From 2e30d7982a1aa6f9c306ee20ee74cd3414e42b2f Mon Sep 17 00:00:00 2001
From: Jan Fousek <jan.fousek@univ-amu.fr>
Date: Sun, 19 Dec 2021 14:46:56 +0100
Subject: [PATCH] added connecitivity gen for 1000Brains
---
setup.py | 2 +-
tvb_ebrains_data/data.py | 14 ++++++++++++++
2 files changed, 15 insertions(+), 1 deletion(-)
diff --git a/setup.py b/setup.py
index 0cf45ff..1150b06 100644
--- a/setup.py
+++ b/setup.py
@@ -3,7 +3,7 @@ from setuptools import find_packages, setup
setup(
name='tvb-ebrains-data',
packages=find_packages(),
- version='0.2.0',
+ version='0.2.1',
install_requires=[
'tvb-library',
]
diff --git a/tvb_ebrains_data/data.py b/tvb_ebrains_data/data.py
index de4dd98..7c67de4 100644
--- a/tvb_ebrains_data/data.py
+++ b/tvb_ebrains_data/data.py
@@ -132,3 +132,17 @@ class Brains1000Dataset(DataProxyConnectivityDataset):
fname = f'{subject}_SC_7NW100parc.txt'
W = np.loadtxt(self.open_file(f'{self.version}/Schaefer/Matrices/{fname}'))
return W
+
+ def get_connectivity(self, subject, scaling_factor=124538.470647693):
+ SC = self.load_sc(subject)
+ SC = SC / scaling_factor
+ conn = connectivity.Connectivity(
+ weights = SC,
+ tract_lengths=np.ones_like(SC),
+ centres = np.zeros(np.shape(SC)[0]),
+ speed = np.r_[np.Inf]
+ )
+ conn.compute_region_labels()
+ logger.warning("Placeholder region names!")
+ return conn
+
--
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