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bug fix in use of ext data file

pull/4/head
Kai Staats 2015-12-23 20:09:15 -07:00
parent 6a4dfe327e
commit 034ba2af59
4 changed files with 28 additions and 14 deletions
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7
RELEASE_NOTES.txt
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@ -14,3 +14,10 @@ Thank you! --kai
2015 12/23
Discovered that when loading external datasets, Karoo was yet extracting variables (terminals) from the data in the files/ directory, according to the selected kernel.
This is now fixed.
Happy holidays! --kai

31
karoo_gp_base_class.py
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@ -2,7 +2,7 @@
# Define the Karoo GP methods and global variables
# by Kai Staats, MSc UCT / AIMS
# Much thanks to Emmanuel Dufourq and Arun Kumar for their support, guidance, and free psychotherapy sessions
# version 0.9
# version 0.9.1.1
import csv
import os
@ -215,22 +215,29 @@ class Base_GP(object):
func_dict = {'a':'files/functions_ABS.csv', 'b':'files/functions_BOOL.csv', 'c':'files/functions_CLASSIFY.csv', 'm':'files/functions_MATCH.csv', 'p':'files/functions_PLAY.csv'}
fitt_dict = {'a':'min', 'b':'max', 'c':'max', 'm':'max', 'p':''}
if len(sys.argv) == 1:
data_x = np.loadtxt(data_dict[self.kernel], skiprows = 1, delimiter = ',', dtype = float); data_x = data_x[:,0:-1]
data_y = np.loadtxt(data_dict[self.kernel], skiprows = 1, usecols = (-1,), delimiter = ',', dtype = float)
if len(sys.argv) == 1: # load data in the files/ directory
data_x = np.loadtxt(data_dict[self.kernel], skiprows = 1, delimiter = ',', dtype = float); data_x = data_x[:,0:-1] # skip right-most column
data_y = np.loadtxt(data_dict[self.kernel], skiprows = 1, usecols = (-1,), delimiter = ',', dtype = float) # load only right-most column (class labels)
elif len(sys.argv) == 2:
print '\n\t\033[36m You have opted to load the alternative dataset:', sys.argv[1], '\033[0;0m'
header = open(data_dict[self.kernel],'r')
self.terminals = header.readline().split(','); self.terminals[-1] = self.terminals[-1].replace('\n','')
self.functions = np.loadtxt(func_dict[self.kernel], delimiter=',', skiprows=1, dtype = str)
self.fitness_type = fitt_dict[self.kernel]
elif len(sys.argv) == 2: # load an external data file
print '\n\t\033[36m You have opted to load an alternative dataset:', sys.argv[1], '\033[0;0m'
data_x = np.loadtxt(sys.argv[1], skiprows = 1, delimiter = ',', dtype = float); data_x = data_x[:,0:-1]
data_y = np.loadtxt(sys.argv[1], skiprows = 1, usecols = (-1,), delimiter = ',', dtype = float)
header = open(sys.argv[1],'r')
self.terminals = header.readline().split(','); self.terminals[-1] = self.terminals[-1].replace('\n','')
self.functions = np.loadtxt(func_dict[self.kernel], delimiter=',', skiprows=1, dtype = str)
self.fitness_type = fitt_dict[self.kernel]
else: print '\n\t\033[31mERROR! You have assigned too many command line arguments at launch. Try again ...\033[0;0m'; sys.exit()
header = open(data_dict[self.kernel],'r')
self.terminals = header.readline().split(','); self.terminals[-1] = self.terminals[-1].replace('\n','')
self.functions = np.loadtxt(func_dict[self.kernel], delimiter=',', skiprows=1, dtype = str)
self.fitness_type = fitt_dict[self.kernel]
### 2) from the dataset, prepare terminals, TRAINING, and TEST data ###
if len(data_x) < 11: # for small datasets we will not split them into TRAINING and TEST components
@ -921,7 +928,7 @@ class Base_GP(object):
Build the Terminal nodes
'''
self.pop_node_depth = self.pop_tree_depth_max # set the final node_depth (same as 'pop_node_depth' + 1)
self.pop_node_depth = self.pop_tree_depth_max # set the final node_depth (same as 'pop_node_depth' + 1gp)
for j in range(1, len(self.tree[3]) ): # increment through all nodes (exclude 0) in array 'tree'

2
karoo_gp_main.py
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@ -2,7 +2,7 @@
# Use Genetic Programming for Classification and Symbolic Regression
# by Kai Staats, MSc UCT / AIMS
# Much thanks to Emmanuel Dufourq and Arun Kumar for their support, guidance, and free psychotherapy sessions
# version 0.9
# version 0.9.1.1
'''
A NOTE TO THE NEWBIE, EXPERT, AND BRAVE

2
karoo_gp_server.py
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@ -2,7 +2,7 @@
# Use Genetic Programming for Classification and Symbolic Regression
# by Kai Staats, MSc UCT / AIMS
# Much thanks to Emmanuel Dufourq and Arun Kumar for their support, guidance, and free psychotherapy sessions
# version 0.9
# version 0.9.1.1
import sys # sys.path.append('modules/') # add the directory 'modules' to the current path
import karoo_gp_base_class; gp = karoo_gp_base_class.Base_GP()