pymoo 0.6.1.5.dev0__cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl

pymoo/cython/mnn.pyx

@@ -0,0 +1,273 @@
+# distutils: language = c++
+# cython: language_level=2, boundscheck=False, wraparound=False, cdivision=True
+
+# This was implemented using the full distances matrix
+# Other strategies can be more efficient depending on the population size and number of objectives
+# This approach was the most promising for N = 3
+# I believe for a large number of objectives M, some strategy based on upper bounds for distances would be helpful
+# Those interested in contributing please contact me at bruscalia12@gmail.com
+
+
+import numpy as np
+
+from pymoo.cython.utils cimport c_get_drop, c_get_argmin, c_get_argmax, c_normalize_array
+
+from libcpp cimport bool
+from libcpp.vector cimport vector
+from libcpp.set cimport set as cpp_set
+
+
+cdef extern from "math.h":
+    double HUGE_VAL
+
+
+def calc_mnn(double[:, :] X, int n_remove=0):
+
+    cdef:
+        int N, M, n
+        cpp_set[int] extremes
+        vector[int] extremes_min, extremes_max
+
+    N = X.shape[0]
+    M = X.shape[1]
+
+    if N <= M:
+        return np.full(N, HUGE_VAL)
+
+    if n_remove <= (N - M):
+        if n_remove < 0:
+            n_remove = 0
+        else:
+            pass
+    else:
+        n_remove = N - M
+
+    extremes_min = c_get_argmin(X)
+    extremes_max = c_get_argmax(X)
+
+    extremes = cpp_set[int]()
+
+    for n in extremes_min:
+        extremes.insert(n)
+
+    for n in extremes_max:
+        extremes.insert(n)
+
+    X = c_normalize_array(X, extremes_max, extremes_min)
+
+    return c_calc_mnn(X, n_remove, N, M, extremes)
+
+
+def calc_2nn(double[:, :] X, int n_remove=0):
+
+    cdef:
+        int N, M, n
+        cpp_set[int] extremes
+        vector[int] extremes_min, extremes_max
+
+    N = X.shape[0]
+    M = X.shape[1]
+
+    if n_remove <= (N - M):
+        if n_remove < 0:
+            n_remove = 0
+        else:
+            pass
+    else:
+        n_remove = N - M
+
+    extremes_min = c_get_argmin(X)
+    extremes_max = c_get_argmax(X)
+
+    extremes = cpp_set[int]()
+
+    for n in extremes_min:
+        extremes.insert(n)
+
+    for n in extremes_max:
+        extremes.insert(n)
+
+    X = c_normalize_array(X, extremes_max, extremes_min)
+
+    M = 2
+
+    return c_calc_mnn(X, n_remove, N, M, extremes)
+
+
+cdef c_calc_mnn(double[:, :] X, int n_remove, int N, int M, cpp_set[int] extremes):
+
+    cdef:
+        int n, mm, i, j, n_removed, k, MM
+        double dij
+        cpp_set[int] calc_items
+        cpp_set[int] H
+        double[:, :] D
+        double[:] d
+        int[:, :] Mnn
+
+    # Define items to calculate distances
+    calc_items = cpp_set[int]()
+    for n in range(N):
+        calc_items.insert(n)
+    for n in extremes:
+        calc_items.erase(n)
+
+    # Define remaining items to evaluate
+    H = cpp_set[int]()
+    for n in range(N):
+        H.insert(n)
+
+    # Instantiate distances array
+    _D = np.empty((N, N), dtype=np.double)
+    D = _D[:, :]
+
+    # Shape of X
+    MM = X.shape[1]
+
+    # Fill values on D
+    for i in range(N - 1):
+        D[i, i] = 0.0
+
+        for j in range(i + 1, N):
+
+            dij = 0
+            for mm in range(MM):
+                dij = dij + (X[j, mm] - X[i, mm]) * (X[j, mm] - X[i, mm])
+
+            D[i, j] = dij
+            D[j, i] = D[i, j]
+
+    D[N-1, N-1] = 0.0
+
+    # Initialize
+    n_removed = 0
+
+    # Initialize neighbors and distances
+    # _Mnn = np.full((N, M), -1, dtype=np.intc)
+    _Mnn = np.argpartition(D, range(1, M+1), axis=1)[:, 1:M+1].astype(np.intc)
+    dd = np.full((N,), HUGE_VAL, dtype=np.double)
+
+    Mnn = _Mnn[:, :]
+    d = dd[:]
+
+    # Obtain distance metrics
+    c_calc_d(d, Mnn, D, calc_items, M)
+
+    # While n_remove not acheived (no need to recalculate if only one item should be removed)
+    while n_removed < (n_remove - 1):
+
+        # Obtain element to drop
+        k = c_get_drop(d, H)
+        H.erase(k)
+
+        # Update index
+        n_removed = n_removed + 1
+
+        # Get items to be recalculated
+        calc_items = c_get_calc_items(Mnn, H, k, M)
+        for n in extremes:
+            calc_items.erase(n)
+
+        # Fill in neighbors and distance matrix
+        c_calc_mnn_iter(
+                X,
+                Mnn,
+                D,
+                N, M,
+                calc_items,
+                H
+            )
+
+        # Obtain distance metrics
+        c_calc_d(d, Mnn, D, calc_items, M)
+
+    return dd
+
+
+cdef c_calc_mnn_iter(
+    double[:, :] X,
+    int[:, :] Mnn,
+    double[:, :] D,
+    int N, int M,
+    cpp_set[int] calc_items,
+    cpp_set[int] H
+    ):
+
+    cdef:
+        int i, j, m
+
+    # Iterate over items to calculate
+    for i in calc_items:
+
+        # Iterate over elements in X
+        for j in H:
+
+            # Go to next if same element
+            if (j == i):
+                continue
+
+            # Replace at least the last neighbor
+            elif (D[i, j] <= D[i, Mnn[i, M-1]]) or (Mnn[i, M-1] == -1):
+
+                # Iterate over current values
+                for m in range(M):
+
+                    # Set to current if unassigned
+                    if (Mnn[i, m] == -1):
+
+                        # Set last neighbor to index
+                        Mnn[i, m] = j
+                        break
+
+                    # Break if checking already corresponding index
+                    elif (j == Mnn[i, m]):
+                        break
+
+                    # Distance satisfies condition
+                    elif (D[i, j] <= D[i, Mnn[i, m]]):
+
+                        # Replace higher values
+                        Mnn[i, m + 1:] = Mnn[i, m:-1]
+
+                        # Replace current value
+                        Mnn[i, m] = j
+                        break
+
+
+# Calculate crowding metric
+cdef c_calc_d(double[:] d, int[:, :] Mnn, double[:, :] D, cpp_set[int] calc_items, int M):
+
+    cdef:
+        int i, m
+
+    for i in calc_items:
+
+        d[i] = 1
+        for m in range(M):
+            d[i] = d[i] * D[i, Mnn[i, m]]
+
+
+# Returns indexes of items to be recalculated after removal
+cdef cpp_set[int] c_get_calc_items(
+    int[:, :] Mnn,
+    cpp_set[int] H,
+    int k, int M):
+
+    cdef:
+        int i, m
+        cpp_set[int] calc_items
+
+    calc_items = cpp_set[int]()
+
+    for i in H:
+
+        for m in range(M):
+
+            if Mnn[i, m] == k:
+
+                Mnn[i, m:-1] = Mnn[i, m + 1:]
+                Mnn[i, M-1] = -1
+
+                calc_items.insert(i)
+
+    return calc_items