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

dendrotweaks/simulators.py

@@ -1,5 +1,6 @@
 from collections import defaultdict
 import warnings
+from functools import cached_property
 
 import matplotlib.pyplot as plt
 import neuron
@@ -9,6 +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
 
@@ -30,34 +32,59 @@ def reset_neuron():
 
 reset_neuron()            
 
+# -------------------------------------------------------
+# SIMULATOR
+# -------------------------------------------------------
+
 class Simulator:
     """
     A generic simulator class.
     """
     def __init__(self):
-        self.vs = None
-        self.t = None
+        self._t = None
         self.dt = None
-        self.recordings = {}
+        self._recordings = {'v': {}}
 
-    def plot_voltage(self, ax=None, segments=None, **kwargs):
+    def plot_var(self, var='v', ax=None, segments=None, **kwargs):
+        if self._t is None:
+            raise ValueError('Simulation has not been run yet.')
+        if var not in self.recordings:
+            raise ValueError(f'Variable {var} not recorded.')
         if ax is None:
             fig, ax = plt.subplots()
         if segments is None:
-            segments = self.recordings.keys()
-        for seg, v in self.vs.items():
+            segments = self.recordings[var].keys()
+        for seg, x in self.recordings[var].items():
             if segments and seg not in segments:
                 continue
-            ax.plot(self.t, v, label=f'{seg.domain} {seg.idx}', **kwargs)
-
+            ax.plot(self.t, x, label=f'{var} {seg.domain} {seg.idx}', **kwargs)
         if len(segments) < 10:
             ax.legend()
-        # ax.set_ylim(-100, 60)
         ax.set_xlabel('Time (ms)')
-        ax.set_ylabel('Voltage (mV)')
+        if var == 'v':
+            ax.set_ylabel('Voltage (mV)')
+        elif var.startswith('i_'):
+            ax.set_ylabel('Current (nA)')
+        return ax
+
+    def plot_voltage(self, **kwargs):
+        """
+        Plot the recorded voltages.
+        """
+        self.plot_var('v', **kwargs)
+    
+    def plot_currents(self, **kwargs):
+        """
+        Plot the recorded currents.
+        """
+        ax = kwargs.pop('ax', None)
+        for var in self.recordings:
+            if var.startswith('i_'):
+                ax = self.plot_var(var, ax=ax, **kwargs)
+            
         
 
-class NEURONSimulator(Simulator):
+class NeuronSimulator(Simulator):
     """
     A class to represent the NEURON simulator.
 
@@ -88,10 +115,33 @@ class NEURONSimulator(Simulator):
         self.temperature = temperature
         self.v_init = v_init * mV
         self._duration = 300
+        
 
         self.dt = dt
         self._cvode = cvode
 
+    @cached_property
+    def recordings(self):
+        return {
+            var:{ seg: vec.to_python() for seg, vec in recs.items() }
+            for var, recs in self._recordings.items()
+        }
+
+    @cached_property
+    def t(self):
+        return self._t.to_python()
+
+    def _clean_cache(self):
+        """
+        Clean the cache of the simulator.
+        """
+        try:
+            del self.recordings
+            del self.t
+        except AttributeError:
+            # Property hasn't been accessed yet, so no need to delete
+            pass
+
 
     def add_recording(self, sec, loc, var='v'):
         """
@@ -107,11 +157,16 @@ class NEURONSimulator(Simulator):
             The variable to record. Default is 'v' (voltage).
         """
         seg = sec(loc)
-        if self.recordings.get(seg):
-            self.remove_recording(sec, loc)
-        self.recordings[seg] = h.Vector().record(getattr(seg._ref, f'_ref_{var}'))
-
-    def remove_recording(self, sec, loc):
+        if not hasattr(seg._ref, f'_ref_{var}'):
+            raise ValueError(f'Segment {seg} does not have variable {var}.')
+        if self._recordings.get(var, {}).get(seg):
+            self.remove_recording(sec, loc, var)
+        if var not in self._recordings:
+            self._recordings[var] = {}
+        self._recordings[var][seg] = h.Vector().record(getattr(seg._ref, f'_ref_{var}'))
+        self._clean_cache()
+
+    def remove_recording(self, sec, loc, var='v'):
         """
         Remove a recording from the simulator.
 
@@ -123,35 +178,45 @@ class NEURONSimulator(Simulator):
             The location along the normalized section length to remove the recording from.
         """
         seg = sec(loc)
-        if self.recordings.get(seg):
-            self.recordings[seg] = None
-            self.recordings.pop(seg)
-
-    def remove_all_recordings(self):
+        if self._recordings[var].get(seg):
+            self._recordings[var][seg] = None
+            self._recordings[var].pop(seg)
+            if not self._recordings[var]:
+                self._recordings.pop(var)
+        self._clean_cache()
+
+    def remove_all_recordings(self, var=None):
         """
         Remove all recordings from the simulator.
         """
-        for seg in list(self.recordings.keys()):
-            sec, loc = seg._section, seg.x
-            self.remove_recording(sec, loc)
-        if self.recordings:
-            warnings.warn(f'Not all recordings were removed: {self.recordings}')
-        self.recordings = {}
+        variables = [var] if var else list(self._recordings.keys())
+        for variable in variables:
+            for seg in list(self._recordings.get(variable, {}).keys()):
+                self.remove_recording(seg._section, seg.x, variable)
+            if self._recordings.get(variable):
+                warnings.warn(f'Not all recordings were removed for variable {variable}: {self._recordings}')
 
 
     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.
@@ -161,35 +226,16 @@ class NEURONSimulator(Simulator):
         duration : float
             The duration of the simulation in milliseconds.
         """
-        self._duration = duration
-
 
-        # vs = list(self.recordings.values())
-        Is = []
+        self._clean_cache()
 
-        # for v in self.recordings.values():
-        #     # v = h.Vector().record(seg._ref_v)
-        #     vs.append(v)
-
-        t = h.Vector().record(h._ref_t)
+        self._duration = duration
 
-        # if self.ch is None:
-        #     pass
-        # else:
-        #     for seg in self.recordings.keys():
-        #         if getattr(seg, f'_ref_i_{self.ch.suffix}', None) is None:
-        #             logger.warning(
-        #                 f'No current recorded for {self.ch.suffix} at {seg}. Make i a RANGE variable in mod file.')
-        #             continue
-        #         I = h.Vector().record(getattr(seg, f'_ref_i_{self.ch.suffix}'))
-        #         Is.append(I)
+        self._t = h.Vector().record(h._ref_t)
 
         self._init_simulation()
 
         h.continuerun(duration * ms)
-
-        self.t = t.to_python()
-        self.vs = {seg: v.to_python() for seg, v in self.recordings.items()}
     
 
     def to_dict(self):

dendrotweaks/stimuli/populations.py

@@ -123,6 +123,17 @@ class Population():
                 spike_times[syn].extend(syn.spike_times)
         return dict(spike_times)
 
+    @property
+    def n_per_seg(self):
+        """
+        Return the number of synapses per segment.
+        """
+        n_per_seg = {seg: 0 for seg in self.segments}
+        for (sec, loc), syns in self.synapses.items():
+            seg = sec(loc)
+            n_per_seg[seg] += len(syns)
+        return dict(n_per_seg)
+            
 
     def update_kinetic_params(self, **params):
         """

{dendrotweaks-0.3.1.dist-info → dendrotweaks-0.4.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dendrotweaks
-Version: 0.3.1
+Version: 0.4.1
 Summary: A toolbox for exploring dendritic dynamics
 Home-page: https://dendrotweaks.dendrites.gr
 Author: Roman Makarov
@@ -15,7 +15,7 @@ Classifier: Operating System :: OS Independent
 Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: neuron>=8.2.6
+Requires-Dist: neuron>=8.2.6; sys_platform == "linux" or sys_platform == "darwin"
 Requires-Dist: neuron-reduce==0.0.7
 Requires-Dist: numpy<2.0.0
 Requires-Dist: pandas

dendrotweaks-0.4.1.dist-info/RECORD

@@ -0,0 +1,56 @@
+dendrotweaks/__init__.py,sha256=t5t6BzFqY45ePdil4bFlkEaQZiKS-KKthacbRUkwDhc,384
+dendrotweaks/model.py,sha256=Y6m9U0FOoMYG3qCLZczxYfl1-nXeL-4uZNuAqrDlwPQ,69113
+dendrotweaks/model_io.py,sha256=xwXKMcUle-Y0HoWFYVZu3G8v4pdQXmeaDfl2Xi65eHw,2137
+dendrotweaks/path_manager.py,sha256=dai5o6UA0nk-ubwKWRu4LFdDBO77zW_SsMf6k0MLBiI,8703
+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=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
+dendrotweaks/biophys/default_mod/CaDyn.mod,sha256=gwc69K_rxu2w_mV7CnOSOnVaCMc8Z-MfdBFf6lAj4kg,1298
+dendrotweaks/biophys/default_mod/GABAa.mod,sha256=jdGRid-Wzw4y9kHvq74oSMogLhSiS-Ac2DDaLOrxVi8,983
+dendrotweaks/biophys/default_mod/Leak.mod,sha256=u0lwMYGgl5kNZN5W4N6YHgRSeVxb-z2oM9fqou5rCV8,420
+dendrotweaks/biophys/default_mod/NMDA.mod,sha256=tT4Q5UPoeztXcQ45uZc2PUO3-8OkDLCmrS7WDsn1yQQ,1185
+dendrotweaks/biophys/default_mod/vecstim.mod,sha256=iSpJgR96O2Z3pLNUFIsZ7YJ529ncKUBaZqDJvA0_oV0,965
+dendrotweaks/biophys/default_templates/NEURON_template.py,sha256=MWSv2fLKGJxdt2zfSO0b74peuBC8U9j_S6AwM5URXts,14945
+dendrotweaks/biophys/default_templates/default.py,sha256=7HEbR2GJEOhgiox1QtZUEuHi5ihNAHDLsXQiQk980tI,2201
+dendrotweaks/biophys/default_templates/standard_channel.mod,sha256=sw80c-JyqfXNA7c7v7pZGLY-0MgFUvd3bPvJcAGXNSk,2923
+dendrotweaks/biophys/default_templates/template_jaxley.py,sha256=t-GsCSUyQ7rDoaLmyuWd9bIxB8W3bCqJdnikD59EVvI,3676
+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=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=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=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=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
+dendrotweaks/morphology/reduce/reduce.py,sha256=5czZDrG3xsvHn3c_tbYhUOlXgST989-RS-ntbhlvvA0,6361
+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/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-0.3.1.dist-info → dendrotweaks-0.4.1.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (77.0.3)
+Generator: setuptools (80.7.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

dendrotweaks/membrane/__init__.py

@@ -1,6 +0,0 @@
-from dendrotweaks.membrane.mechanisms import Mechanism, IonChannel, CaDynamics, StandardIonChannel, LeakChannel
-from dendrotweaks.membrane.mechanisms import LeakChannel
-from dendrotweaks.membrane.groups import SegmentGroup
-from dendrotweaks.membrane.distributions import Distribution
-
-import dendrotweaks.membrane.io as io

dendrotweaks/membrane/io/__init__.py

@@ -1,11 +0,0 @@
-from dendrotweaks.membrane.io.loader import MODFileLoader
-from dendrotweaks.membrane.io.converter import MODFileConverter
-
-from dendrotweaks.membrane.io.reader import MODFileReader
-from dendrotweaks.membrane.io.parser import MODFileParser
-from dendrotweaks.membrane.io.code_generators import PythonCodeGenerator
-from dendrotweaks.membrane.io.code_generators import NMODLCodeGenerator
-
-from dendrotweaks.membrane.io.factories import create_channel
-from dendrotweaks.membrane.io.factories import create_standard_channel
-from dendrotweaks.membrane.io.factories import standardize_channel

dendrotweaks/membrane/io/loader.py

@@ -1,90 +0,0 @@
-import os
-import shutil
-import subprocess
-import neuron
-from neuron import h
-
-from pprint import pprint
-
-class MODFileLoader():
-
-    def __init__(self):
-        self._loaded_mechanisms = set()
-        self.verbose = False
-              
-    # LOADING METHODS
-
-    def _get_mechanism_dir(self, path_to_mod_file: str) -> str:
-        """
-        Get the subdirectory for the given mod file.
-
-        Parameters
-        ----------
-        path_to_mod_file : str
-            Path to the .mod file.
-
-        Returns
-        -------
-        str
-            Path to the subdirectory for the mechanism.
-        """
-        mechanism_name = os.path.basename(path_to_mod_file).replace('.mod', '')
-        parent_dir = os.path.dirname(path_to_mod_file)
-        return os.path.join(parent_dir, mechanism_name)
-
-    def load_mechanism(self, path_to_mod_file: str, 
-                       recompile: bool = False) -> None:
-        """
-        Load a mechanism from the specified mod file.
-        Uses the NEURON neuron.load_mechanisms method to make
-        the mechanism available in the hoc interpreter.
-        Creates a temporary directory for the mechanism files
-        to be able to dynamically load mechanisms.
-
-        Parameters
-        ----------
-        path_to_mod_file : str
-            Path to the .mod file.
-        recompile : bool
-            Force recompilation even if already compiled.
-        """
-        mechanism_name = os.path.basename(path_to_mod_file).replace('.mod', '')
-        mechanism_dir = self._get_mechanism_dir(path_to_mod_file)
-        x86_64_dir = os.path.join(mechanism_dir, 'x86_64')
-
-        if self.verbose: print(f"{'=' * 60}\nLoading mechanism {mechanism_name} to NEURON...\n{'=' * 60}")
-
-        if mechanism_name in self._loaded_mechanisms:
-            if self.verbose: print(f'Mechanism "{mechanism_name}" already loaded')
-            return
-
-        if recompile and os.path.exists(mechanism_dir):
-            shutil.rmtree(mechanism_dir)
-
-        if not os.path.exists(x86_64_dir):
-            if self.verbose: print(f'Compiling mechanism "{mechanism_name}"...')
-            os.makedirs(mechanism_dir, exist_ok=True)
-            shutil.copy(path_to_mod_file, mechanism_dir)
-            self._compile_files(mechanism_dir)
-
-        if hasattr(h, mechanism_name):
-            if self.verbose: print(f'Mechanism "{mechanism_name}" already exists in hoc')
-        else:
-            try:
-                neuron.load_mechanisms(mechanism_dir)
-            except Exception as e:
-                print(f"Failed to load mechanism {mechanism_name}: {e}")
-                return
-        self._loaded_mechanisms.add(mechanism_name)
-        if self.verbose: print(f'Loaded mechanism "{mechanism_name}"')
-
-    # HELPER METHODS
-
-    
-    def _compile_files(self, path: str) -> None:
-        """Compile the MOD files in the specified directory."""
-        try:
-            subprocess.run(["nrnivmodl"], cwd=path, check=True)
-        except subprocess.CalledProcessError as e:
-            print(f"Compilation failed: {e}")
-

dendrotweaks-0.3.1.dist-info/RECORD

@@ -1,56 +0,0 @@
-dendrotweaks/__init__.py,sha256=Oty4wVcVFs_9w7L9peCncnzQKFubqkRHyf4c3HKfwWY,385
-dendrotweaks/model.py,sha256=wy17K85d95bD1ioibhDxs8rcNCzow3BP1OVam1b1bTM,67445
-dendrotweaks/model_io.py,sha256=xwXKMcUle-Y0HoWFYVZu3G8v4pdQXmeaDfl2Xi65eHw,2137
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