ENH: Refactor BatchSimulate Example and Improve Documentation (jone…

…scompneurolab#857)

* ENH BatchSimulate for JSON path handling

Signed-off-by: samadpls <[email protected]>

* Fix: Docstring of dic_to_network

Signed-off-by: samadpls <[email protected]>

* ENH: Reorder the init params

Signed-off-by: samadpls <[email protected]>

* Added record_isec vsec validation test

Signed-off-by: samadpls <[email protected]>

* Removed net_json param and update test

Signed-off-by: samadpls <[email protected]>

* Refactored  Example and initialize parameters

Co-authored-by: Nicholas Tolley <[email protected]>
Signed-off-by: samadpls <[email protected]>

* Enh: visualization of dipole responses in plot_batch_simulate

Co-authored-by: Nicholas Tolley <[email protected]>
Signed-off-by: samadpls <[email protected]>

* Refactor batch simulation parameters and backend

Signed-off-by: samadpls <[email protected]>

* [MRG] Fix indexing for batch simulations (jonescompneurolab#5)

* ENH BatchSimulate for JSON path handling

Signed-off-by: samadpls <[email protected]>

* Fix: Docstring of dic_to_network

Signed-off-by: samadpls <[email protected]>

* ENH: Reorder the init params

Signed-off-by: samadpls <[email protected]>

* Added record_isec vsec validation test

Signed-off-by: samadpls <[email protected]>

* Removed net_json param and update test

Signed-off-by: samadpls <[email protected]>

* Refactored  Example and initialize parameters

Co-authored-by: Nicholas Tolley <[email protected]>
Signed-off-by: samadpls <[email protected]>

* Enh: visualization of dipole responses in plot_batch_simulate

Co-authored-by: Nicholas Tolley <[email protected]>
Signed-off-by: samadpls <[email protected]>

* Refactor batch simulation parameters and backend

Signed-off-by: samadpls <[email protected]>

* batches run in parallel

---------

Signed-off-by: samadpls <[email protected]>
Co-authored-by: samadpls <[email protected]>

* Refactor: Removed joblib from simulate_dipole, and added parallel execution test.

Signed-off-by: samadpls <[email protected]>

* Refactor: Simplify BatchSimulate parameters by removing n_jobs

Signed-off-by: samadpls <[email protected]>

* Remove unused Dask code and simplify BatchSimulate initialization

Signed-off-by: samadpls <[email protected]>

---------

Signed-off-by: samadpls <[email protected]>
Co-authored-by: Nicholas Tolley <[email protected]>

examples/howto/plot_batch_simulate.py

@@ -24,13 +24,25 @@
 from hnn_core import jones_2009_model
 
 # The number of cores may need modifying depending on your current machine.
-n_jobs = 10
+n_jobs = 4
 ###############################################################################
+# The `add_evoked_drive` function simulates external input to the network,
+# mimicking sensory stimulation or other external events.
+#
+# - `evprox` indicates a proximal drive, targeting dendrites near the cell
+#   bodies.
+# - `mu=40` and `sigma=5` define the timing (mean and spread) of the input.
+# - `weights_ampa` and `synaptic_delays` control the strength and
+#   timing of the input.
+#
+# This evoked drive causes the initial positive deflection in the dipole
+# signal, triggering a cascade of activity through the network and
+# resulting in the complex waveforms observed.
 
 
 def set_params(param_values, net=None):
     """
-    Set parameters in the network drives.
+    Set parameters for the network drives.
 
     Parameters
     ----------
@@ -57,16 +69,16 @@ def set_params(param_values, net=None):
                          synaptic_delays=synaptic_delays)
 
 ###############################################################################
-# Define a parameter grid for the batch simulation.
+# Next, we define a parameter grid for the batch simulation.
 
 
 param_grid = {
-    'weight_basket': np.logspace(-4 - 1, 10),
-    'weight_pyr': np.logspace(-4, -1, 10)
+    'weight_basket': np.logspace(-4, -1, 20),
+    'weight_pyr': np.logspace(-4, -1, 20)
 }
 
 ###############################################################################
-# Define a function to calculate summary statistics
+# We then define a function to calculate summary statistics.
 
 
 def summary_func(results):
@@ -95,36 +107,54 @@ def summary_func(results):
 ###############################################################################
 # Run the batch simulation and collect the results.
 
-# Comment off this code, if dask and distributed Python packages are installed
-# from dask.distributed import Client
-# client = Client(threads_per_worker=1, n_workers=5, processes=False)
-
 
-# Run the batch simulation and collect the results.
+# Initialize the network model and run the batch simulation.
 net = jones_2009_model(mesh_shape=(3, 3))
 batch_simulation = BatchSimulate(net=net,
                                  set_params=set_params,
                                  summary_func=summary_func)
 simulation_results = batch_simulation.run(param_grid,
                                           n_jobs=n_jobs,
                                           combinations=False,
-                                          backend='multiprocessing')
-# backend='dask' if installed
+                                          backend='loky')
+
 print("Simulation results:", simulation_results)
 ###############################################################################
 # This plot shows an overlay of all smoothed dipole waveforms from the
-# batch simulation. Each line represents a different set of parameters,
-# allowing us to visualize the range of responses across the parameter space.
+# batch simulation. Each line represents a different set of synaptic strength
+# parameters (`weight_basket`), allowing us to visualize the range of responses
+# across the parameter space.
+# The colormap represents synaptic strengths, from weaker (purple)
+# to stronger (yellow).
+#
+# As drive strength increases, dipole responses show progressively larger
+# amplitudes and more distinct features, reflecting heightened network
+# activity. Weak drives (purple lines) produce smaller amplitude signals with
+# simpler waveforms, while stronger drives (yellow lines) generate
+# larger responses with more pronounced oscillatory features, indicating
+# more robust network activity.
+#
+# The y-axis represents dipole amplitude in nAm (nanoAmpere-meters), which is
+# the product of current flow and distance in the neural tissue.
+#
+# Stronger synaptic connections (yellow lines) generally show larger
+# amplitude responses and more pronounced features throughout the simulation.
 
-dpl_waveforms = []
+dpl_waveforms, param_values = [], []
 for data_list in simulation_results['simulated_data']:
     for data in data_list:
         dpl_smooth = data['dpl'][0].copy().smooth(window_len=30)
         dpl_waveforms.append(dpl_smooth.data['agg'])
+        param_values.append(data['param_values']['weight_basket'])
 
 plt.figure(figsize=(10, 6))
-for waveform in dpl_waveforms:
-    plt.plot(waveform, alpha=0.5, linewidth=3)
+cmap = plt.get_cmap('viridis')
+log_param_values = np.log10(param_values)
+norm = plt.Normalize(log_param_values.min(), log_param_values.max())
+
+for waveform, log_param in zip(dpl_waveforms, log_param_values):
+    color = cmap(norm(log_param))
+    plt.plot(waveform, color=color, alpha=0.7, linewidth=2)
 plt.title('Overlay of Dipole Waveforms')
 plt.xlabel('Time (ms)')
 plt.ylabel('Dipole Amplitude (nAm)')

hnn_core/batch_simulate.py

@@ -16,15 +16,14 @@
 
 
 class BatchSimulate(object):
-    def __init__(self, set_params, net=jones_2009_model(), tstop=170,
-                 dt=0.025, n_trials=1, record_vsec=False,
-                 record_isec=False, postproc=False, save_outputs=False,
+    def __init__(self, set_params, net=jones_2009_model(),
+                 tstop=170, dt=0.025, n_trials=1,
                  save_folder='./sim_results', batch_size=100,
-                 overwrite=True, summary_func=None,
-                 save_dpl=True, save_spiking=False,
-                 save_lfp=False, save_voltages=False,
-                 save_currents=False, save_calcium=False,
-                 clear_cache=False):
+                 overwrite=True, save_outputs=False, save_dpl=True,
+                 save_spiking=False, save_lfp=False, save_voltages=False,
+                 save_currents=False, save_calcium=False, record_vsec=False,
+                 record_isec=False, postproc=False, clear_cache=False,
+                 summary_func=None):
         """Initialize the BatchSimulate class.
 
         Parameters
@@ -37,34 +36,17 @@ def __init__(self, set_params, net=jones_2009_model(), tstop=170,
             where ``net`` is a Network object and ``params`` is a dictionary
             of the parameters that will be set inside the function.
         net : Network object, optional
-            The network model to use for simulations. Must be an instance of
-            jones_2009_model, law_2021_model, or calcium_model.
-            Default is jones_2009_model().
+            The network model to use for simulations. Examples include:
+            - `jones_2009_model`: A network model based on Jones et al. (2009).
+            - `law_2021_model`: A network model based on Law et al. (2021).
+            - `calcium_model`: A network model incorporating calcium dynamics.
+            Default is `jones_2009_model()`
         tstop : float, optional
             The stop time for the simulation. Default is 170 ms.
         dt : float, optional
             The time step for the simulation. Default is 0.025 ms.
         n_trials : int, optional
             The number of trials for the simulation. Default is 1.
-        record_vsec : 'all' | 'soma' | False
-            Option to record voltages from all sections ('all'), or just
-            the soma ('soma'). Default: False.
-        record_isec : 'all' | 'soma' | False
-            Option to record voltages from all sections ('all'), or just
-            the soma ('soma'). Default: False.
-        postproc : bool
-            If True, smoothing (``dipole_smooth_win``) and scaling
-            (``dipole_scalefctr``) values are read from the parameter file, and
-            applied to the dipole objects before returning.
-            Note that this setting
-            only affects the dipole waveforms, and not somatic voltages,
-            possible extracellular recordings etc.
-            The preferred way is to use the
-            :meth:`~hnn_core.dipole.Dipole.smooth` and
-            :meth:`~hnn_core.dipole.Dipole.scale` methods instead.
-            Default: False.
-        save_outputs : bool, optional
-            Whether to save the simulation outputs to files. Default is False.
         save_folder : str, optional
             The path to save the simulation outputs.
             Default is './sim_results'.
@@ -74,9 +56,8 @@ def __init__(self, set_params, net=jones_2009_model(), tstop=170,
         overwrite : bool, optional
             Whether to overwrite existing files and create file paths
             if they do not exist. Default is True.
-        summary_func : callable, optional
-            A function to calculate summary statistics from the simulation
-            results. Default is None.
+        save_outputs : bool, optional
+            Whether to save the simulation outputs to files. Default is False.
         save_dpl : bool
             If True, save dipole results. Note, `save_outputs` must be True.
             Default: True.
@@ -97,9 +78,23 @@ def __init__(self, set_params, net=jones_2009_model(), tstop=170,
             If True, save calcium concentrations.
             Note, `save_outputs` must be True.
             Default: False.
+        record_vsec : 'all' | 'soma' | False
+            Option to record voltages from all sections ('all'), or just
+            the soma ('soma'). Default: False.
+        record_isec : 'all' | 'soma' | False
+            Option to record voltages from all sections ('all'), or just
+            the soma ('soma'). Default: False.
+        postproc : bool
+            If True, smoothing (``dipole_smooth_win``) and scaling
+            (``dipole_scalefctr``) values are read from the parameter file, and
+            applied to the dipole objects before returning.
+            Default: False.
         clear_cache : bool, optional
             Whether to clear the results cache after saving each batch.
             Default is False.
+        summary_func : callable, optional
+            A function to calculate summary statistics from the simulation
+            results. Default is None.
         Notes
         -----
         When `save_output=True`, the saved files will appear as
@@ -201,16 +196,13 @@ def run(self, param_grid, return_output=True,
         param_combinations = self._generate_param_combinations(
             param_grid, combinations)
         total_sims = len(param_combinations)
-        num_sims_per_batch = max(total_sims // self.batch_size, 1)
         batch_size = min(self.batch_size, total_sims)
 
         results = []
         simulated_data = []
-        for i in range(batch_size):
-            start_idx = i * num_sims_per_batch
-            end_idx = start_idx + num_sims_per_batch
-            if i == batch_size - 1:
-                end_idx = len(param_combinations)
+        for i in range(0, total_sims, batch_size):
+            start_idx = i
+            end_idx = min(i + batch_size, total_sims)
             batch_results = self.simulate_batch(
                 param_combinations[start_idx:end_idx],
                 n_jobs=n_jobs,
@@ -388,6 +380,14 @@ def _save(self, results, start_idx, end_idx):
             if getattr(self, f'save_{attr}') and attr in results[0]:
                 save_data[attr] = [result[attr] for result in results]
 
+        metadata = {
+            'batch_size': self.batch_size,
+            'n_trials': self.n_trials,
+            'tstop': self.tstop,
+            'dt': self.dt
+        }
+        save_data['metadata'] = metadata
+
         file_name = os.path.join(self.save_folder,
                                  f'sim_run_{start_idx}-{end_idx}.npz')
         if os.path.exists(file_name) and not self.overwrite:

hnn_core/hnn_io.py

@@ -397,12 +397,12 @@ def dict_to_network(net_data,
 
     Parameters
     ----------
-    fname : str or Path
-        Path to configuration file
-    read_drives : bool
-        Read-in drives to Network object
-    read_external_biases
-        Read-in external biases to Network object
+    net_data : dict
+        Dictionary containing network configurations.
+    read_drives : bool, optional
+        Read-in drives to Network object. Default is True.
+    read_external_biases : bool, optional
+        Read-in external biases to Network object. Default is True.
 
     Returns : Network
     -------

hnn_core/tests/test_batch_simulate.py

@@ -3,13 +3,18 @@
 #          Ryan Thorpe <[email protected]>
 #          Mainak Jas <[email protected]>
 
+from pathlib import Path
+import time
 import pytest
 import numpy as np
 import os
 
 from hnn_core.batch_simulate import BatchSimulate
 from hnn_core import jones_2009_model
 
+hnn_core_root = Path(__file__).parents[1]
+assets_path = Path(hnn_core_root, 'tests', 'assets')
+
 
 @pytest.fixture
 def batch_simulate_instance(tmp_path):
@@ -33,11 +38,12 @@ def set_params(param_values, net):
                              weights_ampa=weights_ampa,
                              synaptic_delays=synaptic_delays)
 
-    net = jones_2009_model()
+    net = jones_2009_model(mesh_shape=(3, 3))
     return BatchSimulate(net=net, set_params=set_params,
-                         tstop=1.,
+                         tstop=10,
                          save_folder=tmp_path,
-                         batch_size=3)
+                         batch_size=3,
+                         n_trials=3,)
 
 
 @pytest.fixture
@@ -75,6 +81,12 @@ def test_parameter_validation():
     with pytest.raises(TypeError, match="net must be"):
         BatchSimulate(net="invalid_network", set_params=lambda x: x)
 
+    with pytest.raises(ValueError, match="'record_vsec' parameter"):
+        BatchSimulate(set_params=lambda x: x, record_vsec="invalid")
+
+    with pytest.raises(ValueError, match="'record_isec' parameter"):
+        BatchSimulate(set_params=lambda x: x, record_isec="invalid")
+
 
 def test_generate_param_combinations(batch_simulate_instance, param_grid):
     """Test generating parameter combinations."""
@@ -280,3 +292,27 @@ def test_load_results(batch_simulate_instance, param_grid, tmp_path):
     # Validation Tests
     with pytest.raises(TypeError, match='results must be'):
         batch_simulate_instance._save("invalid_results", start_idx, end_idx)
+
+
+def test_parallel_execution(batch_simulate_instance, param_grid):
+    """Test parallel execution of simulations and ensure speedup."""
+
+    param_combinations = batch_simulate_instance._generate_param_combinations(
+        param_grid)
+
+    start_time = time.perf_counter()
+    _ = batch_simulate_instance.simulate_batch(
+        param_combinations, n_jobs=1, backend='loky')
+    end_time = time.perf_counter()
+    serial_time = end_time - start_time
+
+    start_time = time.perf_counter()
+    _ = batch_simulate_instance.simulate_batch(
+        param_combinations,
+        n_jobs=2,
+        backend='loky')
+    end_time = time.perf_counter()
+    parallel_time = end_time - start_time
+
+    assert (serial_time > parallel_time
+            ), "Parallel execution is not faster than serial execution!"