first commit

BN_realization/functions.csv

@@ -0,0 +1,9 @@
+Node 1,Node 2,Node 3,Node 4,Node 5
+0,0,0,0,0
+1,1,1,1,0
+1,1,1,-1,0
+1,0,0,-1,0
+0,0,1,-1,0
+1,1,1,-1,0
+1,1,0,-1,0
+1,1,1,-1,1

BN_realization/functions_2.csv

@@ -0,0 +1,3 @@
+Node 1,Node 2,Node 3,Node 4,Node 5,Node 6
+0,0,0,0,0,0
+1,1,1,1,1,1

BN_realization/generateFunctionData.py

@@ -0,0 +1,40 @@
+
+
+# memoryLength should be even so that the majority function is always defined;
+# the input to the majority function includes the current timestep and the
+# previous memoryLength timesteps
+def generateMajorityFunctionData(memoryLength,
+                                 timeseries_filepath,
+                                 function_output_filepath):
+    time_series_file = open(timeseries_filepath)
+    contents = time_series_file.read()
+    time_series = []
+    for char in contents:
+        if char == '1':
+            time_series.append(1)
+        elif char == '0':
+            time_series.append(0)
+    time_series_file.close()
+
+    majority_data = [-1 for _ in range(memoryLength)]
+    for i in range(memoryLength, len(time_series)):
+        numberOfOnes = sum(time_series[i - memoryLength: i + 1])
+        if 2 * numberOfOnes > memoryLength:
+            majority_data.append(1)
+        else:
+            majority_data.append(0)
+
+    # Note that right now this only works with 1 input
+    strToWrite = 'Majority\n'
+    for datum in majority_data:
+        strToWrite += str(datum)
+        strToWrite += '\n'
+    output_file = open(function_output_filepath, 'w')
+    output_file.write(strToWrite)
+
+
+folder = '/Users/maxnotarangelo/Documents/ISB/BN_realization/'
+ts_filepath = folder + 'time_series_data.csv'
+output_filepath = folder + 'function_data.csv'
+
+generateMajorityFunctionData(2, ts_filepath, output_filepath)

BN_realization/generateTimeseries.py

@@ -0,0 +1,39 @@
+import sys
+
+def create_timeseries_csv(input_filepath, output_filepath, numberOfInputs):
+    input_file = open(input_filepath)
+    raw_input = input_file.readlines()
+    input_file.close()
+
+    one_line_input = ''
+    for line in raw_input:
+        one_line_input += line
+
+    list_input = []
+    for char in one_line_input:
+        if char == '1':
+            list_input.append(1)
+        elif char == '0':
+            list_input.append(0)
+
+    strToWrite = ''
+    for i in range(numberOfInputs):
+        strToWrite += 'Input_%d,' % (i + 1)
+    strToWrite = strToWrite[:-1] + '\n'
+
+    for i in range(len(list_input) // numberOfInputs):
+        for j in range(numberOfInputs):
+            strToWrite += str(list_input[numberOfInputs * i + j])
+            strToWrite += ','
+        strToWrite = strToWrite[:-1] + '\n'
+
+    output_file = open(output_filepath, 'w')
+    output_file.write(strToWrite)
+
+
+inputFile = '/Users/maxnotarangelo/Documents/ISB/code/BN_realization/' + \
+                sys.argv[1] # 'time_series_raw_2.txt'
+outputFile = '/Users/maxnotarangelo/Documents/ISB/code/BN_realization/' + \
+                sys.argv[2] # 'time_series_data_3.csv'
+
+create_timeseries_csv(inputFile, outputFile, int(sys.argv[3])) 

BN_realization/initial_nodes.csv

@@ -0,0 +1,2 @@
+Node 1,Node 2,Node 3,Node 4,Node 5
+0,1,1,0,1

BN_realization/initial_nodes_2.csv

@@ -0,0 +1,2 @@
+Node 1,Node 2,Node 3,Node 4,Node 5,Node 6
+0,0,0,0,0,0

BN_realization/linkages.csv

@@ -0,0 +1,4 @@
+Node 1,Node 2,Node 3,Node 4,Node 5
+5,3,3,4,5
+2,5,1,-1,4
+4,4,5,-1,1

BN_realization/linkages_2.csv

@@ -0,0 +1,2 @@
+Node 1,Node 2,Node 3,Node 4,Node 5,Node 6
+1,2,3,4,5,6