diff --git a/multi-area-model.ipynb b/multi-area-model.ipynb
index d86c05ad688177b5321f391471b9aa55f5249f68..0640081e0dac01c4cc2384ac5a695442e8120870 100644
--- a/multi-area-model.ipynb
+++ b/multi-area-model.ipynb
@@ -233,16 +233,17 @@
"id": "a2161477",
"metadata": {},
"source": [
- "1. `scale_down_to` <br>\n",
- "It is the down-scaling factor that defines the ratio by which the full-scale multi-area model is reduced to a model with fewer neurons and indegrees. This reduction is essential to enable simulation on machines with limited computational power, ensuring that simulation results can be obtained in a relatively shorter timeframe. <br> If the value is `1.`, the full-scale network will be simulated. <br> In the pre-set downscale version, it is set as `0.005`, where the number of neurons and indegrees are scaled down to 0.5% of its full-scale amount, where the model can usually be simulated on a local machine. <br> **Warning**: This will not yield reasonable dynamical results from the network and is only meant to demonstrate the simulation workflow <br> \n",
- "2. `cc_weights_factor` <br>\n",
- "This scaling factor controls the cortico-cortical synaptic strength. <br> By default it's set as `1.0`, where the inter-area synaptic strength is the same as the intra-areal. <br> **Important**: This factor changes the network activity from ground state to metastable state. <br>\n",
- "3. `areas_simulated` <br>\n",
- "This parameter specifies the cortical areas included in the simulation process. Its default value is `complete_area_list` meaning all the areas in the complete_area_list will be actually simulated. <br>\n",
- "complete_area_list = `['V1', 'V2', 'VP', 'V3', 'V3A', 'MT', 'V4t', 'V4', 'VOT', 'MSTd', 'PIP', 'PO', 'DP', 'MIP', 'MDP', 'VIP', 'LIP', 'PITv', 'PITd', 'MSTl', 'CITv', 'CITd', 'FEF', 'TF', 'AITv', 'FST', '7a', 'STPp', 'STPa', '46', 'AITd', 'TH']` <br>\n",
- "The value assigned to simulation_areas can be any sublist of the compete_area_list specifying areas a user want to include in his/her simulation. <br>\n",
- "4. `replace_non_simulated_areas` <br>\n",
- "This parameter defines how non-simulated areas will be replaced. <br> It is set as `None` by default when the parameter areas_simulated is set as full_area_list where all areas will be simulated so that no areas need to be replaced. <br> Other options are: `'hom_poisson_stat'`, `'het_poisson_stat'`, and `'het_current_nonstat'`. `'hom_poisson_stat'` is a manually set parameter which can be tuned. When it is set as 'het_poisson_stat' or 'het_current_nonstat', the data to replace the cortico-cortical input is loaded from 'replace_cc_input_source' which is the firing rates of our full scale simulation results. The differenc between 'het_poisson_stat' and 'het_current_nonstat' is that 'het_poisson_stat' is the mean of the time-series firing rate so that it is static, yet 'het_current_nonstat' is time-varying specific current, which is varying by time. "
+ "1. `scale_down_to`: is the down-scaling factor that defines the ratio by which the full-scale multi-area model is reduced to a model with fewer neurons and indegrees. This reduction is essential to enable simulation on machines with limited computational power, ensuring that simulation results can be obtained in a relatively shorter timeframe. <br> If the value is `scale_down_to = 1.`, the full-scale network will be simulated. <br> In the pre-set downscale version, it is set to `scale_down_to = 0.005`, This setting reduces both the number of neurons and indegrees to 0.5 % of their full-scale counterparts, facilitating simulation on a typical local machine. <br> **Warning**: This will not yield reasonable dynamical results from the network and is only meant to demonstrate the simulation workflow <br> \n",
+ "\n",
+ "2. `cc_weights_factor`: This scaling factor controls the cortico-cortical synaptic strength. <br> By default it's set as `1.0`, where the inter-area synaptic strength is the same as the intra-areal. <br> **Important**: This factor changes the network activity from ground state to metastable state. <br>\n",
+ "\n",
+ "3. `areas_simulated`: This parameter specifies the cortical areas to be included in the simulation process. Its default value is `complete_area_list` meaning all the areas in the complete_area_list will be simulated. The value assigned to `areas_simulated` can be any sublist of the list below:\n",
+ "```python\n",
+ "complete_area_list = ['V1', 'V2', 'VP', 'V3', 'V3A', 'MT', 'V4t', 'V4', 'VOT', 'MSTd', 'PIP', 'PO', 'DP', 'MIP', 'MDP', 'VIP', 'LIP', 'PITv', 'PITd', 'MSTl', 'CITv', 'CITd', 'FEF', 'TF', 'AITv', 'FST', '7a', 'STPp', 'STPa', '46', 'AITd', 'TH']\n",
+ "```\n",
+ "<br>\n",
+ "\n",
+ "4. `replace_non_simulated_areas`: This parameter defines how non-simulated areas will be replaced. <br> When all areas are included, it is set as `None` by default. <br> Other options are: `'hom_poisson_stat'`, `'het_poisson_stat'`, and `'het_current_nonstat'`.<br> `'hom_poisson_stat'` replaces the non-simulated areas by Poisson sources with the same global rate `rate_ext`. The `'het_poisson_stat'` and `'het_current_nonstat'` options use the loaded specific rates from `'replace_cc_input_source'`, which contains the area-specific firing rates of our full scale simulation results. The difference between them is that `'het_poisson_stat'` replaces the non-simulated areas by Poisson spike trains and `'het_current_nonstat'` replaces it by a time-varying current input."
]
},
{
@@ -254,23 +255,23 @@
"source": [
"# Downscaling factor\n",
"# Value range/options: (0, 1.]\n",
- "# Value assgined: 0.005\n",
+ "# Value assigned: 0.005\n",
"scale_down_to = 0.005 # Change it to 1. for running the fullscale network\n",
"\n",
"# Scaling factor for cortico-cortical connections (chi) \n",
"# Value range/options: [1., 2.5]\n",
- "# Value assgined: 1.0\n",
+ "# Value assigned: 1.0\n",
"cc_weights_factor = 1.0\n",
"\n",
"# Cortical areas included in the simulation\n",
- "# Value range/options: any sublist of complete_ares_list\n",
- "# where complete_ares_list = ['V1', 'V2', 'VP', 'V3', 'V3A', 'MT', 'V4t', 'V4', 'VOT', 'MSTd', 'PIP', 'PO', 'DP', 'MIP', 'MDP', 'VIP', 'LIP', 'PITv', 'PITd', 'MSTl', 'CITv', 'CITd', 'FEF', 'TF', 'AITv', 'FST', '7a', 'STPp', 'STPa', '46', 'AITd', 'TH']\n",
- "# Value assgined: complete_ares_list\n",
+ "# Value range/options: any sublist of complete_area_list\n",
+ "# where complete_area_list = ['V1', 'V2', 'VP', 'V3', 'V3A', 'MT', 'V4t', 'V4', 'VOT', 'MSTd', 'PIP', 'PO', 'DP', 'MIP', 'MDP', 'VIP', 'LIP', 'PITv', 'PITd', 'MSTl', 'CITv', 'CITd', 'FEF', 'TF', 'AITv', 'FST', '7a', 'STPp', 'STPa', '46', 'AITd', 'TH']\n",
+ "# Value assigned: complete_area_list\n",
"areas_simulated = ['V1', 'V2', 'VP', 'V3', 'V3A', 'MT', 'V4t', 'V4', 'VOT', 'MSTd', 'PIP', 'PO', 'DP', 'MIP', 'MDP', 'VIP', 'LIP', 'PITv', 'PITd', 'MSTl', 'CITv', 'CITd', 'FEF', 'TF', 'AITv', 'FST', '7a', 'STPp', 'STPa', '46', 'AITd', 'TH']\n",
"\n",
"# Firing rates used to replace the non-simulated areas\n",
"# Value range/options: None, 'hom_poisson_stat', 'het_poisson_stat', 'het_current_nonstat'\n",
- "# Value assgined: 'het_poisson_stat'\n",
+ "# Value assigned: 'het_poisson_stat'\n",
"replace_non_simulated_areas = 'het_poisson_stat'"
]
},
@@ -280,7 +281,7 @@
"metadata": {},
"source": [
"### 1.2. Default parameters <a class=\"anchor\" id=\"section_1_2\"></a>\n",
- "We try our best not to confuse users with too many parameters. However, if you want to change more parameters and explore the model, you can do so by passing a dictionary to the `default_params` argument of the `MultiAreaModel` class."
+ "We try our best not to confuse users with too many parameters. However, if you want to change more parameters and explore the model, you can do so by passing a dictionary to the `default_params` argument of the `MultiAreaModel` class. (*NOTE: it should may be moved to the default parameters file in the future.*)"
]
},
{
@@ -292,7 +293,7 @@
"source": [
"# Connection parameters\n",
"conn_params = {\n",
- " 'replace_non_simulated_areas': 'het_poisson_stat', # Whether to replace non-simulated areas by Poisson sources with the same global rate, by default: None\n",
+ " 'replace_non_simulated_areas': replace_non_simulated_areas, # Whether to replace non-simulated areas by Poisson sources with the same global rate, by default: None\n",
" 'g': -11., # It sets the relative inhibitory synaptic strength, by default: -16.\n",
" 'K_stable': 'K_stable.npy', # Whether to apply the stabilization method of Schuecker, Schmidt et al. (2017), by default: None\n",
" 'fac_nu_ext_TH': 1.2, # Increase the external input to 2/3E and 5E in area TH\n",
@@ -496,7 +497,7 @@
"output_type": "stream",
"text": [
"Initializing network from dictionary.\n",
- "RAND_DATA_LABEL 2177\n"
+ "RAND_DATA_LABEL 4858\n"
]
},
{
@@ -578,72 +579,72 @@
"text": [
"Prepared simulation in 0.01 seconds.\n",
"Rank 0: created area V1 with 0 local nodes\n",
- "Memory after V1 : 1514.66 MB\n",
+ "Memory after V1 : 1515.65 MB\n",
"Rank 0: created area V2 with 0 local nodes\n",
- "Memory after V2 : 1541.36 MB\n",
+ "Memory after V2 : 1542.43 MB\n",
"Rank 0: created area VP with 0 local nodes\n",
- "Memory after VP : 1570.57 MB\n",
+ "Memory after VP : 1571.48 MB\n",
"Rank 0: created area V3 with 0 local nodes\n",
- "Memory after V3 : 1598.81 MB\n",
+ "Memory after V3 : 1599.88 MB\n",
"Rank 0: created area V3A with 0 local nodes\n",
- "Memory after V3A : 1618.78 MB\n",
+ "Memory after V3A : 1619.66 MB\n",
"Rank 0: created area MT with 0 local nodes\n",
- "Memory after MT : 1644.28 MB\n",
+ "Memory after MT : 1645.27 MB\n",
"Rank 0: created area V4t with 0 local nodes\n",
- "Memory after V4t : 1669.24 MB\n",
+ "Memory after V4t : 1670.24 MB\n",
"Rank 0: created area V4 with 0 local nodes\n",
- "Memory after V4 : 1696.18 MB\n",
+ "Memory after V4 : 1697.18 MB\n",
"Rank 0: created area VOT with 0 local nodes\n",
- "Memory after VOT : 1720.76 MB\n",
+ "Memory after VOT : 1721.72 MB\n",
"Rank 0: created area MSTd with 0 local nodes\n",
- "Memory after MSTd : 1740.80 MB\n",
+ "Memory after MSTd : 1741.80 MB\n",
"Rank 0: created area PIP with 0 local nodes\n",
- "Memory after PIP : 1762.27 MB\n",
+ "Memory after PIP : 1763.14 MB\n",
"Rank 0: created area PO with 0 local nodes\n",
- "Memory after PO : 1783.68 MB\n",
+ "Memory after PO : 1784.60 MB\n",
"Rank 0: created area DP with 0 local nodes\n",
- "Memory after DP : 1803.82 MB\n",
+ "Memory after DP : 1804.86 MB\n",
"Rank 0: created area MIP with 0 local nodes\n",
- "Memory after MIP : 1825.39 MB\n",
+ "Memory after MIP : 1826.39 MB\n",
"Rank 0: created area MDP with 0 local nodes\n",
- "Memory after MDP : 1846.86 MB\n",
+ "Memory after MDP : 1847.88 MB\n",
"Rank 0: created area VIP with 0 local nodes\n",
- "Memory after VIP : 1868.78 MB\n",
+ "Memory after VIP : 1869.85 MB\n",
"Rank 0: created area LIP with 0 local nodes\n",
- "Memory after LIP : 1892.83 MB\n",
+ "Memory after LIP : 1893.75 MB\n",
"Rank 0: created area PITv with 0 local nodes\n",
- "Memory after PITv : 1918.03 MB\n",
+ "Memory after PITv : 1919.06 MB\n",
"Rank 0: created area PITd with 0 local nodes\n",
- "Memory after PITd : 1943.21 MB\n",
+ "Memory after PITd : 1944.23 MB\n",
"Rank 0: created area MSTl with 0 local nodes\n",
- "Memory after MSTl : 1964.70 MB\n",
+ "Memory after MSTl : 1965.56 MB\n",
"Rank 0: created area CITv with 0 local nodes\n",
- "Memory after CITv : 1983.83 MB\n",
+ "Memory after CITv : 1984.35 MB\n",
"Rank 0: created area CITd with 0 local nodes\n",
- "Memory after CITd : 2003.29 MB\n",
+ "Memory after CITd : 2003.71 MB\n",
"Rank 0: created area FEF with 0 local nodes\n",
- "Memory after FEF : 2024.62 MB\n",
+ "Memory after FEF : 2025.05 MB\n",
"Rank 0: created area TF with 0 local nodes\n",
- "Memory after TF : 2040.30 MB\n",
+ "Memory after TF : 2040.73 MB\n",
"Rank 0: created area AITv with 0 local nodes\n",
- "Memory after AITv : 2062.89 MB\n",
+ "Memory after AITv : 2063.43 MB\n",
"Rank 0: created area FST with 0 local nodes\n",
- "Memory after FST : 2079.61 MB\n",
+ "Memory after FST : 2080.16 MB\n",
"Rank 0: created area 7a with 0 local nodes\n",
- "Memory after 7a : 2100.93 MB\n",
+ "Memory after 7a : 2101.36 MB\n",
"Rank 0: created area STPp with 0 local nodes\n",
- "Memory after STPp : 2119.64 MB\n",
+ "Memory after STPp : 2120.07 MB\n",
"Rank 0: created area STPa with 0 local nodes\n",
- "Memory after STPa : 2138.77 MB\n",
+ "Memory after STPa : 2139.20 MB\n",
"Rank 0: created area 46 with 0 local nodes\n",
- "Memory after 46 : 2154.10 MB\n",
+ "Memory after 46 : 2154.56 MB\n",
"Rank 0: created area AITd with 0 local nodes\n",
- "Memory after AITd : 2176.68 MB\n",
+ "Memory after AITd : 2177.15 MB\n",
"Rank 0: created area TH with 0 local nodes\n",
- "Memory after TH : 2189.35 MB\n",
- "Created areas and internal connections in 2.19 seconds.\n",
- "Created cortico-cortical connections in 22.55 seconds.\n",
- "Simulated network in 80.08 seconds.\n"
+ "Memory after TH : 2189.89 MB\n",
+ "Created areas and internal connections in 2.17 seconds.\n",
+ "Created cortico-cortical connections in 21.79 seconds.\n",
+ "Simulated network in 86.05 seconds.\n"
]
}
],