dendrotweaks 0.3.1__py3-none-any.whl → 0.4.1__py3-none-any.whl

dendrotweaks/model.py

@@ -6,16 +6,16 @@ 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.membrane.groups import SegmentGroup
-from dendrotweaks.membrane.mechanisms import Mechanism, LeakChannel, CaDynamics
-from dendrotweaks.membrane.io import create_channel, standardize_channel, create_standard_channel
-from dendrotweaks.membrane.io import MODFileLoader
+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
+from dendrotweaks.biophys.io import MODFileLoader
 from dendrotweaks.morphology.io import create_point_tree, create_section_tree, create_segment_tree
 from dendrotweaks.stimuli.iclamps import IClamp
-from dendrotweaks.membrane.distributions import Distribution
+from dendrotweaks.biophys.distributions import Distribution
 from dendrotweaks.stimuli.populations import Population
 from dendrotweaks.utils import calculate_lambda_f, dynamic_import
 from dendrotweaks.utils import get_domain_color, timeit
@@ -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)
 
 
@@ -343,11 +343,11 @@ class Model():
         """
         return self.path_manager.list_files('morphology', extension=extension)
 
-    def list_membrane_configs(self, extension='json'):
+    def list_biophys(self, extension='json'):
         """
-        List the membrane configurations available for the model.
+        List the biophysical configurations available for the model.
         """
-        return self.path_manager.list_files('membrane', extension=extension)
+        return self.path_manager.list_files('biophys', extension=extension)
 
     def list_mechanisms(self, extension='mod'):
         """
@@ -355,7 +355,7 @@ class Model():
         """
         return self.path_manager.list_files('mod', extension=extension)
 
-    def list_stimuli_configs(self, extension='json'):
+    def list_stimuli(self, extension='json'):
         """
         List the stimuli configurations available for the model.
         """
@@ -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):
@@ -631,8 +632,8 @@ 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 +710,15 @@ 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 +800,7 @@ 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 +850,7 @@ 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):
@@ -1287,7 +1290,7 @@ class Model():
         print(f'Recording added to sec {sec} at loc {loc}.')
 
 
-    def remove_recording(self, sec, loc):
+    def remove_recording(self, sec, loc, var='v'):
         """
         Remove a recording from the model.
 
@@ -1298,14 +1301,14 @@ class Model():
         loc : float
             The location along the normalized section length to remove the recording from.
         """
-        self.simulator.remove_recording(sec, loc)
+        self.simulator.remove_recording(sec, loc, var)
 
 
-    def remove_all_recordings(self):
+    def remove_all_recordings(self, var=None):
         """
         Remove all recordings from the model.
         """
-        self.simulator.remove_all_recordings()
+        self.simulator.remove_all_recordings(var=var)
 
 
     def run(self, duration=300):
@@ -1402,7 +1405,8 @@ 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 +1438,8 @@ 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 +1471,8 @@ 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())
         
                
@@ -1598,7 +1604,7 @@ class Model():
             'name': self.name,
             },
             'd_lambda': self.d_lambda,
-            'domains': {domain: list(mechs) for domain, mechs in self.domains_to_mechs.items()},
+            'domains': {domain: sorted(list(mechs)) for domain, mechs in self.domains_to_mechs.items()},
             'groups': [
             group.to_dict() for group in self._groups
             ],
@@ -1657,9 +1663,9 @@ class Model():
             
 
 
-    def export_membrane(self, file_name, **kwargs):
+    def export_biophys(self, file_name, **kwargs):
         """
-        Export the membrane properties of the model to a JSON file.
+        Export the biophysical properties of the model to a JSON file.
 
         Parameters
         ----------
@@ -1669,16 +1675,18 @@ class Model():
             Additional keyword arguments to pass to `json.dump`.
         """        
         
-        path_to_json = self.path_manager.get_file_path('membrane', file_name, extension='json')
+        path_to_json = self.path_manager.get_file_path('biophys', file_name, extension='json')
+        if not kwargs.get('indent'):
+            kwargs['indent'] = 4
 
         data = self.to_dict()
         with open(path_to_json, 'w') as f:
             json.dump(data, f, **kwargs)
 
 
-    def load_membrane(self, file_name, recompile=True):
+    def load_biophys(self, file_name, recompile=True):
         """
-        Load the membrane properties of the model from a JSON file.
+        Load the biophysical properties of the model from a JSON file.
 
         Parameters
         ----------
@@ -1688,13 +1696,18 @@ class Model():
             Whether to recompile the mechanisms after loading. Default is True.
         """
         self.add_default_mechanisms()
-        self.add_mechanisms('mod', recompile=recompile)
+        
 
-        path_to_json = self.path_manager.get_file_path('membrane', file_name, extension='json')
+        path_to_json = self.path_manager.get_file_path('biophys', file_name, extension='json')
 
         with open(path_to_json, 'r') as f:
             data = json.load(f)
 
+        for mech_name in {mech for mechs in data['domains'].values() for mech in mechs}:
+            if mech_name in ['Leak', 'CaDyn', 'Independent']:
+                continue
+            self.add_mechanism(mech_name, dir_name='mod', recompile=recompile)            
+
         self.from_dict(data)
 
 
@@ -1715,6 +1728,14 @@ class Model():
                 **self.simulator.to_dict(),
             },
             'stimuli': {
+                'recordings': [
+                    {
+                        'name': f'rec_{i}',
+                        'var': var
+                    } 
+                    for var, recs in self.simulator.recordings.items()
+                    for i, _ in enumerate(recs)
+                ],
                 'iclamps': [
                     {
                         'name': f'iclamp_{i}',
@@ -1743,11 +1764,16 @@ class Model():
         """
         
         rec_data = {
-            'type': ['recording'] * len(self.recordings),
-            'idx': [i for i in range(len(self.recordings))],
-            'sec_idx': [seg._section.idx for seg in self.recordings],
-            'loc': [seg.x for seg in self.recordings],
+            'type': [],
+            'idx': [],
+            'sec_idx': [],
+            'loc': [],
         }
+        for var, recs in self.simulator.recordings.items():
+            rec_data['type'].extend(['rec'] * len(recs))
+            rec_data['idx'].extend([i for i in range(len(recs))])
+            rec_data['sec_idx'].extend([seg._section.idx for seg in recs])
+            rec_data['loc'].extend([seg.x for seg in recs])
 
         iclamp_data = {
             'type': ['iclamp'] * len(self.iclamps),
@@ -1776,6 +1802,7 @@ class Model():
             pd.DataFrame(iclamp_data),
             pd.DataFrame(synapses_data)
         ], ignore_index=True)
+        df['idx'] = df['idx'].astype(int)
         df['sec_idx'] = df['sec_idx'].astype(int)
         if path_to_csv: df.to_csv(path_to_csv, index=False)
 
@@ -1797,6 +1824,8 @@ class Model():
 
         data = self.stimuli_to_dict()
 
+        if not kwargs.get('indent'):
+            kwargs['indent'] = 4
         with open(path_to_json, 'w') as f:
             json.dump(data, f, **kwargs)
 
@@ -1827,13 +1856,9 @@ class Model():
 
         self.simulator.from_dict(data['simulation'])
 
-        # Recordings ---------------------------------------------------------
-
-        df_recs = df_stimuli[df_stimuli['type'] == 'recording']
-        for i, row in df_recs.iterrows():
-            self.add_recording(
-                self.sec_tree.sections[row['sec_idx']], row['loc']
-            )
+        # Clear all stimuli and recordings
+        self.remove_all_stimuli()
+        self.remove_all_recordings()
 
         # IClamps -----------------------------------------------------------
 
@@ -1875,6 +1900,20 @@ class Model():
                 pop.update_input_params(**pop_data['input_params'])
                 self._add_population(pop)
 
+        # Recordings ---------------------------------------------------------
+
+        df_recs = df_stimuli[df_stimuli['type'] == 'rec'].reset_index(drop=True, inplace=False)
+        for i, row in df_recs.iterrows():
+            # TODO: This conditional statement is to account for a recent change
+            # in the JSON structure. It should be removed in the future.
+            if data['stimuli'].get('recordings'):
+                var = data['stimuli']['recordings'][i]['var']
+            else:
+                var = 'v'
+            self.add_recording(
+                self.sec_tree.sections[row['sec_idx']], row['loc'], var
+            )
+
 
     def export_to_NEURON(self, file_name, include_kinetic_params=True):
         """

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)