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lahirujayathilake pushed a commit to branch main
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The following commit(s) were added to refs/heads/main by this push:
new ef9373b v1l3 nest python script
ef9373b is described below
commit ef9373b2391cf1d3164c8002c49aa3c1e2ba25be
Author: lahiruj <[email protected]>
AuthorDate: Fri Oct 4 13:53:43 2024 -0400
v1l3 nest python script
---
resources/scripts/v1l4_nest_notebook.py | 193 ++++++++++++++++++++++++++++++++
1 file changed, 193 insertions(+)
diff --git a/resources/scripts/v1l4_nest_notebook.py
b/resources/scripts/v1l4_nest_notebook.py
new file mode 100644
index 0000000..840085c
--- /dev/null
+++ b/resources/scripts/v1l4_nest_notebook.py
@@ -0,0 +1,193 @@
+#!/usr/bin/env python
+# coding: utf-8
+
+import os
+import argparse
+import shutil
+
+import logging
+import airavata_cerebrum.util.desc_config as cbm_dcfg
+import airavata_cerebrum.view.tree as cbm_tree
+import airavata_cerebrum.model.desc as cbm_desc
+import mousev1.model as mousev1
+
+import json
+import ast
+import numpy as np
+import pandas as pd
+import IPython.display
+
+import mousev1.operations as mousev1ops
+import nest
+import matplotlib.pyplot as plt
+
+
+# Creating the base directory
+v1l4_base_dir = "./v1l4"
+sub_dirs = ["bkg", "network", "description", "components"]
+
+# Create base directory if it doesn't exist
+if not os.path.exists(v1l4_base_dir):
+ os.makedirs(v1l4_base_dir)
+
+# Create each subdirectory within the base directory
+for sub_dir in sub_dirs:
+ dir_path = os.path.join(v1l4_base_dir, sub_dir)
+ if not os.path.exists(dir_path):
+ os.makedirs(dir_path)
+
+print(f"Directories {v1l4_base_dir} and {sub_dirs} have been created.")
+
+# File paths in the current directory
+config_nest_file = 'config_nest.json'
+custom_mod_file = 'custom_mod.json'
+config_file = 'config.json'
+
+# Check that files exist
+if not all(os.path.exists(f) for f in [config_nest_file, custom_mod_file,
config_file]):
+ raise FileNotFoundError("One or more required files are missing in the
current directory.")
+
+# Paths to move the files to
+description_dir = os.path.join(v1l4_base_dir, "description")
+
+# Move config_file and custom_mod_file to ./v1l4/description
+shutil.move(config_file, os.path.join(description_dir, config_file))
+shutil.move(custom_mod_file, os.path.join(description_dir, custom_mod_file))
+
+# Move config_nest_file to ./v1l4
+shutil.move(config_nest_file, os.path.join(v1l4_base_dir, config_nest_file))
+
+print(f"Moved {config_file} to {description_dir}")
+print(f"Moved {custom_mod_file} to {description_dir}")
+print(f"Moved {config_nest_file} to {v1l4_base_dir}")
+
+# Update the file paths to the new locations
+config_nest_file = os.path.join(v1l4_base_dir, config_nest_file)
+custom_mod_file = os.path.join(description_dir, custom_mod_file)
+config_file = os.path.join(description_dir, config_file)
+
+
+# Paths for the source and destination of the symlinks
+source_component_dir = "/home/scigap/projects/data/V1L4/components"
+target_component_dir = os.path.join(v1l4_base_dir, "components")
+
+source_source_data_file =
"/home/scigap/projects/data/V1L4/source_data_output.json"
+target_source_data_file = os.path.join(description_dir,
"source_data_output.json")
+
+source_bkg_file = "/home/scigap/projects/data/V1L4/bkg_spikes_250Hz_3s.h5"
+target_bkg_dir = os.path.join(v1l4_base_dir, "bkg")
+
+# Create symlinks
+try:
+ os.symlink(source_component_dir, target_component_dir)
+ print(f"Symlink created: {target_component_dir} -> {source_component_dir}")
+except FileExistsError:
+ print(f"Symlink already exists: {target_component_dir}")
+
+try:
+ os.symlink(source_source_data_file, target_source_data_file)
+ print(f"Symlink created: {target_source_data_file} ->
{source_source_data_file}")
+except FileExistsError:
+ print(f"Symlink already exists: {target_source_data_file}")
+
+try:
+ os.symlink(source_bkg_file, os.path.join(target_bkg_dir,
"bkg_spikes_250Hz_3s.h5"))
+ print(f"Symlink created: {os.path.join(target_bkg_dir,
'bkg_spikes_250Hz_3s.h5')} -> {source_bkg_file}")
+except FileExistsError:
+ print(f"Symlink already exists: {os.path.join(target_bkg_dir,
'bkg_spikes_250Hz_3s.h5')}")
+
+
+md_desc_config = cbm_dcfg.init_model_desc_config(
+ name="v1l4",
+ base_dir="./",
+ config_files={"config": [config_file], "templates":
["config_template.json"] },
+ config_dir="./v1l4/description/",
+)
+
+model_dex = cbm_desc.ModelDescription(
+ config=md_desc_config.config,
+ region_mapper=mousev1.V1RegionMapper,
+ neuron_mapper=mousev1.V1NeuronMapper,
+ connection_mapper=mousev1.V1ConnectionMapper,
+ network_builder=mousev1.V1BMTKNetworkBuilder,
+ custom_mod=custom_mod_file,
+ save_flag=True,
+)
+
+with open(custom_mod_file) as ifx:
+ custom_mod_dict = json.load(ifx)
+IPython.display.JSON(custom_mod_dict)
+
+# mdb_data = model_dex.download_db_data()
+
+with open("./v1l4/description/db_connect_output.json") as dbf:
+ db_out_data = json.load(dbf)
+ai_syn_data = db_out_data['airavata_cerebrum.dataset.ai_synphys'][0]
+row_keys = set([ast.literal_eval(xk)[0] for xk in ai_syn_data.keys()])
+col_keys = set([ast.literal_eval(xk)[1] for xk in ai_syn_data.keys()])
+col_names = row_names = list(row_keys)
+connect_matrix = np.zeros((len(row_names), len(col_names)))
+for i, cx in enumerate(col_names):
+ for j,rx in enumerate(row_names):
+ connect_matrix[i, j] = ai_syn_data[repr((cx, rx))]
+pd.DataFrame(connect_matrix, index=row_names, columns=col_names)
+
+logging.basicConfig(level=logging.INFO)
+# mdb_data = model_dex.db_post_ops()
+
+msrc = model_dex.map_source_data()
+
+with open(custom_mod_file) as ifx:
+ custom_mod_dict = json.load(ifx)
+IPython.display.JSON(custom_mod_dict)
+
+msrc = model_dex.build_net_struct()
+msrc = model_dex.apply_custom_mod()
+
+bmtk_net_builder = mousev1.V1BMTKNetworkBuilder(model_dex.network_struct)
+bmtk_net = bmtk_net_builder.build()
+
+bmtk_net_builder.net.save(str(model_dex.config.network_dir))
+bmtk_net_builder.bkg_net.save(str(model_dex.config.network_dir))
+
+# Converting to
+mousev1ops.convert_ctdb_models_to_nest("./v1l4/components/point_neuron_models/",
"./v1l4/components/cell_models/")
+
+# Instantiate SonataNetwork
+sonata_net = nest.SonataNetwork(config_nest_file)
+
+# Create and connect nodes
+node_collections = sonata_net.BuildNetwork()
+print("Node Collections", node_collections.keys())
+
+# Connect spike recorder to a population
+spike_rec = nest.Create("spike_recorder")
+nest.Connect(node_collections["v1l4"], spike_rec)
+
+# Attach Multimeter
+multi_meter = nest.Create(
+ "multimeter",
+ params={
+ # "interval": 0.05,
+ "record_from": ["V_m", "I", "I_syn", "threshold", "threshold_spike",
"threshold_voltage", "ASCurrents_sum"],
+ },
+)
+nest.Connect(multi_meter, node_collections["v1l4"])
+
+# Simulate the network
+sonata_net.Simulate()
+
+dmm = multi_meter.get()
+Vms = dmm["events"]["V_m"]
+ts = dmm["events"]["times"]
+plt.figure(1)
+plt.plot(ts, Vms)
+
+spike_data = spike_rec.events
+spike_senders = spike_data["senders"]
+ts = spike_data["times"]
+plt.figure(2)
+plt.plot(ts, spike_senders, ".")
+plt.savefig('nest_combined_plots.png')
+plt.close()
+
