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31 lines
923 B
31 lines
923 B
6 years ago
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import os
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import numpy as np
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from cffi import FFI
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import subprocess
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cluster_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)))
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subprocess.check_call(["make", "-j4"], cwd=cluster_dir)
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cluster_fn = os.path.join(cluster_dir, "libfastcluster.so")
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ffi = FFI()
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ffi.cdef("""
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int hclust_fast(int n, double* distmat, int method, int* merge, double* height);
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void cutree_cdist(int n, const int* merge, double* height, double cdist, int* labels);
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void hclust_pdist(int n, int m, double* pts, double* out);
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void cluster_points_centroid(int n, int m, double* pts, double dist, int* idx);
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""")
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hclust = ffi.dlopen(cluster_fn)
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def cluster_points_centroid(pts, dist):
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pts = np.ascontiguousarray(pts, dtype=np.float64)
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pts_ptr = ffi.cast("double *", pts.ctypes.data)
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n, m = pts.shape
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labels_ptr = ffi.new("int[]", n)
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hclust.cluster_points_centroid(n, m, pts_ptr, dist**2, labels_ptr)
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return list(labels_ptr)
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