Initial script

graph_count.py

@@ -0,0 +1,69 @@
+from pyflagser_count import flagser_count
+from typing import Union, List
+import numpy as np
+import scipy.sparse as sp
+from pathlib import Path
+
+temporary_file_name = "temp"
+
+
+def binary2simplex(address):
+    """From Jason's flagser-count."""
+    X = np.fromfile(address, dtype='uint64')                         #Load binary file
+    S=[]                                                             #Initialise empty list for simplices
+
+    i=0
+    while i < len(X):
+        b = format(X[i], '064b')                                     #Load the 64bit integer as a binary string
+        if b[0] == '0':                                              #If the first bit is 0 this is the start of a new simplex
+            S.append([])
+        t=[int(b[-21:],2), int(b[-42:-21],2), int(b[-63:-42],2)]     #Compute the 21bit ints stored in this 64bit int
+        for j in t:
+            if j != 2097151:                                         #If an int is 2^21 this means we have reached the end of the simplex, so don't add it
+                S[-1].append(j)
+        i+=1
+    return S
+
+
+def biedge_count_per_dimension(conn_matrix: Union[np.ndarray, sp.coo_matrix], repeats: bool = True):
+    result_dict = {}
+
+    for file in Path("").glob(temporary_file_name + "*.binary"):
+        if file.exists():
+            raise FileExistsError("File " + str(file.absolute()) + " already exists. Cannot overwrite it.")
+
+    flagser_count(conn_matrix, binary=temporary_file_name)
+
+    if repeats:
+        for file in Path("").glob(temporary_file_name + "*.binary"):
+            simplices = binary2simplex(file)
+            for simplex in simplices:
+                dimension = len(simplex) - 1
+                result_dict[dimension] = result_dict.setdefault(dimension, 0) +\
+                                         biedge_in_simplex(conn_matrix, simplex)
+            file.unlink()
+
+    else:
+        simplices = []
+        for file in Path("").glob(temporary_file_name + "*.binary"):
+            simplices.extend(binary2simplex(file))
+            file.unlink()
+        for simplex in simplices:
+            dimension = len(simplex) - 1
+            biedge_coordinates = biedges_in_simplex_coordinates(conn_matrix, simplex)
+            for elem in zip(biedge_coordinates):
+                result_dict[dimension] = result_dict.setdefault(dimension, 0) +\
+                                         conn_matrix[elem] * conn_matrix.T[elem]
+                conn_matrix[elem] = False
+                conn_matrix[list(reversed(elem))] = False
+
+
+def biedge_in_simplex(conn_matrix: Union[np.ndarray, sp.csr_matrix], simplex: List[int]):
+    return np.sum(np.tril(conn_matrix[simplex].T[simplex]))
+
+
+def biedges_in_simplex_coordinates(conn_matrix: Union[np.ndarray, sp.csr_matrix], simplex: List[int]):
+    biedges_indices_in_simplex = np.nonzero(np.tril(conn_matrix[simplex].T[simplex]))
+    biedges_rows_in_matrix = simplex[biedges_indices_in_simplex[0]]
+    biedges_cols_in_matrix = simplex[biedges_indices_in_simplex[1]]
+    return biedges_rows_in_matrix, biedges_cols_in_matrix