First commit of MAMMULT code

9 files changed, 421 insertions, 0 deletions

diff --git a/structure/activity/degs_to_activity_overlap.py b/structure/activity/degs_to_activity_overlap.py
new file mode 100644
index 0000000..c96959b
--- /dev/null
+++ b/structure/activity/degs_to_activity_overlap.py
@@ -0,0 +1,36 @@
+####
+##
+## Take a file which contains, on the n-th line, the degrees at each
+## layer of the n-th node, and print on output the corresponding node
+## multi-activity (i.e., the number of layers in which the node is
+## active) and the overlapping degree (i.e., the total number of edges
+## incident on the node)
+## 
+##
+
+
+import sys
+
+def to_binary(l):
+    s = 0
+    e = 0
+    for v in l:
+        s += v * pow(2,e)
+        e +=1
+    return s
+
+if len(sys.argv) < 2:
+    print "Usage: %s <filein>" % sys.argv[0]
+    sys.exit(1)
+
+distr = {}
+
+with open(sys.argv[1]) as f:
+    for l in f:
+        elems = [int(x) for x in l.strip(" \n").split(" ")]
+        ov = sum(elems)
+        new_list = [1 if x>0 else 0 for x in elems]
+        multi_act = sum(new_list)
+        if multi_act and ov:
+            print ov, multi_act
+    
diff --git a/structure/activity/degs_to_binary.py b/structure/activity/degs_to_binary.py
new file mode 100644
index 0000000..cb7aef5
--- /dev/null
+++ b/structure/activity/degs_to_binary.py
@@ -0,0 +1,45 @@
+####
+##
+## Take a file which contains, on the n-th line, the degrees at each
+## layer of the n-th node, and print on output the corresponding node
+## participation bit-strings, i.e. the string which contains "1" if on
+## that layer the node is connected, and zero otherwise
+## 
+## on the stderr, we also dump the distribution of each bit-string
+##
+
+
+import sys
+
+def to_binary(l):
+    s = 0
+    e = 0
+    for v in l:
+        s += v * pow(2,e)
+        e +=1
+    return s
+
+if len(sys.argv) < 2:
+    print "Usage: %s <filein>" % sys.argv[0]
+    sys.exit(1)
+
+distr = {}
+
+with open(sys.argv[1]) as f:
+    for l in f:
+        elems = [int(x) for x in l.strip(" \n").split(" ")]
+        new_list = [1 if x>0 else 0 for x in elems]
+        val = to_binary(new_list)
+        if val in distr:
+            distr[val] += 1
+        else:
+            distr[val] = 1
+        for i in new_list:
+            print i,
+        print
+
+for k in distr:
+    bin_list = bin(k)
+    bin_num = sum([int(x) if x=='1' else 0 for x in bin_list[2:]])
+    sys.stderr.write("%d %028s %d \n" % (bin_num, bin_list[2:], distr[k]))
+    
diff --git a/structure/activity/hamming_dist.py b/structure/activity/hamming_dist.py
new file mode 100644
index 0000000..2a98e64
--- /dev/null
+++ b/structure/activity/hamming_dist.py
@@ -0,0 +1,41 @@
+####
+##
+## Take as input the layers of a multiplex, and provide as output a
+## file where the n-th line contains the activity of the n-th
+## layer. 
+##
+##
+
+
+import sys
+
+if len(sys.argv) < 3:
+    print "Usage: %s <layer1> <layer2> [<layer3>...]" % sys.argv[0]
+    sys.exit(1)
+
+max_N = -1
+
+layers = []
+
+
+for layer in sys.argv[1:]:
+    active = []
+    with open(layer, "r") as lines:
+        for l in lines:
+            if l[0] == "#":
+                continue
+            
+            s, d = [int(x) for x in l.strip(" \n").split(" ")[:2]]
+            if s > max_N:
+                max_N = s
+            if d > max_N:
+                max_N = d
+            active.extend([s,d])
+        active = set(active)
+        layers.append(active)
+
+for i in range(len(layers)):
+    for j in range(i+1, len(layers)):
+        s = layer[i] ^ layer[j]
+        print i, j, len(s)*1.0 / min(len(layer[i]) + len(layer[j]), max_N+1)
+
diff --git a/structure/activity/layer_activity.py b/structure/activity/layer_activity.py
new file mode 100644
index 0000000..bea0416
--- /dev/null
+++ b/structure/activity/layer_activity.py
@@ -0,0 +1,27 @@
+####
+##
+## Take as input the layers of a multiplex, and provide as output a
+## file where the n-th line contains the activity of the n-th
+## layer. 
+##
+##
+
+
+import sys
+
+if len(sys.argv) < 2:
+    print "Usage: %s <layer1> [<layer2>...]" % sys.argv[0]
+    sys.exit(1)
+
+
+for layer in sys.argv[1:]:
+    active = []
+    with open(layer, "r") as lines:
+        for l in lines:
+            if l[0] == "#":
+                continue
+            
+            s, d = [int(x) for x in l.strip(" \n").split(" ")[:2]]
+            active.extend([s,d])
+        active = set(active)
+        print len(active)
diff --git a/structure/activity/layer_activity_vectors.py b/structure/activity/layer_activity_vectors.py
new file mode 100644
index 0000000..f32418d
--- /dev/null
+++ b/structure/activity/layer_activity_vectors.py
@@ -0,0 +1,44 @@
+####
+##
+## Take as input the layers of a multiplex, and provide as output a
+## file where the n-th line contains the activity of the n-th
+## layer. 
+##
+##
+
+
+import sys
+
+if len(sys.argv) < 2:
+    print "Usage: %s <layer1> [<layer2>...]" % sys.argv[0]
+    sys.exit(1)
+
+max_N = -1
+
+layers = []
+
+
+for layer in sys.argv[1:]:
+    active = []
+    with open(layer, "r") as lines:
+        for l in lines:
+            if l[0] == "#":
+                continue
+            
+            s, d = [int(x) for x in l.strip(" \n").split(" ")[:2]]
+            if s > max_N:
+                max_N = s
+            if d > max_N:
+                max_N = d
+            active.extend([s,d])
+        active = set(active)
+        layers.append(active)
+
+for l in layers:
+    for n in range(max_N+1):
+        if n in l:
+            print 1,
+        else:
+            print 0,
+    print
+
diff --git a/structure/activity/multiplexity.py b/structure/activity/multiplexity.py
new file mode 100644
index 0000000..9e038c9
--- /dev/null
+++ b/structure/activity/multiplexity.py
@@ -0,0 +1,41 @@
+####
+##
+## Take as input the layers of a multiplex, and provide as output a
+## file where the n-th line contains the activity of the n-th
+## layer. 
+##
+##
+
+
+import sys
+
+if len(sys.argv) < 3:
+    print "Usage: %s <layer1> <layer2> [<layer3>...]" % sys.argv[0]
+    sys.exit(1)
+
+max_N = -1
+
+layers = []
+
+
+for layer in sys.argv[1:]:
+    active = []
+    with open(layer, "r") as lines:
+        for l in lines:
+            if l[0] == "#":
+                continue
+            
+            s, d = [int(x) for x in l.strip(" \n").split(" ")[:2]]
+            if s > max_N:
+                max_N = s
+            if d > max_N:
+                max_N = d
+            active.extend([s,d])
+        active = set(active)
+        layers.append(active)
+
+for i in range(len(layers)):
+    for j in range(i+1, len(layers)):
+        s = layer[i] & layer[j]
+        print i, j, len(s)*1.0 / (max_N+1)
+
diff --git a/structure/activity/node_activity.py b/structure/activity/node_activity.py
new file mode 100644
index 0000000..6410a68
--- /dev/null
+++ b/structure/activity/node_activity.py
@@ -0,0 +1,51 @@
+####
+##
+## Take as input the layers of a multiplex, and provide as output a
+## file where the n-th line contains the activity of the n-th node. We
+## assume that nodes are numbered sequentially, starting from 0, with
+## no gaps (i.e., missing nodes are treated as isolated nodes)
+##
+##
+##
+
+
+import sys
+
+if len(sys.argv) < 2:
+    print "Usage: %s <layer1> [<layer2>...]" % sys.argv[0]
+    sys.exit(1)
+
+node_activity = {}
+
+max_N = -1
+
+for layer in sys.argv[1:]:
+    active = []
+    with open(layer, "r") as lines:
+        for l in lines:
+            if l[0] == "#":
+                continue
+            
+            s, d = [int(x) for x in l.strip(" \n").split(" ")[:2]]
+            active.extend([s,d])
+            if s > max_N:
+                max_N = s
+            if d > max_N:
+                max_N = d
+        active = set(active)
+        for n in active:
+            if n in node_activity:
+                node_activity[n] += 1
+            else:
+                node_activity[n] = 1
+    
+
+for n in range(max_N+1):
+    if n in node_activity:
+        print node_activity[n]
+    else:
+        print 0
+
+
+
+
diff --git a/structure/activity/node_activity_vectors.py b/structure/activity/node_activity_vectors.py
new file mode 100644
index 0000000..9839334
--- /dev/null
+++ b/structure/activity/node_activity_vectors.py
@@ -0,0 +1,68 @@
+####
+##
+## Take as input the layers of a multiplex, and provide as output a
+## file where the n-th line contains the degrees of the n-th node at
+## each layer, separated by a space, in the format:
+##
+## node1_deglay1 node1_deglay2 .... node1_deglayM
+## node2_deglay1 node2_deglay2 .... node2_deglayM
+## ..............................................
+## nodeN_deglay1 nodeN_deglay2 .... nodeN_deglayM
+##
+##
+
+import sys
+
+if len(sys.argv) < 2:
+    print "Usage: %s <layer1> [<layer2>...]" % sys.argv[0]
+    sys.exit(1)
+
+node_degrees = {}
+
+max_N = -1
+
+num_layer = 0
+
+for layer in sys.argv[1:]:
+    with open(layer, "r") as lines:
+        for l in lines:
+            if l[0] == "#":
+                continue
+            
+            s, d = [int(x) for x in l.strip(" \n").split(" ")[:2]]
+
+            if s > max_N:
+                max_N = s
+            if d > max_N:
+                max_N = d
+
+            if s in node_degrees:
+                if num_layer in node_degrees[s]:
+                    node_degrees[s][num_layer] += 1
+                else:
+                    node_degrees[s][num_layer] = 1
+            else:
+                node_degrees[s] = {}
+                node_degrees[s][num_layer] = 1
+
+            if d in node_degrees:
+                if num_layer in node_degrees[d]:
+                    node_degrees[d][num_layer] += 1
+                else:
+                    node_degrees[d][num_layer] = 1
+            else:
+                node_degrees[d] = {}
+                node_degrees[d][num_layer] = 1
+    num_layer += 1
+
+
+for n in range(max_N+1):
+    for i in range(num_layer):
+        if n in node_degrees:
+            if i in node_degrees[n]:
+                print 1,
+            else:
+                print 0,
+        else:
+            print 0,
+    print
diff --git a/structure/activity/node_degree_vectors.py b/structure/activity/node_degree_vectors.py
new file mode 100644
index 0000000..8863daa
--- /dev/null
+++ b/structure/activity/node_degree_vectors.py
@@ -0,0 +1,68 @@
+####
+##
+## Take as input the layers of a multiplex, and provide as output a
+## file where the n-th line contains the degrees of the n-th node at
+## each layer, separated by a space, in the format:
+##
+## node1_deglay1 node1_deglay2 .... node1_deglayM
+## node2_deglay1 node2_deglay2 .... node2_deglayM
+## ..............................................
+## nodeN_deglay1 nodeN_deglay2 .... nodeN_deglayM
+##
+##
+
+import sys
+
+if len(sys.argv) < 2:
+    print "Usage: %s <layer1> [<layer2>...]" % sys.argv[0]
+    sys.exit(1)
+
+node_degrees = {}
+
+max_N = -1
+
+num_layer = 0
+
+for layer in sys.argv[1:]:
+    with open(layer, "r") as lines:
+        for l in lines:
+            if l[0] == "#":
+                continue
+            
+            s, d = [int(x) for x in l.strip(" \n").split(" ")[:2]]
+
+            if s > max_N:
+                max_N = s
+            if d > max_N:
+                max_N = d
+
+            if s in node_degrees:
+                if num_layer in node_degrees[s]:
+                    node_degrees[s][num_layer] += 1
+                else:
+                    node_degrees[s][num_layer] = 1
+            else:
+                node_degrees[s] = {}
+                node_degrees[s][num_layer] = 1
+
+            if d in node_degrees:
+                if num_layer in node_degrees[d]:
+                    node_degrees[d][num_layer] += 1
+                else:
+                    node_degrees[d][num_layer] = 1
+            else:
+                node_degrees[d] = {}
+                node_degrees[d][num_layer] = 1
+    num_layer += 1
+
+
+for n in range(max_N+1):
+    for i in range(num_layer):
+        if n in node_degrees:
+            if i in node_degrees[n]:
+                print node_degrees[n][i],
+            else:
+                print 0,
+        else:
+            print 0,
+    print