Merge pull request #80 from MunchLab/ReebOfSimplexTree

Updating function names

- `reeb_of_lower_star` is now `computeReeb`
- `LowerStarSC` is now `LowerStar`
- `Torus.plot()` is now `Torus.draw()`

Author: lizliz

README.md

@@ -36,7 +36,7 @@ The code is a compilation of work done by [Elizabeth Munch](http://www.elizabeth
 
 - [Danielle Barnes](https://github.com/barnesd8)
 - [Elena Wang](https://elenaxwang.com)
-- [Ishika Ghsoh](https://www.ishikaghosh.com/)
+- [Ishika Ghosh](https://www.ishikaghosh.com/)
 
 ## Contact Information
 

cereeberus/cereeberus/__init__.py

@@ -1,5 +1,5 @@
 __all__ = [
-	'ReebGraph', 'LowerStarSC', 'reeb_of_lower_star',
+	'ReebGraph', 'LowerStar', 'computeReeb',
 	'MergeTree', 'MapperGraph', 'EmbeddedGraph', 'Interleave', 'Assignment',
 	'data', 'dist', 'reeb', 'compute'
 ]
@@ -9,8 +9,8 @@
 from .reeb.mapper import MapperGraph
 from .reeb.embeddedgraph import EmbeddedGraph
 from .distance.interleave import Interleave, Assignment
-from .reeb.lowerstarSC import LowerStarSC
-from .compute.reeb_of_lower_star import reeb_of_lower_star
+from .reeb.lowerstar import LowerStar
+from .compute.computereeb import computeReeb
 
 # Examples 
 from .data import ex_reebgraphs, ex_mergetrees, ex_mappergraphs, ex_embedgraphs, ex_torus

cereeberus/cereeberus/compute/__init__.py

@@ -1,4 +1,4 @@
-__all__ = ['draw', 'unionfind', 'distance', 'reeb_of_lower_star']
+__all__ = ['draw', 'unionfind', 'computeReeb']
 from .draw import *
 from .unionfind import *
-from .reeb_of_lower_star import *
+from .computereeb import *

…cereeberus/compute/reeb_of_lower_star.py …eberus/cereeberus/compute/computereeb.pycereeberus/cereeberus/compute/reeb_of_lower_star.py renamed to cereeberus/cereeberus/compute/computereeb.py cereeberus/cereeberus/compute/reeb_of_lower_star.py renamed to cereeberus/cereeberus/compute/computereeb.py

@@ -1,5 +1,5 @@
 from .unionfind import UnionFind
-from ..reeb.lowerstarSC import LowerStarSC
+from ..reeb.lowerstar import LowerStar
 import numpy as np
 
 
@@ -19,7 +19,7 @@ def is_face(sigma, tau):
 
 def get_levelset_components(L):
     '''
-    Given a list of simplices L representing a level set, compute the connected components. This function is really only helpful inside of reeb_of_lower_star.
+    Given a list of simplices L representing a level set, compute the connected components. This function is really only helpful inside of computeReeb.
     
     Args:
         L: A list of simplices (each simplex is a list of vertices).
@@ -46,27 +46,27 @@ def get_levelset_components(L):
     return components
 
 
-def reeb_of_lower_star(K: LowerStarSC, verbose = False):
+def computeReeb(K: LowerStar, verbose = False):
     """Computes the Reeb graph of a Lower Star Simplicial Complex K.
 
     Args:
-        K (LowerStarSC): A Lower Star Simplicial Complex with assigned filtration values.
+        K (LowerStar): A Lower Star Simplicial Complex with assigned filtration values.
         verbose (boolean): Make it True if you want lots of printouts.
 
     Returns:
         ReebGraph: The computed Reeb graph.
 
     Example:
-        >>> from cereeberus.reeb.lowerstarSC import LowerStarSC
-        >>> K = LowerStarSC()
+        >>> from cereeberus.reeb.LowerStar import LowerStar
+        >>> K = LowerStar()
         >>> K.insert([0, 1, 2])
         >>> K.insert([1, 3])
         >>> K.insert([2,3])
         >>> K.assign_filtration([0], 0.0)
         >>> K.assign_filtration([1], 3.0)
         >>> K.assign_filtration([2], 5.0)
         >>> K.assign_filtration([3], 7)
-        >>> R = reeb_of_lower_star(K)
+        >>> R = computeReeb(K)
         >>> R.draw()
     """
     from ..reeb.reebgraph import ReebGraph

cereeberus/cereeberus/data/__init__.py

@@ -3,6 +3,6 @@
 
 from .ex_reebgraphs import *
 from .ex_mergetrees import *
-from . import ex_mappergraphs
-from . import ex_embedgraphs
-from . import ex_torus
+from .ex_mappergraphs import *
+from .ex_embedgraphs import *
+from .ex_torus import *

cereeberus/cereeberus/data/ex_torus.py

@@ -1,13 +1,13 @@
-from ..reeb.lowerstarSC import LowerStarSC 
+from ..reeb.lowerstar import LowerStar 
 import matplotlib.pyplot as plt
 import numpy as np
 
-class Torus(LowerStarSC):
+class Torus(LowerStar):
     """
-    Class to create an example torus using the LowerStarSC.
+    Class to create an example torus using the LowerStar.
 
     Inherits from:
-        LowerStarSC: A lower star simplicial complex.
+        LowerStar: A lower star simplicial complex.
 
     Methods:
         __init__(): Initializes the torus by inserting simplices.
@@ -101,7 +101,7 @@ def assign_filtration(self, vertex, value):
 
         super().assign_filtration(vertex, value)
 
-    def plot(self, ax = None, cmap = plt.cm.viridis, **kwargs):
+    def draw(self, ax = None, cmap = plt.cm.viridis, **kwargs):
         """Gives a flat plot of the torus's 1-skeleton using matplotlib.
 
         Args:

cereeberus/cereeberus/reeb/__init__.py

@@ -1,7 +1,7 @@
-__all__ = ['reebgraph', 'merge', 'mapper', 'embeddedgraph', 'lowerstarSC']
+__all__ = ['reebgraph', 'merge', 'mapper', 'embeddedgraph', 'lowerstar']
 
 from .reebgraph import *
 from .merge import *
 from .mapper import *
 from .embeddedgraph import *
-from .lowerstarSC import *
+from .lowerstar import *

cereeberus/cereeberus/reeb/lowerstarSC.py cereeberus/cereeberus/reeb/lowerstar.pycereeberus/cereeberus/reeb/lowerstarSC.py renamed to cereeberus/cereeberus/reeb/lowerstar.py

@@ -1,11 +1,11 @@
-# An example torus built using gudhi's Simplex Tree 
+# An example lower star filtration built using gudhi's Simplex Tree 
 
 from gudhi import SimplexTree
 import numpy as np
 
-class LowerStarSC(SimplexTree):
+class LowerStar(SimplexTree):
     """
-    Class to create a simplicial compex that has a lower star filtration, based on Gudhi's SimplexTree.
+    Class to create a simplicial complex that has a lower star filtration, based on Gudhi's SimplexTree.
 
     Inherits from:
         SimplexTree: A simplex tree structure from the Gudhi library.
@@ -32,7 +32,7 @@ def assign_filtration(self, vertex, value):
         if isinstance(vertex, int):
             vertex = [vertex]
         elif len(vertex) != 1:
-            raise ValueError("vertex must be an integer, or a single-element list.")
+            raise ValueError("Lower star filtration can only by updated by specificying the function value on a vertex. Input -vertex- must be an integer, or a single-element list.")
 
         super().assign_filtration(vertex, value)
 
@@ -87,7 +87,7 @@ def iter_vertices(self):
 
 
 if __name__ == "__main__":
-    LS = LowerStarSC()
+    LS = LowerStar()
     LS.insert([0, 1, 2])
     LS.insert([1, 3])
     LS.insert([2,3])

doc_source/images/SmallComplexExample.jpeg

@@ -1,6 +1,6 @@
 Compute Reeb Graph from Lower Star Filtration
 **********************************************
 
-The ``reeb_of_lower_star`` module provides functionality to compute the Reeb graph from a lower star filtration. Information on the lower star filtration can be found in the `Lower Star Filtration for Simplicial Complexes <../reeb/lowerstarSC.rst>`_ documentation.
+The ``computeReeb`` module provides functionality to compute the Reeb graph from a lower star filtration. Information on the lower star filtration can be found in the `Lower Star Filtration for Simplicial Complexes <../reeb/lowerstar.rst>`_ documentation.
 
-.. autofunction:: cereeberus.compute.reeb_of_lower_star.reeb_of_lower_star
+.. autofunction:: cereeberus.compute.computereeb.computeReeb