bmtool 0.6.2__tar.gz → 0.6.3__tar.gz

{bmtool-0.6.2 → bmtool-0.6.3}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: bmtool
-Version: 0.6.2
+Version: 0.6.3
 Summary: BMTool
 Home-page: https://github.com/cyneuro/bmtool
 Download-URL: 
@@ -31,6 +31,15 @@ Requires-Dist: pynmodlt
 Requires-Dist: xarray
 Requires-Dist: fooof
 Requires-Dist: requests
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license
+Dynamic: requires-dist
+Dynamic: summary
 
 # bmtool
 A collection of modules to make developing [Neuron](https://www.neuron.yale.edu/neuron/) and [BMTK](https://alleninstitute.github.io/bmtk/) models easier.
@@ -44,6 +53,7 @@ A collection of modules to make developing [Neuron](https://www.neuron.yale.edu/
 - [Synapses](#synapses-module)
 - [Connectors](#connectors-module)
 - [Bmplot](#bmplot-module)
+- [SLURM](#slurm-module)
 - [Graphs](#graphs-module)
 
 ## Getting Started
@@ -338,9 +348,10 @@ ex: [https://github.com/tjbanks/two-cell-hco](https://github.com/tjbanks/two-cel
 
 ### Synapses Module
 -[SynapticTuner](#synaptictuner)
+-Gap Junction tuner
 
 #### SynapticTuner - Aids in the tuning of synapses by printing out synaptic properties and giving the user sliders in a Jupyter notebook to tune the synapse. For more info view the example [here](examples/synapses/synaptic_tuner.ipynb)
-
+#### GapJunctionTuner - Provides jupyter sliders to tune for coupling coefficient in a similar style to the SynapticTuner an example can be viewed [here](examples/synapses/gap_junction_tuner.ipynb)
 
 ### Connectors Module
 - [UnidirectionConnector](#unidirectional-connector---unidirectional-connections-in-bmtk-network-model-with-given-probability-within-a-single-population-or-between-two-populations)
@@ -459,7 +470,8 @@ bmplot.plot_network_graph(config='config.json',sources='LA',targets='LA',tids='p
     
 ![png](readme_figures/output_35_0.png)
     
-
+## SLURM Module
+### This is an extremely helpful module that can simplify using SLURM too submit your models. There is also features to enable doing a seedSweep. This will vary the parameters of the simulation and make tuning the model easier. An example can be found [here](examples/SLURM/using_BlockRunner.ipynb) 
 
 
 ## Graphs Module

{bmtool-0.6.2 → bmtool-0.6.3}/README.md

@@ -10,6 +10,7 @@ A collection of modules to make developing [Neuron](https://www.neuron.yale.edu/
 - [Synapses](#synapses-module)
 - [Connectors](#connectors-module)
 - [Bmplot](#bmplot-module)
+- [SLURM](#slurm-module)
 - [Graphs](#graphs-module)
 
 ## Getting Started
@@ -304,9 +305,10 @@ ex: [https://github.com/tjbanks/two-cell-hco](https://github.com/tjbanks/two-cel
 
 ### Synapses Module
 -[SynapticTuner](#synaptictuner)
+-Gap Junction tuner
 
 #### SynapticTuner - Aids in the tuning of synapses by printing out synaptic properties and giving the user sliders in a Jupyter notebook to tune the synapse. For more info view the example [here](examples/synapses/synaptic_tuner.ipynb)
-
+#### GapJunctionTuner - Provides jupyter sliders to tune for coupling coefficient in a similar style to the SynapticTuner an example can be viewed [here](examples/synapses/gap_junction_tuner.ipynb)
 
 ### Connectors Module
 - [UnidirectionConnector](#unidirectional-connector---unidirectional-connections-in-bmtk-network-model-with-given-probability-within-a-single-population-or-between-two-populations)
@@ -425,7 +427,8 @@ bmplot.plot_network_graph(config='config.json',sources='LA',targets='LA',tids='p
     
 ![png](readme_figures/output_35_0.png)
     
-
+## SLURM Module
+### This is an extremely helpful module that can simplify using SLURM too submit your models. There is also features to enable doing a seedSweep. This will vary the parameters of the simulation and make tuning the model easier. An example can be found [here](examples/SLURM/using_BlockRunner.ipynb) 
 
 
 ## Graphs Module

{bmtool-0.6.2 → bmtool-0.6.3}/bmtool/SLURM.py

@@ -379,32 +379,36 @@ class BlockRunner:
         if self.webhook:
             message = "SIMULATION UPDATE: Simulations have been submited in parallel!"
             send_teams_message(self.webhook,message)
-        for i, block in enumerate(self.blocks):
-            if block.component_path == None:
-                raise Exception("Unable to use parallel submitter without defining the component path")
-            new_value = self.param_values[i]
-            
-            source_dir = block.component_path
-            destination_dir = f"{source_dir}{i+1}"
-            block.component_path = destination_dir
-
-            shutil.copytree(source_dir, destination_dir) # create new components folder 
-            json_file_path = os.path.join(destination_dir,self.json_file_path)
-            if self.syn_dict_list == None:
-                json_editor = seedSweep(json_file_path, self.param_name)
-                json_editor.edit_json(new_value)
-            else:
-                json_editor = multiSeedSweep(json_file_path,self.param_name,
-                                             self.syn_dict_list,base_ratio=1)
-                json_editor.edit_all_jsons(new_value)  
+        if self.param_values == None:
+            print(f"skipping json editing for block {block.block_name}",flush=True)
+        else:
+            for i, block in enumerate(self.blocks):
+                if block.component_path == None:
+                    raise Exception("Unable to use parallel submitter without defining the component path")
+                new_value = self.param_values[i]
+                
+                source_dir = block.component_path
+                destination_dir = f"{source_dir}{i+1}"
+                block.component_path = destination_dir
+
+                shutil.copytree(source_dir, destination_dir) # create new components folder 
+                json_file_path = os.path.join(destination_dir,self.json_file_path)
+                if self.syn_dict_list == None:
+                    json_editor = seedSweep(json_file_path, self.param_name)
+                    json_editor.edit_json(new_value)
+                else:
+                    json_editor = multiSeedSweep(json_file_path,self.param_name,
+                                                self.syn_dict_list,base_ratio=1)
+                    json_editor.edit_all_jsons(new_value)  
             
             # submit block with new component path 
             print(f"Submitting block: {block.block_name}", flush=True)
             block.submit_block()
-            if i == len(self.blocks) - 1:  
-                while not block.check_block_completed():
-                    print(f"Waiting for the last block {i} to complete...")
-                    time.sleep(self.check_interval)
+            if i == len(self.blocks) - 1:
+                if self.webook:  
+                    while not block.check_block_completed():
+                        print(f"Waiting for the last block {i} to complete...")
+                        time.sleep(self.check_interval)
                 
         if self.webhook:
             message = "SIMULATION UPDATE: Simulations are Done!"

{bmtool-0.6.2 → bmtool-0.6.3}/bmtool/synapses.py

@@ -653,5 +653,113 @@ class SynapseTuner:
         # run model with default parameters 
         update_ui()
 
+class GapJunctionTuner:
+    def __init__(self, mechanisms_dir: str, templates_dir: str, general_settings: dict, conn_type_settings: dict):
+        neuron.load_mechanisms(mechanisms_dir)
+        h.load_file(templates_dir)
+        
+        self.general_settings = general_settings
+        self.conn_type_settings = conn_type_settings
+        
+        h.tstop = general_settings['tstart'] + general_settings['tdur'] + 100.
+        h.dt = general_settings['dt']  # Time step (resolution) of the simulation in ms
+        h.steps_per_ms = 1 / h.dt
+        h.celsius = general_settings['celsius']
+
+        self.cell_name = conn_type_settings['cell']
+        
+        # set up gap junctions
+        pc = h.ParallelContext()
+
+        self.cell1 = getattr(h, self.cell_name)()
+        self.cell2 = getattr(h, self.cell_name)()
+        
+        self.icl = h.IClamp(self.cell1.soma[0](0.5))
+        self.icl.delay = self.general_settings['tstart'] 
+        self.icl.dur = self.general_settings['tdur'] 
+        self.icl.amp = self.conn_type_settings['iclamp_amp'] # nA
+        
+        sec1 = list(self.cell1.all)[conn_type_settings['sec_id']]
+        sec2 = list(self.cell2.all)[conn_type_settings['sec_id']]
+
+        pc.source_var(sec1(conn_type_settings['sec_x'])._ref_v, 0, sec=sec1)
+        self.gap_junc_1 = h.Gap(sec1(0.5))
+        pc.target_var(self.gap_junc_1 ._ref_vgap, 1)
+
+        pc.source_var(sec2(conn_type_settings['sec_x'])._ref_v, 1, sec=sec2)
+        self.gap_junc_2 = h.Gap(sec2(0.5))
+        pc.target_var(self.gap_junc_2._ref_vgap, 0)
 
-    
+        pc.setup_transfer()
+    
+    def model(self,resistance):
+
+        self.gap_junc_1.g = resistance
+        self.gap_junc_2.g = resistance
+        
+        t_vec = h.Vector()
+        soma_v_1 = h.Vector()
+        soma_v_2 = h.Vector()
+        t_vec.record(h._ref_t)
+        soma_v_1.record(self.cell1.soma[0](0.5)._ref_v)
+        soma_v_2.record(self.cell2.soma[0](0.5)._ref_v)
+        
+        self.t_vec = t_vec
+        self.soma_v_1 = soma_v_1
+        self.soma_v_2 = soma_v_2
+        
+        h.finitialize(-70 * mV)
+        h.continuerun(h.tstop * ms)
+ 
+ 
+    def plot_model(self):
+        t_range = [self.general_settings['tstart'] - 100., self.general_settings['tstart']+self.general_settings['tdur'] + 100.]
+        t = np.array(self.t_vec)
+        v1 = np.array(self.soma_v_1)
+        v2 = np.array(self.soma_v_2)
+        tidx = (t >= t_range[0]) & (t <= t_range[1])
+
+        plt.figure()
+        plt.plot(t[tidx], v1[tidx], 'b', label=f'{self.cell_name} 1')
+        plt.plot(t[tidx], v2[tidx], 'r', label=f'{self.cell_name} 2')
+        plt.title(f"{self.cell_name} gap junction")
+        plt.xlabel('Time (ms)')
+        plt.ylabel('Membrane Voltage (mV)')
+        plt.legend()
+        plt.show()        
+
+
+    def coupling_coefficient(self,t, v1, v2, t_start, t_end, dt=h.dt):
+        t = np.asarray(t)
+        v1 = np.asarray(v1)
+        v2 = np.asarray(v2)
+        idx1 = np.nonzero(t < t_start)[0][-1]
+        idx2 = np.nonzero(t < t_end)[0][-1]
+        return (v2[idx2] - v2[idx1]) / (v1[idx2] - v1[idx1])
+
+    
+    def run_model(self):
+        w_run = widgets.Button(description='Run', icon='history', button_style='primary')
+        values = [i * 10**-4 for i in range(1, 101)]  # From 1e-4 to 1e-2
+
+        # Create the SelectionSlider widget with appropriate formatting
+        resistance = widgets.SelectionSlider(
+            options=[("%g"%i,i) for i in values],  # Use scientific notation for display
+            value=10**-3,  # Default value
+            description='Resistance: ',
+            continuous_update=True
+)
+
+        ui = VBox([w_run,resistance])
+        display(ui)
+        def on_button(*args):
+            clear_output()
+            display(ui)
+            resistance_for_gap = resistance.value
+            self.model(resistance_for_gap)
+            self.plot_model()
+            cc = self.coupling_coefficient(self.t_vec, self.soma_v_1, self.soma_v_2, 500, 1000)
+            print(f"coupling_coefficient is {cc:0.4f}")
+
+        on_button()    
+        w_run.on_click(on_button)

{bmtool-0.6.2 → bmtool-0.6.3}/bmtool.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: bmtool
-Version: 0.6.2
+Version: 0.6.3
 Summary: BMTool
 Home-page: https://github.com/cyneuro/bmtool
 Download-URL: 
@@ -31,6 +31,15 @@ Requires-Dist: pynmodlt
 Requires-Dist: xarray
 Requires-Dist: fooof
 Requires-Dist: requests
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license
+Dynamic: requires-dist
+Dynamic: summary
 
 # bmtool
 A collection of modules to make developing [Neuron](https://www.neuron.yale.edu/neuron/) and [BMTK](https://alleninstitute.github.io/bmtk/) models easier.
@@ -44,6 +53,7 @@ A collection of modules to make developing [Neuron](https://www.neuron.yale.edu/
 - [Synapses](#synapses-module)
 - [Connectors](#connectors-module)
 - [Bmplot](#bmplot-module)
+- [SLURM](#slurm-module)
 - [Graphs](#graphs-module)
 
 ## Getting Started
@@ -338,9 +348,10 @@ ex: [https://github.com/tjbanks/two-cell-hco](https://github.com/tjbanks/two-cel
 
 ### Synapses Module
 -[SynapticTuner](#synaptictuner)
+-Gap Junction tuner
 
 #### SynapticTuner - Aids in the tuning of synapses by printing out synaptic properties and giving the user sliders in a Jupyter notebook to tune the synapse. For more info view the example [here](examples/synapses/synaptic_tuner.ipynb)
-
+#### GapJunctionTuner - Provides jupyter sliders to tune for coupling coefficient in a similar style to the SynapticTuner an example can be viewed [here](examples/synapses/gap_junction_tuner.ipynb)
 
 ### Connectors Module
 - [UnidirectionConnector](#unidirectional-connector---unidirectional-connections-in-bmtk-network-model-with-given-probability-within-a-single-population-or-between-two-populations)
@@ -459,7 +470,8 @@ bmplot.plot_network_graph(config='config.json',sources='LA',targets='LA',tids='p
     
 ![png](readme_figures/output_35_0.png)
     
-
+## SLURM Module
+### This is an extremely helpful module that can simplify using SLURM too submit your models. There is also features to enable doing a seedSweep. This will vary the parameters of the simulation and make tuning the model easier. An example can be found [here](examples/SLURM/using_BlockRunner.ipynb) 
 
 
 ## Graphs Module

{bmtool-0.6.2 → bmtool-0.6.3}/setup.py

@@ -6,7 +6,7 @@ with open("README.md", "r") as fh:
 
 setup(
     name="bmtool",
-    version='0.6.2',
+    version='0.6.3',
     author="Neural Engineering Laboratory at the University of Missouri",
     author_email="gregglickert@mail.missouri.edu",
     description="BMTool",
@@ -41,7 +41,8 @@ setup(
         'Topic :: Software Development :: Libraries :: Python Modules',
         "Operating System :: OS Independent",
     ],
-    packages=find_packages(exclude=['tests']),
+    packages=find_packages(),  # Automatically finds all packages
+    include_package_data=True,
     entry_points={
         'console_scripts': [
             'bmtool = bmtool.manage:cli'