From 29d4d8b021b63bba023bd7fe944605ea97bf1aba Mon Sep 17 00:00:00 2001
From: TeunHuijben <teunhuijben@hotmail.com>
Date: Sun, 14 Jun 2020 17:17:47 +0200
Subject: [PATCH] Add functions for reconnecting the graph

---
 MATLAB/avg/connectGraph.m | 42 +++++++++++++++++++++++++++++++++++++++
 MATLAB/avg/isConnected.m  | 34 +++++++++++++++++++++++++++++++
 2 files changed, 76 insertions(+)
 create mode 100644 MATLAB/avg/connectGraph.m
 create mode 100644 MATLAB/avg/isConnected.m

diff --git a/MATLAB/avg/connectGraph.m b/MATLAB/avg/connectGraph.m
new file mode 100644
index 0000000..66d847b
--- /dev/null
+++ b/MATLAB/avg/connectGraph.m
@@ -0,0 +1,42 @@
+%connectGraph   This function keeps increasing the threshold on the error
+%to include more connections, untill the graph is connected.
+%
+%   SYNOPSIS:
+%       [error_idx] = connectGraph(I,error)
+%
+%   Input: 
+%       I: 2xN matrix of indices indications the connections
+%       error: vector of error values for every combinations in I
+%
+%   Output:
+%       error_idx: indices of the to-be-removed connection in I
+%
+%   NOTE:
+%
+% (C) Copyright 2017                    QI Group
+%     All rights reserved               Faculty of Applied Physics
+%                                       Delft University of Technology
+%                                       Lorentzweg 1
+%                                       2628 CJ Delft
+%                                       The Netherlands
+%
+% Teun Huijben, June 2020.
+
+function error_idx = connectGraph(I,error)
+
+    [a,b] = sort(abs(error));           %sort the errors
+    first_above5 = find(a>5,1);         %find the index of lowest error
+
+    error_idx = abs(error)>5;           %indices of all errors
+    I_new = I; 
+    I_new(:,error_idx) = [];            %remove errors from graph
+
+    start = first_above5; 
+    while (isConnected(I_new)==0 | max(I_new(:))<max(I(:)))
+        error_idx = (abs(error)>abs(error(b(start))));  %indices of all errors including new one
+        I_new = I; 
+        I_new(:,error_idx) = []; 
+        start = start+1; 
+    end
+ 
+end
diff --git a/MATLAB/avg/isConnected.m b/MATLAB/avg/isConnected.m
new file mode 100644
index 0000000..a3ab092
--- /dev/null
+++ b/MATLAB/avg/isConnected.m
@@ -0,0 +1,34 @@
+%isConnected   This function checks whether the graph is connected
+%
+%   SYNOPSIS:
+%       [connected] = isConnected(I)
+%
+%   Input: 
+%       I: 2xN matrix of indices indications the connections
+%
+%   Output:
+%       connected: Boolean indicating whether is connected
+%
+%   NOTE:
+%
+% (C) Copyright 2017                    QI Group
+%     All rights reserved               Faculty of Applied Physics
+%                                       Delft University of Technology
+%                                       Lorentzweg 1
+%                                       2628 CJ Delft
+%                                       The Netherlands
+%
+% Teun Huijben, June 2020.
+
+function connected = isConnected(I)
+
+    Gr = graph(I(1,:),I(2,:));
+    clusters = conncomp(Gr);
+    if max(clusters)==1
+        connected = true;
+    else
+        connected = false; 
+    end
+
+end
+