Support non-simplicial complexes

cechmate/filtrations/base.py

@@ -28,7 +28,7 @@ def __init__(self, maxdim=None, verbose=True):
         self.simplices_ = None
         self.diagrams_ = None
 
-    def diagrams(self, simplices=None, show_inf=False):
+    def diagrams(self, simplices=None, show_inf=False, verbose=True, simplicial=False):
         """Compute persistence diagrams for the simplices.
 
         Parameters
@@ -46,6 +46,6 @@ def diagrams(self, simplices=None, show_inf=False):
 
         """
         simplices = simplices or self.simplices_
-        self.diagrams_ = phat_diagrams(simplices, show_inf)
+        self.diagrams_ = phat_diagrams(simplices, show_inf, verbose, simplicial)
 
         return self.diagrams_

cechmate/filtrations/custom.py

@@ -23,3 +23,11 @@ def build(self, simplices):
         """
 
         self.simplices_ = simplices
+
+    def diagrams(self, simplices=None, show_inf=False, verbose=True, simplicial=True):
+        """
+        Redefine the Custom version of diagrams so that simplicial defaults to True, rather
+        than false.
+        """
+
+        return super().diagrams(simplices,show_inf,verbose,simplicial)

cechmate/solver.py

@@ -5,7 +5,7 @@
 import phat
 
 
-def phat_diagrams(simplices, show_inf=False, verbose=True):
+def phat_diagrams(simplices, show_inf=False, verbose=True, simplicial=False):
     """
     Compute the persistence diagram for :code:`simplices` using Phat.
 
@@ -19,12 +19,21 @@ def phat_diagrams(simplices, show_inf=False, verbose=True):
     show_inf: Boolean
         Determines whether or not to return points that never die.
 
+    simplicial: Boolean
+        Asserts that the filtration is a simplicial complex at every "dist," 
+        not some other kind of topological complex. Defaults to not checking
+        to ensure speed of existing filtrations.
+
     Returns
     --------
     dgms: list of diagrams 
         the persistence diagram for Hk 
     """
 
+    ## Check that the filtration is a simplicial complex at every time step
+    if simplicial:
+        simplices = _assert_simplicial(simplices)
+
     ## Convert simplices representation to sparse pivot column
     #  -- sort by birth time, if tie, use order of simplex
     ordered_simplices = sorted(simplices, key=lambda x: (x[1], len(x[0])))
@@ -59,6 +68,36 @@ def phat_diagrams(simplices, show_inf=False, verbose=True):
 
     return dgms
 
+def _assert_simplicial(simplices):
+
+    # Initialize a set to keep track of simplices
+    existing_simplices = set()
+
+    # Initialize a list which is the (sub)filtration
+    # where the filtration is properly a simplicial
+    # complex at each point
+    simplicial_filtration = list()
+
+    # Sort the filtration by the time at which each simplex is
+    for s,t in sorted(simplices, key = lambda x: (x[1],x[0])):
+
+        # Sort to ensure a uniform representation
+        sorted_simplex = tuple(sorted(s))
+
+        if sorted_simplex in existing_simplices:
+            continue
+
+        else:
+            existing_simplices.add(sorted_simplex)
+
+            # Don't sort in the final filtration because the
+            # user might care about the order in which the
+            # 0-faces are listed
+
+            simplicial_filtration.append((s,t))
+
+    return simplicial_filtration
+
 
 def _simplices_to_sparse_pivot_column(ordered_simplices, verbose=False):
     """