From 72ed76cb55be06b690ad503a63e0ab2898e1cbfe Mon Sep 17 00:00:00 2001
From: shimoura <renanshimoura@gmail.com>
Date: Fri, 5 Apr 2024 17:34:11 +0200
Subject: [PATCH] Removed louvain_communities dependence
The dependence was removed in the jupyter-notebook tutorial. It was replaced by the area list order as used in the reference paper.
---
figures/MAM2EBRAINS/M2E_visualize_fc.py | 22 ++++++----------------
1 file changed, 6 insertions(+), 16 deletions(-)
diff --git a/figures/MAM2EBRAINS/M2E_visualize_fc.py b/figures/MAM2EBRAINS/M2E_visualize_fc.py
index 089f24f..cb38740 100644
--- a/figures/MAM2EBRAINS/M2E_visualize_fc.py
+++ b/figures/MAM2EBRAINS/M2E_visualize_fc.py
@@ -15,7 +15,6 @@ from matplotlib import gridspec
sys.path.append('./figures/Schmidt2018')
from M2E_compute_fc import compute_fc
-from M2E_compute_louvain_communities import compute_communities
cmap = pl.cm.coolwarm
cmap = cmap.from_list('mycmap', [myblue, 'white', myred], N=256)
@@ -94,7 +93,6 @@ def visualize_fc(M, data_path):
# Compute functional connectivity
compute_fc(M, data_path, label)
- compute_communities(M, data_path, label)
"""
Figure layout
@@ -161,21 +159,13 @@ def visualize_fc(M, data_path):
sim_FC[label] = np.load(fn)
label = M.simulation.label
- fn = os.path.join(data_path,
- label,
- 'Analysis',
- 'FC_synaptic_input_communities.json')
- with open(fn, 'r') as f:
- part_sim = json.load(f)
- part_sim_list = [part_sim[area] for area in M.area_list]
- part_sim_index = np.argsort(part_sim_list, kind='mergesort')
- # Manually position MDP in between the two clusters for visual purposes
- ind_MDP = M.area_list.index('MDP')
- ind_MDP_index = np.where(part_sim_index == ind_MDP)[0][0]
- part_sim_index = np.append(part_sim_index[:ind_MDP_index], part_sim_index[ind_MDP_index+1:])
- new_ind_MDP_index = np.where(np.array(part_sim_list)[part_sim_index] == 0.)[0][-1]
- part_sim_index = np.insert(part_sim_index, new_ind_MDP_index+1, ind_MDP)
+ areas_reordered = ['V1', 'V2', 'VP', 'V4t', 'V4', 'VOT', 'MSTd', 'PITv',
+ 'PITd', 'CITv', 'CITd', 'AITv', 'AITd', 'MDP', 'V3', 'V3A',
+ 'MT', 'PIP', 'PO', 'DP', 'MIP', 'VIP', 'LIP', 'MSTI',
+ 'FEF', 'TF', 'FST', '7a', 'STPp', 'STPa', '46', 'TH']
+ part_sim = {area: M.area_list.index(area) for area in areas_reordered if area in M.area_list}
+ part_sim_index = list(part_sim.values())
"""
Plotting
--
GitLab