Add riding eps example

evaluation/1Layer Suscept.py

@@ -51,6 +51,7 @@ def __calc_chi(mode='density'):
     lastkurt=None
     for dim in dims:
         try:
+            1/0
             with open(path+f"magnets/magnetisation_{mode}_dim={dim:02}.txt", 'r', encoding='utf-8') as f:
                 magnet = json.load(f)
             with open(path+f"suscepts/susceptibility_{mode}_dim={dim:02}.txt", 'r', encoding='utf-8') as f:
@@ -87,7 +88,7 @@ def __calc_chi(mode='density'):
                     else:
                         raise NotImplementedError
                         
-                    mag = round(abs(mag),6)
+                    mag = round(abs(dmag),6)
                     fluct = round(mag2-mag**2,6)
                     tail = round(mag4/mag2**2,6)
                     

evaluation/2Layer Sonic.py

@@ -0,0 +1,71 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Tue Aug 30 14:25:12 2022
+
+@author: timof
+"""
+
+import sys
+import os
+import json
+
+# from plot import qtplot
+from scipy.io import wavfile
+
+
+import math as m
+import numpy as np
+
+
+vect = np.vectorize
+
+@vect
+def log2(x):
+    try:
+        return m.log2(x)
+    except ValueError:
+        if x==0:
+            return float(0)
+        else:
+            raise
+
+def new_folder(path):
+    if not os.path.exists(path):
+        os.makedirs(path)
+    return path
+
+phase = np.vectorize(lambda x,y: (m.atan2(y,x)+m.pi)%(2*m.pi)-m.pi)
+diff = np.vectorize(lambda x,y: (y-x+m.pi)%(2*m.pi)-m.pi)
+H2 = lambda x: -x*m.log2(x)-(1-x)*m.log2(1-x)
+
+
+path = '/cloud/Public/_data/neuropercolation/2lay/steps=500000_rising/'
+suffix = ''
+
+chi = chr(967)
+vareps = chr(949)
+
+vals = [[],[]]
+
+runsteps = 1000100
+
+eps_space = np.linspace(0.005, 0.5, 100)
+eps_space = eps_space[1::2]
+
+dims = [121]#+[16,49]
+
+mode='density'
+ma=[]
+s=[]
+k=[]
+mk=[]
+lastkurt=None
+for dim in dims:
+    dimpath = new_folder(path + f'dim={dim:03d}/')
+    for epsilon in [0.000]:
+        with open(dimpath+f"eps={round(epsilon,3):.3f}_activation.txt", 'r', encoding='utf-8') as f:
+            activation = np.array(json.load(f)[::-1])
+        # activation = list(zip(*activation))
+        
+        
+        wavfile.write(dimpath+f"eps={round(epsilon,3):.3f}_activation_48k.wav_rev",48000,activation)

evaluation/2Layer fft.py

@@ -345,13 +345,13 @@ qtplot(f'Q facor for odd automaton sizes',
 #     FWHM=json.load(f)
 
 qtplot(f'Dominant frequency',
-        [[0]+list(eps_space[:-1])]*3,
+        [[0]+list(eps_space[:20])]*3,
-        [[0]+FMAX[-1],[0]+LHM[-1],[0]+UHM[-1]],
+        [[0]+FMAX[:20],[0]+LHM[:20],[0]+UHM[:20]],
         # [f'dim={dim}x{dim}' for dim in dims],
-        ['dominant frequency', 'lesser half maximum', 'upper half maximum'],
+        ['FMAX', 'FMAX-FWHM/2', 'FMAX+FWHM/2'],
-        #colors=['g','r','r'],
+        colors=['r','r','g'],
         y_tag = 'frequency f',
-        y_log = True,
+        y_log = False,
         export=True,
         path=sigpath,
         filename=f'FMAX+FWHMto50_plot_{parts}parts_accum={accum}.png',

evaluation/2Layer phiplot.py

@@ -89,6 +89,7 @@ qtplot(f"Mean effect integration over noise level",
         [[0]+phi for phi in PHI[::-1]],
         [f'dim={dim:02d}x{dim:02d}' for dim in dims[::-1]],
         y_tag = f'effect integration {varphi}',
+        x_tag = f'noise level {vareps}',
         export=True,
         path=dimpath+"",
         filename=f'eps={round(epsilon,3):.3f}_evolution.png',

evaluation/4Layer Sonic.py

@@ -0,0 +1,77 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Tue Aug 30 14:25:12 2022
+
+@author: timof
+"""
+
+import sys
+import os
+import json
+
+from plot import qtplot
+
+
+import math as m
+import numpy as np
+
+
+vect = np.vectorize
+
+@vect
+def log2(x):
+    try:
+        return m.log2(x)
+    except ValueError:
+        if x==0:
+            return float(0)
+        else:
+            raise
+
+def new_folder(path):
+    if not os.path.exists(path):
+        os.makedirs(path)
+    return path
+
+path = '/cloud/Public/_data/neuropercolation/4lay/cons=27-knight_steps=100100_causal/dim=09/batch=0/'
+suffix = ''
+
+chi = chr(967)
+vareps = chr(949)
+
+vals = [[],[]]
+
+runsteps = 1000100
+
+eps_space = np.linspace(0.005, 0.5, 100)
+eps_space = eps_space[1::2]
+
+dims = list(range(3,10))#+[16,49]
+
+mode='density'
+ma=[]
+s=[]
+k=[]
+mk=[]
+lastkurt=None
+for dim in dims[-1:]:
+    dimpath = new_folder(path + f'dim={dim:02}/')
+    for epsilon in eps_space[:]:
+        with open(path+f"eps={round(epsilon,3):.3f}_phase_diff.txt", 'r', encoding='utf-8') as f:
+            phase_diff = np.array(json.load(f)[:500])
+        with open(path+f"eps={round(epsilon,3):.3f}_ei.txt", 'r', encoding='utf-8') as f:
+            phase_diff = np.array(json.load(f)[:500])
+        
+        qtplot(f"Phase relation time series for eps={round(epsilon,3):.3f}",
+                [list(range(500))]*2,
+                [phase_diff],
+                x_tag = 'time step',
+                y_tag = f'phase diffe´rence',
+                y_range = (-m.pi,m.pi),
+                export=True,
+                path=dimpath+"evolution/",
+                filename=f'eps={round(epsilon,3):.3f}_evolution.png',
+                close=False) 
+
+mode = 'density'
+#%%

evaluation/4laysign.py

@@ -71,20 +71,20 @@ for _eps in _epses[11:21]:
     #     sign_p_list.append(sign_p)
         
         
-    # with open(savepath+f"phasediff_means.txt", 'w', encoding='utf-8') as f:
+    with open(savepath+f"phasediff_means.txt", 'w', encoding='utf-8') as f:
-    #     json.dump(meanlist, f, indent=1)
+        json.dump(meanlist, f, indent=1)
-    # with open(savepath+f"phasediff_stds.txt", 'w', encoding='utf-8') as f:
+    with open(savepath+f"phasediff_stds.txt", 'w', encoding='utf-8') as f:
-    #     json.dump(stdlist, f, indent=1)
+        json.dump(stdlist, f, indent=1)
-    # with open(savepath+f"phasediff_integrals.txt", 'w', encoding='utf-8') as f:
+    with open(savepath+f"phasediff_integrals.txt", 'w', encoding='utf-8') as f:
-    #     json.dump(integrallist, f, indent=1)
+        json.dump(integrallist, f, indent=1)
-    # with open(savepath+f"phasediff_cohends.txt", 'w', encoding='utf-8') as f:
+    with open(savepath+f"phasediff_cohends.txt", 'w', encoding='utf-8') as f:
-    #     json.dump(cohendlist, f, indent=1)
+        json.dump(cohendlist, f, indent=1)
-    # with open(savepath+f"phasediff_norm_ps.txt", 'w', encoding='utf-8') as f:
+    with open(savepath+f"phasediff_norm_ps.txt", 'w', encoding='utf-8') as f:
-    #     json.dump(norm_p_list, f, indent=1)
+        json.dump(norm_p_list, f, indent=1)
-    # with open(savepath+f"phasediff_ttest_ps.txt", 'w', encoding='utf-8') as f:
+    with open(savepath+f"phasediff_ttest_ps.txt", 'w', encoding='utf-8') as f:
-    #     json.dump(ttest_p_list, f, indent=1)
+        json.dump(ttest_p_list, f, indent=1)
-    # with open(savepath+f"phasediff_sign_ps.txt", 'w', encoding='utf-8') as f:
+    with open(savepath+f"phasediff_sign_ps.txt", 'w', encoding='utf-8') as f:
-    #     json.dump(sign_p_list, f, indent=1)
+        json.dump(sign_p_list, f, indent=1)
     
 # stdlowlist = [meanlist[eps] - stdlist[eps] for eps in range(len(meanlist))]
 # stdhighlist = [meanlist[eps] + stdlist[eps] for eps in range(len(meanlist))]
@@ -105,19 +105,19 @@ for _eps in _epses[11:21]:
             filename=f'Resultant reduction disconnect eps={_eps} dim={_dim} extremes={_ext}.png',
             close=True)
     
-# qtplot(f'Mean causal phase reduction for dt={_dt} dim={_dim} with 4 layers',
+qtplot(f'Mean causal phase reduction for dt={_dt} dim={_dim} with 4 layers',
-#         [_epsilons]*3,
+        [_epsilons]*3,
-#         [stdlowlist, stdhighlist, meanlist],
+        [stdlowlist, stdhighlist, meanlist],
-#         ['Low standard deviation',
+        ['Low standard deviation',
-#           'High standard deviation',
+          'High standard deviation',
-#           'Mean'],
+          'Mean'],
-#         colors=['r','r','g'],
+        colors=['r','r','g'],
-#         x_tag = f'noise level {chr(949)}',
+        x_tag = f'noise level {chr(949)}',
-#         y_tag = 'abs phase reduction',
+        y_tag = 'abs phase reduction',
-#         export=True,
+        export=True,
-#         path=savepath,
+        path=savepath,
-#         filename=f'Mean phase reduction dim={_dim} extremes={_ext}.png',
+        filename=f'Mean phase reduction dim={_dim} extremes={_ext}.png',
-#         close=True)
+        close=True)
 # qtplot(f'Phase reduction probability for dt={_dt} dim={_dim} with 4 layers',
 #         [_epsilons],
 #         [integrallist],

evaluation/phi.py

@@ -13,11 +13,12 @@ from numpy.linalg import norm
 from datetime import datetime
 from random import sample as choose
 from random import random
-from numba import jit, njit, prange
+import itertools
+#from numba import jit, njit, prange
 
-from plot import qtplot
+# from plot import qtplot
 
-from neuropercolation import Simulate4Layers
+# from neuropercolation import Simulate4Layers
 
 eps_space = list(np.linspace(0.01,0.2,20))
 def new_folder(path):
@@ -29,7 +30,7 @@ phase = np.vectorize(lambda x,y: (m.atan2(y,x)+m.pi)%(2*m.pi)-m.pi)
 diff = np.vectorize(lambda x,y: (y-x+m.pi)%(2*m.pi)-m.pi)
 H2 = lambda x: -x*m.log2(x)-(1-x)*m.log2(1-x)
 
-@njit
+
 def neighbor(digit0, digit1, lenght):
     layer = int(lenght)
     dim = int(np.sqrt(layer))
@@ -43,9 +44,11 @@ def neighbor(digit0, digit1, lenght):
     else:
         return False
     
-@njit
+
 def kcomb(zp,zm):
-    if zp>2:
+    if zp+zm>5:
+        val=None
+    elif zp>2:
         val=1
     elif zm>2:
         val=0
@@ -62,7 +65,24 @@ def kcomb(zp,zm):
     else:
         raise NotImplementedError(zp,zm)
     return val
+#%%
+neighbourcomb = [[(i,j) for j in range(6)] for i in range(6)]
+probcombs = [[kcomb(*n) for n in row] for row in neighbourcomb]
+posscombs = {val for row in probcombs for val in row}
 
+probcombs1 = [kcomb(n,4-n) for n in range(5)]
+
+eta = lambda eps: 1-eps
+etastar = lambda eps,kp: kp*(1-eps)+(1-kp)*eps
+epsstar = lambda eps,kp: kp*eps+(1-kp)*(1-eps)
+KL = lambda eps,kp: eta(eps)*m.log2(eta(eps)/etastar(eps,kp)) + eps*m.log2(eps/epsstar(eps,kp)) if kp is not None else 0
+phi_mat = lambda eps: [[KL(eps,kcomb(i,j)) for j in range(6)] for i in range(6)]
+phi_vals = lambda eps,df=4: sorted({sum([KL(eps,kp) for kp in kps]) for kps in itertools.product(*[[1,0.5]]*df)})
+phi_sing = lambda eps: KL(eps,kcomb(1,0))
+phi_lims = lambda eps: [phi_sing(eps)+val for val in phi_vals(eps)]
+
+
+#%%
 path = new_folder('/cloud/Public/_data/neuropercolation/1lay/mips/')
 
 
@@ -125,22 +145,29 @@ def MIP(dim,statestr,eps):
     
     return mip,lophi
 
-def calc_mips(dim,eps):
+def calc_mips(dim,eps,save=True):
-    mip = []
+    mips = [[] for i in range(5)]
     statestr='0'*dim**2
+    lims = phi_lims(eps)
     # statestr=statestr.translate(str.maketrans('','','.-='))
     for parti in range(1,2**(dim**2-1)):
         partstr = bin(parti)[2:].zfill(dim**2)
         curphi = phi(dim,statestr,partstr,eps)
-        mip.append(round(curphi,6))
+        for cha,mip in enumerate(mips):
+            if curphi<lims[cha]:
+                mip.append(parti)
+                print(f'Part {partstr} in mips[{cha}] with phi={curphi}')
     
     mipath = new_folder(path+f'dim={dim:02d}/')
-    with open(mipath+f"eps={round(eps,3):.3f}_mips.txt", 'w', encoding='utf-8') as f:
+    for cha,mip in enumerate(mips):
-        json.dump(mip, f, indent=1)
+        with open(mipath+f"eps={round(eps,3):.3f}_mipis_{cha}.txt", 'w', encoding='utf-8') as f:
-        
+            json.dump(mip, f, indent=1) if save else None
+    return mips
+
 def smartMIP(dim,statestr,eps):
     lophi=np.inf
     mip = []
+    phi_lims = phi_vals(eps)
     
     for parti in range(0,dim**2):
         partstr = bin(2**parti)[2:].zfill(dim**2)

evaluation/plots/bootstrap_plot.py

@@ -23,7 +23,8 @@ for eps in eps_ep:
         boots.append(ps)
         
 
-
+    lower=[0.001]*len(ps)
+    higher=[0.999]*len(ps)
 
    
-    qtplot(f"Bootstrapping p-value for noise level {eps}",[range(dt+1)],boots[-1:],[f''],y_tag='p-value',y_log=False) 
+    qtplot(f"Bootstrapping p-value for noise level {eps}",[range(dt+1)]*3,[lower,higher,ps],[f'right-sided p-value','p=0.999 limit','p=0.001 limit'],colors=['w','r','g'],y_tag='p-value',y_log=False) 

evaluation/plots/significance_plot.py

@@ -0,0 +1,25 @@
+from plot import qtplot
+import json
+import math as ma
+import numpy as np
+
+path='/cloud/Public/_data/neuropercolation/4lay/cons=27-knight_steps=1000100_diares/dim=09/batch=0/allpos_ei_samples=10000/dt=1/'
+eps_sp=np.linspace(0.005,0.2,40)
+eps_ep=eps_sp
+
+extremes=10000
+strength=100000
+
+savepath=path+f'extremes={extremes}_bootstrength={strength}/'
+
+with open(path+f"phasediff_means.txt", 'r', encoding='utf-8') as f:
+    means=json.load(f)
+with open(path+f"phasediff_stds.txt", 'r', encoding='utf-8') as f:
+    stds=json.load(f)
+        
+
+hirim=[means[i]+stds[i] for i in range(len(means))]
+lorim=[means[i]-stds[i] for i in range(len(means))]
+
+   
+qtplot(f'Reduction of phase deviation to noise level',[[0]+list(eps_sp[:40])]*3,[[0]+lorim,[0]+means,[0]+hirim],['mean-std','mean','mean+std'],colors=['r','g','r'],y_tag='phase difference',y_log=False) 

examples/Simulate2Layers rising eps.py

@@ -0,0 +1,29 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Fri Aug 18 19:05:04 2023
+
+@author: astral
+"""
+
+from datetime import datetime
+import numpy as np
+from neuropercolation import Simulate2Layers
+
+eps_space = np.linspace(0.005,0.5,100)
+#eps_space = np.linspace(0.135,0.15,4)
+
+dims=list(range(21,27,2))
+for dim in [33]:
+    for eps in [0]:
+        eps = round(eps,3)
+        sim = Simulate2Layers(dim,
+                       eps,
+                       steps=5000,
+                       draw='pygame',
+                       save='simple',
+                       path=f'/cloud/Public/_data/neuropercolation/2lay/steps=500000_rising/dim={dim:02}/',
+                       rising=True,
+                       fps=60,
+                       )
+        print(f'Done eps={eps:.3f} with dim={dim} at {datetime.now()}')

examples/Simulate4Layers.py

@@ -19,7 +19,7 @@ eps_space = np.linspace(0.005,0.5,100)
 #eps_space = np.linspace(0.135,0.15,4)
 
 stp = 1000100
-dims = range(9,10)
+dims = range(25,26)
 batches = 1
 
 path = f'/cloud/Public/_data/neuropercolation/4lay/cons=27-knight_steps=1000100_diares/dim=09/batch=0/'
@@ -40,7 +40,7 @@ for dim in dims:
     for batch in range(max_bat, max_bat+batches):
         savepath = dimpath + f'batch={batch}'
         new_folder(savepath)
-        for eps in [0.3]:#list(eps_space[61::2]):
+        for eps in [0.05]:#list(eps_space[61::2]):
             eps = round(eps,3)
             initstate = [[0,0],[0,0]]
             sim = Simulate4Layers(dim,
@@ -49,10 +49,10 @@ for dim in dims:
                            init=initstate,
                            steps=stp,
                            noeffect=-1,
-                           #fps=20,
+                           fps=60,
-                           draw=None,
+                           draw='pygame',
-                           res=6,
+                           res=10,
-                           save='all',
+                           save=None,
                            path=path,
                            )
             print(f'Done eps={eps:.3f} with dim={dim} at {datetime.now()}')

neuropercolation/automaton.py

@@ -279,7 +279,7 @@ class NeuropercolationCoupled(CellularAutomatonCreator, abc.ABC):
             self.__evolve_cells(self._current_state, self._next_state)
             self._current_state, self._next_state = self._next_state, self._current_state
             self._evolution_step += 1
-
+            
     def __evolve_cells(self, this_state, next_state): #this will be overwritten by heir
         evolve_cell = self.__evolve_cell
         evolution_rule = self.evolve_rule

neuropercolation/display.py

@@ -248,6 +248,7 @@ class Simulate2Layers:
                  save=None,
                  path='/cloud/Public/_data/neuropercolation/test/',
                  state_to_color_cb=None,
+                 rising=False,
                  *args, **kwargs):
         """
         Creates a window to render a 2D CellularAutomaton.
@@ -275,6 +276,7 @@ class Simulate2Layers:
         self.__state_list = []
         self.__activation_list = []
         self.__channel_list = []
+        self.__rising = rising
         self.run(evolutions_per_second=fps, last_evolution_step=steps)
         
     def run(self,
@@ -293,6 +295,9 @@ class Simulate2Layers:
             while self.__active and self._not_at_the_end(last_evolution_step):
                 time_ca_start = time.time()
                 self._cellular_automaton.evolve(evolutions_per_draw)
+                if self.__rising:
+                    self._cellular_automaton.epsilon = self._cellular_automaton.evolution_step/last_evolution_step*0.5
+
                 self._track()
                 if self.__draw_engine is not None:
                     time_ca_end = time.time()