From bdb5bb5bb9af58e4e61acae13ea1c35b52bde2e7 Mon Sep 17 00:00:00 2001
From: Gard Spreemann <gspreemann@gmail.com>
Date: Wed, 30 Mar 2016 15:09:27 +0200
Subject: Some documentation for general simplicial complexes.

---
 README.md               | 39 +++++++++++++++++++++++++++++++++++++++
 phstuff/diphawrapper.py | 17 +++++++++++++----
 2 files changed, 52 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index b2bc29b..e1afff0 100644
--- a/README.md
+++ b/README.md
@@ -147,6 +147,45 @@ environment variables.
     bc.plot(ax, dipharunner.barcode[1], weights.min(), weights.max())
     plt.show()
 
+### PH of an arbitrary simplicial complex (EXPERIMENTAL)
+
+The code for arbitrary simplicial complexes, the `simplicial` module,
+is dirty, fragile and inefficient. Its API and behavior may change at
+any time.
+
+    import phstuff.diphawrapper as dipha
+    import phstuff.barcode as bc
+    import matplotlib.pyplot as plt
+    import phstuff.simplicial as simpl
+
+    cplx = simpl.Complex()
+
+    cplx.add([0], 0)
+    cplx.add([1], 0)
+    cplx.add([2], 0)
+    cplx.add([3], 0)
+    cplx.add([4], 0)
+    cplx.add([0,1], 0)
+    cplx.add([0,2], 0)
+    cplx.add([2,4], 0)
+    cplx.add([3,4], 0)
+    cplx.add([1,3], 1)
+    cplx.add([0,3], 2)
+    cplx.add([2,3], 3)
+    cplx.add([0,2,3], 10)
+    cplx.add([0,1,3], 20)
+
+    dipharunner = dipha.DiphaRunner(2) # Compute up to 2-simplices.
+    dipharunner.simplicial(cplx)
+    dipharunner.run()
+
+    for interval in dipharunner.barcode[1]:
+        print(interval)
+
+    fig = plt.figure()
+    ax = fig.add_subplot(1,1,1)
+    bc.plot(ax, dipharunner.barcode[1], 0.0, 20.0)
+    plt.show()
 
 
 ### PH of an alpha complex made with CGAL
diff --git a/phstuff/diphawrapper.py b/phstuff/diphawrapper.py
index b2c9444..4d1742e 100644
--- a/phstuff/diphawrapper.py
+++ b/phstuff/diphawrapper.py
@@ -187,6 +187,19 @@ def save_cubical(fname, array):
             f.write(struct.pack("<d", float(w)))
 
 def save_simplicial(fname, complex):
+    """*EXPERIMENTAL*. Save a filtered simplicial complex.
+
+    Corresponds to DIPHA's "weighted boundary matrix".
+
+    Parameters:
+    -----------
+    
+    fname: Name of file to write.
+
+    complex: Simplicial complex to save.
+
+    """
+        
     complex.order()
     assert(complex.is_ordered())
     
@@ -221,10 +234,6 @@ def save_simplicial(fname, complex):
                 f.write(struct.pack("<q", bnode.i))
             
             
-    
-    
-            
-
 def load_barcode(fname, top_dim = None):
 
     """Load a barcode as written by DIPHA.
-- 
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