UQPyL 2.0.7__tar.gz → 2.0.9__tar.gz

{UQPyL-2.0.7 → UQPyL-2.0.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: UQPyL
-Version: 2.0.7
+Version: 2.0.9
 Summary: A python package for parameter uncertainty quantification and optimization
 Author: wmtSky
 Author-email: wmtSky <wmtsky@hhu.edu.cn>

{UQPyL-2.0.7 → UQPyL-2.0.9}/UQPyL/DoE/__init__.py

@@ -5,4 +5,6 @@ from .samplerABC import Sampler
 from .sobol_sequence import Sobol_Sequence
 from .fast_sequence import FAST_Sequence
 from .morris_sequence import Morris_Sequence
-__all__=['LHS', 'FFD', 'Random', 'Sobol_Sequence', 'Morris_Sequence','FAST_Sequence','Sampler']
+from .saltelli_sequence import Saltelli_Sequence
+
+__all__=['LHS', 'FFD', 'Random', 'Saltelli_Sequence','Sobol_Sequence', 'Morris_Sequence','FAST_Sequence','Sampler']

{UQPyL-2.0.7 → UQPyL-2.0.9}/UQPyL/DoE/morris_sequence.py

@@ -9,23 +9,23 @@ class Morris_Sequence(Sampler):
     The sample technique for Morris analysis
     
     Parameters:
-        num_levels (p): each x_i would take value on {0, 1/(p-1), 2/(p-1), ..., 1}. 
-                        Morris et al[1]. recommend the num_levels to be even and range from 4 and 10.
+        numLevels (p): each x_i would take value on {0, 1/(p-1), 2/(p-1), ..., 1}. 
+                        Morris et al[1]. recommend the numLevels to be even and range from 4 and 10.
     
     Methods:
         __call__ or sample: Generate a sample for FAST method
     
     Examples:
-        >>> mor_seq=Morris_Sequence(num_levels=4)
+        >>> mor_seq=Morris_Sequence(numLevels=4)
         >>> mor_seq.sample(100, 4) or mor_seq(100, 4)
     
     Reference:
         [1] Max D. Morris (1991) Factorial Sampling Plans for Preliminary Computational Experiments, Technometrics, 33:2, 161-174
     '''
-    def __init__(self, num_levels: int=4):
+    def __init__(self, numLevels: int=4):
         
         super().__init__()
-        self.num_levels=num_levels
+        self.numLevels=numLevels
         
     def _generate(self, nt: int, nx: int):
         '''
@@ -65,11 +65,11 @@ class Morris_Sequence(Sampler):
         
         nx=problem.nInput if problem is not None else nx
         
-        self._generate(nt, nx)
+        return self._generate(nt, nx)
         
     def _generate_trajectory(self, nx: int):
         
-        delta=self.num_levels/(2*(self.num_levels-1))
+        delta=self.numLevels/(2*(self.numLevels-1))
         
         B=np.tril(np.ones([nx + 1, nx], dtype=int), -1)
         
@@ -77,7 +77,7 @@ class Morris_Sequence(Sampler):
         D_star = np.diag(np.random.choice([-1, 1], nx)) #step1
         J=np.ones((nx+1, nx))
         
-        levels_grids=np.linspace(0, 1-delta, int(self.num_levels / 2))
+        levels_grids=np.linspace(0, 1-delta, int(self.numLevels / 2))
         x_star=np.random.choice(levels_grids, nx).reshape(1,-1) #step2
         
         P_star=np.zeros((nx,nx))

UQPyL-2.0.9/UQPyL/DoE/saltelli_sequence.py

@@ -0,0 +1,90 @@
+import numpy as np
+from typing import Optional
+from scipy.stats import qmc
+from .samplerABC import Sampler, decoratorRescale
+from ..problems import ProblemABC as Problem
+
+class Saltelli_Sequence(Sampler):
+    
+    def __init__(self, scramble: bool=True, skipValue: int=0, calSecondOrder: bool=False):
+        
+        super().__init__()
+        
+        self.scramble=scramble
+        self.skipValue=skipValue
+        self.calSecondOrder=calSecondOrder
+        
+    @decoratorRescale
+    def sample(self, nt: int, nx: Optional[int] = None, problem: Optional[Problem] = None, random_seed: Optional[int] = None):
+        
+        if random_seed is not None:
+            self.random_state = np.random.RandomState(random_seed)
+        else:
+            self.random_state = np.random.RandomState()
+
+        if problem is not None and nx is not None:
+            if(problem.nInput!=nx):
+                raise ValueError('The input dimensions of the problem and the samples must be the same')
+        elif problem is None and nx is None:
+            raise ValueError('Either the problem or the input dimensions must be provided')
+        
+        nx=problem.nInput if problem is not None else nx
+        
+        return self._generate(nt, nx)
+    
+    def _generate(self, nt: int, nx: int):
+        
+        N=nt
+        nInput=nx
+        skipValue=self.skipValue
+        
+        calSecondOrder=self.calSecondOrder
+        
+        M=None
+        if skipValue>0 and isinstance(skipValue, int):
+            
+            M=skipValue
+            
+            if not((M&(M-1))==0 and (M!=0 and M-1!=0)):
+                raise ValueError("skip value must be a power of 2!")
+            
+            if N<M:
+                raise ValueError("N must be greater than skip value you set!")
+        
+        elif skipValue<0 or not isinstance(skipValue, int):
+            raise ValueError("skip value must be a positive integer!")
+        
+        sampler=qmc.Sobol(nInput*2, scramble=self.scramble, seed=1)
+        
+        if M:
+            sampler.fast_forward(M)
+        
+        if calSecondOrder:
+            saltelliSequence=np.zeros(((2*nInput+2)*N, nInput))
+        else:
+            saltelliSequence=np.zeros(((nInput+2)*N, nInput))
+        
+        baseSequence=sampler.random(N)
+        
+        index=0
+        for i in range(N):
+            
+            saltelliSequence[index, :]=baseSequence[i, :nInput]
+
+            index+=1
+            
+            saltelliSequence[index:index+nInput,:]=np.tile(baseSequence[i, :nInput], (nInput, 1))
+            saltelliSequence[index:index+nInput,:][np.diag_indices(nInput)]=baseSequence[i, nInput:]               
+            index+=nInput
+           
+            if calSecondOrder:
+                saltelliSequence[index:index+nInput,:]=np.tile(baseSequence[i, nInput:], (nInput, 1))
+                saltelliSequence[index:index+nInput,:][np.diag_indices(nInput)]=baseSequence[i, :nInput] 
+                index+=nInput
+            
+            saltelliSequence[index,:]=baseSequence[i, nInput:nInput*2]
+            index+=1
+        
+        xSample=saltelliSequence
+        
+        return xSample

{UQPyL-2.0.7 → UQPyL-2.0.9}/UQPyL/DoE/sobol_sequence.py

@@ -19,12 +19,12 @@ class Sobol_Sequence(Sampler):
     __call__ or sample: generate the shape of (nt*nx, nx) and numpy array Sobol sequence. 
     
     '''
-    def __init__(self, scramble: bool=True, skip_value: int=0):
+    def __init__(self, scramble: bool=True, skipValue: int=0):
         
         super().__init__()
         
         self.scramble=scramble
-        self.skip_value=skip_value
+        self.skipValue=skipValue
         
     def _generate(self, nt: int, nx: int):
         '''
@@ -32,9 +32,9 @@ class Sobol_Sequence(Sampler):
         '''
         
         sampler=Sobol(d=nx, scramble=self.scramble)
-        xInit=sampler.random(nt+self.skip_value)
+        xInit=sampler.random(nt+self.skipValue)
         
-        return xInit[self.skip_value:, :]
+        return xInit[self.skipValue:, :]
     
     @decoratorRescale
     def sample(self, nt: int, nx: Optional[int] = None, problem: Optional[Problem] = None, random_seed: Optional[int] = None) -> np.ndarray:

{UQPyL-2.0.7 → UQPyL-2.0.9}/UQPyL/__init__.py

@@ -1,6 +1,6 @@
 from . import problems, surrogates, optimization, sensibility, DoE, utility
 
-__version__ = "2.0.7"
+__version__ = "2.0.9"
 __author__ = "wmtSky"
 
 __all__=[

{UQPyL-2.0.7 → UQPyL-2.0.9}/UQPyL/optimization/algorithmABC.py

@@ -58,8 +58,12 @@ class Algorithm(metaclass=abc.ABCMeta):
     
     def checkTermination(self):
         
-        if self.FEs<=self.maxFEs:
-            if self.maxIter is None or self.iters<=self.maxIter:
+        if Verbose.isStop: #TODO
+            
+            return False
+        
+        if self.FEs<self.maxFEs:
+            if self.maxIter is None or self.iters<self.maxIter:
                 if self.maxTolerateTimes is None or self.tolerateTimes<=self.maxTolerateTimes:
                     self.iters+=1
                     return True

{UQPyL-2.0.7 → UQPyL-2.0.9}/UQPyL/sensibility/fast.py

@@ -146,7 +146,7 @@ class FAST(SA):
             idx=np.arange(i*n, (i+1)*n)
             Y_sub=Y[idx]
             #fft
-            f=np.fft.fft(Y_sub.ravel())
+            f=np.fft.fft(Y_sub)
             # Sp = np.power(np.absolute(f[np.arange(1, np.ceil((self.N_within_sampler-1)/2), dtype=np.int32)-1])/self.N_within_sampler, 2) #TODO 1-(NS-1)/2 
             Sp = np.power(np.absolute(f[np.arange(1, np.ceil(n / 2), dtype=np.int32)]) / n, 2)
             V=2.0*np.sum(Sp)

{UQPyL-2.0.7 → UQPyL-2.0.9}/UQPyL/sensibility/morris.py

@@ -144,6 +144,9 @@ class Morris(SA):
         self.record('mu_star', problem.x_labels, mu_star)
         self.record('sigma', problem.x_labels, sigma)
 
+        self.record('S1', problem.x_labels, mu)
+        self.record('ST', problem.x_labels, sigma)
+        
         return self.result
     
     def summary(self):

{UQPyL-2.0.7 → UQPyL-2.0.9}/UQPyL/sensibility/rbd_fast.py

@@ -134,7 +134,7 @@ class RBD_FAST(SA):
             S1[i]=S1_sub
         
         self.record('S1', problem.x_labels, S1)
-            
+        
         return self.result
      
         

{UQPyL-2.0.7 → UQPyL-2.0.9}/UQPyL/sensibility/rsa.py

@@ -106,19 +106,39 @@ class RSA(SA):
         
         X, Y=self.__check_and_scale_xy__(X, Y)
         
-        seq = np.linspace(0, 1, nRegion + 1)
+        seq = np.linspace(0.0, 1.0, nRegion + 1)
         results = np.full((nRegion, nInput), np.nan)
         X_di = np.empty(X.shape[0])
         
+        trr=Y.ravel()
+        mrr=X_di
+        
         for d_i in range(nInput):
-                X_di = X[:, d_i]
-                for bin_index in range(nRegion):
-                    lower_bound, upper_bound = seq[bin_index], seq[bin_index + 1]
-                    b = (lower_bound < X_di) & (X_di <= upper_bound)
-                    if np.count_nonzero(b) > 0 and np.unique(X[b]).size > 1:
-                        r_s = cramervonmises_2samp(Y[b].ravel(), Y[~b].ravel()).statistic
-                        results[bin_index, d_i] = r_s
-
-        self.record("S1", problem.x_labels, results)
+            X_di[:] = X[:, d_i]
+            
+            quants=np.quantile(trr, seq)
+            
+            b = (quants[0] <= trr) & (trr <= quants[1])
+            if self._has_samples(Y, b):
+                results[0, d_i] = cramervonmises_2samp(mrr[b].ravel(), mrr[~b].ravel()).statistic
+             
+            for bin_index in range(1, nRegion):
+                
+                b = (quants[bin_index] < trr) & (trr <= quants[bin_index+1])
+                
+                if self._has_samples(Y, b):
+                    results[bin_index, d_i] = cramervonmises_2samp(mrr[b].ravel(), mrr[~b].ravel()).statistic
+        
+        
+        self.record("S1", problem.x_labels, np.mean(results, axis=0))
+        self.record("S1_Detail", problem.x_labels, np.mean(results, axis=0))
+        
+        return self.result
+    
+    def _has_samples(self, y, sel):
         
-        return self.result
+        return(
+            (np.count_nonzero(sel) !=0)
+             and (len(y[~sel])!=0 )
+             and np.unique(y[sel]).size > 1
+        )

{UQPyL-2.0.7 → UQPyL-2.0.9}/UQPyL/sensibility/sobol.py

@@ -100,8 +100,8 @@ class Sobol(SA):
             if not((M&(M-1))==0 and (M!=0 and M-1!=0)):
                 raise ValueError("skip value must be a power of 2!")
             
-            if N>M:
-                raise ValueError("skip value must be greater than N you set!")
+            if N<M:
+                raise ValueError("N must be greater than skip value you set!")
         
         elif skipValue<0 or not isinstance(skipValue, int):
             raise ValueError("skip value must be a positive integer!")
@@ -200,10 +200,10 @@ class Sobol(SA):
                     S_Labels.append(f"{problem.x_labels[j]}-{problem.x_labels[k]}")
         
         #Record Data
-        self.record('S1(First Order)', problem.x_labels, S1)
+        self.record('S1', problem.x_labels, S1)
         if calSecondOrder:
-            self.record('S2(Second Order)', S_Labels, S2) 
-        self.record('ST(Total Order)', problem.x_labels, ST)
+            self.record('S2', S_Labels, S2) 
+        self.record('ST', problem.x_labels, ST)
         
         return self.result
     

{UQPyL-2.0.7 → UQPyL-2.0.9}/UQPyL/utility/verbose.py

@@ -18,6 +18,10 @@ class Verbose():
     saveFlag=False
     verbose=False
     workDir=os.getcwd()
+    iterEmit=None
+    verboseEmit=None
+    isStop=False
+    total_width=os.get_terminal_size().columns
     @staticmethod    
     def output(obj):
         
@@ -25,20 +29,24 @@ class Verbose():
             obj=str(obj)+'\n'
         
         if Verbose.logFlag:
+            
             Verbose.logLines.append(obj)
         
+        if Verbose.verboseEmit:
+            
+            Verbose.verboseEmit.send(obj)
+        
         if Verbose.verbose:
+            
             print(obj)
     
     @staticmethod
     def verboseSetting(obj):
-    
-        total_width=os.get_terminal_size().columns
         
         if obj.verbose or obj.logFlag:
             
             title=obj.name+" Setting"
-            spacing=int((total_width-len(title))/2)
+            spacing=int((Verbose.total_width-len(title))/2)
             Verbose.output("="*spacing+title+"="*spacing)
             keys=obj.setting.keys
             values=obj.setting.values
@@ -126,17 +134,20 @@ class Verbose():
         @functools.wraps(func)
         def wrapper(obj, *args, **kwargs):
             
+            if Verbose.iterEmit:
+                
+                Verbose.iterEmit.send()
+            
             func(obj, *args, **kwargs)
             
             if obj.verbose and obj.iters%obj.verboseFreq==0:
-                total_width=os.get_terminal_size().columns
                 title="FEs: "+str(obj.FEs)+" | Iters: "+str(obj.iters)
-                spacing=int((total_width-len(title))/2)
+                spacing=int((Verbose.total_width-len(title))/2)
                 Verbose.output("="*spacing+title+"="*spacing)
                 if obj.problem.nOutput==1:
-                    Verbose.verboseSingleSolutions(obj.result.bestDec, obj.result.bestObj, obj.problem.x_labels, obj.problem.y_labels, obj.FEs, obj.iters, total_width)
+                    Verbose.verboseSingleSolutions(obj.result.bestDec, obj.result.bestObj, obj.problem.x_labels, obj.problem.y_labels, obj.FEs, obj.iters, Verbose.total_width)
                 else:
-                    Verbose.verboseMultiSolutions(obj.result.bestDec, obj.result.bestMetric, obj.FEs, obj.iters, total_width)
+                    Verbose.verboseMultiSolutions(obj.result.bestDec, obj.result.bestMetric, obj.FEs, obj.iters, Verbose.total_width)
         return wrapper
     
     @staticmethod
@@ -220,9 +231,8 @@ class Verbose():
                 
             if  Verbose.verbose or Verbose.logFlag:
                 
-                total_width=os.get_terminal_size().columns
                 title=obj.name+" Setting"
-                spacing=int((total_width-len(title))/2)
+                spacing=int((Verbose.total_width-len(title))/2)
                 Verbose.output("="*spacing+title+"="*spacing)
                 
                 keys=obj.setting.keys
@@ -231,6 +241,11 @@ class Verbose():
                 table.add_row(values)
                 Verbose.output(table)
             
+            #TODO
+            if Verbose.iterEmit:
+                
+                Verbose.iterEmit.send()
+            
             startTime=time.time()
             res=func(obj, *args, **kwargs)
             endTime=time.time()
@@ -239,16 +254,16 @@ class Verbose():
             if Verbose.verbose:
                 
                 title="Conclusion"
-                spacing=int((total_width-len(title))/2)
+                spacing=int((Verbose.total_width-len(title))/2)
                 Verbose.output("="*spacing+title+"="*spacing)
                 Verbose.output("Time:  "+Verbose.formatTime(totalTime))
                 Verbose.output(f"Used FEs:    {obj.FEs}  |  Iters:  {obj.iters}")
                 Verbose.output(f"Best Objs and Best Decision with the FEs")
                 
                 if obj.problem.nOutput==1:
-                    Verbose.verboseSingleSolutions(res.bestDec, res.bestObj, obj.problem.x_labels, obj.problem.y_labels, res.appearFEs, res.appearIters, total_width)
+                    Verbose.verboseSingleSolutions(res.bestDec, res.bestObj, obj.problem.x_labels, obj.problem.y_labels, res.appearFEs, res.appearIters, Verbose.total_width)
                 else:
-                    Verbose.verboseMultiSolutions(res.bestDec, res.bestMetric, res.appearFEs, res.appearIters, total_width)
+                    Verbose.verboseMultiSolutions(res.bestDec, res.bestMetric, res.appearFEs, res.appearIters, Verbose.total_width)
 
             if Verbose.saveFlag:
                 
@@ -258,6 +273,13 @@ class Verbose():
                 
                 Verbose.saveLog(obj, folder_log)
 
+            #TODO
+            if Verbose.isStop:
+                Verbose.iterEmit.unfinished()
+            else:
+                Verbose.iterEmit.finished()
+            
+            
             Verbose.logFlag, Verbose.verbose, Verbose.saveFlag=record
             
             return res
@@ -297,9 +319,9 @@ class Verbose():
                 folder_data, folder_log=Verbose.checkDir()
             
             if Verbose.verbose or Verbose.logFlag:
-                total_width=os.get_terminal_size().columns
+
                 title=obj.name+" Setting"
-                spacing=int((total_width-len(title))/2)
+                spacing=int((Verbose.total_width-len(title))/2)
                 Verbose.output("="*spacing+title+"="*spacing)
 
                 keys=obj.setting.keys()
@@ -310,7 +332,7 @@ class Verbose():
                 Verbose.output(table)
                 
                 title="Attribute"
-                spacing=int((total_width-len(title))/2)
+                spacing=int((Verbose.total_width-len(title))/2)
                 Verbose.output("="*spacing+title+"="*spacing)
                 
                 Verbose.output(f"First Order Sensitivity: {obj.firstOrder}")
@@ -320,16 +342,16 @@ class Verbose():
             res=func(obj, *args, **kwargs)
             
             if Verbose.verbose or Verbose.logFlag:
-                total_width=os.get_terminal_size().columns
+      
                 title="Conclusion"
-                spacing=int((total_width-len(title))/2)
+                spacing=int((Verbose.total_width-len(title))/2)
                 Verbose.output("="*spacing+title+"="*spacing)
                 
                 for key, values in obj.result.Si.items():
                     title=key
-                    spacing=int((total_width-len(title))/2)
+                    spacing=int((Verbose.total_width-len(title))/2)
                     Verbose.output("-"*spacing+title+"-"*spacing)
-                    Verbose.verboseSi(values[0], values[1], total_width)
+                    Verbose.verboseSi(values[0], values[1], Verbose.total_width)
                     
             if Verbose.logFlag:
                 

{UQPyL-2.0.7 → UQPyL-2.0.9}/UQPyL.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: UQPyL
-Version: 2.0.7
+Version: 2.0.9
 Summary: A python package for parameter uncertainty quantification and optimization
 Author: wmtSky
 Author-email: wmtSky <wmtsky@hhu.edu.cn>

{UQPyL-2.0.7 → UQPyL-2.0.9}/UQPyL.egg-info/SOURCES.txt

@@ -14,6 +14,7 @@ UQPyL/DoE/full_fact.py
 UQPyL/DoE/lhs.py
 UQPyL/DoE/morris_sequence.py
 UQPyL/DoE/random.py
+UQPyL/DoE/saltelli_sequence.py
 UQPyL/DoE/samplerABC.py
 UQPyL/DoE/sobol_sequence.py
 UQPyL/optimization/__init__.py

{UQPyL-2.0.7 → UQPyL-2.0.9}/pyproject.toml

@@ -12,7 +12,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "UQPyL"
-version = "2.0.7"
+version = "2.0.9"
 authors = [
     {name = "wmtSky", email = "wmtsky@hhu.edu.cn"}
 ]

{UQPyL-2.0.7 → UQPyL-2.0.9}/setup.py

@@ -32,7 +32,7 @@ extensions=cythonize(cython_extensions, compiler_directives={'cdivision': True,
 setup(
     name="UQPyL",
     author="wmtSky",
-    version="2.0.7",
+    version="2.0.9",
     author_email="wmtsky@hhu.edu.cn",
     ext_modules=extensions,  
     packages=find_packages(),