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Improve use of max_iter_harmony + max_iter_kmeans #8

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Aug 11, 2020
Merged

Improve use of max_iter_harmony + max_iter_kmeans #8

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11 changes: 6 additions & 5 deletions harmonypy/harmony.py
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Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,8 @@ def run_harmony(
nclust = None,
tau = 0,
block_size = 0.05,
max_iter_kmeans = 10,
max_iter_harmony = 10,
max_iter_kmeans = 20,
epsilon_cluster = 1e-5,
epsilon_harmony = 1e-4,
plot_convergence = False,
Expand Down Expand Up @@ -121,7 +122,7 @@ def run_harmony(
np.random.seed(random_state)

ho = Harmony(
data_mat, phi, phi_moe, Pr_b, sigma, theta, max_iter_kmeans,
data_mat, phi, phi_moe, Pr_b, sigma, theta, max_iter_harmony, max_iter_kmeans,
epsilon_cluster, epsilon_harmony, nclust, block_size, lamb_mat, verbose
)

Expand All @@ -130,8 +131,8 @@ def run_harmony(
class Harmony(object):
def __init__(
self, Z, Phi, Phi_moe, Pr_b, sigma,
theta, max_iter_kmeans, epsilon_kmeans,
epsilon_harmony, K, block_size,
theta, max_iter_harmony, max_iter_kmeans,
epsilon_kmeans, epsilon_harmony, K, block_size,
lamb, verbose
):
self.Z_corr = np.array(Z)
Expand Down Expand Up @@ -168,7 +169,7 @@ def __init__(

self.allocate_buffers()
self.init_cluster()
self.harmonize(self.max_iter_kmeans, self.verbose)
self.harmonize(self.max_iter_harmony, self.verbose)

def result(self):
return self.Z_corr
Expand Down