flacco has been integrated w rpy2 - basic function

.idea/.gitignore

@@ -0,0 +1,3 @@
+# Default ignored files
+/shelf/
+/workspace.xml

.idea/MDAF-GitLAB.iml

@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<module type="PYTHON_MODULE" version="4">
+  <component name="NewModuleRootManager">
+    <content url="file://$MODULE_DIR$" />
+    <orderEntry type="jdk" jdkName="Python 3.9" jdkType="Python SDK" />
+    <orderEntry type="sourceFolder" forTests="false" />
+  </component>
+</module>

.idea/aws.xml

@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="accountSettings">
+    <option name="activeRegion" value="us-east-1" />
+    <option name="recentlyUsedRegions">
+      <list>
+        <option value="us-east-1" />
+      </list>
+    </option>
+  </component>
+</project>

.idea/inspectionProfiles/profiles_settings.xml

@@ -0,0 +1,6 @@
+<component name="InspectionProjectProfileManager">
+  <settings>
+    <option name="USE_PROJECT_PROFILE" value="false" />
+    <version value="1.0" />
+  </settings>
+</component>

.idea/misc.xml

@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ProjectRootManager" version="2" project-jdk-name="Python 3.9" project-jdk-type="Python SDK" />
+  <component name="PyCharmProfessionalAdvertiser">
+    <option name="shown" value="true" />
+  </component>
+</project>

.idea/modules.xml

@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ProjectModuleManager">
+    <modules>
+      <module fileurl="file://$PROJECT_DIR$/.idea/MDAF-GitLAB.iml" filepath="$PROJECT_DIR$/.idea/MDAF-GitLAB.iml" />
+    </modules>
+  </component>
+</project>

.idea/vcs.xml

@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="VcsDirectoryMappings">
+    <mapping directory="$PROJECT_DIR$" vcs="Git" />
+  </component>
+</project>

.spyproject/config/backups/codestyle.ini.bak

@@ -0,0 +1,8 @@
+[codestyle]
+indentation = True
+edge_line = True
+edge_line_columns = 79
+
+[main]
+version = 0.2.0
+

.spyproject/config/backups/encoding.ini.bak

@@ -0,0 +1,6 @@
+[encoding]
+text_encoding = utf-8
+
+[main]
+version = 0.2.0
+

.spyproject/config/backups/vcs.ini.bak

@@ -0,0 +1,7 @@
+[vcs]
+use_version_control = False
+version_control_system = 
+
+[main]
+version = 0.2.0
+

.spyproject/config/backups/workspace.ini.bak

@@ -0,0 +1,12 @@
+[workspace]
+restore_data_on_startup = True
+save_data_on_exit = True
+save_history = True
+save_non_project_files = False
+project_type = empty-project-type
+recent_files = ['SourceCode/AlgorithmAnalyser.py']
+
+[main]
+version = 0.2.0
+recent_files = []
+

.spyproject/config/codestyle.ini

@@ -0,0 +1,8 @@
+[codestyle]
+indentation = True
+edge_line = True
+edge_line_columns = 79
+
+[main]
+version = 0.2.0
+

.spyproject/config/defaults/defaults-codestyle-0.2.0.ini

@@ -0,0 +1,5 @@
+[codestyle]
+indentation = True
+edge_line = True
+edge_line_columns = 79
+

.spyproject/config/defaults/defaults-encoding-0.2.0.ini

@@ -0,0 +1,3 @@
+[encoding]
+text_encoding = utf-8
+

.spyproject/config/defaults/defaults-vcs-0.2.0.ini

@@ -0,0 +1,4 @@
+[vcs]
+use_version_control = False
+version_control_system = 
+

.spyproject/config/defaults/defaults-workspace-0.2.0.ini

@@ -0,0 +1,6 @@
+[workspace]
+restore_data_on_startup = True
+save_data_on_exit = True
+save_history = True
+save_non_project_files = False
+

.spyproject/config/encoding.ini

@@ -0,0 +1,6 @@
+[encoding]
+text_encoding = utf-8
+
+[main]
+version = 0.2.0
+

.spyproject/config/vcs.ini

@@ -0,0 +1,7 @@
+[vcs]
+use_version_control = False
+version_control_system = 
+
+[main]
+version = 0.2.0
+

.spyproject/config/workspace.ini

@@ -0,0 +1,12 @@
+[workspace]
+restore_data_on_startup = True
+save_data_on_exit = True
+save_history = True
+save_non_project_files = False
+project_type = empty-project-type
+recent_files = ['SourceCode/AlgorithmAnalyser.py']
+
+[main]
+version = 0.2.0
+recent_files = []
+

.vscode/settings.json

@@ -1,5 +1,5 @@
 {
-    "python.pythonPath": "/usr/bin/python3.8",
+    "python.pythonPath": "/usr/sbin/python",
     "python.testing.pytestArgs": [
         "Sample codes"
     ],

SourceCode/AlgorithmAnalyser.py

@@ -1,5 +1,6 @@
 # directly running the DOE because existing surrogates can be explored with another workflow
 from os import path
+from os import sys
 import importlib.util
 import  multiprocessing
 import time
@@ -15,6 +16,11 @@ import itertools
 import matplotlib.pyplot as plt
 from mpl_toolkits.mplot3d import Axes3D
 
+# Test function representation
+from rpy2 import robjects as robjs
+from rpy2.robjects.packages import importr
+from rpy2 import rinterface
+
 # Test function characteristics
 import statistics as st
 from scipy import signal, misc, ndimage
@@ -140,93 +146,30 @@ def representfunc(funcpath):
 
         # Automatically generate the representation if the docstrings did not return anything
         if not ('Represented' in results):
-            print("Warning, the Representation of the Test Function has not specified\n===\n******Calculating the Characteristics******")
+            print("Warning, the Representation of the Test Function has not been specified\n===\n******Calculating the Characteristics******")
             n = int(results['dimmensions'])
             
-            # pickle these steps
+            execpath = sys.executable
-            coords = arange(-10,10,0.5)
-            samplemx = array([*itertools.product(coords, repeat=n)])
-            funcmap = array([* map(funcmodule.main, samplemx)])
-            
-            # Arrays for plotting the test function
-            X = array([tp[0] for tp in samplemx])
-            Y = array([tp[1] for tp in samplemx])
-            Z = array(funcmap)
-            
-            # reshaping the array into a 3D topology
-            topology = reshape(Z,(coords.size,coords.size))
-            ck = topology
-            
-            # Plotting the test function
-            fig = plt.figure()
-            ax = fig.add_subplot(111, projection='3d')
-            ax.plot_trisurf(X, Y, Z)
-            # plt.show()
-            
             
+            # creating the r functions
+            rlist = robjs.r['list']
+            rapply = robjs.r['apply']
+            rtestfunc = rinterface.rternalize(funcmodule.main)
 
-            # Number of Modes filter the data for local optima: look for circle like shapes, or squares or rectangles of very low derivative (tip of modes)
+            ###
+            lower =-10
+            upper = 10
+            X = flacco.createInitialSample(n_obs = 500, dim = 2, control = rlist(init_sample_type = 'lhs', init_sample_lower = lower, init_sample_upper = upper))
+            y = rapply(X, 1, rtestfunc)
+            testfuncobj = flacco.createFeatureObject(X = X, y = y, fun = rtestfunc, lower = lower, upper = upper, blocks = 10)
+            
+            rawfeats = flacco.calculateFeatureSet(testfuncobj, set='ela_meta')
+
+            pyfeat = asarray(rawfeats)
             
             
             
-            # Valleys and Bassins
             
-            # Alternative filter used for calculating derivatives
-            #derfilt = array([1.0, -2, 1.0], dtype=float32)
-            #alpha = signal.sepfir2d(ck, derfilt, [1]) + signal.sepfir2d(ck, [1], derfilt)
-            
-            # Currently used filter for Valley detection
-            hor = array([[0,1,1],[-1,0,1], [-1,-1,0]])
-            vert = array([[-1,-1,0], [-1,0,1], [0,1,1]])
-            
-            for i in range(1): betaH = signal.convolve(ck,hor,mode='valid')
-            for i in range(1): betaV = signal.convolve(ck,vert, mode='valid')
-            
-            beta = sqrt(betaH ** 2 + betaV ** 2)
-            
-                        
-            #beta = beta[5:-5][5:-5]
-            
-            norm = linalg.norm(beta)
-            beta/= norm  # normalized matrix
-            
-            
-            # custom filter for detection should light up the locaton of pattern
-            kernel = array([[1,1,1], [1,100,1], [1,1,1]])
-            beta = beta < average(beta)
-            beta = beta * 1
-            for i in range(100):
-                    beta = ndimage.convolve(beta,kernel)
-                    beta = beta >= 101
-                    beta = beta * 1
-            
-            if any(beta): results['Valleys'] = True
-            
-            
-            # Separability: calculate the derivatives in one dimension and see if independant from other dimension
-            
-            
-            # Dimensionality: number of objectives, inputs: call function once and see what it gives | for number of inputs call until it works; try catch
-            
-            
-            # Pareto fronts: 
-            
-            
-            # Noisyness: use the previously generated DOE and calculate a noisyness factor; average of derivative
-            
-            # Displaying the plots for development purposes
-            #img1 = plt.figure()
-            #ax2 = img1.add_subplot(111)
-            #ax2.imshow(alpha)
-            
-            img2 = plt.figure()
-            ax3 = img2.add_subplot(111)
-            ax3.imshow(beta)
-            
-            plt.show()
-            
-            # Writing the calculated representation into the test function file
-            # results['Represented'] = True
             writerepresentation(funcpath, results)
 
 
@@ -285,14 +228,23 @@ if __name__ == '__main__':
     funcnames = ["Bukin2", "Bukin4", "Brown"]
     # testfunctionpaths = ["/home/remi/Documents/MDAF-GitLAB/SourceCode/TestFunctions/Bukin4.py"]
     # funcnames = ["Bukin4"]
-    
+
+    # Installing the packages needed for FLACCO
+    utils = importr('utils')
+    #utils.install_packages('flacco', repos='https://utstat.toronto.edu/cran/')
+    #utils.install_packages('list', repos='https://utstat.toronto.edu/cran/')
+    ####utils.install_packages('reticulate', repos='https://utstat.toronto.edu/cran/')
+
+    reticulate = importr('reticulate')
+    flacco = importr('flacco')
+
     objs = 0
     args = {"high": 200, "low": -200, "t": 1000, "p": 0.95}
     scale = 1
         
-    data = doe (heuristicpath, heuristic_name, testfunctionpaths, funcnames, objs, args, scale)
+    # data = doe (heuristicpath, heuristic_name, testfunctionpaths, funcnames, objs, args, scale)
-    print(data['Bukin2'][1][2])
+    # print([point[2] for point in data['Bukin2'][1]])
-    #representfunc("TestFunctions/Bukin6.py")
+    representfunc("TestFunctions/Bukin2.py")
 
 
 # %%

SourceCode/SampleAlgorithms/SimmulatedAnnealing.py

@@ -72,7 +72,7 @@ def main(func, obj, S, args):
             route.append(Best[:])
             print(route)
             
-        if t < 0 or Quality(Best,y,func) > 200:
+        if t < 0 or Quality(Best,y,func) > 50:
             break
     #print('the Best Quality obtained was:{}'.format(Quality(Best,y)))
     print("Final Quality is: {}".format(Quality(Best,y,func)))

SourceCode/TestFunctions/Bukin6.py

@@ -5,88 +5,5 @@ def main(args):
     '''
     #_# dimmensions: 2
     
-	#_# dimmensions: 2.0
-	
-	#_# dimmensions: 2.0
-	
-	#_# dimmensions: 2.0
-	
-	#_# dimmensions: 2.0
-	
-	#_# dimmensions: 2.0
-	
-	#_# dimmensions: 2.0
-	
-	#_# dimmensions: 2.0
-	
-	#_# dimmensions: 2.0
-	
-	#_# dimmensions: 2.0
-	
-	#_# dimmensions: 2.0
-	
-	#_# dimmensions: 2.0
-	
-	#_# dimmensions: 2.0
-	
-	#_# dimmensions: 2.0
-	
-	#_# dimmensions: 2.0
-	
-	#_# dimmensions: 2.0
-	
-	#_# dimmensions: 2.0
-	
-	#_# dimmensions: 2.0
-	
-	#_# dimmensions: 2.0
-	
-	#_# dimmensions: 2.0
-	
-	#_# dimmensions: 2.0
-	
-	#_# dimmensions: 2.0
-	
-	#_# dimmensions: 2.0
-	
-	#_# dimmensions: 2.0
-	
-	#_# dimmensions: 2.0
-	
-	#_# dimmensions: 2.0
-	
-	#_# dimmensions: 2.0
-	
-	#_# dimmensions: 2.0
-	
-	#_# dimmensions: 2.0
-	#_# Valleys: True
-	
-	#_# dimmensions: 2.0
-	#_# Valleys: True
-	
-	#_# dimmensions: 2.0
-	#_# Valleys: True
-	
-	#_# dimmensions: 2.0
-	#_# Valleys: True
-	
-	#_# dimmensions: 2.0
-	#_# Valleys: True
-	
-	#_# dimmensions: 2.0
-	#_# Valleys: True
-	
-	#_# dimmensions: 2.0
-	#_# Valleys: True
-	
-	#_# dimmensions: 2.0
-	#_# Valleys: True
-	
-	#_# dimmensions: 2.0
-	#_# Valleys: True
-	
-	#_# dimmensions: 2.0
-	#_# Valleys: True
 	'''
     return 100*sqrt(fabs(args[1]-0.01*args[0]**2))+0.01*fabs(args[0]+10)

SourceCode/Testingground.py

@@ -0,0 +1,31 @@
+from mpl_toolkits.mplot3d import Axes3D
+import matplotlib.pyplot as plt
+from matplotlib import cm
+from matplotlib.ticker import LinearLocator, FormatStrFormatter
+import numpy as np
+
+
+fig = plt.figure()
+ax = fig.gca(projection='3d')
+
+# Make data.
+X = np.arange(-5, 5, 0.25)
+Y = np.arange(-5, 5, 0.25)
+X, Y = np.meshgrid(X, Y)
+R = np.sqrt(X**2 + Y**2)
+Z = np.sin(R)
+print(Z[1])
+
+# Plot the surface.
+surf = ax.plot_surface(X, Y, Z, cmap=cm.coolwarm,
+                       linewidth=0, antialiased=False)
+
+# Customize the z axis.
+ax.set_zlim(-1.01, 1.01)
+ax.zaxis.set_major_locator(LinearLocator(10))
+ax.zaxis.set_major_formatter(FormatStrFormatter('%.02f'))
+
+# Add a color bar which maps values to colors.
+fig.colorbar(surf, shrink=0.5, aspect=5)
+
+plt.show()

SourceCode/calcFeatures.R

@@ -0,0 +1,31 @@
+library(reticulate)
+library(flacco)
+library(parallelMap)
+library(parallel)
+
+# Other packages to install
+# plyr
+# RANN
+# numDeriv
+# e1071
+# mda - needs to install gcc-fortran on Operating system
+
+
+genTestFeatures <- function(path,pypath, upper=10, lower=-10, n) {
+    
+    use_python(pypath)
+    source_python(path)
+    
+    X = createInitialSample(n.obs = 500, dim = n, control = list(init_sample.type = 'lhs', init_sample.lower = lower, init_sample.upper = upper))
+    
+    y = apply(X, 1, main)
+    
+    testfunc <- createFeatureObject(X = X, y = y, fun = main, lower = lower, upper = upper, blocks = 10)
+    
+    n.cores = detectCores()
+    parallelStart(mode = "local", logging = FALSE, show.info = FALSE)
+    system.time((levelset.par = calculateFeatures(testfunc , control = list('cm_angle.show_warnings'=TRUE, 'cm_grad.show_warnings'=TRUE, 'ic.show_warnings'=TRUE))))
+    parallelStop()
+    
+    
+}