change project structure and using .ini as config file

algorithms/neat/genome/aggregations.py

@@ -1,109 +0,0 @@
-"""
-aggregations, two special case need to consider:
-1. extra 0s
-2. full of 0s
-"""
-
-import jax
-import jax.numpy as jnp
-import numpy as np
-from jax import jit
-
-
-@jit
-def sum_agg(z):
-    z = jnp.where(jnp.isnan(z), 0, z)
-    return jnp.sum(z, axis=0)
-
-
-@jit
-def product_agg(z):
-    z = jnp.where(jnp.isnan(z), 1, z)
-    return jnp.prod(z, axis=0)
-
-
-@jit
-def max_agg(z):
-    z = jnp.where(jnp.isnan(z), -jnp.inf, z)
-    return jnp.max(z, axis=0)
-
-
-@jit
-def min_agg(z):
-    z = jnp.where(jnp.isnan(z), jnp.inf, z)
-    return jnp.min(z, axis=0)
-
-
-@jit
-def maxabs_agg(z):
-    z = jnp.where(jnp.isnan(z), 0, z)
-    abs_z = jnp.abs(z)
-    max_abs_index = jnp.argmax(abs_z)
-    return z[max_abs_index]
-
-
-@jit
-def median_agg(z):
-
-    non_zero_mask = ~jnp.isnan(z)
-    n = jnp.sum(non_zero_mask, axis=0)
-
-    z = jnp.where(jnp.isnan(z), jnp.inf, z)
-    sorted_valid_values = jnp.sort(z)
-
-    def _even_case():
-        return (sorted_valid_values[n // 2 - 1] + sorted_valid_values[n // 2]) / 2
-
-    def _odd_case():
-        return sorted_valid_values[n // 2]
-
-    median = jax.lax.cond(n % 2 == 0, _even_case, _odd_case)
-
-    return median
-
-
-@jit
-def mean_agg(z):
-    non_zero_mask = ~jnp.isnan(z)
-    valid_values_sum = sum_agg(z)
-    valid_values_count = jnp.sum(non_zero_mask, axis=0)
-    mean_without_zeros = valid_values_sum / valid_values_count
-    return mean_without_zeros
-
-
-AGG_TOTAL_LIST = [sum_agg, product_agg, max_agg, min_agg, maxabs_agg, median_agg, mean_agg]
-
-agg_name2key = {
-    'sum': 0,
-    'product': 1,
-    'max': 2,
-    'min': 3,
-    'maxabs': 4,
-    'median': 5,
-    'mean': 6,
-}
-
-
-@jit
-def agg(idx, z):
-    idx = jnp.asarray(idx, dtype=jnp.int32)
-
-    def full_nan():
-        return 0.
-
-    def not_full_nan():
-        return jax.lax.switch(idx, AGG_TOTAL_LIST, z)
-
-    return jax.lax.cond(jnp.all(jnp.isnan(z)), full_nan, not_full_nan)
-
-
-vectorized_agg = jax.vmap(agg, in_axes=(0, 0))
-
-if __name__ == '__main__':
-    array = jnp.asarray([1, 2, np.nan, np.nan, 3, 4, 5, np.nan, np.nan, np.nan, np.nan], dtype=jnp.float32)
-    for names in agg_name2key.keys():
-        print(names, agg(agg_name2key[names], array))
-
-    array2 = jnp.asarray([0, 0, 0, 0], dtype=jnp.float32)
-    for names in agg_name2key.keys():
-        print(names, agg(agg_name2key[names], array2))