1ARUHVU,6576
 dendrotweaks/morphology/__init__.py,sha256=JwXmSmdn9e_jqslITEdiU9kWvzxcxT9Aw_kUkXLbm5o,353
-dendrotweaks/morphology/domains.py,sha256=Y4txcGdBdl2aK1DfbTRziNtDyd6bChczwpCWE7lTFzg,2391
+dendrotweaks/morphology/domains.py,sha256=l57KVR5eo1LlH_fCd1AOMiG_SsYLBPBTGQ5R78BHfdM,2545
 dendrotweaks/morphology/point_trees.py,sha256=5dUPaQXYPdJbWoD3pFI2DV2XnuFRhB5d0wTBlfmmIeI,21600
-dendrotweaks/morphology/sec_trees.py,sha256=fj-1kBj7InkqB27Ux-jPidGQXts7FAPXa1m2LdzekNY,35816
+dendrotweaks/morphology/sec_trees.py,sha256=eKLC-yNhsn_rPdTE7w7p6STa1onYkBTGcpBKBpEWZUI,36957
 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
@@ -47,10 +47,10 @@ dendrotweaks/morphology/reduce/reduce.py,sha256=5czZDrG3xsvHn3c_tbYhUOlXgST989-R
 dendrotweaks/morphology/reduce/reduced_cylinder.py,sha256=jGJ4J-amukRr-3DPirVR5pzNO-6H7_sZF1N_X57ZGdw,5132
 dendrotweaks/stimuli/__init__.py,sha256=bFfSEZhCVpwOVEBgLe65iiY3SdpjKPhyLemC1z5OX9I,153
 dendrotweaks/stimuli/iclamps.py,sha256=NjkhhwZKJR1f_g3N9BVxMVoO9ubBk5WkQ6h9Bnf9xgA,1681
-dendrotweaks/stimuli/populations.py,sha256=y85v8smiMifINIqXm1O3mOINAlDTz-SPGLS78alhX5A,8325
+dendrotweaks/stimuli/populations.py,sha256=vq2NUOaxaltUwlcT7wuCe8z1JWc8rk6HfPmfEd1kK68,8335
 dendrotweaks/stimuli/synapses.py,sha256=g4MgWTske2TZ2i9FIIOE8-KXNx_3dWa3zEhB2rcqYig,5470
-dendrotweaks-0.4.1.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-dendrotweaks-0.4.1.dist-info/METADATA,sha256=zX87vndTAiJHfWJkywrmMiqa7lNxcg4Kwfbf6tQ0OKs,2740
-dendrotweaks-0.4.1.dist-info/WHEEL,sha256=A8Eltl-h0W-qZDVezsLjjslosEH_pdYC2lQ0JcbgCzs,91
-dendrotweaks-0.4.1.dist-info/top_level.txt,sha256=OzT_2BSI5j5zxC447K6Y-0W-GHbued7iX-_hFGAKMxY,13
-dendrotweaks-0.4.1.dist-info/RECORD,,
+dendrotweaks-0.4.3.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+dendrotweaks-0.4.3.dist-info/METADATA,sha256=KV5Ev0CC98m0JrqsvOG5szTc8Yqi_RjcKuOK4C7yHZo,2740
+dendrotweaks-0.4.3.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+dendrotweaks-0.4.3.dist-info/top_level.txt,sha256=OzT_2BSI5j5zxC447K6Y-0W-GHbued7iX-_hFGAKMxY,13
+dendrotweaks-0.4.3.dist-info/RECORD,,

{dendrotweaks-0.4.1.dist-info → dendrotweaks-0.4.3.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.7.0)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: true
 Tag: py3-none-any