def _run_interface(self, runtime):
int_mat_file = self.inputs.int_mat_file
threshold = self.inputs.threshold
print("loading int_mat_file")
int_mat = np.load(int_mat_file)
if not isdefined(threshold):
threshold = 0
int_list = return_int_net_list(int_mat, threshold)
net_List_file = os.path.abspath('int_List.txt')
export_List_net_from_list(net_List_file, int_list)
# int correl_mat as Louvain format
if self.inputs.export_Louvain:
coords = np.loadtxt(self.inputs.coords_file)
net_Louvain_file = os.path.abspath('Z_Louvain.txt')
export_Louvain_net_from_list(net_Louvain_file, int_list, coords)
return runtime
def test_export_Louvain_net_from_list():
"""testing Louvain Traag file building (for sake of compatibility of older
codes)"""
coords = np.loadtxt(coords_file)
Z_list = np.loadtxt(Z_list_file)
Z_Louvain_file = os.path.join(tmp_dir, "Z_Louvain.txt")
export_Louvain_net_from_list(Z_Louvain_file, Z_list, coords)
assert os.path.exists(Z_Louvain_file)
def _run_interface(self, runtime):
Z_cor_mat_file = self.inputs.Z_cor_mat_file
threshold = self.inputs.threshold
density = self.inputs.density
Z_cor_mat = np.load(Z_cor_mat_file)
if threshold != traits.Undefined and density == traits.Undefined:
Z_cor_mat[np.abs(Z_cor_mat) < threshold] = 0.0
Z_list = return_net_list(Z_cor_mat)
elif threshold == traits.Undefined and density != traits.Undefined:
Z_list = return_net_list(Z_cor_mat)
N = int(Z_list.shape[0] * density)
all_sorted_indexes = (-np.abs(Z_list[:, 2])).argsort()
sorted_indexes = all_sorted_indexes[:N]
max_thr_for_den_file = os.path.abspath('max_thr_for_den.txt')
if N == Z_list.shape[0]:
N = N - 1
max_thr_for_den = np.array(Z_list[all_sorted_indexes[N], 2])
with open(max_thr_for_den_file, "w") as f:
f.write("max_thr_for_den:{}".format(max_thr_for_den))
Z_list = Z_list[sorted_indexes, :]
else:
Z_list = return_net_list(Z_cor_mat)
# Z correl_mat as list of edges
net_List_file = os.path.abspath('Z_List.txt')
export_List_net_from_list(net_List_file, Z_list)
if self.inputs.export_Louvain:
coords = np.loadtxt(self.inputs.coords_file)
net_Louvain_file = os.path.abspath('Z_Louvain.txt')
export_Louvain_net_from_list(net_Louvain_file, Z_list, coords)
if self.inputs.export_np_bin:
bin_mat = np.zeros(shape=Z_cor_mat.shape, dtype="int")
bin_mat[Z_list[:, 0] - 1, Z_list[:, 1] - 1] = 1
np_bin_mat_file = os.path.abspath("bin_mat.npy")
np.save(np_bin_mat_file, bin_mat)
return runtime