timeawarepc 1.2.0__py2.py3-none-any.whl

timeawarepc/__init__.py

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+"""
+Time-Aware PC Algorithm for estimating Causal Functional Connectivity from Time Series
+"""
+
+__version__ = "0.0.1"
+__all__ = ["tpc_helpers","tpc","find_cfc","pcalg","pcalg_helpers","simulate_data"]

timeawarepc/find_cfc.py

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+"""Convenient wrapper for functions in the library.
+"""
+__all__ = ["find_cfc"]
+from timeawarepc.tpc import *
+def find_cfc(data,method_name,alpha=0.05,maxdelay=1,niter=50,thresh=0.25,isgauss=False):
+    """Estimate Causal Functional Connectivity (CFC) between nodes from time series.
+        This is a wrapper for functions cfc_tpc, cfc_pc, cfc_gc in tpc.py.
+        Refer to the individual functions for their details.
+
+    Args:
+        data: (numpy.array) of shape (n,p) with n time-recordings for p nodes
+        method_name: (string)
+            'TPC': Implements TPC Algorithm,
+            'PC': PC Algorithm,
+            'GC': Granger Causality.
+        alpha: (float) Significance level
+        isgauss: (boolean) Arg used for method_name == 'PC' or 'TPC'.
+            True: Assume Gaussian Noise distribution, 
+            False: Distribution free.
+        maxdelay: (int) Maximum time-delay of interactions. Arg used for method_name == 'GC' or 'TPC'.
+        subsampsize: (int) Bootstrap window width in TPC. Arg used for method_name == 'TPC'.
+        niter: (int) Number of bootstrap iterations in TPC. Arg used for method_name == 'TPC'.
+        thresh: (float) Bootstrap stability cut-off in TPC. Arg used for method_name == 'TPC'.
+
+    Returns:
+        adjacency: (numpy.array) Adcajency matrix of estimated CFC by chosen method.
+        weights: (numpy.array) Connectivity Weights in the CFC
+
+    """
+
+    if method_name == 'TPC':
+        adjacency, weights = cfc_tpc(data,maxdelay=maxdelay,alpha=alpha,niter=niter,thresh=thresh,isgauss=isgauss)
+    elif method_name == 'PC':
+        adjacency, weights = cfc_pc(data,alpha,isgauss=isgauss)
+    elif method_name == 'GC':
+        from timeawarepc.gc import cfc_gc 
+        adjacency, weights = cfc_gc(data,maxdelay,alpha)
+    return adjacency,weights

timeawarepc/gc.py

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+import numpy as np
+import nitime.analysis as nta
+import nitime.timeseries as ts
+def cfc_gc(data,maxdelay,alpha):
+    """Estimate Causal Functional Connectivity using Granger Causality.
+
+    Args:
+        data: (numpy.array) of shape (n,p) with n samples for p nodes 
+        maxdelay: Maximum time-delay of interactions. 
+        alpha: (float) Significance level for conditional independence tests
+
+    Returns:
+        adjacency: (numpy.array) Adcajency matrix of shape (p,p) of estimated CFC by Granger Causality.
+        weights: (numpy.array) Connectivity Weight matrix of shape (p,p).
+
+    """
+    TR = 1
+    thresh = 0
+    time_series = ts.TimeSeries(data.T, sampling_interval=TR)
+    order=maxdelay
+    G = nta.GrangerAnalyzer(time_series, order=order)
+    adj_mat = np.zeros((data.shape[1],data.shape[1]))
+
+    adj_mat=np.mean(np.nan_to_num(G.causality_xy[:, :]),-1)+np.mean(np.nan_to_num(G.causality_yx[:, :]),-1).T
+    adjmat1=np.mean(np.nan_to_num(G.causality_xy[:, :]),-1)
+    adjmat2=np.mean(np.nan_to_num(G.causality_yx[:, :]),-1)
+    adj_mat=adjmat1+adjmat2.T
+    weights = adj_mat
+    thresh = np.percentile(adj_mat,(1-alpha)*100)
+    adjacency=(adj_mat > thresh).astype(int)
+    return adjacency, weights