more evaluations

evaluation/1Layer Activity.py

@@ -0,0 +1,75 @@
+# -*- 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/1lay/steps=1000100/'
+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(dimpath+f"eps={round(epsilon,3):.3f}_activation.txt", 'r', encoding='utf-8') as f:
+            activation = np.array(json.load(f)[:500])
+            
+        qtplot(f"Activity time series for eps={round(epsilon,3):.3f}",
+                [list(range(500))],
+                [activation],
+                x_tag = 'time step',
+                y_tag = f'activity density',
+                y_range = (-1,1),
+                export=True,
+                path=dimpath+"evolution/",
+                filename=f'eps={round(epsilon,3):.3f}_evolution.png',
+                close=True) 
+
+mode = 'density'
+#%%

evaluation/1Layer PHI.py

@@ -0,0 +1,91 @@
+# -*- 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 phi import MIP,calc_mips,smartMIP
+
+import math as m
+import numpy as np
+from datetime import datetime
+
+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/1lay/steps=1000100/'
+suffix = ''
+
+chi = chr(967)
+vareps = chr(949)
+varphi = chr(981)
+
+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
+phinum=10000
+PHIS=[]
+for dim in dims[:1]:
+    dimpath = new_folder(path + f'dim={dim:02}/')
+    for epsilon in eps_space:
+        try:
+            with open(dimpath+f"eps={round(epsilon,3):.3f}_phi_{phinum}.txt", 'r', encoding='utf-8') as f:
+                phis=json.load(f)
+                PHIS.append(np.average(phis))
+            print(f'Loaded and Done eps={epsilon:.3f} with dim={dim} at {datetime.now()}')
+        except:
+            with open(dimpath+f"eps={round(epsilon,3):.3f}_states.txt", 'r', encoding='utf-8') as f:
+                states = np.array(json.load(f)[100:phinum+100])
+            
+            phis = [smartMIP(dim,state.translate(str.maketrans('','','.-=')),epsilon)[1] for state in states]
+            with open(dimpath+f"eps={round(epsilon,3):.3f}_phi_{phinum}.txt", 'w', encoding='utf-8') as f:
+                json.dump(phis, f, indent=1)
+            PHIS.append(np.average(phis))
+            print(f'Generated and Done eps={epsilon:.3f} with dim={dim} at {datetime.now()}')
+    #%%
+    qtplot(f"Average phi for different noise parameters",
+        [eps_space],
+        [PHIS],
+        [''],
+        colors='w',
+        x_tag = f'noise level {vareps}',
+        y_tag = f'effect integration {varphi}',
+        export=False,
+        path=dimpath+"evolution/",
+        filename=f'eps={round(epsilon,3):.3f}_evolution.png',
+        close=False) 
+
+mode = 'density'
+#%%

evaluation/1Layer Suscept.py

@@ -0,0 +1,183 @@
+# -*- 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
+            
+path = '/cloud/Public/_data/neuropercolation/1lay/steps=1000100/'
+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]
+
+def __calc_chi(mode='density'):
+    ma=[]
+    s=[]
+    k=[]
+    mk=[]
+    lastkurt=None
+    for dim in dims:
+        try:
+            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:
+                suscept = json.load(f)
+            with open(path+f"kurts/kurtosis_{mode}_dim={dim:02}.txt", 'r', encoding='utf-8') as f:
+                kurt = json.load(f)
+        except:
+            magnet = []
+            suscept = []
+            kurt = []
+            jumped=False
+            print('magnets or suscept or kurt file not found')
+            if not os.path.exists(path+"magnets/"):
+                os.makedirs(path+"magnets/")
+            if not os.path.exists(path+"suscepts/"):
+                os.makedirs(path+"suscepts/")
+            if not os.path.exists(path+"kurts/"):
+                os.makedirs(path+"kurts/")
+            for epsilon in eps_space:
+                try:
+                    with open(path+f"dim={dim:02}/eps={round(epsilon,3):.3f}_activation.txt", 'r', encoding='utf-8') as f:
+                        activation = np.array(json.load(f)[100:])
+                    
+                    if mode=='absolute':
+                        dmag = np.sum(activation*dim**2)/len(activation)
+                        mag = np.sum(np.abs(activation*dim**2))/len(activation)
+                        mag2 = np.sum(activation**2*dim**4)/len(activation)
+                        mag4 = np.sum(activation**4*dim**8)/len(activation)
+                    elif mode=='density':
+                        dmag = np.sum(activation)/len(activation)
+                        mag = np.sum(np.abs(activation))/len(activation)
+                        mag2 = np.sum(activation**2)/len(activation)
+                        mag4 = np.sum(activation**4)/len(activation)
+                    else:
+                        raise NotImplementedError
+                        
+                    mag = round(abs(mag),6)
+                    fluct = round(mag2-mag**2,6)
+                    tail = round(mag4/mag2**2,6)
+                    
+                    magnet.append(mag)
+                    suscept.append(fluct)
+                    kurt.append(tail)
+                    print(f"Done dim={dim:02} eps={round(epsilon,3):.3f}: mag={mag}")
+                    print(f"Done dim={dim:02} eps={round(epsilon,3):.3f}: fluct={fluct}")
+                    print(f"Done dim={dim:02} eps={round(epsilon,3):.3f}: tail={tail}")
+                    jumped=True
+                except:
+                    if not jumped:
+                        magnet.append(1)
+                    elif jumped:
+                        magnet.append(0)
+                    suscept.append(0)
+                    if not jumped:
+                        kurt.append(1)
+                    elif jumped:
+                        kurt.append(3)
+                    print(f"Missing dim={dim:02} eps={round(epsilon,3):.3f}")
+            with open(path+f"magnets/magnetisation_{mode}_dim={dim:02}.txt", 'w', encoding='utf-8') as f:
+                json.dump(magnet, f, ensure_ascii=False, indent=1)
+            with open(path+f"suscepts/susceptibility_{mode}_dim={dim:02}.txt", 'w', encoding='utf-8') as f:
+                json.dump(suscept, f, ensure_ascii=False, indent=1)
+            with open(path+f"kurts/kurtosis_{mode}_dim={dim:02}.txt", 'w', encoding='utf-8') as f:
+                json.dump(kurt, f, ensure_ascii=False, indent=1)
+            
+        if lastkurt is not None:
+            pos=0
+            while kurt[pos]<lastkurt[pos]:
+                pos+=1
+            currdiff = kurt[pos]-lastkurt[pos]
+            lastdiff = kurt[pos-1]-lastkurt[pos-1]
+            crossres = currdiff/(currdiff-lastdiff)
+            crosspoint = eps_space[pos] - crossres*(eps_space[pos]-eps_space[pos-1])
+            assert eps_space[pos-1]<crosspoint<eps_space[pos]
+            mk.append(crosspoint)
+        lastkurt = kurt
+        ma.append(magnet)
+        s.append(suscept)
+        k.append(kurt)
+        
+    
+    return ma,s,k,mk
+
+mode = 'absolute'
+ma,s,k,mk = __calc_chi(mode=mode)
+#%%
+qtplot(f"Magnetisation {mode} evolution for different automaton sizes",
+        [[0]+list(eps_space)]*len(ma),
+        [[1]+ls for d,ls in enumerate(ma[::-1])],
+        [f'dim={dim}x{dim}' for dim in dims[::-1]],
+        x_tag = f'noise parameter {vareps}',
+        y_tag = f'magnetisation {m}',
+        export=True,
+        path=path+"magnets/",
+        filename=f'eps_magnetisation_{mode}_dims=3-9_steps={runsteps}_extra.png',
+        close=False)
+
+qtplot(f"Susceptibility evolution for different automaton sizes",
+        [[0]+list(eps_space)]*len(s),
+        [[0]+ls for ls in s[::-1]],
+        [f'dim={dim}x{dim}' for dim in dims[::-1]],
+        x_tag = f'noise parameter {vareps}',
+        y_tag = f'susceptibility {chi}',
+        export=True,
+        path=path+"suscepts/",
+        filename=f'eps_susceptibility_{mode}_dims=3-9_steps={runsteps}_extra.png',
+        close=False)
+
+qtplot("Kurtosis evolution for different automaton sizes",
+        [[0]+list(eps_space)]*len(k),
+        [[1]+ls for ls in k[::-1]],
+        [f'dim={dim}x{dim}' for dim in dims[::-1]],
+        x_tag = f'noise parameter {vareps}',
+        y_tag = f'kurtosis U',
+        export=True,
+        path=path+"kurts/",
+        filename=f'eps_kurtosis_dims=3-9_steps={runsteps}_extra.png',
+        close=False)
+
+qtplot("Kurtosis crossing for different automaton sizes",
+        [[dim+0.5 for dim in dims[:-1]]],
+        [mk],
+        ['epsilon of kurtosis crosspoint'],
+        x_tag = 'size',
+        y_tag = f'epsilon {vareps}',
+        export=True,
+        path=path+"kurts/",
+        filename=f'kurtosis_cross_dims=3-9_steps={runsteps}_extra.png',
+        close=False)
+

evaluation/1LayerPHI.py

@@ -0,0 +1,118 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Wed Sep 27 04:39:54 2023
+
+@author: astral
+"""
+import os
+import json
+import math as m
+import numpy as np
+from numpy.linalg import norm
+from datetime import datetime
+from random import sample as choose
+from random import random
+
+from plot import qtplot
+
+from neuropercolation import Simulate4Layers
+
+eps_space = list(np.linspace(0.01,0.2,20))
+def new_folder(path):
+    if not os.path.exists(path):
+        os.makedirs(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)
+
+def neighbor(digit0, digit1, lenght):
+    layer = int(lenght)
+    dim = int(np.sqrt(layer))
+    digit0, digit1 = np.array([digit0%dim, digit0//dim]), np.array([digit1%dim, digit1//dim])
+    #print(digit0,digit1)
+    coord_dif = list(map(abs,digit1 - digit0))
+    layer_nbor = 0 in coord_dif and len(set([1,dim-1]).intersection(set(coord_dif))) != 0
+    #print(coord_dif, set([1,dim-1]).intersection(set(coord_dif)))
+    if layer_nbor:
+        return True
+    else:
+        return False
+    
+def kcomb(zp,zm):
+    if zp>2:
+        val=1
+    elif zm>2:
+        val=0
+    elif zp==zm:
+        val=0.5
+    elif zm==2:
+        val=0.5**(3-zp)
+    elif zp==2:
+        val=1-0.5**(3-zm)
+    elif zm==0 and zp==1:
+        val=9/16
+    elif zp==0 and zm==1:
+        val=7/16
+    else:
+        raise NotImplementedError(zp,zm)
+    return val
+
+path = '/cloud/Public/_data/neuropercolation/1lay/steps=100000/'
+
+def phi(dim,statestr,partstr,eps):
+    length = dim**2
+    eta = 1-eps
+    
+    state = np.array([int(q) for q in statestr])
+    state = list(state.reshape((dim,dim)))
+    state = [list([int(cell) for cell in row]) for row in state]
+
+    part = np.array([int(p) for p in partstr])
+    part = list(part.reshape((dim,dim)))
+    part = [list([int(cell) for cell in row]) for row in part]
+
+    inp = [[q+sum([state[(i+1)%dim][j],
+                   state[(i-1)%dim][j],
+                   state[i][(j+1)%dim],
+                   state[i][(j-1)%dim]
+                   ]) for j,q in enumerate(row)] for i,row in enumerate(state)]
+    
+    beps = [[int(inp[i][j]>2)*eta+int(inp[i][j]<3)*eps for j,q in enumerate(row)] for i,row in enumerate(state)]
+    
+    zplus = [[q+sum([state[(i+1)%dim][j]*(part[i][j]==part[(i+1)%dim][j]),
+                     state[(i-1)%dim][j]*(part[i][j]==part[(i-1)%dim][j]),
+                     state[i][(j+1)%dim]*(part[i][j]==part[i][(j+1)%dim]),
+                     state[i][(j-1)%dim]*(part[i][j]==part[i][(j-1)%dim])
+                     ]) for j,q in enumerate(row)] for i,row in enumerate(state)]
+    zminus = [[sum([(1-state[(i+1)%dim][j])*(part[i][j]==part[(i+1)%dim][j]),
+                    (1-state[(i-1)%dim][j])*(part[i][j]==part[(i-1)%dim][j]),
+                    (1-state[i][(j+1)%dim])*(part[i][j]==part[i][(j+1)%dim]),
+                    (1-state[i][(j-1)%dim])*(part[i][j]==part[i][(j-1)%dim])
+                    ]) for j,q in enumerate(row)] for i,row in enumerate(state)]
+    
+    kplus = [[kcomb(zplus[i][j],zminus[i][j]) for j,q in enumerate(row)] for i,row in enumerate(state)]
+    
+    pi = [[eps*(1-kplus[i][j]) + eta*kplus[i][j] for j,q in enumerate(row)] for i,row in enumerate(state)]
+    
+    crossent = [[-beps[i][j]*m.log2(pi[i][j])-(1-beps[i][j])*m.log2(1-pi[i][j]) for j,q in enumerate(row)] for i,row in enumerate(state)]
+    
+    return np.sum(crossent) - length*H2(eps)
+
+def MIP(dim,statestr,eps):
+    lophi=np.inf
+    mip = []
+    for parti in range(1,2**(dim**2-1)):
+        partstr = bin(parti)[2:].zfill(dim**2)
+        print(partstr)
+        curphi = phi(dim,statestr,partstr,eps)
+        
+        if curphi<lophi:
+            lophi=curphi
+            mip = [partstr]
+        elif curphi==lophi:
+            mip.append(partstr)
+    
+    return mip,lophi
+            

evaluation/2Layer Activity.py

@@ -0,0 +1,81 @@
+# -*- 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
+
+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=100100/'
+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(dimpath+f"eps={round(epsilon,3):.3f}_activation.txt", 'r', encoding='utf-8') as f:
+            activation = np.array(json.load(f)[:500])
+        activation = list(zip(*activation))
+        
+        qtplot(f"Activity time series for eps={round(epsilon,3):.3f}",
+                [list(range(500))]*2,
+                activation,
+                x_tag = 'time step',
+                y_tag = f'activity density',
+                y_range = (-1,1),
+                export=True,
+                path=dimpath+"evolution/",
+                filename=f'eps={round(epsilon,3):.3f}_evolution.png',
+                close=True) 
+
+mode = 'density'
+#%%

evaluation/2Layer Suscept.py

@@ -0,0 +1,155 @@
+# -*- 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
+            
+path = '/cloud/Public/_data/neuropercolation/2lay/steps=100100/'
+suspath = path + 'suscepts_euk/'
+kurpath = path + 'kurts_euk/'
+chi = chr(967)
+vareps = chr(949)
+kappa = chr(954)
+rho=chr(961)
+
+vals = [[],[]]
+
+runsteps = 100000
+
+#eps_space = np.linspace(0.005, 0.1, 20)
+eps_space = np.linspace(0.005, 0.5, 100)
+
+epses=20
+
+dims = list(range(3,27,2))#+[16]
+
+def __calc_chi(mode='density'):
+    ma=[]
+    s=[]
+    k=[]
+    
+    suffix = mode
+
+    for dim in dims:
+        try:
+            with open(suspath+f"radium_{suffix}_dim={dim:02}.txt", 'r', encoding='utf-8') as f:
+                magnet = json.load(f)
+            with open(suspath+f"susceptibility_{suffix}_dim={dim:02}.txt", 'r', encoding='utf-8') as f:
+                suscept = json.load(f)
+            with open(kurpath+f"kurtosis_{suffix}_dim={dim:02}.txt", 'r', encoding='utf-8') as f:
+                kurt = []+json.load(f)
+        except:
+            magnet=[]
+            suscept = []
+            kurt = []
+            jumped = False
+            print('suscept or kurt file not found')
+            if not os.path.exists(suspath):
+                os.makedirs(suspath)
+            if not os.path.exists(kurpath):
+                os.makedirs(kurpath)
+            for epsilon in eps_space:
+                try:
+                    with open(path+f"dim={dim:02}/eps={round(epsilon,3):.3f}_activation.txt", 'r', encoding='utf-8') as f:
+                        activation = np.array(json.load(f)[100:])
+                    
+                    if mode=='density':
+                        mag = np.sum(np.linalg.norm(activation,axis=1))/len(activation)                  # density
+                        mag2 = np.sum(np.linalg.norm(activation,axis=1)**2)/len(activation)              # density
+                        mag4 = np.sum(np.linalg.norm(activation,axis=1)**4)/len(activation)              # density
+                    elif mode=='absolute':
+                        mag = np.sum(np.linalg.norm(activation*dim**2,axis=1))/len(activation)                 # density
+                        mag2 = np.sum(np.linalg.norm(activation*dim**2,axis=1)**2)/len(activation)              # density
+                        mag4 = np.sum(np.linalg.norm(activation*dim**2,axis=1)**4)/len(activation)              # density
+                    
+                        
+                    mag = round(mag,6)
+                    fluct = round(mag2-mag**2,6)
+                    tail = round(mag4/mag2**2,6)
+                    
+                    magnet.append(mag)
+                    suscept.append(fluct)
+                    kurt.append(tail)
+                    print(f"Done dim={dim:02} eps={round(epsilon,3):.3f}: mag={mag}")
+                    print(f"Done dim={dim:02} eps={round(epsilon,3):.3f}: fluct={fluct}")
+                    print(f"Done dim={dim:02} eps={round(epsilon,3):.3f}: tail ={tail}")
+                    print(f"===========================================================")
+                    jumped=True
+                except:
+                    suscept.append(0)
+                    if not jumped:
+                        kurt.append(1)
+                    elif jumped:
+                        kurt.append(3)
+                    print(f"Missing dim={dim:02} eps={round(epsilon,3):.3f}")
+            with open(suspath+f"radium_{suffix}_dim={dim:02}.txt", 'w', encoding='utf-8') as f:
+                json.dump(magnet, f, ensure_ascii=False, indent=1)
+            with open(suspath+f"susceptibility_{suffix}_dim={dim:02}.txt", 'w', encoding='utf-8') as f:
+                json.dump(suscept, f, ensure_ascii=False, indent=1)
+            with open(kurpath+f"kurtosis_{suffix}_dim={dim:02}.txt", 'w', encoding='utf-8') as f:
+                json.dump(kurt, f, ensure_ascii=False, indent=1)
+                
+        ma.append([1]+magnet[:epses])
+        s.append([0]+suscept[:epses])
+        k.append([1]+kurt[:epses])
+    
+    return ma,s,k
+
+ma,s,k = __calc_chi()
+#%%
+qtplot(f"Magnetisation evolution for different automaton sizes",
+        [[0]+list(eps_space[:epses])]*len(ma),
+        [[dims[len(dims)-1-d]**2]+list(dims[len(dims)-1-d]**2*np.array(ls[1:])) for d,ls in enumerate(ma[::-1])],
+        [f'dim={dim}x{dim}' for dim in dims[::-1]],
+        y_tag = f'mean cycle {kappa}',
+        export=True,
+        path=path+"magnets/",
+        filename=f'ep_radius_density_dims=3-9_steps={runsteps}_extra.png',
+        close=False)
+
+qtplot(f"Susceptibility evolution for different automaton sizes",
+        [[0]+list(eps_space[:epses])]*len(ma),
+        [[0]+list(np.array(sus[1:])*dims[len(dims)-1-i]**2) for i,sus in enumerate(s[::-1])],
+        [f'dim={dim}x{dim}' for dim in dims[::-1]],
+        y_tag = f'susceptibility {chi}',
+        export=True,
+        path=suspath,
+        filename=f'eps+0_susceptibility_density_dims=3-15_odd_steps={runsteps}_extra.png',
+        close=False)
+
+qtplot("Kurtosis evolution for different automaton sizes",
+        [[0]+list(eps_space[:epses])]*len(k),
+        k[::-1],
+        [f'dim={dim}x{dim}' for dim in dims[::-1]],
+        y_tag = f'kurtosis U',
+        y_range = (1,2),
+        y_log=True,
+        export=True,
+        path=kurpath,
+        filename=f'eps+0_kurtosis_density_dims=3-15_odd_steps={runsteps}_extra.png',
+        close=False)
+

evaluation/2Layer fft.py

@@ -0,0 +1,433 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Tue Aug 30 14:25:12 2022
+
+@author: timof
+"""
+
+from plot import qtplot
+
+import sys
+import os
+import json
+
+import pyqtgraph as qt
+import pyqtgraph.exporters
+
+
+import math as m
+import numpy as np
+from scipy.fftpack import fft, fftfreq
+from scipy.stats import cauchy
+
+vect = np.vectorize
+
+
+
+@vect
+def log2(x):
+    try:
+        return m.log2(x)
+    except ValueError:
+        if x==0:
+            return float(0)
+        else:
+            raise
+        
+basepath = f'/cloud/Public/_data/neuropercolation/2lay/steps=1000100/'
+vals = [[],[]]
+    
+
+TOTP_eps=[]
+TOTP_eps = []
+SIGP_eps = []
+SN_eps = []
+STON_eps = []
+FMAX_eps = []
+FWHM_eps = []
+Q_eps = []
+LHM_eps = []
+UHM_eps = []
+SOS_eps = []
+SPECC_eps=[]
+LORENTZ_eps=[]
+
+dims=[9]
+runsteps = 1000000
+for dim in dims:
+    path=basepath+f'dim={dim:02}/'
+    eps_space = np.linspace(0.005, 0.5, 100)
+    eps_space=eps_space[1::2]
+    TOTP = []
+    SIGP = []
+    SN = []
+    STON = []
+    FMAX = []
+    FWHM = []
+    Q = []
+    LHM=[]
+    UHM=[]
+    SOS=[]
+    #%%
+    for eps in eps_space:
+        eps=round(eps,3)
+        halfh_parts = []
+        sigtonoi_parts = []
+        noisefloor_parts = []
+        totalpower_parts = []
+        sigpower_parts = []
+        sn_parts = []
+        freqmax_parts = []
+        freqfwhm_parts = []
+        specc_list = []
+        lorentz_list = []
+        
+        subfreqmax_parts = []
+        subfreqfwhm_parts = []
+        totlorentz_list = []
+        lhm_list=[]
+        uhm_list=[]
+    
+        parts = 1
+        partlen = int(runsteps/parts)
+        for part in range(0,runsteps,partlen):
+            with open(path+f"eps={eps:.3f}_activation.txt", 'r', encoding='utf-8') as f:
+                activation = json.load(f)[100+part:100+part+partlen]
+            phases = []
+            for act in activation:
+                ph = m.atan2(*act[::-1])
+                phase = act[0] + act[1]*1j #m.e**(ph*1j)
+                phases.append(phase)
+        
+            spectrum = abs(fft(phases))**2
+            freqs = fftfreq(partlen, 1)
+            
+            accum = 1#int(500/parts)
+            
+        
+            if accum==1:
+                try:
+                    with open(path+f"eps={eps:.3f}_smooth_spectrum.txt", 'r', encoding='utf-8') as f:
+                        specc = json.load(f)
+                    freqqs = np.array([freqs[pos] for pos in range(-int(partlen/2),int(partlen/2))])
+                    print(f'Loaded specc for eps={eps:.3f}')
+                except:
+                    freqqs = np.array([freqs[pos] for pos in range(-int(partlen/2),int(partlen/2))])
+                    spec = np.array([spectrum[pos] for pos in range(-int(partlen/2),int(partlen/2))])
+                    
+                    kernelres=2500
+                    kernelbase = np.linspace(-1,1,2*kernelres+1)
+                    kernel = np.exp(-1/(1-np.abs(kernelbase)**2))
+                    kernel=kernel/np.sum(kernel)
+                    
+                    spec_ext = np.hstack((spec[-kernelres:],spec,spec[:kernelres]))
+                    
+                    specc=np.convolve(spec_ext,kernel,mode='same')[kernelres:-kernelres]
+                    with open(path+f"eps={eps:.3f}_smooth_spectrum.txt", 'w', encoding='utf-8') as f:
+                        json.dump(list(specc),f,indent=1)
+            else:
+                freqqs = np.array([freqs[pos]
+                                   for pos in range(int((-partlen+accum)/2), int((partlen+accum)/2),accum)])
+                specc = np.array([( spectrum[pos-int(accum/2)]/2 + sum(spectrum[pos-int(accum/2)+1:pos+int(accum/2)-1]) + spectrum[pos+int(accum/2)-1] + spectrum[pos+int(accum/2)]/2 )/accum
+                                   for pos in range(int((-partlen+accum)/2), int((partlen+accum)/2),accum)])
+            
+            halfh = (max(specc)+min(specc))/2
+            
+            #sigtonoi = sum([specc[pos] for pos in range(len(specc)) if specc[pos]>=halfh])/sum([specc[pos] for pos in range(len(specc)) if specc[pos]<halfh])
+            
+            fars = int(runsteps/accum/100)
+            noisefloor = min(np.average(specc[:fars]),np.average(specc[-fars:]))
+            speccnorm = specc - noisefloor
+            
+            totalpower = sum(specc)
+            sigpower = sum(speccnorm)
+            sig = max(specc)
+            sn = sigpower/(totalpower-sigpower)
+            sigtonoi = sig/(totalpower-sig)
+            
+            halfh_parts.append(halfh)
+            sigtonoi_parts.append(sigtonoi)
+            noisefloor_parts.append(noisefloor)
+            totalpower_parts.append(totalpower)
+            sigpower_parts.append(sig)
+            sn_parts.append(sn)
+            specc_list.append(specc)
+            
+        
+            cumspecc = [speccnorm[0]]
+            for pos in range(1,len(speccnorm)):
+                cumspecc.append(cumspecc[pos-1]+speccnorm[pos])
+        
+            for pos in range(len(specc)):
+                if cumspecc[pos+1]>=sigpower/2:
+                    median = pos
+                    stepdiff = speccnorm[pos]
+                    halfdiff = sum(speccnorm[:pos+1]) - sigpower/2
+                    
+                    freqstep = freqqs[pos] - freqqs[pos-1]
+                    freqmax  = freqqs[pos] - freqstep * halfdiff/stepdiff
+                    
+                    break
+                
+            for pos in range(median, len(speccnorm)):
+                if cumspecc[pos+1]>=sigpower*3/4:
+                    stepdiff = speccnorm[pos]
+                    halfdiff = sum(speccnorm[:pos+1]) - sigpower*3/4
+                    
+                    
+                    freqstep = freqqs[pos] - freqqs[pos-1]
+                    freqquart3  = freqqs[pos] - freqstep * halfdiff/stepdiff
+            
+                    break   
+            for pos in range(median+1):
+                if cumspecc[pos+1]>=sigpower/4:
+                    stepdiff = speccnorm[pos]
+                    halfdiff = sum(speccnorm[:pos+1]) - sigpower/4
+                    
+                    freqstep = freqqs[pos] - freqqs[pos-1]
+                    freqquart1  = freqqs[pos] - freqstep * halfdiff/stepdiff
+        
+                    break
+            
+            
+        
+            freqfwhm = freqquart3-freqquart1
+            gamma = freqfwhm/2
+            
+            freqmax_parts.append(freqmax)
+            freqfwhm_parts.append(freqfwhm)
+            
+            print(gamma**2/median**2)
+            
+            lorentz = sigpower/m.pi * accum/partlen * gamma/((freqqs-freqmax)**2+gamma**2) + noisefloor
+            lorentz_list.append(lorentz)
+            
+            speccpdf = speccnorm/sigpower
+            deviation = np.sqrt(sum((specc-lorentz)**2)/len(specc))/sigpower
+            
+            maxpos = 0
+            for i in range(len(freqqs)):
+                if abs(freqqs[i]-freqmax)<abs(freqqs[maxpos]-freqmax):
+                    maxpos = i
+            pos=maxpos
+            try:
+                while lorentz[pos]>lorentz[maxpos]/2:
+                    pos-=1
+                lhm=freqqs[pos]
+            except:
+                lhm=freqqs[0]
+            pos=maxpos
+            try:
+                while lorentz[pos]>lorentz[maxpos]/2:
+                    pos+=1
+                uhm=freqqs[pos]
+            except:
+                uhm=freqqs[-1]
+                
+        SPECC = np.average(specc_list,axis=0)
+        LORENTZ = np.average(lorentz_list,axis=0)
+        DEV = np.sqrt(sum((SPECC-LORENTZ)**2)/len(SPECC))/sum(SPECC)
+    
+        TOTP.append(np.average(totalpower_parts))
+        SIGP.append(np.average(sigpower_parts))
+        SN.append(np.average(sn_parts))
+        STON.append(sigtonoi)
+    
+        FMAX.append(np.average(freqmax_parts))
+        FWHM.append(np.average(freqfwhm_parts))
+        LHM.append(lhm)
+        UHM.append(uhm)
+        Q.append(np.average(freqmax_parts)/np.average(freqfwhm_parts))
+        SOS.append(DEV)
+        #%%
+        with open(path+f"signal/SN_{parts}_accum={accum}_dim={dim}_runsteps={runsteps}.txt", 'w', encoding='utf-8') as f:
+            json.dump(SN, f, ensure_ascii=False, indent=4)
+        with open(path+f"signal/FMAX_{parts}_accum={accum}_dim={dim}_runsteps={runsteps}.txt", 'w', encoding='utf-8') as f:
+            json.dump(FMAX, f, ensure_ascii=False, indent=4)
+        with open(path+f"signal/FWHM_{parts}_accum={accum}_dim={dim}_runsteps={runsteps}.txt", 'w', encoding='utf-8') as f:
+            json.dump(FWHM, f, ensure_ascii=False, indent=4)
+        with open(path+f"signal/LHM_{parts}_accum={accum}_dim={dim}_runsteps={runsteps}.txt", 'w', encoding='utf-8') as f:
+            json.dump(LHM, f, ensure_ascii=False, indent=4)
+        with open(path+f"signal/UHM_{parts}_accum={accum}_dim={dim}_runsteps={runsteps}.txt", 'w', encoding='utf-8') as f:
+            json.dump(UHM, f, ensure_ascii=False, indent=4)
+        with open(path+f"signal/TOTP_{parts}_accum={accum}_dim={dim}_runsteps={runsteps}.txt", 'w', encoding='utf-8') as f:
+            json.dump(TOTP, f, ensure_ascii=False, indent=4)
+        with open(path+f"signal/SIGP_{parts}_accum={accum}_dim={dim}_runsteps={runsteps}.txt", 'w', encoding='utf-8') as f:
+            json.dump(SIGP, f, ensure_ascii=False, indent=4)
+        with open(path+f"signal/Q_{parts}_accum={accum}_dim={dim}_runsteps={runsteps}.txt", 'w', encoding='utf-8') as f:
+            json.dump(Q, f, ensure_ascii=False, indent=4)
+        with open(path+f"signal/STON_{parts}_accum={accum}_dim={dim}_runsteps={runsteps}.txt", 'w', encoding='utf-8') as f:
+            json.dump(STON, f, ensure_ascii=False, indent=4)
+        
+        #%%
+        plotpath = path + 'spectra/'
+        # qtplot(f'Frequency spectrum for dim={dim} eps={eps:.3f}',
+        #         [freqqs]*2,
+        #         [LORENTZ,SPECC],
+        #         [f'lorentz regression dev={DEV}','spectrum'],
+        #         x_tag = 'frequency f',
+        #         y_tag = 'spectral power p',
+        #         y_log = False,
+        #         export=True,
+        #         lw=1,
+        #         path=plotpath,
+        #         filename=f'Lorentz and Cauchy fit to spectrum {parts} parts accum={accum} eps={round(eps,3):.3f}.png',
+        #         close=True)
+        
+        
+        #%%
+    
+        print("Power {}, Signal {}".format(round(totalpower), round(sigpower)))
+        
+        print("Done {:.3f}: DEV {}, FMAX {}, FWHM {}".format(eps, round(deviation,3), round(freqmax,5), round(FWHM[-1],5)))
+    
+        LORENTZ_eps.append(LORENTZ)
+        SPECC_eps.append(SPECC)
+    
+    #%%
+    # vareps=chr(949)
+    # qtplot(f'Frequency spectra to noise level',
+    #         [freqqs[50::100]]*len(eps_space),
+    #         [SPECC[50::100] for SPECC in SPECC_eps],
+    #         [f'{vareps}={eps:.3f}' for eps in eps_space],
+    #         x_tag = 'frequency f',
+    #         y_tag = 'energy spectral density',
+    #         y_log = True,
+    #         export=False,
+    #         lw=2,
+    #         path=plotpath,
+    #         filename=f'Lorentz and Cauchy fit to spectrum log {parts} parts accum={accum} eps={round(eps,3):.3f}.png',
+    #         close=False)
+    #%%
+    TOTP_eps.append(TOTP)
+    SIGP_eps.append(SIGP)
+    SN_eps.append(SN)
+    STON_eps.append(STON)
+    FMAX_eps.append(FMAX)
+    FWHM_eps.append(FWHM)
+    Q_eps.append(Q)
+    LHM_eps.append(LHM)
+    UHM_eps.append(UHM)
+    SOS_eps.append(SOS)
+
+    #%%
+sigpath = basepath + 'signal/'
+if not os.path.exists(sigpath):
+    os.makedirs(sigpath)
+    
+# qtplot(f'Signal to noise for dim={dim} eps={eps:.3f}',
+#         [eps_space],
+#         [SN],
+#         ['signalpower to noisefloor'],
+#         x_tag = 'epsilon',
+#         y_tag = 'ratio',
+#         y_log = False,
+#         export=True,
+#         path=sigpath,
+#         filename=f'SN_plot.png',
+#         close=True)
+
+qtplot(f'Q facor for odd automaton sizes',
+        [eps_space]*3,
+        Q_eps,
+        [f'dim={dim}x{dim}' for dim in dims],
+        y_tag = 'purity',
+        y_log = False,
+        export=True,
+        path=sigpath,
+        filename=f'Q_plot_{parts}parts_accum={accum}.png',
+        close=False)
+#%%
+
+# with open(path+f"signal/FMAX_1_accum={accum}_dim={dim}_runsteps={runsteps}.txt", 'r', encoding='utf-8') as f:
+#     FMAX=json.load(f)
+# with open(path+f"signal/FWHM_1_accum={accum}_dim={dim}_runsteps={runsteps}.txt", 'r', encoding='utf-8') as f:
+#     FWHM=json.load(f)
+
+qtplot(f'Dominant frequency',
+        [[0]+list(eps_space[:-1])]*3,
+        [[0]+FMAX[-1],[0]+LHM[-1],[0]+UHM[-1]],
+        # [f'dim={dim}x{dim}' for dim in dims],
+        ['dominant frequency', 'lesser half maximum', 'upper half maximum'],
+        #colors=['g','r','r'],
+        y_tag = 'frequency f',
+        y_log = True,
+        export=True,
+        path=sigpath,
+        filename=f'FMAX+FWHMto50_plot_{parts}parts_accum={accum}.png',
+        close=False)
+#%%
+qtplot(f'Dominant frequency',
+        [[0]+list(eps_space[:-1])]*3,
+        [[0]+FMAX[:-1] for FMAX in FMAX_eps],#, [[0]+LHM[i][:50] for LHM in LHM_eps], [[0]+UHM[i][:50] for UHM in UHM_eps],
+        [f'dim={dim}x{dim}' for dim in dims],
+        #[['dominant frequency', 'lesser half maximum', 'upper half maximum'],
+        #colors=['g','r','r'],
+        y_tag = 'frequency f',
+        y_log = True,
+        export=True,
+        path=sigpath,
+        filename=f'FMAX+FWHMto50_plot_{parts}parts_accum={accum}.png',
+        close=False)
+#%%
+qtplot(f'Total and signal energy to noise level',
+        [eps_space]*6,
+        list(np.array(SIGP_eps)/runsteps*accum)+list(np.array(TOTP_eps)/runsteps*accum),
+        [f'signal energy for dim={dim:02d}' for dim in dims]+[f'total energy for dim={dim:02d}' for dim in dims],
+        colors=['b','g','r','c','y','m'],
+        y_tag = f'energy',
+        y_log = True,
+        export=True,
+        path=sigpath,
+        filename=f'POWER_plot_{parts}parts_accum={accum}.png',
+        close=False)
+#%%
+qtplot(f'Signal-to-noise ratio to noise level',
+        [eps_space]*len(dims),
+        STON_eps,
+        [f'dim={dim:02d}x{dim:02d}' for dim in dims],
+        y_tag = f'ratio S/N',
+        y_log = True,
+        export=True,
+        path=sigpath,
+        filename=f'SN_plot_{parts}parts_accum={accum}.png',
+        close=False)
+#%%
+qtplot(f'Goodness of fit to Lorentz curve',
+        [eps_space]*len(dims),
+        SOS_eps,
+        [f'dim={dim:02d}x{dim:02d}' for dim in dims],
+        y_tag = f'mean deviation',
+        y_log = False,
+        export=True,
+        path=sigpath,
+        filename=f'DEV_plot_{parts}parts_accum={accum}.png',
+        close=False)
+#%%
+with open(basepath+f"signal/SN_{parts}_accum={accum}_dim={dim}_runsteps={runsteps}.txt", 'w', encoding='utf-8') as f:
+    json.dump(SN_eps, f, ensure_ascii=False, indent=4)
+with open(basepath+f"signal/FMAX_{parts}_accum={accum}_dim={dim}_runsteps={runsteps}.txt", 'w', encoding='utf-8') as f:
+    json.dump(FMAX_eps, f, ensure_ascii=False, indent=4)
+with open(basepath+f"signal/FWHM_{parts}_accum={accum}_dim={dim}_runsteps={runsteps}.txt", 'w', encoding='utf-8') as f:
+    json.dump(FWHM_eps, f, ensure_ascii=False, indent=4)
+with open(basepath+f"signal/LHM_{parts}_accum={accum}_dim={dim}_runsteps={runsteps}.txt", 'w', encoding='utf-8') as f:
+    json.dump(LHM_eps, f, ensure_ascii=False, indent=4)
+with open(basepath+f"signal/UHM_{parts}_accum={accum}_dim={dim}_runsteps={runsteps}.txt", 'w', encoding='utf-8') as f:
+    json.dump(UHM_eps, f, ensure_ascii=False, indent=4)
+with open(basepath+f"signal/TOTP_{parts}_accum={accum}_dim={dim}_runsteps={runsteps}.txt", 'w', encoding='utf-8') as f:
+    json.dump(TOTP_eps, f, ensure_ascii=False, indent=4)
+with open(basepath+f"signal/SIGP_{parts}_accum={accum}_dim={dim}_runsteps={runsteps}.txt", 'w', encoding='utf-8') as f:
+    json.dump(SIGP_eps, f, ensure_ascii=False, indent=4)
+with open(basepath+f"signal/Q_{parts}_accum={accum}_dim={dim}_runsteps={runsteps}.txt", 'w', encoding='utf-8') as f:
+    json.dump(Q_eps, f, ensure_ascii=False, indent=4)
+with open(basepath+f"signal/STON_{parts}_accum={accum}_dim={dim}_runsteps={runsteps}.txt", 'w', encoding='utf-8') as f:
+    json.dump(STON_eps, f, ensure_ascii=False, indent=4)
+with open(basepath+f"signal/Q_{parts}_accum={accum}_dim={dim}_runsteps={runsteps}.txt", 'w', encoding='utf-8') as f:
+    json.dump(Q_eps, f, ensure_ascii=False, indent=4)
+with open(basepath+f"signal/STON_{parts}_accum={accum}_dim={dim}_runsteps={runsteps}.txt", 'w', encoding='utf-8') as f:
+    json.dump(STON_eps, f, ensure_ascii=False, indent=4)
+
+def plot_execute():
+    if sys.flags.interactive != 1 or not hasattr(qt.QtCore, 'PYQT_VERSION'):
+        qt.QtGui.QApplication.exec_()
+

evaluation/2Layer phiplot.py

@@ -0,0 +1,98 @@
+# -*- 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
+
+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=100100/'
+suffix = ''
+
+chi = chr(967)
+vareps = chr(949)
+varphi = chr(981)
+
+vals = [[],[]]
+
+runsteps = 1000100
+
+eps_space = np.linspace(0.005, 0.5, 100)
+eps_space = eps_space[1::2]
+
+dims = list(range(3,10,2))#+[16,49]
+
+mode='density'
+ma=[]
+s=[]
+k=[]
+mk=[]
+PHI=[]
+lastkurt=None
+for dim in dims:
+    phis=[]
+    con_gap = 3
+    cons = [(n,(2*n+m)%dim) for n in range(dim) for m in range(0,dim-2,con_gap)]
+    dimpath = new_folder(path + f'dim={dim:02}/')
+    for epsilon in eps_space:
+        try:
+            with open(dimpath+f"eps={round(epsilon,3):.3f}_ei.txt", 'r', encoding='utf-8') as f:
+                ei = np.array(json.load(f)[100:])
+        except:
+            print(f'Calcing phi for eps={epsilon}')
+            with open(dimpath+f"eps={round(epsilon,3):.3f}_channels.txt", 'r', encoding='utf-8') as f:
+                channels = np.array(json.load(f)[100:])
+                
+            ei = np.sum(channels,axis=0)*(1-H2(epsilon))
+            ei=list(ei)
+            with open(dimpath+f"eps={round(epsilon,3):.3f}_ei.txt", 'w', encoding='utf-8') as f:
+                json.dump(list(ei),f, ensure_ascii=False,indent=1)
+                
+        phi=np.average(ei)
+        phis.append(phi)
+    PHI.append(phis)
+    #%%
+qtplot(f"Mean effect integration over noise level",
+        [[0]+list(eps_space)]*len(dims),
+        [[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}',
+        export=True,
+        path=dimpath+"",
+        filename=f'eps={round(epsilon,3):.3f}_evolution.png',
+        close=False) 
+
+mode = 'density'
+#%%

evaluation/2axplot.py

@@ -0,0 +1,60 @@
+"""
+Demonstrates a way to put multiple axes around a single plot. 
+
+(This will eventually become a built-in feature of PlotItem)
+"""
+
+
+import pyqtgraph as pg
+
+pg.mkQApp()
+
+pw = pg.PlotWidget()
+pw.show()
+pw.setWindowTitle('pyqtgraph example: MultiplePlotAxes')
+p1 = pw.plotItem
+p1.setLabels(left='axis 1')
+
+## create a new ViewBox, link the right axis to its coordinate system
+p2 = pg.ViewBox()
+p1.showAxis('right')
+p1.scene().addItem(p2)
+p1.getAxis('right').linkToView(p2)
+p2.setXLink(p1)
+p1.getAxis('right').setLabel('axis2', color='#0000ff')
+
+## create third ViewBox. 
+## this time we need to create a new axis as well.
+p3 = pg.ViewBox()
+ax3 = pg.AxisItem('right')
+p1.layout.addItem(ax3, 2, 3)
+p1.scene().addItem(p3)
+ax3.linkToView(p3)
+p3.setXLink(p1)
+ax3.setZValue(-10000)
+ax3.setLabel('axis 3', color='#ff0000')
+
+
+## Handle view resizing 
+def updateViews():
+    ## view has resized; update auxiliary views to match
+    global p1, p2, p3
+    p2.setGeometry(p1.vb.sceneBoundingRect())
+    p3.setGeometry(p1.vb.sceneBoundingRect())
+    
+    ## need to re-update linked axes since this was called
+    ## incorrectly while views had different shapes.
+    ## (probably this should be handled in ViewBox.resizeEvent)
+    p2.linkedViewChanged(p1.vb, p2.XAxis)
+    p3.linkedViewChanged(p1.vb, p3.XAxis)
+
+updateViews()
+p1.vb.sigResized.connect(updateViews)
+
+
+p1.plot([1,2,4,8,16,32])
+p2.addItem(pg.PlotCurveItem([10,20,40,80,40,20], pen='b'))
+p3.addItem(pg.PlotCurveItem([3200,1600,800,400,200,100], pen='r'))
+
+if __name__ == '__main__':
+    pg.exec()

evaluation/4Layer Activity.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/4Layer Bootstrap Resultant.py

@@ -0,0 +1,286 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Mon Aug 21 14:59:22 2023
+
+@author: astral
+"""
+
+import os
+import json
+import math as m
+import numpy as np
+from numpy.linalg import norm
+from datetime import datetime
+from random import sample as choose
+from random import random
+
+from plot import qtplot
+
+from neuropercolation import Simulate4Layers
+
+
+def resultant(sample):
+    phase_x = [m.cos(ind) for ind in sample]
+    phase_y = [m.sin(ind) for ind in sample]
+    
+    return (np.average(phase_x), np.average(phase_y))
+
+def coherence(sample):
+    phase_x = [m.cos(ind) for ind in sample]
+    
+    return np.average(phase_x)
+
+
+def bootstrap_stat(whole, sub, strength=10000, estimator='resultant'):
+    k = len(sub)
+    
+    if estimator=='resultant':
+        whole_est = norm(resultant(whole))
+        sub_est = norm(resultant(sub))
+        
+        boot_dist = []
+        for i in range(strength):
+            boot_dist.append(norm(resultant(choose(whole,k))))
+            if i%1000==999:
+                print(f'Done {i:0{len(str(strength))}d} bootstraps')
+        
+        confidence = len([val for val in boot_dist if (val-whole_est)<max(sub_est-whole_est,0)])/len(boot_dist)
+        
+    return confidence
+
+def bootstrap_res(whole, sub, strength=10000):
+    k = len(sub)
+    
+    resultants = []
+    for i in range(strength):
+        resultants.append(norm(resultant(choose(whole,k))))
+        if i%1000==999:
+            print(f'Done {i:0{len(str(strength))}d} bootstraps')
+    return resultants
+
+def sample_parts(wholes, subs):
+    ks = [len(s) for s in subs]
+    sample = [pha for j in range(len(wholes)) for pha in choose(wholes[j],ks[j])]
+            
+    return sample
+
+def bootstrap_parts(wholes, subs, strength=10000, estimator='resultant',sided='right'):
+    ks = [len(s) for s in subs]
+    
+    whole = [w for whole in wholes for w in whole]
+    sub   = [s for sub   in subs   for s in sub]
+    
+    if estimator=='resultant':
+        whole_est = norm(resultant(whole))
+        sub_est = norm(resultant(sub))
+        
+        boot_dist = []
+        for i in range(strength):
+            sample = [pha for j in range(len(wholes)) for pha in choose(wholes[j],ks[j])]
+            boot_dist.append(norm(resultant(sample)))
+            if i%1000==999:
+                print(f'Done {i:0{len(str(strength))}d} bootstraps')
+        
+    if sided=='right':
+        confidence = len([val for val in boot_dist if val<sub_est])/len(boot_dist)
+    elif sided=='double':
+        confidence = len([val for val in boot_dist if abs(val-whole_est)<abs(sub_est-whole_est)])/len(boot_dist)
+    elif sided=='left':
+        confidence = len([val for val in boot_dist if val>sub_est])/len(boot_dist)
+    else:
+        raise NotImplemented
+    return confidence
+
+def bootstrap_res_parts(wholes, subs, strength=10000):
+    ks = [len(s) for s in subs]
+    
+    whole = [w for whole in wholes for w in whole]    
+    whole_est = norm(resultant(whole))
+    
+    resultants = []
+    for i in range(strength):
+        sample = [pha for j in range(len(wholes)) for pha in choose(wholes[j],ks[j])]
+        resultants.append(norm(resultant(sample)))
+        if i%1000==999:
+            print(f'Done {i:0{len(str(strength))}d} bootstraps')
+        
+    return resultants
+
+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)
+
+extremes = None
+maxdt = 250
+
+stp = 1000100
+batch = 0
+
+eps_space = list(np.linspace(0.01,0.5,50))
+
+print(f'Started at {datetime.now()}')
+
+for dim in [9]:
+    for eps in eps_space[:1]:#list(eps_space[3:8])+list(eps_space[:3])+list(eps_space[8:]):
+        eps = round(eps,3)
+        path='/cloud/Public/_data/neuropercolation/4lay/cons=dimtimesdimby3_steps=100100/dim=09_cons=27/batch=0/'
+        
+        try:
+            with open(path+f"eps={round(eps,3):.3f}_phase_diff.txt", 'r', encoding='utf-8') as f:
+                phase_diff = json.load(f)
+        except:
+            with open(path+f"eps={round(eps,3):.3f}_activation.txt", 'r', encoding='utf-8') as f:
+                activation = json.load(f)[100:]
+        
+            osc = list(zip(*activation))
+            phase_abs = np.array([[np.arctan2(*act[::-1]) for act in osc[i]] for i in range(2)])
+            phase_diff = diff(phase_abs[0],phase_abs[1])
+            phase_diff = [round(pha,6) for pha in phase_diff]
+            
+            with open(path+f"eps={round(eps,3):.3f}_phase_diff.txt", 'w', encoding='utf-8') as f:
+                json.dump(list(phase_diff), f, indent=1)
+    
+        
+        all_res = norm(resultant(phase_diff))
+        av_diff = np.arccos(all_res)
+        
+        try:
+            with open(path+f"eps={round(eps,3):.3f}_ei.txt", 'r', encoding='utf-8') as f:
+                ei = json.load(f)
+        except:
+            with open(path+f"eps={round(eps,3):.3f}_channels.txt", 'r', encoding='utf-8') as f:
+                channels = json.load(f)[100:]
+            
+            ei = [round(np.sum(cha)*(1-H2(eps)),6) for cha in channels]
+            
+            with open(path+f"eps={round(eps,3):.3f}_ei.txt", 'w', encoding='utf-8') as f:
+                json.dump(ei, f, indent=1)
+        
+        strength = 100000
+        extremes = 10000 #[l//2 for l in lens]
+        ext_rat = extremes/(stp-100)
+        
+        circparts = 100
+        pha_dev = m.pi/circparts
+        pha_max = np.max(np.abs(phase_diff))
+        
+        phase_in_part = lambda ph, i: abs(ph)<=pha_max/circparts if i==0 else i*pha_max/circparts<abs(ph)<=(i+1)*pha_max/circparts
+        
+        dev_parts = [sorted([i for i,val in enumerate(ei[:-maxdt]) if phase_in_part(phase_diff[i],j)],
+                            key = lambda i: ei[i]) for j in range(circparts)]
+        
+        ext_fracs = [round(len(dev_parts[i])*ext_rat,6) for i in range(circparts)]
+        ext_parts = [int(ext_fracs[i]) for i in range(circparts)]
+        ext_probs = [round(ext_fracs[i]%1,6) for i in range(circparts)]
+        
+        exts = [ext_parts[i]+(random()<ext_probs[i]) for i in range(circparts)]
+    
+        top_parts = [dev_parts[i][-exts[i]:] if exts[i]>0 else [] for i in range(circparts)]
+        
+        pha_parts = [[phase_diff[i] for i in part] for part in dev_parts]
+        syn_parts = [[phase_diff[i] for i in part] for part in top_parts]
+        ran_sam = sample_parts(dev_parts, top_parts)
+        top_sam = sample_parts(top_parts, top_parts)
+        
+        dev = []
+        for part in dev_parts:
+            dev.extend(part)
+        top = []
+        for part in top_parts:
+            top.extend(part)
+        
+        assert sorted(top)==sorted(top_sam)
+        
+        ran_res = []
+        top_res = []
+        tot_res = []
+        
+        bot_ei = []
+        top_ei = []
+        
+        maxdt = 250
+        for dt in range(maxdt):
+            tot_pha = phase_diff[dt:dt-maxdt]
+            ran_pha = [(phase_diff[i+dt]) for i in ran_sam]
+            top_pha = [(phase_diff[i+dt]) for i in top_sam]
+            
+            tot_res.append( norm(resultant(tot_pha)) )
+            ran_res.append( norm(resultant(ran_pha)) )
+            top_res.append( norm(resultant(top_pha)) )
+            
+
+        sampling = 'samedist_varmaxpha'
+        plotpath = new_folder(path+f'{sampling}_causal_roll{pha_dev:.3f}/')#'bootstrap={strength}/'
+        savepath=new_folder(plotpath+f'extremes={extremes}_bootstrength={strength}/')
+        
+        newpath = new_folder(path+f'extremes={extremes}_bootstrength={strength}/')
+        resultant_stat = bootstrap_res(phase_diff,top,strength=strength)
+        
+        confs = []
+        confdt = 250
+        for dt in range(confdt+1):
+            pha_evs = [[phase_diff[i+dt] for i in part] for part in dev_parts]
+            syn_evs = [[phase_diff[i+dt] for i in part] for part in top_parts]
+            phas = [phase_diff[i+dt] for i in top]
+            res_pha = norm(resultant(phas))
+            
+            conf = len([val for val in resultant_stat if val<res_pha])/len(resultant_stat)
+            confs.append((dt, conf))
+            print(f'Confidence for dim={dim} dt={dt}: {conf}')
+        with open(newpath+f"eps={round(eps,3):.3f}_dt={confdt}_simpbootstrap.txt", 'w', encoding='utf-8') as f:
+            json.dump(list(confs), f, indent=1)
+
+        qtplot(f'Diachronic resultant for dim={dim} eps={eps:.3f} with 4 layers',
+                [np.array(range(maxdt))]*3,
+                [tot_res, ran_res, top_res],
+                ['Average Resultant', f'random sample of {extremes}',
+                    f'top sample of {extremes} ei'],
+                x_tag = 'dt',
+                y_tag = 'concentration',
+                export=True,
+                path=newpath,
+                filename=f'Random Diachronic Resultant Norm eps={round(eps,3):.3f} dim={dim} extremes={extremes}.png',
+                close=True)
+        
+        # qtplot(f'Diachronic resultant phase for dim={dim} eps={eps:.3f} with 4 layers',
+        #         [np.array(range(maxdt))]*3,
+        #         [top_ph[0], dis_ph[0], tot_ph],
+        #         ['top {extremes} ei', 'dis {extremes} ei',
+        #          'Average'],
+        #         x_tag = 'dt',
+        #         y_tag = 'phase',
+        #         export=True,
+        #         path=plotpath,
+        #         filename=f'All Diachronic Resultant Phase eps={round(eps,3):.3f} dim={dim} extremes={extremes} roll{pha_dev:.3f}.png',
+        #         close=True)
+        
+        # qtplot(f'Diachronic ei for dim={dim} with 4 layers',
+        #         [np.array(range(maxdt))]*4,
+        #         [bot_ei, top_ei, dev_ei, tot_ei],
+        #         ['EI ev of bottom {extremes} ei', 'EI ev of top {extremes} ei',
+        #          'EI ev of phase filtered ei', 'Average EI'],
+        #         x_tag = 'dt',
+        #         y_tag = 'average ei',
+        #         export=True,
+        #         path=path+'plots/',
+        #         filename=f'Diachronic EI balanced for eps={round(eps,3):.3f} dim={dim} extremes={extremes} roll{pha_dev:.3f}.png',
+        #         close=True)
+        
+        print(f'Done eps={eps:.3f} with dim={dim} at {datetime.now()}')
+        
+    # qtplot(f'Resultant and EI evolution for dim={dim} with 4 layers',
+    #         [[0]+eps_space]*2,
+    #         [max(av_ei)*diff_res, av_ei],
+    #         ['Resultant', 'avEI'],
+    #         export=True,
+    #         path=path,
+    #         filename=f'Resultant and EI for dim={dim}.png',
+    #         close=True)
+        
+        

evaluation/4Layer Causal 4way resultant.py

@@ -0,0 +1,369 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Mon Aug 21 14:59:22 2023
+
+@author: astral
+"""
+
+import json
+import math as m
+import numpy as np
+from numpy.linalg import norm
+from datetime import datetime
+from random import sample as choose
+
+from plot import qtplot
+
+from neuropercolation import Simulate4Layers
+
+eps_space = list(np.linspace(0.01,0.2,20))
+
+def resultant(sample):
+    phase_x = [m.cos(ind) for ind in sample]
+    phase_y = [m.sin(ind) for ind in sample]
+    
+    return (np.average(phase_x), np.average(phase_y))
+
+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)
+
+extremes = None
+maxdt = 300
+
+stp = 10100
+batch = 0
+
+for dim in [9]:
+    for eps in eps_space[1:41:2]:
+        path=f'/cloud/Public/_data/neuropercolation/4lay/cons=27-knight_steps={stp}/dim={dim:02}/batch={batch}/'
+        
+        try:
+            with open(path+f"eps={round(eps,3):.3f}_phase_diff.txt", 'r', encoding='utf-8') as f:
+                phase_diff = json.load(f)
+        except:
+            with open(path+f"eps={round(eps,3):.3f}_activation.txt", 'r', encoding='utf-8') as f:
+                activation = json.load(f)[100:]
+        
+            osc = list(zip(*activation))
+            phase_abs = np.array([[np.arctan2(*act[::-1]) for act in osc[i]] for i in range(2)])
+            phase_diff = diff(phase_abs[0],phase_abs[1])
+            
+            with open(path+f"eps={round(eps,3):.3f}_phase_diff.txt", 'w', encoding='utf-8') as f:
+                json.dump(list(phase_diff), f, indent=1)
+    
+        
+        all_res = norm(resultant(phase_diff))
+        av_diff = np.arccos(all_res)
+        
+        try:
+            with open(path+f"eps={round(eps,3):.3f}_ei.txt", 'r', encoding='utf-8') as f:
+                ei = json.load(f)
+        except:
+            with open(path+f"eps={round(eps,3):.3f}_channels.txt", 'r', encoding='utf-8') as f:
+                channels = json.load(f)[100:]
+            
+            ei = [np.sum(cha)*(1-H2(eps)) for cha in channels]
+            
+            with open(path+f"eps={round(eps,3):.3f}_ei.txt", 'w', encoding='utf-8') as f:
+                json.dump(ei, f, indent=1)
+        
+        pha_center = av_diff
+        pha_dev = m.pi/32
+        
+        from_sync = lambda i: True if abs(phase_diff[i])<0.08*m.pi else False if 0.42*m.pi<abs(phase_diff[i])<0.58*m.pi else from_sync(i-1) if i>0 else None
+        to_sync = lambda i: True if abs(phase_diff[i])<0.08*m.pi else False if 0.42*m.pi<abs(phase_diff[i])<0.58*m.pi else to_sync(i+1) if i+1<len(phase_diff) else None
+        
+        dev_ind = sorted([i for i,val in enumerate(ei[:-maxdt]) if (pha_center-pha_dev)<=abs(phase_diff[i])<=(pha_center+pha_dev)], key = lambda i: ei[i])
+        dev_00 = [i for i in dev_ind if from_sync(i)          and to_sync(i)         ]
+        dev_01 = [i for i in dev_ind if from_sync(i)          and to_sync(i) is False]
+        dev_10 = [i for i in dev_ind if from_sync(i) is False and to_sync(i)         ]
+        dev_11 = [i for i in dev_ind if from_sync(i) is False and to_sync(i) is False]
+        
+        lens = [len(dev_00),len(dev_01),len(dev_10),len(dev_11)]
+        
+        #if not extremes:
+        extremes = [100]*4 #[l//2 for l in lens]
+
+        print(lens)
+        #print(all_res, av_diff)
+        
+        
+        # bot_00 = dev_00[:extremes[0]]
+        # bot_01 = dev_01[:extremes[1]]
+        # bot_10 = dev_10[:extremes[2]]
+        # bot_11 = dev_11[:extremes[3]]
+        
+        top_00 = dev_00[-extremes[0]:]
+        top_01 = dev_01[-extremes[1]:]
+        top_10 = dev_10[-extremes[2]:]
+        top_11 = dev_11[-extremes[3]:]
+        
+        with open(path+f"eps={round(eps,3):.3f}_states.txt", 'r', encoding='utf-8') as f:
+            states = json.load(f)[100:]
+        with open(path+f"eps={round(eps,3):.3f}_coupling.txt", 'r', encoding='utf-8') as f:
+            coupling = json.load(f)
+            coupling = [tuple(edge) for edge in coupling]
+        
+        for top,name in [(top_00,'top_00'),(top_01,'top_01'),(top_10,'top_10'),(top_11,'top_11')]:
+            for i in top:
+                causal_init = states[i].translate(str.maketrans('', '', '.-='))
+                path_c = path+f'causal_maxdt={maxdt}/{name}/{i:0{len(str(stp))}}/'
+                
+                try:
+                    with open(path_c+f'eps={round(eps,3):.3f}_phase_diff.txt', 'r', encoding='utf-8') as f:
+                        phasediff = json.load(f)
+                except:
+                    sim=Simulate4Layers(dim,
+                                        eps,
+                                        coupling=coupling,
+                                        init=causal_init,
+                                        noeffect=0,
+                                        steps=maxdt,
+                                        draw=None,
+                                        save='all',
+                                        path=path_c,
+                                        )
+                    
+                    with open(path_c+f"eps={round(eps,3):.3f}_activation.txt", 'r', encoding='utf-8') as f:
+                        activation = json.load(f)
+                
+                    osc = list(zip(*activation))
+                    phase_abs = np.array([[np.arctan2(*act[::-1]) for act in osc[i]] for i in range(2)])
+                    phasediff = diff(phase_abs[0],phase_abs[1])
+                    
+                    with open(path_c+f"eps={round(eps,3):.3f}_phase_diff.txt", 'w', encoding='utf-8') as f:
+                        json.dump(list(phasediff), f, indent=1)
+        
+        for top,name in [(top_00,'top_00'),(top_01,'top_01'),(top_10,'top_10'),(top_11,'top_11')]:
+            for i in top:
+                causal_init = states[i].translate(str.maketrans('', '', '.-='))
+                path_c = path+f'original_maxdt={maxdt}/{name}/{i:0{len(str(stp))}}/'
+                
+                try:
+                    with open(path_c+f'eps={round(eps,3):.3f}_phase_diff.txt', 'r', encoding='utf-8') as f:
+                        phasediff = json.load(f)
+                except:
+                    sim=Simulate4Layers(dim,
+                                        eps,
+                                        coupling=coupling,
+                                        init=causal_init,
+                                        noeffect=-1,
+                                        steps=maxdt,
+                                        draw=None,
+                                        save='all',
+                                        path=path_c,
+                                        )
+                    
+                    with open(path_c+f"eps={round(eps,3):.3f}_activation.txt", 'r', encoding='utf-8') as f:
+                        activation = json.load(f)
+                
+                    osc = list(zip(*activation))
+                    phase_abs = np.array([[np.arctan2(*act[::-1]) for act in osc[i]] for i in range(2)])
+                    phasediff = diff(phase_abs[0],phase_abs[1])
+                    
+                    with open(path_c+f"eps={round(eps,3):.3f}_phase_diff.txt", 'w', encoding='utf-8') as f:
+                        json.dump(list(phasediff), f, indent=1)
+        
+            
+        
+        
+        
+        # bot_res = []
+        top_res = []
+        dis_res = []
+        tot_res = []
+        
+        # bot_ph = []
+        top_ph = []
+        dis_ph = []
+        tot_ph = []
+        
+        # bot_ei = []
+        top_ei = []
+        # dev_ei = []
+        tot_ei = []
+        for dt in range(maxdt):
+            # bot_pha = [[abs(phase_diff[i+dt]) for i in bot_00],
+            #            [abs(phase_diff[i+dt]) for i in bot_01],
+            #            [abs(phase_diff[i+dt]) for i in bot_10],
+            #            [abs(phase_diff[i+dt]) for i in bot_11]]
+            
+            top_pha = [[abs(phase_diff[i+dt]) for i in top_00],
+                       [abs(phase_diff[i+dt]) for i in top_01],
+                       [abs(phase_diff[i+dt]) for i in top_10],
+                       [abs(phase_diff[i+dt]) for i in top_11]]
+            
+            dis_00 = []
+            dis_01 = []
+            dis_10 = []
+            dis_11 = []
+            for i in top_00:
+                path_c = path+f'causal_maxdt={maxdt}/top_00/{i:0{len(str(stp))}}/'
+                with open(path_c+f'eps={round(eps,3):.3f}_phase_diff.txt', 'r', encoding='utf-8') as f:
+                    dis_00.append(abs(json.load(f)[dt]))
+            for i in top_01:
+                path_c = path+f'causal_maxdt={maxdt}/top_01/{i:0{len(str(stp))}}/'
+                with open(path_c+f'eps={round(eps,3):.3f}_phase_diff.txt', 'r', encoding='utf-8') as f:
+                    dis_01.append(abs(json.load(f)[dt]))
+            for i in top_10:
+                path_c = path+f'causal_maxdt={maxdt}/top_10/{i:0{len(str(stp))}}/'
+                with open(path_c+f'eps={round(eps,3):.3f}_phase_diff.txt', 'r', encoding='utf-8') as f:
+                    dis_10.append(abs(json.load(f)[dt]))
+            for i in top_11:
+                path_c = path+f'causal_maxdt={maxdt}/top_11/{i:0{len(str(stp))}}/'
+                with open(path_c+f'eps={round(eps,3):.3f}_phase_diff.txt', 'r', encoding='utf-8') as f:
+                    dis_11.append(abs(json.load(f)[dt]))
+            
+            dis_pha = [dis_00, dis_01, dis_10, dis_11]
+            
+            tot_pha = np.abs(phase_diff[dt:dt-maxdt])
+            
+            # bot_res.append( [norm(resultant(bot_pha[i])) for i in range(4)] )
+            top_res.append( [norm(resultant(top_pha[i])) for i in range(4)] )
+            dis_res.append( [norm(resultant(dis_pha[i])) for i in range(4)] )
+            tot_res.append( norm(resultant(tot_pha)) )
+            
+            # bot_ph.append( [phase(*resultant(bot_pha[i])) for i in range(4)] )
+            top_ph.append( [phase(*resultant(top_pha[i])) for i in range(4)] )
+            dis_ph.append( [phase(*resultant(dis_pha[i])) for i in range(4)] )
+            tot_ph.append( phase(*resultant(tot_pha)) )
+            
+            # bot_ei.append( [np.average([ei[i+dt] for i in bot]) for bot in [bot_00,bot_01,bot_10,bot_11]] )
+            top_ei.append( [np.average([ei[i+dt] for i in top]) for top in [top_00,top_01,top_10,top_11]] )
+            # dev_ei.append( [np.average([ei[i+dt] for i in dev]) for dev in [dev_00,dev_01,dev_10,dev_11]] )
+            tot_ei.append( np.average(ei[dt:dt-maxdt]) )
+            
+            if dt%10==0:
+                print(f'Done dt={dt}')
+        
+        # bot_res = list(zip(*bot_res))
+        top_res = list(zip(*top_res))
+        dis_res = list(zip(*dis_res))
+        
+        # bot_ph = list(zip(*bot_ph))
+        top_ph = list(zip(*top_ph))
+        dis_ph = list(zip(*dis_ph))
+
+        # bot_ei = list(zip(*bot_ei))
+        top_ei = list(zip(*top_ei))
+        # dev_ei = list(zip(*dev_ei))
+        
+        plotpath = path+'4waycausal/'
+
+        qtplot(f'Diachronic resultant sync to sync for dim={dim} with 4 layers',
+                [np.array(range(maxdt))]*3,
+                [top_res[0], dis_res[0], tot_res],
+                
+                ['sync to sync top {extremes} ei',
+                 'sync to sync dis {extremes} ei', 'Average Resultant'],
+                x_tag = 'dt',
+                y_tag = 'concentration',
+                export=True,
+                path=plotpath,
+                filename=f'Diachronic Resultant Norm eps={round(eps,3):.3f} sts dim={dim} extremes={extremes} roll{pha_dev:.3f}.png',
+                close=True)
+        qtplot(f'Diachronic resultant sync to orth for dim={dim} with 4 layers',
+                [np.array(range(maxdt))]*3,
+                [top_res[1], dis_res[1], tot_res],
+                ['sync to orth top {extremes} ei', 'sync to orth dis {extremes} ei',
+                 'Average Resultant'],
+                x_tag = 'dt',
+                y_tag = 'concentration',
+                export=True,
+                path=plotpath,
+                filename=f'Diachronic Resultant Norm eps={round(eps,3):.3f} sto dim={dim} extremes={extremes} roll{pha_dev:.3f}.png',
+                close=True)
+        qtplot(f'Diachronic resultant orth to sync for dim={dim} with 4 layers',
+                [np.array(range(maxdt))]*3,
+                [top_res[2], dis_res[2], tot_res],
+                ['orth to sync top {extremes} ei', 'orth to sync dis {extremes} ei',
+                 'Average Resultant'],
+                x_tag = 'dt',
+                y_tag = 'concentration',
+                export=True,
+                path=plotpath,
+                filename=f'Diachronic Resultant Norm eps={round(eps,3):.3f} ots dim={dim} extremes={extremes} roll{pha_dev:.3f}.png',
+                close=True)
+        qtplot(f'Diachronic resultant orth to orth for dim={dim} with 4 layers',
+                [np.array(range(maxdt))]*3,
+                [top_res[3], dis_res[3], tot_res],
+                ['orth to orth top {extremes} ei', 'orth to orth dis {extremes} ei',
+                 'Average Resultant'],
+                x_tag = 'dt',
+                y_tag = 'concentration',
+                export=True,
+                path=plotpath,
+                filename=f'Diachronic Resultant Norm eps={round(eps,3):.3f} oto dim={dim} extremes={extremes} roll{pha_dev:.3f}.png',
+                close=True)
+        
+        qtplot(f'Diachronic resultant phase sync to sync for dim={dim} with 4 layers',
+                [np.array(range(maxdt))]*3,
+                [top_ph[0], dis_ph[0], tot_ph],
+                ['sync to sync top {extremes} ei', 'sync to sync dis {extremes} ei',
+                 'Average'],
+                x_tag = 'dt',
+                y_tag = 'phase',
+                export=True,
+                path=plotpath,
+                filename=f'Diachronic Resultant Phase eps={round(eps,3):.3f} sts dim={dim} extremes={extremes} roll{pha_dev:.3f}.png',
+                close=True)
+        qtplot(f'Diachronic resultant phase sync to orth for dim={dim} with 4 layers',
+                [np.array(range(maxdt))]*3,
+                [top_ph[1], dis_ph[1], tot_ph],
+                ['sync to orth top {extremes} ei', 'sync to orth dis {extremes} ei',
+                 'Average'],
+                x_tag = 'dt',
+                y_tag = 'phase',
+                export=True,
+                path=plotpath,
+                filename=f'Diachronic Resultant Phase eps={round(eps,3):.3f} sto dim={dim} extremes={extremes} roll{pha_dev:.3f}.png',
+                close=True)
+        qtplot(f'Diachronic resultant phase orth to sync for dim={dim} with 4 layers',
+                [np.array(range(maxdt))]*3,
+                [top_ph[2], dis_ph[2], tot_ph],
+                ['orth to sync top {extremes} ei', 'orth to sync dos {extremes} ei',
+                 'Average'],
+                x_tag = 'dt',
+                y_tag = 'phase',
+                export=True,
+                path=plotpath,
+                filename=f'Diachronic Resultant Phase eps={round(eps,3):.3f} ots dim={dim} extremes={extremes} roll{pha_dev:.3f}.png',
+                close=True)
+        qtplot(f'Diachronic resultant phase orth to orth for dim={dim} with 4 layers',
+                [np.array(range(maxdt))]*3,
+                [top_ph[3], dis_ph[3], tot_ph],
+                ['orth to orth top {extremes} ei', 'orth to orth dis {extremes} ei',
+                 'Average'],
+                x_tag = 'dt',
+                y_tag = 'phase',
+                export=True,
+                path=plotpath,
+                filename=f'Diachronic Resultant Phase eps={round(eps,3):.3f} oto dim={dim} extremes={extremes} roll{pha_dev:.3f}.png',
+                close=True)
+        
+        # qtplot(f'Diachronic ei for dim={dim} with 4 layers',
+        #         [np.array(range(maxdt))]*4,
+        #         [bot_ei, top_ei, dev_ei, tot_ei],
+        #         ['EI ev of bottom {extremes} ei', 'EI ev of top {extremes} ei',
+        #          'EI ev of phase filtered ei', 'Average EI'],
+        #         x_tag = 'dt',
+        #         y_tag = 'average ei',
+        #         export=True,
+        #         path=path+'plots/',
+        #         filename=f'Diachronic EI balanced for eps={round(eps,3):.3f} dim={dim} extremes={extremes} roll{pha_dev:.3f}.png',
+        #         close=True)
+        
+        print(f'Done eps={eps:.3f} with dim={dim} at {datetime.now()}')
+        
+    # qtplot(f'Resultant and EI evolution for dim={dim} with 4 layers',
+    #         [[0]+eps_space]*2,
+    #         [max(av_ei)*diff_res, av_ei],
+    #         ['Resultant', 'avEI'],
+    #         export=True,
+    #         path=path,
+    #         filename=f'Resultant and EI for dim={dim}.png',
+    #         close=True)
+        
+        

evaluation/4Layer Causal Significance.py

@@ -0,0 +1,191 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Sat Sep  9 22:23:30 2023
+
+@author: astral
+"""
+
+import os
+import json
+import math as m
+import numpy as np
+from numpy.linalg import norm
+from datetime import datetime
+from random import sample as choose
+
+from plot import qtplot
+
+from neuropercolation import Simulate4Layers
+
+eps_space = list(np.linspace(0.01,0.2,20))
+
+def resultant(sample):
+    phase_x = [m.cos(ind) for ind in sample]
+    phase_y = [m.sin(ind) for ind in sample]
+    
+    return (np.average(phase_x), np.average(phase_y))
+
+def new_folder(path):
+    if not os.path.exists(path):
+        os.makedirs(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)
+
+extremes = None
+maxdt = 200
+
+stp = 1000100
+batch = 0
+
+print(f'Started at {datetime.now()}')
+
+for dim in [9]:
+    for eps in eps_space[4:]:
+        eps = round(eps,3)
+        path='/cloud/Public/_data/neuropercolation/4lay/cons=27-knight_steps=1000100/dim=09/batch=0/'
+        
+        try:
+            with open(path+f"eps={round(eps,3):.3f}_phase_diff.txt", 'r', encoding='utf-8') as f:
+                phase_diff = json.load(f)
+        except:
+            with open(path+f"eps={round(eps,3):.3f}_activation.txt", 'r', encoding='utf-8') as f:
+                activation = json.load(f)[100:]
+        
+            osc = list(zip(*activation))
+            phase_abs = np.array([[np.arctan2(*act[::-1]) for act in osc[i]] for i in range(2)])
+            phase_diff = diff(phase_abs[0],phase_abs[1])
+            phase_diff = [round(pha,6) for pha in phase_diff]
+            
+            with open(path+f"eps={round(eps,3):.3f}_phase_diff.txt", 'w', encoding='utf-8') as f:
+                json.dump(list(phase_diff), f, indent=1)
+    
+        
+        all_res = norm(resultant(phase_diff))
+        av_diff = np.arccos(all_res)
+        
+        try:
+            with open(path+f"eps={round(eps,3):.3f}_ei.txt", 'r', encoding='utf-8') as f:
+                ei = json.load(f)
+        except:
+            with open(path+f"eps={round(eps,3):.3f}_channels.txt", 'r', encoding='utf-8') as f:
+                channels = json.load(f)[100:]
+            
+            ei = [round(np.sum(cha)*(1-H2(eps)),6) for cha in channels]
+            
+            with open(path+f"eps={round(eps,3):.3f}_ei.txt", 'w', encoding='utf-8') as f:
+                json.dump(ei, f, indent=1)
+        
+        extremes = 10000 #[l//2 for l in lens]
+        
+        ei_ind = [i for i,val in enumerate(ei[:-maxdt]) if val>0]
+        
+        print(f'{len(ei_ind)} states with positive EI')
+        
+        samples = choose(ei_ind, extremes)
+        sampling = 'allpos_ei'
+        
+        with open(path+f"eps={round(eps,3):.3f}_states.txt", 'r', encoding='utf-8') as f:
+            states = json.load(f)[100:]
+        with open(path+f"eps={round(eps,3):.3f}_coupling.txt", 'r', encoding='utf-8') as f:
+            coupling = json.load(f)
+            coupling = [tuple(edge) for edge in coupling]
+        
+        phase_pairs = []
+        ei_pairs = []
+        for num,i in enumerate(samples):
+            causal_init = states[i].translate(str.maketrans('', '', '.-='))
+            
+            sim = Simulate4Layers(  dim,
+                                    eps,
+                                    coupling=coupling,
+                                    init=causal_init,
+                                    noeffect=0,
+                                    steps=1,
+                                    draw=None,
+                                    )
+                
+            activation = sim._activations()
+            channel = sim._channels()
+        
+            osc = list(zip(*activation))
+            phase_abs = np.array([[np.arctan2(*act[::-1]) for act in osc[i]] for i in range(2)])
+            phasediff_c = np.round(diff(phase_abs[0],phase_abs[1]),6)
+            ei_c = [round(np.sum(cha)*(1-H2(eps)),6) for cha in channel]
+            max_ei_c = max([np.sum(cha) for cha in channel])
+
+            sim = Simulate4Layers(  dim,
+                                    eps,
+                                    coupling=coupling,
+                                    init=causal_init,
+                                    noeffect=-1,
+                                    steps=1,
+                                    draw=None,
+                                    )
+                
+            activation = sim._activations()
+            channel = sim._channels()
+            
+            osc = list(zip(*activation))
+            phase_abs = np.array([[np.arctan2(*act[::-1]) for act in osc[i]] for i in range(2)])
+            phasediff_i = np.round(diff(phase_abs[0],phase_abs[1]),6)
+            ei_i = [round(np.sum(cha)*(1-H2(eps)),6) for cha in channel]
+            max_ei_i = max([np.sum(cha) for cha in channel])
+
+            phase_pairs.append((phasediff_i[-1], phasediff_c[-1]))
+            ei_pairs.append((ei_i[-1], ei_c[-1]))
+            
+            savepath = path + sampling + '/'
+            new_folder(savepath)
+            
+            if num%100==99:
+                print(f'Done {num:0{len(str(extremes))}d}')
+        
+        with open(savepath+f"eps={round(eps,3):.3f}_phase_pairs.txt", 'w', encoding='utf-8') as f:
+            json.dump(phase_pairs, f, indent=1)
+        with open(savepath+f"eps={round(eps,3):.3f}_ei_pairs.txt", 'w', encoding='utf-8') as f:
+            json.dump(ei_pairs, f, indent=1)
+            
+        phases_i, phases_c = zip(*phase_pairs)
+        ei_i, ei_c = zip(*ei_pairs)
+        
+        phase_space = np.linspace(0,m.pi,100+1)
+        ei_space = np.linspace(0,np.max([ei_i,ei_c]),100+1)
+        
+        phase_dist_i = [len([ph for ph in phases_i if low<=ph<high])/extremes for low,high in zip(phase_space[:-1],phase_space[1:])]
+        phase_dist_c = [len([ph for ph in phases_c if low<=ph<high])/extremes for low,high in zip(phase_space[:-1],phase_space[1:])]
+        
+        max_ei = max(max_ei_i, max_ei_c)
+        
+        ei_dist_i = [len([e for e in ei_i if round(e/(1-H2(eps)))==val])/extremes for val in range(max_ei)]
+        ei_dist_c = [len([e for e in ei_c if round(e/(1-H2(eps)))==val])/extremes for val in range(max_ei)]
+
+        qtplot(f'Phase distribution for dim={dim} eps={eps:.3f} with 4 layers',
+                [phase_space[:-1]]*2,
+                [phase_dist_i, phase_dist_c],
+                ['Phase dist with ei',
+                 'Phase dist without ei'],
+                x_tag = 'phase',
+                y_tag = 'density',
+                export=True,
+                path=savepath,
+                filename=f'Phase dist eps={round(eps,3):.3f} dim={dim} extremes={extremes}.png',
+                close=True)
+        
+        qtplot(f'EI distribution for dim={dim} eps={eps:.3f} with 4 layers',
+                [range(max_ei)]*2,
+                [ei_dist_i, ei_dist_c],
+                ['EI dist with ei',
+                 'EI dist without ei'],
+                x_tag = 'ei',
+                y_tag = 'density',
+                export=True,
+                path=savepath,
+                filename=f'EI dist eps={round(eps,3):.3f} dim={dim} extremes={extremes}.png',
+                close=True)
+      
+        print(f'Done eps={eps:.3f} with dim={dim} at {datetime.now()}')
+        
+    

evaluation/4Layer Causal resultant.py

@@ -0,0 +1,405 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Mon Aug 21 14:59:22 2023
+
+@author: astral
+"""
+
+import os
+import json
+import math as m
+import numpy as np
+from numpy.linalg import norm
+from datetime import datetime
+#from random import sample as choose
+
+from plot import qtplot
+
+from neuropercolation import Simulate4Layers
+
+eps_space = list(np.linspace(0.01,0.2,20))
+
+def resultant(sample):
+    phase_x = [m.cos(ind) for ind in sample]
+    phase_y = [m.sin(ind) for ind in sample]
+    
+    return (np.average(phase_x), np.average(phase_y))
+
+def new_folder(path):
+    if not os.path.exists(path):
+        os.makedirs(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)
+
+extremes = None
+maxdt = 200
+
+stp = 1000100
+batch = 0
+
+print(f'Started at {datetime.now()}')
+
+for dim in [9]:
+    for eps in eps_space[14:]:
+        eps = round(eps,3)
+        path='/cloud/Public/_data/neuropercolation/4lay/cons=27-knight_steps=1000100/dim=09/batch=0/'
+        
+        try:
+            with open(path+f"eps={round(eps,3):.3f}_phase_diff.txt", 'r', encoding='utf-8') as f:
+                phase_diff = json.load(f)
+        except:
+            with open(path+f"eps={round(eps,3):.3f}_activation.txt", 'r', encoding='utf-8') as f:
+                activation = json.load(f)[100:]
+        
+            osc = list(zip(*activation))
+            phase_abs = np.array([[np.arctan2(*act[::-1]) for act in osc[i]] for i in range(2)])
+            phase_diff = diff(phase_abs[0],phase_abs[1])
+            phase_diff = [round(pha,6) for pha in phase_diff]
+            
+            with open(path+f"eps={round(eps,3):.3f}_phase_diff.txt", 'w', encoding='utf-8') as f:
+                json.dump(list(phase_diff), f, indent=1)
+    
+        
+        all_res = norm(resultant(phase_diff))
+        av_diff = np.arccos(all_res)
+        
+        try:
+            with open(path+f"eps={round(eps,3):.3f}_ei.txt", 'r', encoding='utf-8') as f:
+                ei = json.load(f)
+        except:
+            with open(path+f"eps={round(eps,3):.3f}_channels.txt", 'r', encoding='utf-8') as f:
+                channels = json.load(f)[100:]
+            
+            ei = [round(np.sum(cha)*(1-H2(eps)),6) for cha in channels]
+            
+            with open(path+f"eps={round(eps,3):.3f}_ei.txt", 'w', encoding='utf-8') as f:
+                json.dump(ei, f, indent=1)
+        
+        extremes = 10000 #[l//2 for l in lens]
+        ext_rat = extremes/(stp-100)
+        
+        circparts = 32
+        pha_dev = m.pi/circparts
+        pha_max = np.max(np.abs(phase_diff))
+        
+        phase_in_part = lambda ph, i: abs(ph)<=pha_max/circparts if i==0 else i*pha_max/circparts<abs(ph)<=(i+1)*pha_max/circparts
+        
+        dev_parts = [sorted([i for i,val in enumerate(ei[:-maxdt]) if phase_in_part(phase_diff[i],j)],
+                            key = lambda i: ei[i]) for j in range(circparts)]
+        
+        ext_parts = [int(np.ceil(len(dev_parts[i])*ext_rat)) for i in range(circparts)]
+        
+        top_parts = [dev_parts[i][-ext_parts[i]:] if ext_parts[i]>0 else [] for i in range(circparts)]
+        bot_parts = [dev_parts[i][:ext_parts[i]] if ext_parts[i]>0 else [] for i in range(circparts)]
+
+        top = []
+        for part in top_parts:
+            top.extend(part)
+        bot = []
+        for part in bot_parts:
+            bot.extend(part)
+        
+        print(len(top), len(bot), extremes, 'equal?')
+        sampling = 'samedist_varmaxpha'
+    
+        # pha_center = av_diff
+        # pha_dev = m.pi/8
+        
+        # from_sync = lambda i: True if abs(phase_diff[i])<0.08*m.pi else False if 0.42*m.pi<abs(phase_diff[i])<0.58*m.pi else from_sync(i-1) if i>0 else None
+        # to_sync = lambda i: True if abs(phase_diff[i])<0.08*m.pi else False if 0.42*m.pi<abs(phase_diff[i])<0.58*m.pi else to_sync(i+1) if i+1<len(phase_diff) else None
+        
+        # infra_phase = lambda ph: (pha_center-pha_dev)<=abs(ph)<=(pha_center        )
+        # supra_phase = lambda ph: (pha_center        )< abs(ph)<=(pha_center+pha_dev)
+
+        # dev_inf = sorted([i for i,val in enumerate(ei[:-maxdt]) if infra_phase(phase_diff[i])], key = lambda i: ei[i])
+        # dev_sup = sorted([i for i,val in enumerate(ei[:-maxdt]) if supra_phase(phase_diff[i])], key = lambda i: ei[i])
+        
+        # ext_inf = round(extremes*len(dev_inf)/(len(dev_inf)+len(dev_sup)))
+        # ext_sup = round(extremes*len(dev_sup)/(len(dev_inf)+len(dev_sup)))
+
+        # top_inf = dev_inf[-ext_inf:]
+        # top_sup = dev_sup[-ext_sup:]
+        
+        # top = top_inf + top_sup
+        
+        # print(len(top), extremes, 'equal?')
+        # sampling = 'biequal'
+        
+        with open(path+f"eps={round(eps,3):.3f}_states.txt", 'r', encoding='utf-8') as f:
+            states = json.load(f)[100:]
+        with open(path+f"eps={round(eps,3):.3f}_coupling.txt", 'r', encoding='utf-8') as f:
+            coupling = json.load(f)
+            coupling = [tuple(edge) for edge in coupling]
+        
+        for i in top:
+            causal_maxdt=0
+            for file in os.listdir(path):
+                f = os.path.join(path, file)
+                if not os.path.isfile(f):
+                    c_maxdt = file.replace('causal_maxdt=','')
+                    if c_maxdt != file:
+                        causal_maxdt = int(c_maxdt)
+            
+            if causal_maxdt>=maxdt:
+                path_c = path+f'causal_maxdt={causal_maxdt}/eps={round(eps,3):.3f}/{i:0{len(str(stp))}}/'
+            else:
+                path_c = path+f'causal_maxdt={maxdt}/eps={round(eps,3):.3f}/{i:0{len(str(stp))}}/'
+            
+            causal_init = states[i].translate(str.maketrans('', '', '.-='))
+            
+            try:
+                with open(path_c+f"eps={round(eps,3):.3f}_phase_diff.txt", 'r', encoding='utf-8') as f:
+                    phasediff = json.load(f)
+            except:
+                sim=Simulate4Layers(dim,
+                                    eps,
+                                    coupling=coupling,
+                                    init=causal_init,
+                                    noeffect=0,
+                                    steps=maxdt,
+                                    draw=None,
+                                    save='simple',
+                                    path=path_c,
+                                    )
+                
+                with open(path_c+f"eps={round(eps,3):.3f}_activation.txt", 'r', encoding='utf-8') as f:
+                    activation = json.load(f)
+            
+                osc = list(zip(*activation))
+                phase_abs = np.array([[np.arctan2(*act[::-1]) for act in osc[i]] for i in range(2)])
+                phasediff = diff(phase_abs[0],phase_abs[1])
+                
+                with open(path_c+f"eps={round(eps,3):.3f}_phase_diff.txt", 'w', encoding='utf-8') as f:
+                    json.dump(list(phasediff), f, indent=1)
+        
+        for i in []:#top:
+            original_maxdt=0
+            for file in os.listdir(path):
+                f = os.path.join(path, file)
+                if not os.path.isfile(f):
+                    o_maxdt = file.replace('original_maxdt=','')
+                    if c_maxdt != file:
+                        original_maxdt = int(o_maxdt)
+            
+            if original_maxdt>=maxdt:
+                path_c = path+f'original_maxdt={original_maxdt}/eps={round(eps,3):.3f}/{i:0{len(str(stp))}}/'
+            else:
+                path_c = path+f'original_maxdt={maxdt}/eps={round(eps,3):.3f}/{i:0{len(str(stp))}}/'
+            
+            causal_init = states[i].translate(str.maketrans('', '', '.-='))
+            
+            try:
+                with open(path_c+f"eps={round(eps,3):.3f}_phase_diff.txt", 'r', encoding='utf-8') as f:
+                    phasediff = json.load(f)
+            except:
+                sim=Simulate4Layers(dim,
+                                    eps,
+                                    coupling=coupling,
+                                    init=causal_init,
+                                    noeffect=-1,
+                                    steps=maxdt,
+                                    draw=None,
+                                    save='simple',
+                                    path=path_c,
+                                    )
+                
+                with open(path_c+f"eps={round(eps,3):.3f}_activation.txt", 'r', encoding='utf-8') as f:
+                    activation = json.load(f)
+            
+                osc = list(zip(*activation))
+                phase_abs = np.array([[np.arctan2(*act[::-1]) for act in osc[i]] for i in range(2)])
+                phasediff = diff(phase_abs[0],phase_abs[1])
+                phasediff = [round(pha,6) for pha in phasediff]
+                
+                with open(path_c+f"eps={round(eps,3):.3f}_phase_diff.txt", 'w', encoding='utf-8') as f:
+                    json.dump(list(phasediff), f, indent=1)
+        
+        
+        
+        bot_res = []
+        top_res = []
+        dis_res = []
+        tot_res = []
+        
+        bot_ph = []
+        top_ph = []
+        dis_ph = []
+        tot_ph = []
+        
+        bot_ei = []
+        top_ei = []
+        dis_ei = []
+        tot_ei = []
+        
+        
+        present_dt=0
+        for file in os.listdir(path):
+            f = os.path.join(path, file)
+            if not os.path.isfile(f):
+                p_maxdt = file.replace(f'{sampling}_causal_roll{pha_dev:.3f}_maxdt=','')
+                if p_maxdt != file:
+                    present_dt = int(p_maxdt)
+        
+        if present_dt>0:
+            try:
+                datapath = path + f"{sampling}_causal_roll{pha_dev:.3f}_maxdt={present_dt}/data/"
+                with open(datapath+f"eps={round(eps,3):.3f}_bot_dia_res.txt", 'r', encoding='utf-8') as f:
+                    bot_res = json.load(f)
+                with open(datapath+f"eps={round(eps,3):.3f}_top_dia_res.txt", 'r', encoding='utf-8') as f:
+                    top_res = json.load(f)
+                with open(datapath+f"eps={round(eps,3):.3f}_dis_dia_res.txt", 'r', encoding='utf-8') as f:
+                    dis_res = json.load(f)
+                with open(datapath+f"eps={round(eps,3):.3f}_bot_dia_ei.txt", 'r', encoding='utf-8') as f:
+                    bot_ei = json.load(f)
+                with open(datapath+f"eps={round(eps,3):.3f}_top_dia_ei.txt", 'r', encoding='utf-8') as f:
+                    top_ei = json.load(f)
+                with open(datapath+f"eps={round(eps,3):.3f}_dis_dia_ei.txt", 'r', encoding='utf-8') as f:
+                    dis_ei = json.load(f)
+            except:
+                present_dt=0
+                bot_res = []
+                top_res = []
+                dis_res = []
+        
+        for dt in range(present_dt,maxdt):
+            top_pha = [(phase_diff[i+dt]) for i in top]
+            bot_pha = [(phase_diff[i+dt]) for i in bot]
+            
+            dis = []
+            for i in top:
+                causal_maxdt=0
+                for file in os.listdir(path):
+                    f = os.path.join(path, file)
+                    if not os.path.isfile(f):
+                        c_maxdt = file.replace('causal_maxdt=','')
+                        if c_maxdt != file:
+                            causal_maxdt = int(c_maxdt)
+                
+                if causal_maxdt>=maxdt:
+                    path_c = path+f'causal_maxdt={causal_maxdt}/eps={round(eps,3):.3f}/{i:0{len(str(stp))}}/'
+                else:
+                    path_c = path+f'causal_maxdt={maxdt}/eps={round(eps,3):.3f}/{i:0{len(str(stp))}}/'
+                
+                with open(path_c+f'eps={round(eps,3):.3f}_phase_diff.txt', 'r', encoding='utf-8') as f:
+                    dis.append((json.load(f)[dt]))
+            
+            dei = []
+            for i in top:
+                causal_maxdt=0
+                for file in os.listdir(path):
+                    f = os.path.join(path, file)
+                    if not os.path.isfile(f):
+                        c_maxdt = file.replace('causal_maxdt=','')
+                        if c_maxdt != file:
+                            causal_maxdt = int(c_maxdt)
+                
+                if causal_maxdt>=maxdt:
+                    path_c = path+f'causal_maxdt={causal_maxdt}/eps={round(eps,3):.3f}/{i:0{len(str(stp))}}/'
+                else:
+                    path_c = path+f'causal_maxdt={maxdt}/eps={round(eps,3):.3f}/{i:0{len(str(stp))}}/'
+                
+                with open(path_c+f'eps={round(eps,3):.3f}_channels.txt', 'r', encoding='utf-8') as f:
+                    dei.append(np.sum(json.load(f)[dt])*(1-H2(eps)))
+            
+            dis_pha = dis
+            tot_pha = (phase_diff[dt:dt-maxdt])
+            
+            bot_res.append( [norm(resultant(bot_pha))] )
+            top_res.append( [norm(resultant(top_pha))] )
+            dis_res.append( [norm(resultant(dis_pha))] )
+            tot_res.append( norm(resultant(tot_pha)) )
+            
+            # bot_ph.append( [phase(*resultant(bot_pha[i])) for i in range(1)] )
+            # top_ph.append( [phase(*resultant(top_pha[i])) for i in range(1)] )
+            # dis_ph.append( [phase(*resultant(dis_pha[i])) for i in range(1)] )
+            # tot_ph.append( phase(*resultant(tot_pha)) )
+            
+            bot_ei.append( [np.average([ei[i+dt] for i in bot])] )
+            top_ei.append( [np.average([ei[i+dt] for i in top])] )
+            dis_ei.append( [np.average(dei)] )
+            tot_ei.append( np.average(ei[dt:dt-maxdt]) )
+            
+            if dt%10==9:
+                print(f'Done dt={dt:{len(str(maxdt))}d}')
+        
+        plotpath = path+f'{sampling}_causal_roll{pha_dev:.3f}_maxdt={maxdt}/'
+        new_folder(plotpath+'data/')
+        
+        with open(plotpath+f"data/eps={round(eps,3):.3f}_bot_dia_res.txt", 'w', encoding='utf-8') as f:
+            json.dump(list(bot_res), f, indent=1)
+        with open(plotpath+f"data/eps={round(eps,3):.3f}_top_dia_res.txt", 'w', encoding='utf-8') as f:
+            json.dump(list(top_res), f, indent=1)
+        with open(plotpath+f"data/eps={round(eps,3):.3f}_dis_dia_res.txt", 'w', encoding='utf-8') as f:
+            json.dump(list(dis_res), f, indent=1)
+        with open(plotpath+f"data/eps={round(eps,3):.3f}_bot_dia_ei.txt", 'w', encoding='utf-8') as f:
+            json.dump(list(bot_ei), f, indent=1)
+        with open(plotpath+f"data/eps={round(eps,3):.3f}_top_dia_ei.txt", 'w', encoding='utf-8') as f:
+            json.dump(list(top_ei), f, indent=1)
+        with open(plotpath+f"data/eps={round(eps,3):.3f}_dis_dia_ei.txt", 'w', encoding='utf-8') as f:
+            json.dump(list(dis_ei), f, indent=1)
+        
+        bot_res = list(zip(*bot_res))
+        top_res = list(zip(*top_res))
+        dis_res = list(zip(*dis_res))
+        
+        # bot_ph = list(zip(*bot_ph))
+        # top_ph = list(zip(*top_ph))
+        # dis_ph = list(zip(*dis_ph))
+
+        bot_ei = list(zip(*bot_ei))
+        top_ei = list(zip(*top_ei))
+        dis_ei = list(zip(*dis_ei))
+        
+        
+
+        qtplot(f'Diachronic resultant for dim={dim} eps={eps:.3f} with 4 layers',
+                [np.array(range(maxdt))]*4,
+                [tot_res, bot_res[0], dis_res[0], top_res[0]],
+                ['Average Resultant', f'bottom {extremes} ei'
+                 f'dis {extremes} ei', f'top {extremes} ei'],
+                x_tag = 'dt',
+                y_tag = 'concentration',
+                export=True,
+                path=plotpath,
+                filename=f'All Diachronic Resultant Norm eps={round(eps,3):.3f} dim={dim} extremes={extremes}.png',
+                close=True)
+        
+        # qtplot(f'Diachronic resultant phase for dim={dim} eps={eps:.3f} with 4 layers',
+        #         [np.array(range(maxdt))]*3,
+        #         [top_ph[0], dis_ph[0], tot_ph],
+        #         ['top {extremes} ei', 'dis {extremes} ei',
+        #          'Average'],
+        #         x_tag = 'dt',
+        #         y_tag = 'phase',
+        #         export=True,
+        #         path=plotpath,
+        #         filename=f'All Diachronic Resultant Phase eps={round(eps,3):.3f} dim={dim} extremes={extremes} roll{pha_dev:.3f}.png',
+        #         close=True)
+        
+        # qtplot(f'Diachronic ei for dim={dim} with 4 layers',
+        #         [np.array(range(maxdt))]*4,
+        #         [bot_ei, top_ei, dev_ei, tot_ei],
+        #         ['EI ev of bottom {extremes} ei', 'EI ev of top {extremes} ei',
+        #          'EI ev of phase filtered ei', 'Average EI'],
+        #         x_tag = 'dt',
+        #         y_tag = 'average ei',
+        #         export=True,
+        #         path=path+'plots/',
+        #         filename=f'Diachronic EI balanced for eps={round(eps,3):.3f} dim={dim} extremes={extremes} roll{pha_dev:.3f}.png',
+        #         close=True)
+        
+        print(f'Done eps={eps:.3f} with dim={dim} at {datetime.now()}')
+        
+    # qtplot(f'Resultant and EI evolution for dim={dim} with 4 layers',
+    #         [[0]+eps_space]*2,
+    #         [max(av_ei)*diff_res, av_ei],
+    #         ['Resultant', 'avEI'],
+    #         export=True,
+    #         path=path,
+    #         filename=f'Resultant and EI for dim={dim}.png',
+    #         close=True)
+        
+        

evaluation/4Layer Res+EI.py

@@ -14,6 +14,7 @@ from datetime import datetime
 from plot import qtplot
 
 eps_space = list(np.linspace(0.005,0.5,100))
+eps_space= eps_space[1::2]
 
 def resultant(sample):
     phase_x = [m.cos(ind) for ind in sample]
@@ -24,37 +25,68 @@ def resultant(sample):
 def H2(x):
     return -x*m.log2(x)-(1-x)*m.log2(1-x)
 
-for dim in [7]:
+dims=list(range(3,10))
-    diff_res = [0]
+
+R=[]
+EI=[]
+for dim in dims:
+    cons = [(n,(2*n+m)%dim) for n in range(dim) for m in range(0,dim-2,3)]
+    path=f'/cloud/Public/_data/neuropercolation/4lay/cons=dimtimesdimby3_steps=100100/dim={dim:02d}_cons={len(cons)}/batch=0/'
+    
+    diff_res = [1]
     av_ei = [0]
     for eps in eps_space:
-        path=f'/cloud/Public/_data/neuropercolation/4lay/steps=100000/dim={dim:02}/'
+        try:
+            with open(path+f"eps={round(eps,3):.3f}_phase_diff.txt", 'r', encoding='utf-8') as f:
+                phase_diff = json.load(f)[100:]
+            with open(path+f"eps={round(eps,3):.3f}_ei.txt", 'r', encoding='utf-8') as f:
+                ei = json.load(f)[100:]
+        except:
+            with open(path+f"eps={round(eps,3):.3f}_activation.txt", 'r', encoding='utf-8') as f:
+                activation = json.load(f)[100:]
+            with open(path+f"eps={round(eps,3):.3f}_channels.txt", 'r', encoding='utf-8') as f:
+                channels = json.load(f)[100:]
         
-        with open(path+f"eps={round(eps,3):.3f}_activation.txt", 'r', encoding='utf-8') as f:
+            osc = list(zip(*activation))
-            activation = json.load(f)[100:]
+            phase = np.array([[np.arctan2(*act[::-1]) for act in osc[i]] for i in range(2)])
-        
+            phase_diff = (phase[1]-phase[0]+m.pi)%(2*m.pi)-m.pi
-        osc = list(zip(*activation))
+            ei = [np.sum(cha)*(1-H2(eps)) for cha in channels]
-        phase = np.array([[np.arctan2(*act[::-1]) for act in osc[i]] for i in range(2)])
-        phase_diff = (phase[1]-phase[0]+m.pi)%(2*m.pi)-m.pi
         
         res = np.linalg.norm(resultant(phase_diff))
         diff_res.append(res)
         
-        with open(path+f"eps={round(eps,3):.3f}_channels.txt", 'r', encoding='utf-8') as f:
-            channels = json.load(f)[100:]
-        
-        ei = [np.sum(cha)*(1-H2(eps)) for cha in channels]
         av_ei.append(np.average(ei))
         
+        with open(path+f"eps={round(eps,3):.3f}_phase_diff.txt", 'w', encoding='utf-8') as f:
+            json.dump(list(phase_diff), f, indent=1)
+
+        with open(path+f"eps={round(eps,3):.3f}_ei.txt", 'w', encoding='utf-8') as f:
+            json.dump(ei, f, indent=1)
         print(f'Done eps={eps:.3f} with dim={dim} at {datetime.now()}')
-        
+    R.append(diff_res)
-    qtplot(f'Resultant and EI evolution for dim={dim} with 4 layers',
+    EI.append(av_ei)
-           [[0]+eps_space]*2,
+
-           [diff_res, av_ei],
+    #%%
-           ['Resultant', 'avEI'],
+savepath=f'/cloud/Public/_data/neuropercolation/4lay/cons=dimtimesdimby3_steps=100100/plots/'
-           export=True,
+
-           path=path,
+qtplot(f'Total resultant of phase-difference',
-           filename=f'Resultant and EI for dim={dim}.png',
+       [[0]+eps_space]*len(dims),
-           close=True)
+       R[::-1],
+       [f'{dim}x{dim}' for dim in dims[::-1]],
+       y_tag = 'concentration',
+       export=False,
+       path=savepath,
+       filename=f'Resultant_ev.png',
+       close=False)
+      
+qtplot(f'Average Effect Integrated Information',
+       [[0]+eps_space]*len(dims),
+       EI[::-1],
+       [f'{dim}x{dim}' for dim in dims[::-1]],
+       y_tag='integrated information',
+       export=False,
+       path=savepath,
+       filename=f'EI_ev.png',
+       close=False)
         
         

evaluation/4Layer Resultant 4way Phase Evolution.py

@@ -0,0 +1,277 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Mon Aug 21 14:59:22 2023
+
+@author: astral
+"""
+
+import json
+import math as m
+import numpy as np
+from numpy.linalg import norm
+from datetime import datetime
+from random import sample as choose
+
+from plot import qtplot
+
+eps_space = list(np.linspace(0.01,0.2,20))
+
+def resultant(sample):
+    phase_x = [m.cos(ind) for ind in sample]
+    phase_y = [m.sin(ind) for ind in sample]
+    
+    return (np.average(phase_x), np.average(phase_y))
+
+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)
+
+extremes = None
+maxdt = 300
+
+for dim in [9]:
+    for eps in eps_space:
+        path=f'/cloud/Public/_data/neuropercolation/4lay/steps=100100/dim=09/'
+        
+        try:
+            with open(path+f"eps={round(eps,3):.3f}_phase_diff.txt", 'r', encoding='utf-8') as f:
+                phase_diff = json.load(f)
+        except:
+            with open(path+f"eps={round(eps,3):.3f}_activation.txt", 'r', encoding='utf-8') as f:
+                activation = json.load(f)[100:]
+        
+            osc = list(zip(*activation))
+            phase_abs = np.array([[np.arctan2(*act[::-1]) for act in osc[i]] for i in range(2)])
+            phase_diff = diff(phase_abs[0],phase_abs[1])
+            
+            with open(path+f"eps={round(eps,3):.3f}_phase_diff.txt", 'w', encoding='utf-8') as f:
+                json.dump(list(phase_diff), f, indent=1)
+    
+        
+        all_res = norm(resultant(phase_diff))
+        av_diff = np.arccos(all_res)
+        
+        try:
+            with open(path+f"eps={round(eps,3):.3f}_ei.txt", 'r', encoding='utf-8') as f:
+                ei = json.load(f)
+        except:
+            with open(path+f"eps={round(eps,3):.3f}_channels.txt", 'r', encoding='utf-8') as f:
+                channels = json.load(f)[100:]
+            
+            ei = [np.sum(cha)*(1-H2(eps)) for cha in channels]
+            
+            with open(path+f"eps={round(eps,3):.3f}_ei.txt", 'w', encoding='utf-8') as f:
+                json.dump(ei, f, indent=1)
+        
+        pha_center = av_diff
+        pha_dev = m.pi/32
+        
+        from_sync = lambda i: True if abs(phase_diff[i])<0.08*m.pi else False if 0.42*m.pi<abs(phase_diff[i])<0.58*m.pi else from_sync(i-1) if i>0 else None
+        to_sync = lambda i: True if abs(phase_diff[i])<0.08*m.pi else False if 0.42*m.pi<abs(phase_diff[i])<0.58*m.pi else to_sync(i+1) if i+1<len(phase_diff) else None
+        
+        dev_ind = sorted([i for i,val in enumerate(ei[:-maxdt]) if (pha_center-pha_dev)<=abs(phase_diff[i])<=(pha_center+pha_dev)], key = lambda i: ei[i])
+        dev_00 = [i for i in dev_ind if from_sync(i)          and to_sync(i)         ]
+        dev_01 = [i for i in dev_ind if from_sync(i)          and to_sync(i) is False]
+        dev_10 = [i for i in dev_ind if from_sync(i) is False and to_sync(i)         ]
+        dev_11 = [i for i in dev_ind if from_sync(i) is False and to_sync(i) is False]
+        
+        lens = [len(dev_00),len(dev_01),len(dev_10),len(dev_11)]
+        
+        #if not extremes:
+        extremes = [1000]*4 #[l//2 for l in lens]
+
+        print(lens)
+        #print(all_res, av_diff)
+        
+        
+        # bot_00 = dev_00[:extremes[0]]
+        # bot_01 = dev_01[:extremes[1]]
+        # bot_10 = dev_10[:extremes[2]]
+        # bot_11 = dev_11[:extremes[3]]
+        
+        top_00 = dev_00[-extremes[0]:]
+        top_01 = dev_01[-extremes[1]:]
+        top_10 = dev_10[-extremes[2]:]
+        top_11 = dev_11[-extremes[3]:]
+        
+        
+        # bot_res = []
+        top_res = []
+        # dev_res = []
+        tot_res = []
+        
+        # bot_ph = []
+        top_ph = []
+        # dev_ph = []
+        tot_ph = []
+        
+        # bot_ei = []
+        top_ei = []
+        # dev_ei = []
+        tot_ei = []
+        for dt in range(maxdt):
+            # bot_pha = [[abs(phase_diff[i+dt]) for i in bot_00],
+            #            [abs(phase_diff[i+dt]) for i in bot_01],
+            #            [abs(phase_diff[i+dt]) for i in bot_10],
+            #            [abs(phase_diff[i+dt]) for i in bot_11]]
+            
+            top_pha = [[abs(phase_diff[i+dt]) for i in top_00],
+                       [abs(phase_diff[i+dt]) for i in top_01],
+                       [abs(phase_diff[i+dt]) for i in top_10],
+                       [abs(phase_diff[i+dt]) for i in top_11]]
+            
+            # dev_pha = [[abs(phase_diff[i+dt]) for i in dev_00],
+            #            [abs(phase_diff[i+dt]) for i in dev_01],
+            #            [abs(phase_diff[i+dt]) for i in dev_10],
+            #            [abs(phase_diff[i+dt]) for i in dev_11]]
+            
+            tot_pha = np.abs(phase_diff[dt:dt-maxdt])
+            
+            # bot_res.append( [norm(resultant(bot_pha[i])) for i in range(4)] )
+            top_res.append( [norm(resultant(top_pha[i])) for i in range(4)] )
+            # dev_res.append( [norm(resultant(dev_pha[i])) for i in range(4)] )
+            tot_res.append( norm(resultant(tot_pha)) )
+            
+            # bot_ph.append( [phase(*resultant(bot_pha[i])) for i in range(4)] )
+            top_ph.append( [phase(*resultant(top_pha[i])) for i in range(4)] )
+            # dev_ph.append( [phase(*resultant(dev_pha[i])) for i in range(4)] )
+            tot_ph.append( phase(*resultant(tot_pha)) )
+            
+            # bot_ei.append( [np.average([ei[i+dt] for i in bot]) for bot in [bot_00,bot_01,bot_10,bot_11]] )
+            top_ei.append( [np.average([ei[i+dt] for i in top]) for top in [top_00,top_01,top_10,top_11]] )
+            # dev_ei.append( [np.average([ei[i+dt] for i in dev]) for dev in [dev_00,dev_01,dev_10,dev_11]] )
+            tot_ei.append( np.average(ei[dt:dt-maxdt]) )
+            
+            if dt%10==0:
+                print(f'Done dt={dt}')
+        
+        # bot_res = list(zip(*bot_res))
+        top_res = list(zip(*top_res))
+        # dev_res = list(zip(*dev_res))
+        
+        # bot_ph = list(zip(*bot_ph))
+        top_ph = list(zip(*top_ph))
+        # dev_ph = list(zip(*dev_ph))
+
+        # bot_ei = list(zip(*bot_ei))
+        top_ei = list(zip(*top_ei))
+        # dev_ei = list(zip(*dev_ei))
+        
+        plotpath = path+'4waymedian/'
+
+        qtplot(f'Diachronic resultant sync to sync for dim={dim} with 4 layers',
+                [np.array(range(maxdt))]*4,
+                # [bot_res[0], top_res[0], dev_res[0], tot_res],
+                [top_res[0], cau_res[0]]
+                ['sync to sync bottom {extremes} ei', 'sync to sync top {extremes} ei',
+                 'sync to sync {len(dev_00)} ei', 'Average Resultant'],
+                x_tag = 'dt',
+                y_tag = 'concentration',
+                export=True,
+                path=plotpath,
+                filename=f'Diachronic Resultant Norm eps={round(eps,3):.3f} sts dim={dim} extremes={extremes} roll{pha_dev:.3f}.png',
+                close=True)
+        qtplot(f'Diachronic resultant sync to orth for dim={dim} with 4 layers',
+                [np.array(range(maxdt))]*4,
+                [bot_res[1], top_res[1], dev_res[1], tot_res],
+                ['sync to orth bottom {extremes} ei', 'sync to orth top {extremes} ei',
+                 'sync to orth {len(dev_01)} ei', 'Average Resultant'],
+                x_tag = 'dt',
+                y_tag = 'concentration',
+                export=True,
+                path=plotpath,
+                filename=f'Diachronic Resultant Norm eps={round(eps,3):.3f} sto dim={dim} extremes={extremes} roll{pha_dev:.3f}.png',
+                close=True)
+        qtplot(f'Diachronic resultant orth to sync for dim={dim} with 4 layers',
+                [np.array(range(maxdt))]*4,
+                [bot_res[2], top_res[2], dev_res[2], tot_res],
+                ['orth to sync bottom {extremes} ei', 'orth to sync top {extremes} ei',
+                 'orth to sync {len(dev_10)} ei', 'Average Resultant'],
+                x_tag = 'dt',
+                y_tag = 'concentration',
+                export=True,
+                path=plotpath,
+                filename=f'Diachronic Resultant Norm eps={round(eps,3):.3f} ots dim={dim} extremes={extremes} roll{pha_dev:.3f}.png',
+                close=True)
+        qtplot(f'Diachronic resultant orth to orth for dim={dim} with 4 layers',
+                [np.array(range(maxdt))]*4,
+                [bot_res[3], top_res[3], dev_res[3], tot_res],
+                ['orth to orth bottom {extremes} ei', 'orth to orth top {extremes} ei',
+                 'orth to orth {len(dev_11)} ei', 'Average Resultant'],
+                x_tag = 'dt',
+                y_tag = 'concentration',
+                export=True,
+                path=plotpath,
+                filename=f'Diachronic Resultant Norm eps={round(eps,3):.3f} oto dim={dim} extremes={extremes} roll{pha_dev:.3f}.png',
+                close=True)
+        
+        qtplot(f'Diachronic resultant phase sync to sync for dim={dim} with 4 layers',
+                [np.array(range(maxdt))]*4,
+                [bot_ph[0], top_ph[0], dev_ph[0], tot_ph],
+                ['sync to sync bottom {extremes} ei', 'sync to sync top {extremes} ei',
+                 'sync to sync {len(dev_in_ind)} ei', 'Average'],
+                x_tag = 'dt',
+                y_tag = 'phase',
+                export=True,
+                path=plotpath,
+                filename=f'Diachronic Resultant Phase eps={round(eps,3):.3f} sts dim={dim} extremes={extremes} roll{pha_dev:.3f}.png',
+                close=True)
+        qtplot(f'Diachronic resultant phase sync to orth for dim={dim} with 4 layers',
+                [np.array(range(maxdt))]*4,
+                [bot_ph[1], top_ph[1], dev_ph[1], tot_ph],
+                ['sync to orth bottom {extremes} ei', 'sync to orth top {extremes} ei',
+                 'sync to orth {len(dev_out_ind)} ei', 'Average'],
+                x_tag = 'dt',
+                y_tag = 'phase',
+                export=True,
+                path=plotpath,
+                filename=f'Diachronic Resultant Phase eps={round(eps,3):.3f} sto dim={dim} extremes={extremes} roll{pha_dev:.3f}.png',
+                close=True)
+        qtplot(f'Diachronic resultant phase orth to sync for dim={dim} with 4 layers',
+                [np.array(range(maxdt))]*4,
+                [bot_ph[2], top_ph[2], dev_ph[2], tot_ph],
+                ['orth to sync bottom {extremes} ei', 'orth to sync top {extremes} ei',
+                 'orth to sync {len(dev_in_ind)} ei', 'Average'],
+                x_tag = 'dt',
+                y_tag = 'phase',
+                export=True,
+                path=plotpath,
+                filename=f'Diachronic Resultant Phase eps={round(eps,3):.3f} ots dim={dim} extremes={extremes} roll{pha_dev:.3f}.png',
+                close=True)
+        qtplot(f'Diachronic resultant phase orth to orth for dim={dim} with 4 layers',
+                [np.array(range(maxdt))]*4,
+                [bot_ph[3], top_ph[3], dev_ph[3], tot_ph],
+                ['orth to orth bottom {extremes} ei', 'orth to orth top {extremes} ei',
+                 'orth to orth {len(dev_out_ind)} ei', 'Average'],
+                x_tag = 'dt',
+                y_tag = 'phase',
+                export=True,
+                path=plotpath,
+                filename=f'Diachronic Resultant Phase eps={round(eps,3):.3f} oto dim={dim} extremes={extremes} roll{pha_dev:.3f}.png',
+                close=True)
+        
+        # qtplot(f'Diachronic ei for dim={dim} with 4 layers',
+        #         [np.array(range(maxdt))]*4,
+        #         [bot_ei, top_ei, dev_ei, tot_ei],
+        #         ['EI ev of bottom {extremes} ei', 'EI ev of top {extremes} ei',
+        #          'EI ev of phase filtered ei', 'Average EI'],
+        #         x_tag = 'dt',
+        #         y_tag = 'average ei',
+        #         export=True,
+        #         path=path+'plots/',
+        #         filename=f'Diachronic EI balanced for eps={round(eps,3):.3f} dim={dim} extremes={extremes} roll{pha_dev:.3f}.png',
+        #         close=True)
+        
+        print(f'Done eps={eps:.3f} with dim={dim} at {datetime.now()}')
+        
+    # qtplot(f'Resultant and EI evolution for dim={dim} with 4 layers',
+    #         [[0]+eps_space]*2,
+    #         [max(av_ei)*diff_res, av_ei],
+    #         ['Resultant', 'avEI'],
+    #         export=True,
+    #         path=path,
+    #         filename=f'Resultant and EI for dim={dim}.png',
+    #         close=True)
+        
+        

evaluation/4Layer Resultant Phase Evolution.py

@@ -32,7 +32,7 @@ maxdt = 300
 
 for dim in [7]:
     for eps in eps_space:
-        path=f'/cloud/Public/_data/neuropercolation/4lay/cons=7-knight_steps=1000100/dim=07/batch=0/'
+        path=f'/cloud/Public/_data/neuropercolation/4lay/cons=9-3dist_steps=1000100/dim=09/batch=1/'
         
         try:
             with open(path+f"eps={round(eps,3):.3f}_phase_diff.txt", 'r', encoding='utf-8') as f:
@@ -67,11 +67,14 @@ for dim in [7]:
         pha_center = av_diff
         pha_dev = m.pi/32
         
-        from_sync = lambda i: True if abs(phase_diff[i])<0.08*m.pi else False if 0.42*m.pi<abs(phase_diff[i])<0.58*m.pi else from_sync(i-1)
+        from_sync = lambda i: True if abs(phase_diff[i])<0.08*m.pi else False if 0.42*m.pi<abs(phase_diff[i])<0.58*m.pi else from_sync(i-1) if i>0 else None
+        to_sync = lambda i: True if abs(phase_diff[i])<0.08*m.pi else False if 0.42*m.pi<abs(phase_diff[i])<0.58*m.pi else to_sync(i+1) if i+1<len(phase_diff) else None
         
         dev_ind = sorted([i for i,val in enumerate(ei[:-maxdt]) if (pha_center-pha_dev)<=abs(phase_diff[i])<=(pha_center+pha_dev)], key = lambda i: ei[i])
-        dev_in_ind = [i for i in dev_ind if not from_sync(i)]
+        dev_00_ind = [i for i in dev_ind if from_sync(i)          and to_sync(i)         ]
-        dev_out_ind = [i for i in dev_ind if from_sync(i)]
+        dev_01_ind = [i for i in dev_ind if from_sync(i)          and to_sync(i) is False]
+        dev_10_ind = [i for i in dev_ind if from_sync(i) is False and to_sync(i)         ]
+        dev_11_ind = [i for i in dev_ind if from_sync(i) is False and to_sync(i) is False]
         
         devm_in_ind = [i for i in dev_in_ind if phase_diff[i]<0]
         devp_in_ind = [i for i in dev_in_ind if phase_diff[i]>0]
@@ -108,19 +111,22 @@ for dim in [7]:
         dev_ei = []
         tot_ei = []
         for dt in range(maxdt):
-            bot_pha = [abs(phase_diff[i+dt]) for i in bot_ind]
+            bot_pha = [[abs(phase_diff[i+dt]) for i in bot_in_ind],
-            top_pha = [abs(phase_diff[i+dt]) for i in top_ind]
+                       [abs(phase_diff[i+dt]) for i in bot_out_ind]]
-            dev_pha = [abs(phase_diff[i+dt]) for i in dev_ind]
+            top_pha = [[abs(phase_diff[i+dt]) for i in top_in_ind],
+                       [abs(phase_diff[i+dt]) for i in top_out_ind]]
+            dev_pha = [[abs(phase_diff[i+dt]) for i in dev_in_ind],
+                       [abs(phase_diff[i+dt]) for i in dev_out_ind]]
             tot_pha = np.abs(phase_diff[dt:dt-maxdt])
             
-            bot_res.append( norm(resultant(bot_pha)) )
+            bot_res.append( [norm(resultant(bot_pha[i])) for i in [0,1]] )
-            top_res.append( norm(resultant(top_pha)) )
+            top_res.append( [norm(resultant(top_pha[i])) for i in [0,1]] )
-            dev_res.append( norm(resultant(dev_pha)) )
+            dev_res.append( [norm(resultant(dev_pha[i])) for i in [0,1]] )
             tot_res.append( norm(resultant(tot_pha)) )
             
-            bot_ph.append( phase(*resultant(bot_pha)) )
+            bot_ph.append( [phase(*resultant(bot_pha[i])) for i in [0,1]] )
-            top_ph.append( phase(*resultant(top_pha)) )
+            top_ph.append( [phase(*resultant(top_pha[i])) for i in [0,1]] )
-            dev_ph.append( phase(*resultant(dev_pha)) )
+            dev_ph.append( [phase(*resultant(dev_pha[i])) for i in [0,1]] )
             tot_ph.append( phase(*resultant(tot_pha)) )
             
             bot_ei.append( np.average([ei[i+dt] for i in bot_ind]) )
@@ -130,29 +136,59 @@ for dim in [7]:
             
             if dt%100==99:
                 print(f'Done dt={dt}')
-            
+        
+        bot_res = list(zip(*bot_res))
+        top_res = list(zip(*top_res))
+        dev_res = list(zip(*dev_res))
+        
+        bot_ph = list(zip(*bot_ph))
+        top_ph = list(zip(*top_ph))
+        dev_ph = list(zip(*dev_ph))
+
         qtplot(f'Diachronic resultant for dim={dim} with 4 layers',
                 [np.array(range(maxdt))]*4,
-                [bot_res, top_res, dev_res, tot_res],
+                [bot_res[0], top_res[0], dev_res[0], tot_res],
-                ['Resultant ev of bottom {extremes} ei', 'Resultant ev of top {extremes} ei',
+                ['in bottom {extremes} ei', 'in top {extremes} ei',
-                  'Resultant ev of phase filtered ei', 'Average Resultant'],
+                 'in all filtered {len(dev_in_ind)} ei', 'Average Resultant'],
                 x_tag = 'dt',
                 y_tag = 'concentration',
                 export=True,
-                path=path+'plots/',
+                path=path+'inout/',
-                filename=f'Diachronic Resultant Norm balanced eps={round(eps,3):.3f} dim={dim} extremes={extremes} roll{pha_dev:.3f}.png',
+                filename=f'Diachronic Resultant Norm in eps={round(eps,3):.3f} dim={dim} extremes={extremes} roll{pha_dev:.3f}.png',
+                close=True)
+        qtplot(f'Diachronic resultant for dim={dim} with 4 layers',
+                [np.array(range(maxdt))]*4,
+                [bot_res[1], top_res[1], dev_res[1], tot_res],
+                ['out bottom {extremes} ei', 'out top {extremes} ei',
+                 'out all filtered {len(dev_out_ind)} ei', 'Average Resultant'],
+                x_tag = 'dt',
+                y_tag = 'concentration',
+                export=True,
+                path=path+'inout/',
+                filename=f'Diachronic Resultant Norm out eps={round(eps,3):.3f} dim={dim} extremes={extremes} roll{pha_dev:.3f}.png',
                 close=True)
         
         qtplot(f'Diachronic resultant phase for dim={dim} with 4 layers',
                 [np.array(range(maxdt))]*4,
-                [bot_ph, top_ph, dev_ph, tot_ph],
+                [bot_ph[0], top_ph[0], dev_ph[0], tot_ph],
-                ['bottom {extremes} ei', 'top {extremes} ei',
+                ['in bottom {extremes} ei', 'in top {extremes} ei',
-                  'all filtered ei', 'Average'],
+                 'in all filtered {len(dev_in_ind)} ei', 'Average'],
                 x_tag = 'dt',
-                y_tag = 'concentration',
+                y_tag = 'phase',
                 export=True,
-                path=path+'plots/',
+                path=path+'inout/',
-                filename=f'Diachronic Resultant Phase balanced eps={round(eps,3):.3f} dim={dim} extremes={extremes} roll{pha_dev:.3f}.png',
+                filename=f'Diachronic Resultant Phase in eps={round(eps,3):.3f} dim={dim} extremes={extremes} roll{pha_dev:.3f}.png',
+                close=True)
+        qtplot(f'Diachronic resultant phase for dim={dim} with 4 layers',
+                [np.array(range(maxdt))]*4,
+                [bot_ph[1], top_ph[1], dev_ph[1], tot_ph],
+                ['out bottom {extremes} ei', 'out top {extremes} ei',
+                 'out all filtered {len(dev_out_ind)} ei', 'Average'],
+                x_tag = 'dt',
+                y_tag = 'phase',
+                export=True,
+                path=path+'inout/',
+                filename=f'Diachronic Resultant Phase out eps={round(eps,3):.3f} dim={dim} extremes={extremes} roll{pha_dev:.3f}.png',
                 close=True)
         
         # qtplot(f'Diachronic ei for dim={dim} with 4 layers',

evaluation/4Layer Resultant.py

@@ -0,0 +1,106 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Mon Aug 21 14:59:22 2023
+
+@author: astral
+"""
+
+import os
+import json
+import math as m
+import numpy as np
+from numpy.linalg import norm
+from datetime import datetime
+from random import sample as choose
+
+from plot import qtplot
+
+eps_space = list(np.linspace(0.005,0.5,100))
+
+def resultant(sample):
+    phase_x = [m.cos(ind) for ind in sample]
+    phase_y = [m.sin(ind) for ind in sample]
+    
+    return (np.average(phase_x), np.average(phase_y))
+
+def H2(x):
+    return -x*m.log2(x)-(1-x)*m.log2(1-x)
+def new_folder(p):
+    if not os.path.exists(p):
+        os.makedirs(p)
+    return p
+
+extremes = None
+maxdt = 300
+
+path=f'/cloud/Public/_data/neuropercolation/4lay/steps=100000_diares_manydim/'
+
+
+dims = list(range(7,9))
+
+resus = []
+phalocks = []
+for dim in dims:
+    resu = []
+    phalock = []
+    for eps in eps_space:
+        dimpath=f'/cloud/Public/_data/neuropercolation/4lay/steps=100000_diares_manydim/dim={dim:02d}/'
+        
+        try:
+            with open(dimpath+f"eps={round(eps,3):.3f}_phase_diff.txt", 'r', encoding='utf-8') as f:
+                phase_diff = json.load(f)
+        except:
+            with open(dimpath+f"eps={round(eps,3):.3f}_activation.txt", 'r', encoding='utf-8') as f:
+                activation = json.load(f)[100:]
+        
+            osc = list(zip(*activation))
+            phase = np.array([[np.arctan2(*act[::-1]) for act in osc[i]] for i in range(2)])
+            phase_diff = (phase[1]-phase[0]+m.pi)%(2*m.pi)-m.pi
+            
+            with open(dimpath+f"eps={round(eps,3):.3f}_phase_diff.txt", 'w', encoding='utf-8') as f:
+                json.dump(list(phase_diff), f, indent=1)
+    
+        
+        all_res = norm(resultant(phase_diff))
+        av_diff = np.arccos(all_res)
+        all_pha = np.arctan2(*resultant(phase_diff)[::-1])
+        
+        resu.append(all_res)
+        phalock.append(all_pha)
+    
+    plotpath = new_folder(dimpath + 'resplot/')
+    with open(plotpath+f"resultants.txt", 'w', encoding='utf-8') as f:
+        json.dump(list(resu), f, indent=1)
+    with open(plotpath+f"mainphase.txt", 'w', encoding='utf-8') as f:
+        json.dump(list(phalock), f, indent=1)
+
+    resus.append(resu)
+    phalocks.append(phalock)
+
+plotspath = new_folder(path + 'resplot/')
+
+#%%
+qtplot(f'Resultant evolution with 4 layers',
+        [eps_space]*len(dims),
+        resus,
+        [f'Resultant for size {dim}x{dim}' for dim in dims],
+        x_tag = 'epsilon',
+        y_tag = 'resultant',
+        lw=3,
+        export=True,
+        path=plotspath,
+        filename=f'resultant.png',
+        close=False)
+
+qtplot(f'Dominant phase evolution with 4 layers',
+        [eps_space]*len(dims),
+        phalocks,
+        [f'dominant phase for size {dim}x{dim}' for dim in dims],
+        x_tag = 'epsilon',
+        y_tag = 'resultant',
+        lw=3,
+        export=True,
+        path=plotspath,
+        filename=f'mainphase.png',
+        close=True)

evaluation/4Layer Significance.py

@@ -0,0 +1,25 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Sun Sep 10 07:07:28 2023
+
+@author: astral
+"""
+
+import sys as _sys
+from sign import significance as _sign
+import numpy as _np
+
+import gc as _gc
+
+_dim = 9
+_epsilons = _np.linspace(0.01,0.20,20)
+
+for _eps in _epsilons[_sys.argv[1]]:
+    _sign(_dim,_eps)
+    
+    for name in dir():
+        if not name.startswith('_'):
+            del globals()[name]
+    
+    _gc.collect()

evaluation/4Layer phiplot.py

@@ -0,0 +1,98 @@
+# -*- 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
+
+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/4lay/cons=dimtimesdimby3_steps=100100/'
+suffix = ''
+
+chi = chr(967)
+vareps = chr(949)
+varphi = chr(981)
+
+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=[]
+PHI=[]
+lastkurt=None
+for dim in dims:
+    phis=[]
+    con_gap = 3
+    cons = [(n,(2*n+m)%dim) for n in range(dim) for m in range(0,dim-2,con_gap)]
+    dimpath = new_folder(path + f'dim={dim:02}_cons={len(cons)}/batch=0/')
+    for epsilon in eps_space:
+        try:
+            with open(dimpath+f"eps={round(epsilon,3):.3f}_ei.txt", 'r', encoding='utf-8') as f:
+                ei = np.array(json.load(f)[100:])
+        except:
+            print('Calcing phi')
+            with open(dimpath+f"eps={round(epsilon,3):.3f}_channels.txt", 'r', encoding='utf-8') as f:
+                channels = np.array(json.load(f)[100:])
+                
+            ei = channels*(1-H2(epsilon))
+            
+            with open(dimpath+f"eps={round(epsilon,3):.3f}_ei.txt", 'r', encoding='utf-8') as f:
+                json.dump(ei,f,indent=1)
+                
+        phi=np.average(ei)
+        phis.append(phi)
+    PHI.append(phis)
+    #%%
+qtplot(f"Mean effect integration over noise level",
+        [eps_space]*len(dims),
+        PHI[::-1],
+        [f'dim={dim:02d}x{dim:02d}' for dim in dims[::-1]],
+        y_tag = f'effect integration {varphi}',
+        export=True,
+        path=dimpath+"",
+        filename=f'eps={round(epsilon,3):.3f}_evolution.png',
+        close=False) 
+
+mode = 'density'
+#%%

evaluation/4laysign.py

@@ -0,0 +1,173 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Sun Sep 10 07:07:28 2023
+
+@author: astral
+"""
+
+import sys as _sys
+from sign import sampling as _samp
+from sign import plotting as _plot
+from sign import full_stats as _stats
+import numpy as _np
+import json
+from plot import qtplot
+
+import gc as _gc
+
+_dim = 9
+_epsilons = _np.linspace(0.005,0.20,40)
+_noeffects = list(range(1,41,5))
+try:
+    _exeps = int(_sys.argv[1])
+    _epses=_epsilons[_exeps-1:_exeps]
+    _nf = int(_sys.argv[2])
+    _nfs = _noeffects[_nf-1:_nf]
+except:
+    _epses=_epsilons
+    _nfs = list(range(1,41,5))
+_samplemethod = 'allpos_ei'
+_ext = 5000
+_dt=40
+
+path='/cloud/Public/_data/neuropercolation/4lay/cons=27-knight_steps=1000100/dim=09/batch=0/'
+plotpath = path + _samplemethod + f'_samples={_ext}/'
+savepath = path + _samplemethod + f'_samples={_ext}/dt={_dt}/'
+
+meanlist = []
+stdlist = []
+integrallist = []
+cohendlist = []
+norm_p_list = []
+ttest_p_list = []
+sign_p_list = []
+
+
+resultant_i = []
+resultant_c = []
+for _eps in _epses[11:21]:
+    res_evol_i = []
+    res_evol_c = []
+    for nf in _nfs:
+        #_samp(_dim,_eps,_samplemethod,_ext,_dt,noeff=nf)
+        resultant_i = []
+        resultant_c = []
+        for t in range(1,_dt):
+            res_i, res_c = _stats(_dim,_eps,_samplemethod,_ext,t,noeff=nf,ret='phases')
+            resultant_i.append(res_i)
+            resultant_c.append(res_c)
+        
+        res_evol_i.append(resultant_i)
+        res_evol_c.append(resultant_c)
+    #     mean,std,integral,cohend,norm_p,ttest_p,sign_p = _stats(_dim,_eps,_samplemethod,_ext,1)
+        
+    #     meanlist.append(mean)
+    #     stdlist.append(std)
+    #     integrallist.append(integral)
+    #     cohendlist.append(-cohend)
+    #     norm_p_list.append(norm_p)
+    #     ttest_p_list.append(ttest_p)
+    #     sign_p_list.append(sign_p)
+        
+        
+    # with open(savepath+f"phasediff_means.txt", 'w', encoding='utf-8') as f:
+    #     json.dump(meanlist, f, indent=1)
+    # with open(savepath+f"phasediff_stds.txt", 'w', encoding='utf-8') as f:
+    #     json.dump(stdlist, f, indent=1)
+    # with open(savepath+f"phasediff_integrals.txt", 'w', encoding='utf-8') as f:
+    #     json.dump(integrallist, f, indent=1)
+    # with open(savepath+f"phasediff_cohends.txt", 'w', encoding='utf-8') as f:
+    #     json.dump(cohendlist, f, indent=1)
+    # with open(savepath+f"phasediff_norm_ps.txt", 'w', encoding='utf-8') as f:
+    #     json.dump(norm_p_list, f, indent=1)
+    # with open(savepath+f"phasediff_ttest_ps.txt", 'w', encoding='utf-8') as f:
+    #     json.dump(ttest_p_list, f, indent=1)
+    # with open(savepath+f"phasediff_sign_ps.txt", 'w', encoding='utf-8') as f:
+    #     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))]
+
+# norm_conf = [1-p for p in norm_p_list]
+# ttest_conf = [1-p for p in ttest_p_list]
+# sign_conf = [1-p for p in sign_p_list]
+    res_tot_i = _np.average(res_evol_i,axis=0)
+    res_evol_c.append(res_tot_i)
+    qtplot(f'Resultant reduction disconnect eps={_eps} dim={_dim} with 4 layers',
+            [list(range(_dt-1))]*(len(_nfs)+1),
+            res_evol_c,
+            [f'{nf} disconnected steps' for nf in _nfs]+['connected steps'],
+            x_tag = 'dt',
+            y_tag = 'resultant',
+            export=True,
+            path=plotpath,
+            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',
+#         [_epsilons]*3,
+#         [stdlowlist, stdhighlist, meanlist],
+#         ['Low standard deviation',
+#           'High standard deviation',
+#           'Mean'],
+#         colors=['r','r','g'],
+#         x_tag = f'noise level {chr(949)}',
+#         y_tag = 'abs phase reduction',
+#         export=True,
+#         path=savepath,
+#         filename=f'Mean phase reduction dim={_dim} extremes={_ext}.png',
+#         close=True)
+# qtplot(f'Phase reduction probability for dt={_dt} dim={_dim} with 4 layers',
+#         [_epsilons],
+#         [integrallist],
+#         ['probability of phase reduction'],
+#         x_tag = f'noise level {chr(949)}',
+#         y_tag = 'abs phase reduction',
+#         export=True,
+#         path=savepath,
+#         filename=f'Probability of phase reduction dim={_dim} extremes={_ext}.png',
+#         close=True)
+# qtplot(f'Effect size phase reduction for dt={_dt} dim={_dim} with 4 layers',
+#         [_epsilons],
+#         [cohendlist],
+#         ["Absolute Cohen's d (negative)"],
+#         x_tag = f'noise level {chr(949)}',
+#         y_tag = 'effect size',
+#         x_range = (0,0.2),
+#         # y_range = (0.05,1),
+#         y_log = True,
+#         export=True,
+#         path=savepath,
+#         filename=f'Effect size phase reduction dim={_dim} extremes={_ext}.png',
+#         close=False)
+# qtplot(f'Test p-values for dt={_dt} dim={_dim} with 4 layers',
+#         [_epsilons]*5,
+#         [[0.001 for eps in _epsilons],[0.0001 for eps in _epsilons],
+#           norm_p_list,ttest_p_list,sign_p_list],
+#         ['0.001 limit','0.0001 limit',
+#           'p-value for normality', 'p-value for mean difference', 'p-value for median'],
+#         x_tag = f'noise level {chr(949)}',
+#         y_tag = 'p-value',
+#         y_range = (0,0.01),
+#         lw=2,
+#         export=True,
+#         path=savepath,
+#         filename=f'P-values phase reduction dim={_dim} extremes={_ext}.png',
+#         close=True)
+# qtplot(f'Test confidences for dt={_dt} dim={_dim} with 4 layers',
+#         [_epsilons]*5,
+#         [[0.999 for eps in _epsilons],[0.9999 for eps in _epsilons],
+#           norm_conf,ttest_conf,sign_conf],
+#         ['0.999 limit', '0.999 limit',
+#           'confidence for normality', 'confidence for mean difference', 'confidence for median'],
+#         x_tag = f'noise level {chr(949)}',
+#         y_tag = 'confidence´',
+#         y_range = (0.99,1),
+#         lw=2,
+#         export=True,
+#         path=savepath,
+#         filename=f'Confidences phase reduction dim={_dim} extremes={_ext}.png',
+#         close=True)
+
+

evaluation/phi.py

@@ -0,0 +1,173 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Wed Sep 27 04:39:54 2023
+
+@author: astral
+"""
+import os
+import json
+import math as m
+import numpy as np
+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
+
+from plot import qtplot
+
+from neuropercolation import Simulate4Layers
+
+eps_space = list(np.linspace(0.01,0.2,20))
+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)
+
+@njit
+def neighbor(digit0, digit1, lenght):
+    layer = int(lenght)
+    dim = int(np.sqrt(layer))
+    digit0, digit1 = np.array([digit0%dim, digit0//dim]), np.array([digit1%dim, digit1//dim])
+    #print(digit0,digit1)
+    coord_dif = list(map(abs,digit1 - digit0))
+    layer_nbor = 0 in coord_dif and len(set([1,dim-1]).intersection(set(coord_dif))) != 0
+    #print(coord_dif, set([1,dim-1]).intersection(set(coord_dif)))
+    if layer_nbor:
+        return True
+    else:
+        return False
+    
+@njit
+def kcomb(zp,zm):
+    if zp>2:
+        val=1
+    elif zm>2:
+        val=0
+    elif zp==zm:
+        val=0.5
+    elif zm==2:
+        val=0.5**(3-zp)
+    elif zp==2:
+        val=1-0.5**(3-zm)
+    elif zm==0 and zp==1:
+        val=9/16
+    elif zp==0 and zm==1:
+        val=7/16
+    else:
+        raise NotImplementedError(zp,zm)
+    return val
+
+path = new_folder('/cloud/Public/_data/neuropercolation/1lay/mips/')
+
+
+def phi(dim,statestr,partstr,eps):
+    length = dim**2
+    eta = 1-eps
+    # statestr=statestr.translate(str.maketrans('','','.-='))
+    
+    state = np.array([int(q) for q in statestr])
+    state = list(state.reshape((dim,dim)))
+    state = [list([int(cell) for cell in row]) for row in state]
+
+    part = np.array([int(p) for p in partstr])
+    part = list(part.reshape((dim,dim)))
+    part = [list([int(cell) for cell in row]) for row in part]
+
+    inp = [[q+sum([state[(i+1)%dim][j],
+                   state[(i-1)%dim][j],
+                   state[i][(j+1)%dim],
+                   state[i][(j-1)%dim]
+                   ]) for j,q in enumerate(row)] for i,row in enumerate(state)]
+    
+    beps = [[int(inp[i][j]>2)*eta+int(inp[i][j]<3)*eps for j,q in enumerate(row)] for i,row in enumerate(state)]
+    
+    zplus = [[q+sum([state[(i+1)%dim][j]*(part[i][j]==part[(i+1)%dim][j]),
+                     state[(i-1)%dim][j]*(part[i][j]==part[(i-1)%dim][j]),
+                     state[i][(j+1)%dim]*(part[i][j]==part[i][(j+1)%dim]),
+                     state[i][(j-1)%dim]*(part[i][j]==part[i][(j-1)%dim])
+                     ]) for j,q in enumerate(row)] for i,row in enumerate(state)]
+    zminus = [[(1-q)+sum([(1-state[(i+1)%dim][j])*(part[i][j]==part[(i+1)%dim][j]),
+                    (1-state[(i-1)%dim][j])*(part[i][j]==part[(i-1)%dim][j]),
+                    (1-state[i][(j+1)%dim])*(part[i][j]==part[i][(j+1)%dim]),
+                    (1-state[i][(j-1)%dim])*(part[i][j]==part[i][(j-1)%dim])
+                    ]) for j,q in enumerate(row)] for i,row in enumerate(state)]
+    
+    kplus = [[kcomb(zplus[i][j],zminus[i][j]) for j,q in enumerate(row)] for i,row in enumerate(state)]
+    
+    pi = [[eps*(1-kplus[i][j]) + eta*kplus[i][j] for j,q in enumerate(row)] for i,row in enumerate(state)]
+    
+    crossent = [[-beps[i][j]*m.log2(pi[i][j])-(1-beps[i][j])*m.log2(1-pi[i][j]) for j,q in enumerate(row)] for i,row in enumerate(state)]
+    
+    return np.sum(crossent) - length*H2(eps)
+
+
+def MIP(dim,statestr,eps):
+    lophi=np.inf
+    mip = []
+    # 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)
+        
+        if curphi<lophi:
+            lophi=curphi
+            mip = [partstr]
+        elif curphi==lophi:
+            mip.append(partstr)
+            
+    print(f'Done with {dim},{eps} = {mip},{lophi}')
+    
+    return mip,lophi
+
+def calc_mips(dim,eps):
+    mip = []
+    statestr='0'*dim**2
+    # 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))
+    
+    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:
+        json.dump(mip, f, indent=1)
+        
+def smartMIP(dim,statestr,eps):
+    lophi=np.inf
+    mip = []
+    
+    for parti in range(0,dim**2):
+        partstr = bin(2**parti)[2:].zfill(dim**2)
+        curphi = phi(dim,statestr,partstr,eps)
+    
+        if curphi<lophi:
+            lophi=curphi
+            mip = [partstr]
+        elif curphi==lophi:
+            mip.append(partstr)
+    
+    mipath = new_folder(path+f'dim={dim:02d}/')
+    with open(mipath+f"eps={round(eps,3):.3f}_mips.txt", 'r', encoding='utf-8') as f:
+        mips=json.load(f) 
+    
+    for parti in range(1,2**(dim**2-1)):
+        partstr = bin(parti)[2:].zfill(dim**2)
+        if mips[parti-1]<curphi:
+            curphi = phi(dim,statestr,partstr,eps)
+        
+            if curphi<lophi:
+                lophi=curphi
+                mip = [partstr]
+            elif curphi==lophi:
+                mip.append(partstr)
+    
+    return mip,lophi
+    
+    
+            

evaluation/plot.py

@@ -17,6 +17,11 @@ from PyQt5.QtGui import QFont
 import math as m
 import numpy as np
 
+def new_folder(path):
+    if not os.path.exists(path):
+        os.makedirs(path)
+    return path
+
 def __get_color(factor, gamma=0.8):
     frequency=380+factor*(750-380)
     
@@ -75,7 +80,10 @@ def plot_execute():
     if sys.flags.interactive != 1 or not hasattr(qt.QtCore, 'PYQT_VERSION'):
         qt.QtGui.QApplication.exec_()
 
-def qtplot(titletext, spaces, vals, names, x_tag=f'noise level {chr(949)}', y_tag=None, colors=None, export=False, path=None, filename=None, lw=4, close=False):
+def qtplot(titletext, spaces, vals, names=None, 
+           x_tag=f'noise {chr(949)}', y_tag=None, x_log=False, y_log=False, x_range=None, y_range=None,
+           colors=None,
+           export=False, path=None, filename=None, lw=3, close=False):
     linewidth = lw
     
     if not close:
@@ -83,15 +91,23 @@ def qtplot(titletext, spaces, vals, names, x_tag=f'noise level {chr(949)}', y_ta
     
     ph = qt.plot()
     ph.showGrid(x=True,y=True)
-    ph.setXRange(min([min(sp) for sp in spaces]), max([max(sp) for sp in spaces]))
+    if x_range is not None:
-    # ph.setYRange(0.0, 6)
+        ph.setXRange(*x_range)
+    else:
+        ph.setXRange(min([min(sp) for sp in spaces]), max([max(sp) for sp in spaces]))
+    if y_range is not None:
+        ph.setYRange(*y_range)
+    else:
+        ph.setYRange(min([min(v) for v in vals]), max([max(v) for v in vals]))
+    ph.setLogMode(x=x_log, y=y_log)
     
-    #ph.setTitle(title='Susceptibility density evolution for different automaton sizes', offset=(1000,500))#.format(dim))
+    ph.setTitle(title=titletext, offset=(1000,500))#.format(dim))
     ph.setLabel('left', y_tag)
     ph.setLabel('bottom', x_tag)
     #ph.setXRange(0, 0.15)
     
-    ph.addLegend(offset=(400, 30))
+    if names is not None:
+        ph.addLegend(offset=(400, 30))
     
     
     #s = ph.plot(np.linspace(0.01,0.32,32), eps_max_freq0, title=sp_Title, pen='w')
@@ -105,22 +121,30 @@ def qtplot(titletext, spaces, vals, names, x_tag=f'noise level {chr(949)}', y_ta
                 (100,100,0), (0,100,100), (100,0,100),
                 (100,200,0), (0,100,200), (200,0,100),
                 (200,100,0), (0,200,100), (100,0,200)]
+    else:
+        colors = colors[::-1]
     
     
-    for i in range(len(vals)):
+    for i in range(len(vals)-1,-1,-1):
-        s = ph.plot(spaces[i], vals[i], 
+        try:
-                              name=names[i], pen=qt.mkPen(colors[i], width=linewidth))
+            s = ph.plot(spaces[i],
-    
+                        vals[i], 
-    title_item = qt.TextItem(text=titletext, anchor=(0.5, 7), color='grey')
+                        name=names[i] if names is not None else None,
-    ph.addItem(title_item)
+                        pen=qt.mkPen(colors[i],
-    title_item.setPos(ph.getViewBox().viewRect().center())
+                        width=linewidth))
-    font = QFont()
+        except:
-    font.setPointSize(14)  # Adjust the font size as needed
+            print('Failed plotting '+names[i])
-    title_item.setFont(font)
+            raise
+            
+    #title_item = qt.TextItem(text=titletext, anchor=(0.5, 7), color='grey')
+    #ph.addItem(title_item)
+    #title_item.setPos(ph.getViewBox().viewRect().center())
+    #font = QFont()
+    #font.setPointSize(14)  # Adjust the font size as needed
+    #title_item.setFont(font)
 
     if export:
-        if not os.path.exists(path):
+        new_folder(path)
-            os.makedirs(path)
         
         exporter = qt.exporters.ImageExporter(ph.plotItem)
     

evaluation/plots/bootstrap_plot.py

@@ -0,0 +1,29 @@
+from plot import qtplot
+import json
+import math as ma
+import numpy as np
+
+path='/cloud/Public/_data/neuropercolation/4lay/cons=dimtimesdimby3_steps=100100/dim=09_cons=27/batch=0/'
+eps_sp=np.linspace(0.01,0.2,20)
+eps_ep=eps_sp
+
+extremes=10000
+strength=100000
+
+savepath=path+f'extremes={extremes}_bootstrength={strength}/'
+
+dt=250
+boots=[]
+for eps in eps_ep:
+    eps=round(eps,3)
+    with open(savepath+f'eps={eps:.3f}_dt={dt}_simpbootstrap.txt','r') as f:
+        
+        confs=list(zip(*json.load(f)))[1]
+        ps=[1-conf for conf in confs]
+        boots.append(ps)
+        
+
+
+
+   
+    qtplot(f"Bootstrapping p-value for noise level {eps}",[range(dt+1)],boots[-1:],[f''],y_tag='p-value',y_log=False) 

evaluation/plots/plot.py

@@ -0,0 +1,169 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Mon Aug 21 16:12:53 2023
+
+@author: astral
+"""
+
+import sys
+import os
+
+import pyqtgraph as qt
+import pyqtgraph.exporters
+from PyQt5.QtGui import QFont
+
+
+import math as m
+import numpy as np
+
+def new_folder(path):
+    if not os.path.exists(path):
+        os.makedirs(path)
+    return path
+
+def __get_color(factor, gamma=0.8):
+    frequency=380+factor*(750-380)
+    
+    lightfrequency = 0.4*(3*np.log10(frequency/2)-2)/4
+    
+    wavelength = 300/lightfrequency
+    
+    '''steps of 10Hz: 22 means 220Hz'''
+
+    '''This converts a given wavelength of light to an 
+    approximate RGB color value. The wavelength must be given
+    in values between 0 and 1 for 0=380nm through 1=750nm
+    (789 THz through 400 THz).
+
+    Based on code by Dan Bruton
+    http://www.physics.sfasu.edu/astro/color/spectra.html
+    '''
+
+    wavelength = float(wavelength)
+    if wavelength >= 380 and wavelength <= 440:
+        attenuation = 0.3 + 0.7 * (wavelength - 380) / (440 - 380)
+        R = ((-(wavelength - 440) / (440 - 380)) * attenuation) ** gamma
+        G = 0.0
+        B = (1.0 * attenuation) ** gamma
+    elif wavelength >= 440 and wavelength <= 490:
+        R = 0.0
+        G = ((wavelength - 440) / (490 - 440)) ** gamma
+        B = 1.0
+    elif wavelength >= 490 and wavelength <= 510:
+        R = 0.0
+        G = 1.0
+        B = (-(wavelength - 510) / (510 - 490)) ** gamma
+    elif wavelength >= 510 and wavelength <= 580:
+        R = ((wavelength - 510) / (580 - 510)) ** gamma
+        G = 1.0
+        B = 0.0
+    elif wavelength >= 580 and wavelength <= 645:
+        R = 1.0
+        G = (-(wavelength - 645) / (645 - 580)) ** gamma
+        B = 0.0
+    elif wavelength >= 645 and wavelength <= 750:
+        attenuation = 0.3 + 0.7 * (750 - wavelength) / (750 - 645)
+        R = (1.0 * attenuation) ** gamma
+        G = 0.0
+        B = 0.0
+    else:
+        R = 0.0
+        G = 0.0
+        B = 0.0
+    R *= 255
+    G *= 255
+    B *= 255
+    return (int(R), int(G), int(B))
+
+def plot_execute():
+    if sys.flags.interactive != 1 or not hasattr(qt.QtCore, 'PYQT_VERSION'):
+        qt.QtGui.QApplication.exec_()
+
+def qtplot(titletext, spaces, vals, names=None, 
+           x_tag=f'noise level {chr(949)}', y_tag=None, x_log=False, y_log=False, x_range=None, y_range=None,
+           colors=None,
+           export=False, path=None, filename=None, lw=3, close=False):
+    linewidth = lw
+    
+    if not close:
+        app = qt.mkQApp()
+    
+    ph = qt.plot()
+    ph.showGrid(x=True,y=True)
+    if x_range is not None:
+        ph.setXRange(*x_range)
+    else:
+        ph.setXRange(min([min(sp) for sp in spaces]), max([max(sp) for sp in spaces]))
+    if y_range is not None:
+        ph.setYRange(*y_range)
+    else:
+        ph.setYRange(min([min(v) for v in vals]), max([max(v) for v in vals]))
+    ph.setLogMode(x=x_log, y=y_log)
+    
+    ph.setTitle(title=titletext, offset=(1000,500))#.format(dim))
+    ph.setLabel('left', y_tag)
+    ph.setLabel('bottom', x_tag)
+    #ph.setXRange(0, 0.15)
+    ph.setFlag(ph.ItemIgnoresTransformations, False)   # the relevant line
+
+    if names is not None:
+        ph.addLegend(offset=(400, 30),size=20)
+    
+    
+    #s = ph.plot(np.linspace(0.01,0.32,32), eps_max_freq0, title=sp_Title, pen='w')
+    #s = ph.plot(np.linspace(0.01,0.32,32), eps_max_freq1, title=sp_Title, pen='w')
+    
+    
+    if colors=='rgb':
+        colors=[__get_color(fac/(len(vals)-1)) for fac in range(len(vals))]
+    elif colors is None:
+        colors=['r', 'g', 'b', 'y', 'c', 'm', 'w',
+                (100,100,0), (0,100,100), (100,0,100),
+                (100,200,0), (0,100,200), (200,0,100),
+                (200,100,0), (0,200,100), (100,0,200)]
+    else:
+        colors = colors[::-1]
+    
+    
+    for i in range(len(vals)-1,-1,-1):
+        try:
+            s = ph.plot(spaces[i],
+                        vals[i], 
+                        name=names[i] if names is not None else None,
+                        pen=qt.mkPen(colors[i],
+                        width=linewidth))
+        except:
+            print('Failed plotting '+names[i])
+            raise
+            
+    #title_item = qt.TextItem(text=titletext, anchor=(0.5, 7), color='grey')
+    #ph.addItem(title_item)
+    #title_item.setPos(ph.getViewBox().viewRect().center())
+    #font = QFont()
+    #font.setPointSize(14)  # Adjust the font size as needed
+    #title_item.setFont(font)
+
+    if export:
+        new_folder(path)
+        
+        exporter = qt.exporters.ImageExporter(ph.plotItem)
+    
+        # set export parameters if needed
+        exporter.parameters()['width'] = 1200   # (note this also affects height parameter)
+        
+        # save to file
+        exporter.export(path+filename)
+        
+        print(f'Saving to {path+filename}')
+    
+    def handleAppExit():
+        # Add any cleanup tasks here
+        print("closing")
+    
+    if close:
+        ph.close()
+    else:
+        app.aboutToQuit.connect(handleAppExit)
+        app.exec_()
+    

evaluation/sign.py

@@ -0,0 +1,374 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Sat Sep  9 22:23:30 2023
+
+@author: astral
+"""
+
+
+
+def sampling(dim,eps,samplemethod,extremes,dtmax,noeff=1):
+    print(f'Starting causal simulation with dim={dim}, eps={eps:.3f}, {samplemethod}, {extremes} extremes for dt={dtmax} and noeff={noeff:03d}')
+    
+    import os
+    import json
+    import math as m
+    import numpy as np
+    from numpy.linalg import norm
+    from datetime import datetime
+    from random import sample as choose
+
+    from plot import qtplot
+
+    from neuropercolation import Simulate4Layers
+
+    eps_space = list(np.linspace(0.01,0.2,20))
+
+    def resultant(sample):
+        phase_x = [m.cos(ind) for ind in sample]
+        phase_y = [m.sin(ind) for ind in sample]
+        
+        return (np.average(phase_x), np.average(phase_y))
+
+    def new_folder(path):
+        if not os.path.exists(path):
+            os.makedirs(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)    
+    
+    #print(f'Started at {datetime.now()} with eps={eps:.3f}')
+    
+    eps = round(eps,3)
+    path='/cloud/Public/_data/neuropercolation/4lay/cons=27-knight_steps=1000100/dim=09/batch=0/'
+    
+    try:
+        with open(path+f"eps={round(eps,3):.3f}_phase_diff.txt", 'r', encoding='utf-8') as f:
+            phase_diff = json.load(f)
+    except:
+        with open(path+f"eps={round(eps,3):.3f}_activation.txt", 'r', encoding='utf-8') as f:
+            activation = json.load(f)[100:]
+    
+        osc = list(zip(*activation))
+        phase_abs = np.array([[np.arctan2(*act[::-1]) for act in osc[i]] for i in range(2)])
+        phase_diff = diff(phase_abs[0],phase_abs[1])
+        phase_diff = [round(pha,6) for pha in phase_diff]
+        
+        with open(path+f"eps={round(eps,3):.3f}_phase_diff.txt", 'w', encoding='utf-8') as f:
+            json.dump(list(phase_diff), f, indent=1)
+
+    
+    all_res = norm(resultant(phase_diff))
+    av_diff = np.arccos(all_res)
+    
+    try:
+        with open(path+f"eps={round(eps,3):.3f}_ei.txt", 'r', encoding='utf-8') as f:
+            ei = json.load(f)
+    except:
+        with open(path+f"eps={round(eps,3):.3f}_channels.txt", 'r', encoding='utf-8') as f:
+            channels = json.load(f)[100:]
+        
+        ei = [round(np.sum(cha)*(1-H2(eps)),6) for cha in channels]
+        
+        with open(path+f"eps={round(eps,3):.3f}_ei.txt", 'w', encoding='utf-8') as f:
+            json.dump(ei, f, indent=1)
+    
+    ei_ind = [i for i,val in enumerate(ei) if val>0]
+    
+    print(f'{len(ei_ind)} states with positive EI')
+    
+    samples = choose(ei_ind, extremes)
+    
+    with open(path+f"eps={round(eps,3):.3f}_states.txt", 'r', encoding='utf-8') as f:
+        states = json.load(f)[100:]
+    with open(path+f"eps={round(eps,3):.3f}_coupling.txt", 'r', encoding='utf-8') as f:
+        coupling = json.load(f)
+        coupling = [tuple(edge) for edge in coupling]
+    
+    phase_pairs = [[] for dt in range(dtmax+1)]
+    ei_pairs = [[] for dt in range(dtmax+1)]
+    for num,i in enumerate(samples):
+        causal_init = states[i].translate(str.maketrans('', '', '.-='))
+        
+        sim = Simulate4Layers(  dim,
+                                eps,
+                                coupling=coupling,
+                                init=causal_init,
+                                noeffect=noeff-1,
+                                steps=dtmax,
+                                draw=None,
+                                )
+            
+        activation = sim._activations()
+        channel = sim._channels()
+    
+        osc = list(zip(*activation))
+        phase_abs = np.array([[np.arctan2(*act[::-1]) for act in osc[i]] for i in range(2)])
+        phasediff_c = diff(phase_abs[0],phase_abs[1])
+        ei_c = [round(np.sum(cha)*(1-H2(eps)),6) for cha in channel]
+        max_ei_c = max([np.sum(cha) for cha in channel])
+
+        sim = Simulate4Layers(  dim,
+                                eps,
+                                coupling=coupling,
+                                init=causal_init,
+                                noeffect=-1,
+                                steps=dtmax,
+                                draw=None,
+                                )
+            
+        activation = sim._activations()
+        channel = sim._channels()
+        
+        osc = list(zip(*activation))
+        phase_abs = np.array([[np.arctan2(*act[::-1]) for act in osc[i]] for i in range(2)])
+        phasediff_i = diff(phase_abs[0],phase_abs[1])
+        ei_i = [round(np.sum(cha)*(1-H2(eps)),6) for cha in channel]
+        max_ei_i = max([np.sum(cha) for cha in channel])
+        
+        for dt in range(1,dtmax+1):
+            phase_pairs[dt].append((i, phasediff_i[dt], phasediff_c[dt]))
+            ei_pairs[dt].append((i, ei_i[dt], ei_c[dt]))
+                    
+        if num%1000==999:
+            print(f'Done {num:0{len(str(extremes))}d}')
+    
+    
+    for dt in range(1,dtmax+1):
+        savepath = path + samplemethod + f'_samples={extremes}/dt={dt}/noeff={noeff:03d}/'
+        new_folder(savepath)
+        with open(savepath+f"eps={round(eps,3):.3f}_phase_pairs.txt", 'w', encoding='utf-8') as f:
+            json.dump(phase_pairs[dt], f, indent=1)
+        with open(savepath+f"eps={round(eps,3):.3f}_ei_pairs.txt", 'w', encoding='utf-8') as f:
+            json.dump(ei_pairs[dt], f, indent=1)
+
+def plotting(dim,eps,samplemethod,extremes,dt):
+    import os
+    import json
+    import math as m
+    import numpy as np
+    from numpy.linalg import norm
+    from datetime import datetime
+    from random import sample as choose
+
+    from plot import qtplot
+
+    from neuropercolation import Simulate4Layers
+
+    eps_space = list(np.linspace(0.01,0.2,20))
+
+    def resultant(sample):
+        phase_x = [m.cos(ind) for ind in sample]
+        phase_y = [m.sin(ind) for ind in sample]
+        
+        return (np.average(phase_x), np.average(phase_y))
+
+    def new_folder(path):
+        if not os.path.exists(path):
+            os.makedirs(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)
+
+    
+    print(f'Started at {datetime.now()} with eps={eps:.3f}')
+    
+    eps = round(eps,3)
+    path='/cloud/Public/_data/neuropercolation/4lay/cons=27-knight_steps=1000100/dim=09/batch=0/'
+    
+    savepath = path + samplemethod + f'_samples={extremes}/dt={dt}/'
+    
+    try:
+        with open(savepath+f"eps={round(eps,3):.3f}_phase_pairs.txt", 'r', encoding='utf-8') as f:
+            phase_pairs = json.load(f)
+        with open(savepath+f"eps={round(eps,3):.3f}_ei_pairs.txt", 'r', encoding='utf-8') as f:
+            ei_pairs = json.load(f)
+    except:
+        sampling(dim,eps,samplemethod,extremes,dt)
+        with open(savepath+f"eps={round(eps,3):.3f}_phase_pairs.txt", 'r', encoding='utf-8') as f:
+            phase_pairs = json.load(f)
+        with open(savepath+f"eps={round(eps,3):.3f}_ei_pairs.txt", 'r', encoding='utf-8') as f:
+            ei_pairs = json.load(f)
+        
+    t, phases_i, phases_c = zip(*phase_pairs)
+    t, ei_i, ei_c = zip(*ei_pairs)
+    
+    extremes = len(t)
+    
+    phases_cdiff = [abs(phases_i[i])-abs(phases_c[i]) for i in range(len(t))]
+    
+    phase_space = np.linspace(-m.pi,m.pi,101)
+    absph_space = np.linspace(0,m.pi,50+1)
+    cdiff_space = np.linspace(min(phases_cdiff),max(phases_cdiff),51)
+    
+    phase_dist_i = [len([ph for ph in phases_i if (phase_space[j]+phase_space[j-1])/2<=ph<(phase_space[j]+phase_space[j+1])/2])/len(t)
+                    for j in range(100)]
+    phase_dist_c = [len([ph for ph in phases_c if (phase_space[j]+phase_space[j-1])/2<=ph<(phase_space[j]+phase_space[j+1])/2])/len(t)
+                    for j in range(100)]
+     
+    absph_dist_i = [len([ph for ph in phases_i if low<=abs(ph)<high])/len(t) for low,high in zip(absph_space[:-1],absph_space[1:])]
+    absph_dist_c = [len([ph for ph in phases_c if low<=abs(ph)<high])/len(t) for low,high in zip(absph_space[:-1],absph_space[1:])]
+    
+    cdiff_dist = [len([diff for diff in phases_cdiff if low<=diff<high])/len(t) for low,high in zip(cdiff_space[:-1],cdiff_space[1:])]
+    
+    max_cha_i = max([round(e/(1-H2(eps))) for e in ei_i])
+    max_cha_c = max([round(e/(1-H2(eps))) for e in ei_c])
+
+    max_cha = max(max_cha_i, max_cha_c)
+    ei_space = np.linspace(0,np.max([ei_i,ei_c]),max_cha+1)
+    
+    ei_dist_i = [len([e for e in ei_i if round(e/(1-H2(eps)))==val])/len(t) for val in range(max_cha)]
+    ei_dist_c = [len([e for e in ei_c if round(e/(1-H2(eps)))==val])/len(t) for val in range(max_cha)]
+
+    qtplot(f'Phase distribution for dt={dt} dim={dim} eps={eps:.3f} with 4 layers',
+            [absph_space[:-1]]*2,
+            [absph_dist_i, absph_dist_c],
+            ['Phase dist with ei',
+              'Phase dist without ei'],
+            x_tag = 'phase',
+            y_tag = 'density',
+            export=True,
+            path=savepath,
+            filename=f'Phase dist eps={round(eps,3):.3f} dim={dim} extremes={extremes}.png',
+            close=True)
+    
+    qtplot(f'Phase distribution for dt={dt} dim={dim} eps={eps:.3f} with 4 layers',
+            [phase_space[:-1]]*2,
+            [phase_dist_i, phase_dist_c],
+            ['Phase dist with ei',
+             'Phase dist without ei'],
+            x_tag = 'phase',
+            y_tag = 'density',
+            export=True,
+            path=savepath,
+            filename=f'Phase original dist eps={round(eps,3):.3f} dim={dim} extremes={extremes}.png',
+            close=True)
+    
+    qtplot(f'Phase causal diff distribution for dt={dt} dim={dim} eps={eps:.3f} with 4 layers',
+            [cdiff_space[:-1]],
+            [cdiff_dist],
+            ['Phase causal difference dist with ei'],
+            x_tag = 'sync raise',
+            y_tag = 'density',
+            export=True,
+            path=savepath,
+            filename=f'Phase causal diff dist eps={round(eps,3):.3f} dim={dim} extremes={extremes}.png',
+            close=True)
+    
+    qtplot(f'EI distribution for dt={dt} dim={dim} eps={eps:.3f} with 4 layers',
+            [ei_space[:-1]]*2,
+            [ei_dist_i, ei_dist_c],
+            ['EI dist with ei',
+              'EI dist without ei'],
+            x_tag = 'ei',
+            y_tag = 'density',
+            export=True,
+            path=savepath,
+            filename=f'EI dist eps={round(eps,3):.3f} dim={dim} extremes={extremes}.png',
+            close=True)
+    
+    ttest(dim,eps,samplemethod,extremes,dt)
+    
+    print(f'Done eps={eps:.3f} with dim={dim} at {datetime.now()}')
+    
+def ttest(dim,eps,samplemethod,extremes,dt):
+    from scipy.stats import ttest_rel, ttest_1samp, normaltest
+    import numpy as np
+    import json
+    
+    eps = round(eps,3)
+    path='/cloud/Public/_data/neuropercolation/4lay/cons=27-knight_steps=1000100/dim=09/batch=0/'
+    
+    savepath = path + samplemethod + f'_samples={extremes}/dt={dt}/'
+
+    try:
+        with open(savepath+f"eps={round(eps,3):.3f}_phase_pairs.txt", 'r', encoding='utf-8') as f:
+            phase_pairs = json.load(f)
+        with open(savepath+f"eps={round(eps,3):.3f}_ei_pairs.txt", 'r', encoding='utf-8') as f:
+            ei_pairs = json.load(f)
+    except:
+        sampling(dim,eps,samplemethod,extremes,dt)
+        with open(savepath+f"eps={round(eps,3):.3f}_phase_pairs.txt", 'r', encoding='utf-8') as f:
+            phase_pairs = json.load(f)
+        with open(savepath+f"eps={round(eps,3):.3f}_ei_pairs.txt", 'r', encoding='utf-8') as f:
+            ei_pairs = json.load(f)
+    
+    t, phases_i, phases_c = zip(*phase_pairs)
+    t, ei_i, ei_c = zip(*ei_pairs)
+    
+    phases_cdiff = [abs(phases_i[i])-abs(phases_c[i]) for i in range(len(t))]
+    
+    stat = phases_cdiff
+    stat_av = np.average(stat)
+    
+    print('===============')
+    print(f'For eps={eps} and dt={dt}: Mean={stat_av}')
+    print('normaltest: pval='+str(normaltest(stat).pvalue))
+    print('ttest: pval='+str(ttest_1samp(stat,0).pvalue))
+    print('===============')
+    
+def full_stats(dim,eps,samplemethod,extremes,dt,ret='stats',noeff=1):
+    from scipy.stats import ttest_rel, ttest_1samp, normaltest, wilcoxon
+    import numpy as np
+    import json
+    import math as m
+    from random import random
+    from numpy.linalg import norm
+    
+    def resultant(sample):
+        phase_x = [m.cos(ind) for ind in sample]
+        phase_y = [m.sin(ind) for ind in sample]
+        
+        return (np.average(phase_x), np.average(phase_y))
+
+    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)
+
+    eps = round(eps,3)
+    path='/cloud/Public/_data/neuropercolation/4lay/cons=27-knight_steps=1000100/dim=09/batch=0/'
+    
+    savepath = path + samplemethod + f'_samples={extremes}/dt={dt}/noeff={noeff:03d}/'
+
+    try:
+        with open(savepath+f"eps={round(eps,3):.3f}_phase_pairs.txt", 'r', encoding='utf-8') as f:
+            phase_pairs = json.load(f)
+        with open(savepath+f"eps={round(eps,3):.3f}_ei_pairs.txt", 'r', encoding='utf-8') as f:
+            ei_pairs = json.load(f)
+    except:
+        sampling(dim,eps,samplemethod,extremes,dt,noeff=noeff)
+        with open(savepath+f"eps={round(eps,3):.3f}_phase_pairs.txt", 'r', encoding='utf-8') as f:
+            phase_pairs = json.load(f)
+        with open(savepath+f"eps={round(eps,3):.3f}_ei_pairs.txt", 'r', encoding='utf-8') as f:
+            ei_pairs = json.load(f)
+    
+    t, phases_i, phases_c = zip(*phase_pairs)
+    t, ei_i, ei_c = zip(*ei_pairs)
+    
+    phases_cdiff = [abs(phases_i[i])-abs(phases_c[i]) if abs(abs(phases_i[i])-abs(phases_c[i]))!=m.pi else m.pi*(-1)**(random()<0.5)
+                    for i in range(len(t))]
+    
+    print('phases with pi diff: '+str(len([i for i in range(len(t)) if abs(abs(phases_i[i])-abs(phases_c[i]))==m.pi])))
+    
+    stat = phases_cdiff
+    mean = np.average(stat)
+    std = np.std(stat)
+    integral = sum([1 for val in stat if val<0])/len(stat)
+    cohend = mean / (np.var(np.abs(phases_i),ddof=1)/2+np.var(np.abs(phases_c),ddof=1)/2)
+    norm_p = normaltest(stat).pvalue
+    ttest_p = ttest_1samp(stat,0,alternative='less').pvalue
+    sign_p = wilcoxon(stat,alternative='less').pvalue
+    print('===============')
+    print(f'For eps={eps} and dt={dt}: Mean={mean}')
+    print('normaltest: pval='+str(norm_p))
+    print('ttest: pval='+str(ttest_p))
+    print('sign: pval='+str(sign_p))
+    print('===============')
+    
+    if ret=='stats':
+        return mean,std,integral,cohend,norm_p,ttest_p,sign_p
+    elif ret=='phases':
+        return norm(resultant(phases_i)), norm(resultant(phases_c))

evaluation/simpleplot.py

@@ -0,0 +1,28 @@
+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/samedist_varmaxpha_causal_roll0.031/'
+eps_sp=np.linspace(0.01,0.2,20)
+eps_ep=eps_sp[3:4]
+
+extremes=200
+strength=200
+
+savepath=path+f'extremes={extremes}_bootstrength={strength}/'
+
+boots=[]
+for eps in eps_ep:
+    
+    with open(savepath+f'eps={eps:.3f}_dt=60_bootstrap.txt','r') as f:
+        
+        confs=list(zip(*json.load(f)))[1]
+        ps=[1-conf for conf in confs]
+        boots.append(ps)
+        
+
+
+
+   
+qtplot("Bootstrapping confidence",[range(61)]*len(eps_sp),boots,[f'{eps}' for eps in eps_sp],y_tag='p-value',y_log=False)

evaluation/updated_bib_file.bib

@@ -0,0 +1,353 @@
+@book{barrat2008,
+	title={Dynamical Processes on Complex Networks},
+	author={Barrat, A. and Barth{\'e}lemy, M. and Vespignani, A.},
+	isbn={9781107377424},
+	url={https://books.google.pt/books?id=fUAhAwAAQBAJ},
+	year={2008},
+	publisher={Cambridge University Press}
+}
+
+@article{Varela2001,
+	title={The brainweb: Phase synchronization and large-scale integration},
+	author={Francisco J. Varela and Jean-Philippe Lachaux and Eugenio Rodriguez and Jacques Martinerie},
+	journal={Nature Reviews Neuroscience},
+	year={2001},
+	volume={2},
+	pages={229-239}
+}
+
+@article{Carmichael2002,
+	title={Synchronous Neuronal Activity Is a Signal for Axonal Sprouting after Cortical Lesions in the Adult},
+	author={S. Thomas Carmichael and M. -F. Chesselet},
+	journal={The Journal of Neuroscience},
+	year={2002},
+	volume={22},
+	pages={6062 - 6070}
+}
+
+@ARTICLE{Otsuka2000,
+	author = {{Otsuka}, Kenju and {Kawai}, Ryoji and {Hwong}, Siao-Lung and {Ko}, Jing-Yuan and {Chern}, Jyh-Long},
+	title = "{Synchronization of Mutually Coupled Self-Mixing Modulated Lasers}",
+	journal = {Phys. Rev. Lett.},
+	year = {2000},
+	month = {apr},
+	volume = {84},
+	number = {14},
+	pages = {3049-3052},
+	doi = {10.1103/PhysRevLett.84.3049},
+	adsurl = {https://ui.adsabs.harvard.edu/abs/2000PhRvL..84.3049O},
+	adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@ARTICLE{Hansel1992,
+	author = {{Hansel}, D. and {Sompolinsky}, H.},
+	title = "{Synchronization and computation in a chaotic neural network}",
+	journal = {Phys. Rev. Lett.},
+	keywords = {87.10.+e, 05.45.+b, General theory and mathematical aspects},
+	year = 1992,
+	month = feb,
+	volume = {68},
+	number = {5},
+	pages = {718-721},
+	doi = {10.1103/PhysRevLett.68.718},
+	adsurl = {https://ui.adsabs.harvard.edu/abs/1992PhRvL..68..718H},
+	adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@ARTICLE{Glass2001,
+	author = {{Glass}, Leon},
+	title = "{Synchronization and rhythmic processes in physiology}",
+	journal = {Nature},
+	year = 2001,
+	month = mar,
+	volume = {410},
+	number = {6825},
+	pages = {277-284},
+	doi = {10.1038/35065745},
+	adsurl = {https://ui.adsabs.harvard.edu/abs/2001Natur.410..277G},
+	adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@article{BIEBERICH2002145,
+	title = {Recurrent fractal neural networks: a strategy for the exchange of local and global information processing in the brain},
+	journal = {Biosystems},
+	volume = {66},
+	number = {3},
+	pages = {145-164},
+	year = {2002},
+	issn = {0303-2647},
+	doi = {https://doi.org/10.1016/S0303-2647(02)00040-0},
+	url = {https://www.sciencedirect.com/science/article/pii/S0303264702000400},
+	author = {Erhard Bieberich},
+	keywords = {Networks, Fractal, Brain, Mind, Consciousness, Neuron},
+	abstract = {The regulation of biological networks relies significantly on convergent feedback signaling loops that render a global output locally accessible. Ideally, the recurrent connectivity within these systems is self-organized by a time-dependent phase-locking mechanism. This study analyzes recurrent fractal neural networks (RFNNs), which utilize a self-similar or fractal branching structure of dendrites and downstream networks for phase-locking of reciprocal feedback loops: output from outer branch nodes of the network tree enters inner branch nodes of the dendritic tree in single neurons. This structural organization enables RFNNs to amplify re-entrant input by over-the-threshold signal summation from feedback loops with equivalent signal traveling times. The columnar organization of pyramidal neurons in the neocortical layers V and III is discussed as the structural substrate for this network architecture. RFNNs self-organize spike trains and render the entire neural network output accessible to the dendritic tree of each neuron within this network. As the result of a contraction mapping operation, the local dendritic input pattern contains a downscaled version of the network output coding structure. RFNNs perform robust, fractal data compression, thus coping with a limited number of feedback loops for signal transport in convergent neural networks. This property is discussed as a significant step toward the solution of a fundamental problem in neuroscience: how is neuronal computation in separate neurons and remote brain areas unified as an instance of experience in consciousness? RFNNs are promising candidates for engaging neural networks into a coherent activity and provide a strategy for the exchange of global and local information processing in the human brain, thereby ensuring the completeness of a transformation from neuronal computation into conscious experience.}
+}
+
+
+@incollection{Chalmers2000,
+	title = {What is a Neural Correlate of Consciousness?},
+	booktitle = {Neural Correlates of Consciousness},
+	author = {David J. Chalmers},
+	publisher = {MIT Press},
+	year = {2000},
+	editor = {Thomas Metzinger}
+}
+
+@inproceedings{Crick1990,
+	title={Towards a neurobiological theory of consciousness},
+	author={Crick, Francis and Koch, Christof},
+	booktitle={Seminars in the Neurosciences (Vol.2)},
+	year={1990},
+	organization={Saunders Scientific Publications}
+}
+
+
+@article{Hidaka2018,
+	doi = {10.1371/journal.pone.0201126},
+	author = {Hidaka, Shohei AND Oizumi, Masafumi},
+	journal = {PLOS ONE},
+	publisher = {Public Library of Science},
+	title = {Fast and exact search for the partition with minimal information loss},
+	year = {2018},
+	month = {09},
+	volume = {13},
+	url = {https://doi.org/10.1371/journal.pone.0201126},
+	pages = {1-14},
+	number = {9},
+	
+}
+
+@Article{Mediano2019,
+	AUTHOR = {Mediano, Pedro A.M. and Seth, Anil K. and Barrett, Adam B.},
+	TITLE = {Measuring Integrated Information: Comparison of Candidate Measures in Theory and Simulation},
+	JOURNAL = {Entropy},
+	VOLUME = {21},
+	YEAR = {2019},
+	NUMBER = {1},
+	ARTICLE-NUMBER = {17},
+	URL = {https://www.mdpi.com/1099-4300/21/1/17},
+	ISSN = {1099-4300}
+}
+
+@incollection{ENGEL2016,
+	title = {Chapter 3 - Neuronal Oscillations, Coherence, and Consciousness},
+	editor = {Steven Laureys and Olivia Gosseries and Giulio Tononi},
+	booktitle = {The Neurology of Conciousness (Second Edition)},
+	publisher = {Academic Press},
+	edition = {Second Edition},
+	address = {San Diego},
+	pages = {49-60},
+	year = {2016},
+	author = {Andreas K. Engel and Pascal Fries}}
+
+
+@article{FRIES2015,
+	title = {Rhythms for Cognition: Communication through Coherence},
+	journal = {Neuron},
+	volume = {88},
+	number = {1},
+	pages = {220-235},
+	year = {2015},
+	author = {Pascal Fries}
+}
+
+
+@article{OIZUMI2014,
+	author = {Oizumi, Masafumi AND Albantakis, Larissa AND Tononi, Giulio},
+	journal = {PLOS Computational Biology},
+	publisher = {Public Library of Science},
+	title = {From the Phenomenology to the Mechanisms of Consciousness: Integrated Information Theory 3.0},
+	year = {2014},
+	month = {05},
+	volume = {10},
+	pages = {1-25},
+	number = {5}
+}
+
+@article{DOERIG2019,
+	title = {The unfolding argument: Why IIT and other causal structure theories cannot explain consciousness},
+	author = {Doerig, Adrien and Schurger, Aaron and Hess, Kathryn and Herzog, Michael H.},
+	journal = {Consciousness and Cognition},
+	volume = {72},
+	year = {2019}
+}
+
+@book{BARRAT2008,
+	title={Dynamical Processes on Complex Networks},
+	author={Barrat, A. and Barth{\'e}lemy, M. and Vespignani, A.},
+	year={2008},
+	publisher={Cambridge University Press}
+}
+
+
+
+@article{Tononi2004,
+	title={An information integration theory of consciousness},
+	author={Giulio Tononi},
+	journal={BMC Neuroscience},
+	year={2004},
+	volume={5},
+	pages={42 - 42}
+}
+
+@article{Rezaei2020,
+	author = {Rezaei, Hedyeh AND Aertsen, Ad AND Kumar, Arvind AND Valizadeh, Alireza},
+	journal = {PLOS Computational Biology},
+	publisher = {Public Library of Science},
+	title = {Facilitating the propagation of spiking activity in feedforward networks by including feedback},
+	year = {2020},
+	month = {08},
+	volume = {16},
+	pages = {1-27},
+	number = {8}	
+}
+
+
+@book{BARRAT2008,
+	title={Dynamical Processes on Complex Networks},
+	author={Barrat, A. and Barth{\'e}lemy, M. and Vespignani, A.},
+	year={2008},
+	publisher={Cambridge University Press}
+}
+
+
+@ARTICLE{LLINAS2014,
+	
+	AUTHOR={Llinás, Rodolfo R.},   
+	
+	TITLE={Intrinsic electrical properties of mammalian neurons and CNS function: a historical perspective},      
+	
+	JOURNAL={Frontiers in Cellular Neuroscience},     
+	
+	YEAR={2014}
+}
+
+@article{Mayner2018,
+	author = {Mayner, William G. P. AND Marshall, William AND Albantakis, Larissa AND Findlay, Graham AND Marchman, Robert AND Tononi, Giulio},
+	journal = {PLOS Computational Biology},
+	publisher = {Public Library of Science},
+	title = {PyPhi: A toolbox for integrated information theory},
+	year = {2018},
+	month = {07},
+	volume = {14},
+	pages = {1-21},
+	number = {7}	
+}
+
+@article{Hahn2014CommunicationTR,
+	title={Communication through Resonance in Spiking Neuronal Networks},
+	author={Gerald Hahn and Alejandro F. Bujan and Yves Fr{\'e}gnac and Ad Aertsen and Arvind Kumar},
+	journal={PLoS Computational Biology},
+	year={2014},
+	volume={10}
+}
+ 
+@article{Fries2005AMF,
+	title={A mechanism for cognitive dynamics: neuronal communication through neuronal coherence},
+	author={Pascal Fries},
+	journal={Trends in Cognitive Sciences},
+	year={2005},
+	volume={9},
+	pages={474-480},
+	url={}
+}
+
+@book{neuroscience6th,
+	title = {Neuroscience},
+	edition = {Sixth},
+	editor = {Purves, Dale and Augustine, George J. and Fitzpatrick, David and Hall, William C. and LaMantia, Anthony-Samuel and Mooney, Richard D. and Platt, Michael L. and White, Leonard E.},
+	year = {2017},
+	publisher = {Sinauer Associates},
+	address = {Sunderland, MA},
+	isbn = {9781605353807},
+	pages = {960},
+	month = {October 12},
+}
+
+@article{Bennett2020AnAA,
+	title={An Attempt at a Unified Theory of the Neocortical Microcircuit in Sensory Cortex},
+	author={Max Bennett},
+	journal={Frontiers in Neural Circuits},
+	year={2020},
+	volume={14},
+	url={}
+}
+
+@article{vanKerkoerle2014AlphaAG,
+	title={Alpha and gamma oscillations characterize feedback and feedforward processing in monkey visual cortex},
+	author={Timo van Kerkoerle and Matthew W. Self and Bruno Dagnino and Marie-Alice Gariel-Mathis and Jasper Poort and Chris van der Togt and Pieter R. Roelfsema},
+	journal={Proceedings of the National Academy of Sciences},
+	year={2014},
+	volume={111},
+	pages={14332 - 14341},
+	url={}
+}
+
+@article {Westerberg2022,
+	article_type = {journal},
+	title = {Laminar microcircuitry of visual cortex producing attention-associated electric fields},
+	author = {Westerberg, Jacob A and Schall, Michelle S and Maier, Alexander and Woodman, Geoffrey F and Schall, Jeffrey D},
+	editor = {Ray, Supratim and Baker, Chris I and Luck, Steven J and Nandy, Anirvan S},
+	volume = 11,
+	year = 2022,
+	month = {jan},
+	pub_date = {2022-01-28},
+	pages = {e72139},
+	citation = {eLife 2022;11:e72139},
+	doi = {10.7554/eLife.72139},
+	url = {https://doi.org/10.7554/eLife.72139},
+	keywords = {CSD, ECoG, EEG, LFP, N2pc, V4},
+	journal = {eLife},
+	issn = {2050-084X},
+	publisher = {eLife Sciences Publications, Ltd},
+}
+@inproceedings{Presigny2021MultiscaleMO,
+	title={Multiscale modeling of brain network organization},
+	author={Charley Presigny and Fabrizio De Vico Fallani},
+	year={2021},
+	url={}
+}
+
+@article{Mejas2016FeedforwardAF,
+	title={Feedforward and feedback frequency-dependent interactions in a large-scale laminar network of the primate cortex},
+	author={Jorge F. Mej{\'i}as and John D. Murray and Henry Kennedy and Xiao-Jing Wang},
+	journal={Science Advances},
+	year={2016},
+	volume={2},
+	url={}
+}
+
+@article{Rezaei2019FacilitatingTP,
+	title={Facilitating the propagation of spiking activity in feedforward networks by including feedback},
+	author={Hedyeh Rezaei and Ad Aertsen and Alireza Valizadeh and Arvind Kumar},
+	journal={PLoS Computational Biology},
+	year={2019},
+	volume={16},
+	url={}
+}
+
+@article{Hahn2014CommunicationTR,
+	title={Communication through Resonance in Spiking Neuronal Networks},
+	author={Gerald Hahn and Alejandro F. Bujan and Yves Fr{\'e}gnac and Ad Aertsen and Arvind Kumar},
+	journal={PLoS Computational Biology},
+	year={2014},
+	volume={10},
+	url={}
+}
+
+@article{Jensen2014HumanBO,
+	title={Human Brain Oscillations: From Physiological Mechanisms to Analysis and Cognition},
+	author={Ole Jensen and Eelke Spaak and Johanna M. Zumer},
+	journal={Magnetoencephalography},
+	year={2014},
+	url={}
+}
+
+@article{Lowet2015InputDependentFM,
+	title={Input-Dependent Frequency Modulation of Cortical Gamma Oscillations Shapes Spatial Synchronization and Enables Phase Coding},
+	author={Eric Lowet and M. Roberts and Avgis Hadjipapas and Alina Peter and Jan van der Eerden and Peter de Weerd},
+	journal={PLoS Computational Biology},
+	year={2015},
+	volume={11},
+	url={}
+}

evaluation/updated_sync.bib

@@ -0,0 +1,353 @@
+@book{barrat2008,
+	title={Dynamical Processes on Complex Networks},
+	author={Barrat, A. and Barth{\'e}lemy, M. and Vespignani, A.},
+	isbn={9781107377424},
+	url={https://books.google.pt/books?id=fUAhAwAAQBAJ},
+	year={2008},
+	publisher={Cambridge University Press}
+}
+
+@article{Varela2001,
+	title={The brainweb: Phase synchronization and large-scale integration},
+	author={Francisco J. Varela and Jean-Philippe Lachaux and Eugenio Rodriguez and Jacques Martinerie},
+	journal={Nature Reviews Neuroscience},
+	year={2001},
+	volume={2},
+	pages={229-239}
+}
+
+@article{Carmichael2002,
+	title={Synchronous Neuronal Activity Is a Signal for Axonal Sprouting after Cortical Lesions in the Adult},
+	author={S. Thomas Carmichael and M. -F. Chesselet},
+	journal={The Journal of Neuroscience},
+	year={2002},
+	volume={22},
+	pages={6062 - 6070}
+}
+
+@ARTICLE{Otsuka2000,
+	author = {{Otsuka}, Kenju and {Kawai}, Ryoji and {Hwong}, Siao-Lung and {Ko}, Jing-Yuan and {Chern}, Jyh-Long},
+	title = "{Synchronization of Mutually Coupled Self-Mixing Modulated Lasers}",
+	journal = {Phys. Rev. Lett.},
+	year = {2000},
+	month = {apr},
+	volume = {84},
+	number = {14},
+	pages = {3049-3052},
+	doi = {10.1103/PhysRevLett.84.3049},
+	adsurl = {https://ui.adsabs.harvard.edu/abs/2000PhRvL..84.3049O},
+	adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@ARTICLE{Hansel1992,
+	author = {{Hansel}, D. and {Sompolinsky}, H.},
+	title = "{Synchronization and computation in a chaotic neural network}",
+	journal = {Phys. Rev. Lett.},
+	keywords = {87.10.+e, 05.45.+b, General theory and mathematical aspects},
+	year = 1992,
+	month = feb,
+	volume = {68},
+	number = {5},
+	pages = {718-721},
+	doi = {10.1103/PhysRevLett.68.718},
+	adsurl = {https://ui.adsabs.harvard.edu/abs/1992PhRvL..68..718H},
+	adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@ARTICLE{Glass2001,
+	author = {{Glass}, Leon},
+	title = "{Synchronization and rhythmic processes in physiology}",
+	journal = {Nature},
+	year = 2001,
+	month = mar,
+	volume = {410},
+	number = {6825},
+	pages = {277-284},
+	doi = {10.1038/35065745},
+	adsurl = {https://ui.adsabs.harvard.edu/abs/2001Natur.410..277G},
+	adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@article{BIEBERICH2002145,
+	title = {Recurrent fractal neural networks: a strategy for the exchange of local and global information processing in the brain},
+	journal = {Biosystems},
+	volume = {66},
+	number = {3},
+	pages = {145-164},
+	year = {2002},
+	issn = {0303-2647},
+	doi = {https://doi.org/10.1016/S0303-2647(02)00040-0},
+	url = {https://www.sciencedirect.com/science/article/pii/S0303264702000400},
+	author = {Erhard Bieberich},
+	keywords = {Networks, Fractal, Brain, Mind, Consciousness, Neuron},
+	abstract = {The regulation of biological networks relies significantly on convergent feedback signaling loops that render a global output locally accessible. Ideally, the recurrent connectivity within these systems is self-organized by a time-dependent phase-locking mechanism. This study analyzes recurrent fractal neural networks (RFNNs), which utilize a self-similar or fractal branching structure of dendrites and downstream networks for phase-locking of reciprocal feedback loops: output from outer branch nodes of the network tree enters inner branch nodes of the dendritic tree in single neurons. This structural organization enables RFNNs to amplify re-entrant input by over-the-threshold signal summation from feedback loops with equivalent signal traveling times. The columnar organization of pyramidal neurons in the neocortical layers V and III is discussed as the structural substrate for this network architecture. RFNNs self-organize spike trains and render the entire neural network output accessible to the dendritic tree of each neuron within this network. As the result of a contraction mapping operation, the local dendritic input pattern contains a downscaled version of the network output coding structure. RFNNs perform robust, fractal data compression, thus coping with a limited number of feedback loops for signal transport in convergent neural networks. This property is discussed as a significant step toward the solution of a fundamental problem in neuroscience: how is neuronal computation in separate neurons and remote brain areas unified as an instance of experience in consciousness? RFNNs are promising candidates for engaging neural networks into a coherent activity and provide a strategy for the exchange of global and local information processing in the human brain, thereby ensuring the completeness of a transformation from neuronal computation into conscious experience.}
+}
+
+
+@incollection{Chalmers2000,
+	title = {What is a Neural Correlate of Consciousness?},
+	booktitle = {Neural Correlates of Consciousness},
+	author = {David J. Chalmers},
+	publisher = {MIT Press},
+	year = {2000},
+	editor = {Thomas Metzinger}
+}
+
+@inproceedings{Crick1990,
+	title={Towards a neurobiological theory of consciousness},
+	author={Crick, Francis and Koch, Christof},
+	booktitle={Seminars in the Neurosciences (Vol.2)},
+	year={1990},
+	organization={Saunders Scientific Publications}
+}
+
+
+@article{Hidaka2018,
+	doi = {10.1371/journal.pone.0201126},
+	author = {Hidaka, Shohei AND Oizumi, Masafumi},
+	journal = {PLOS ONE},
+	publisher = {Public Library of Science},
+	title = {Fast and exact search for the partition with minimal information loss},
+	year = {2018},
+	month = {09},
+	volume = {13},
+	url = {https://doi.org/10.1371/journal.pone.0201126},
+	pages = {1-14},
+	number = {9},
+	
+}
+
+@Article{Mediano2019,
+	AUTHOR = {Mediano, Pedro A.M. and Seth, Anil K. and Barrett, Adam B.},
+	TITLE = {Measuring Integrated Information: Comparison of Candidate Measures in Theory and Simulation},
+	JOURNAL = {Entropy},
+	VOLUME = {21},
+	YEAR = {2019},
+	NUMBER = {1},
+	ARTICLE-NUMBER = {17},
+	URL = {https://www.mdpi.com/1099-4300/21/1/17},
+	ISSN = {1099-4300}
+}
+
+@incollection{ENGEL2016,
+	title = {Chapter 3 - Neuronal Oscillations, Coherence, and Consciousness},
+	editor = {Steven Laureys and Olivia Gosseries and Giulio Tononi},
+	booktitle = {The Neurology of Conciousness (Second Edition)},
+	publisher = {Academic Press},
+	edition = {Second Edition},
+	address = {San Diego},
+	pages = {49-60},
+	year = {2016},
+	author = {Andreas K. Engel and Pascal Fries}}
+
+
+@article{FRIES2015,
+	title = {Rhythms for Cognition: Communication through Coherence},
+	journal = {Neuron},
+	volume = {88},
+	number = {1},
+	pages = {220-235},
+	year = {2015},
+	author = {Pascal Fries}
+}
+
+
+@article{OIZUMI2014,
+	author = {Oizumi, Masafumi AND Albantakis, Larissa AND Tononi, Giulio},
+	journal = {PLOS Computational Biology},
+	publisher = {Public Library of Science},
+	title = {From the Phenomenology to the Mechanisms of Consciousness: Integrated Information Theory 3.0},
+	year = {2014},
+	month = {05},
+	volume = {10},
+	pages = {1-25},
+	number = {5}
+}
+
+@article{DOERIG2019,
+	title = {The unfolding argument: Why IIT and other causal structure theories cannot explain consciousness},
+	author = {Doerig, Adrien and Schurger, Aaron and Hess, Kathryn and Herzog, Michael H.},
+	journal = {Consciousness and Cognition},
+	volume = {72},
+	year = {2019}
+}
+
+@book{BARRAT2008,
+	title={Dynamical Processes on Complex Networks},
+	author={Barrat, A. and Barth{\'e}lemy, M. and Vespignani, A.},
+	year={2008},
+	publisher={Cambridge University Press}
+}
+
+
+
+@article{Tononi2004,
+	title={An information integration theory of consciousness},
+	author={Giulio Tononi},
+	journal={BMC Neuroscience},
+	year={2004},
+	volume={5},
+	pages={42 - 42}
+}
+
+@article{Rezaei2020,
+	author = {Rezaei, Hedyeh AND Aertsen, Ad AND Kumar, Arvind AND Valizadeh, Alireza},
+	journal = {PLOS Computational Biology},
+	publisher = {Public Library of Science},
+	title = {Facilitating the propagation of spiking activity in feedforward networks by including feedback},
+	year = {2020},
+	month = {08},
+	volume = {16},
+	pages = {1-27},
+	number = {8}	
+}
+
+
+@book{BARRAT2008,
+	title={Dynamical Processes on Complex Networks},
+	author={Barrat, A. and Barth{\'e}lemy, M. and Vespignani, A.},
+	year={2008},
+	publisher={Cambridge University Press}
+}
+
+
+@ARTICLE{LLINAS2014,
+	
+	AUTHOR={Llinás, Rodolfo R.},   
+	
+	TITLE={Intrinsic electrical properties of mammalian neurons and CNS function: a historical perspective},      
+	
+	JOURNAL={Frontiers in Cellular Neuroscience},     
+	
+	YEAR={2014}
+}
+
+@article{Mayner2018,
+	author = {Mayner, William G. P. AND Marshall, William AND Albantakis, Larissa AND Findlay, Graham AND Marchman, Robert AND Tononi, Giulio},
+	journal = {PLOS Computational Biology},
+	publisher = {Public Library of Science},
+	title = {PyPhi: A toolbox for integrated information theory},
+	year = {2018},
+	month = {07},
+	volume = {14},
+	pages = {1-21},
+	number = {7}	
+}
+
+@article{Hahn2014CommunicationTR,
+	title={Communication through Resonance in Spiking Neuronal Networks},
+	author={Gerald Hahn and Alejandro F. Bujan and Yves Fr{\'e}gnac and Ad Aertsen and Arvind Kumar},
+	journal={PLoS Computational Biology},
+	year={2014},
+	volume={10}
+}
+ 
+@article{Fries2005AMF,
+	title={A mechanism for cognitive dynamics: neuronal communication through neuronal coherence},
+	author={Pascal Fries},
+	journal={Trends in Cognitive Sciences},
+	year={2005},
+	volume={9},
+	pages={474-480},
+	url={}
+}
+
+@book{neuroscience6th,
+	title = {Neuroscience},
+	edition = {Sixth},
+	editor = {Purves, Dale and Augustine, George J. and Fitzpatrick, David and Hall, William C. and LaMantia, Anthony-Samuel and Mooney, Richard D. and Platt, Michael L. and White, Leonard E.},
+	year = {2017},
+	publisher = {Sinauer Associates},
+	address = {Sunderland, MA},
+	isbn = {9781605353807},
+	pages = {960},
+	month = {October 12},
+}
+
+@article{Bennett2020AnAA,
+	title={An Attempt at a Unified Theory of the Neocortical Microcircuit in Sensory Cortex},
+	author={Max Bennett},
+	journal={Frontiers in Neural Circuits},
+	year={2020},
+	volume={14},
+	url={}
+}
+
+@article{vanKerkoerle2014AlphaAG,
+	title={Alpha and gamma oscillations characterize feedback and feedforward processing in monkey visual cortex},
+	author={Timo van Kerkoerle and Matthew W. Self and Bruno Dagnino and Marie-Alice Gariel-Mathis and Jasper Poort and Chris van der Togt and Pieter R. Roelfsema},
+	journal={Proceedings of the National Academy of Sciences},
+	year={2014},
+	volume={111},
+	pages={14332 - 14341},
+	url={}
+}
+
+@article {Westerberg2022,
+	article_type = {journal},
+	title = {Laminar microcircuitry of visual cortex producing attention-associated electric fields},
+	author = {Westerberg, Jacob A and Schall, Michelle S and Maier, Alexander and Woodman, Geoffrey F and Schall, Jeffrey D},
+	editor = {Ray, Supratim and Baker, Chris I and Luck, Steven J and Nandy, Anirvan S},
+	volume = 11,
+	year = 2022,
+	month = {jan},
+	pub_date = {2022-01-28},
+	pages = {e72139},
+	citation = {eLife 2022;11:e72139},
+	doi = {10.7554/eLife.72139},
+	url = {https://doi.org/10.7554/eLife.72139},
+	keywords = {CSD, ECoG, EEG, LFP, N2pc, V4},
+	journal = {eLife},
+	issn = {2050-084X},
+	publisher = {eLife Sciences Publications, Ltd},
+}
+@inproceedings{Presigny2021MultiscaleMO,
+	title={Multiscale modeling of brain network organization},
+	author={Charley Presigny and Fabrizio De Vico Fallani},
+	year={2021},
+	url={}
+}
+
+@article{Mejas2016FeedforwardAF,
+	title={Feedforward and feedback frequency-dependent interactions in a large-scale laminar network of the primate cortex},
+	author={Jorge F. Mej{\'i}as and John D. Murray and Henry Kennedy and Xiao-Jing Wang},
+	journal={Science Advances},
+	year={2016},
+	volume={2},
+	url={}
+}
+
+@article{Rezaei2019FacilitatingTP,
+	title={Facilitating the propagation of spiking activity in feedforward networks by including feedback},
+	author={Hedyeh Rezaei and Ad Aertsen and Alireza Valizadeh and Arvind Kumar},
+	journal={PLoS Computational Biology},
+	year={2019},
+	volume={16},
+	url={}
+}
+
+@article{Hahn2014CommunicationTR,
+	title={Communication through Resonance in Spiking Neuronal Networks},
+	author={Gerald Hahn and Alejandro F. Bujan and Yves Fr{\'e}gnac and Ad Aertsen and Arvind Kumar},
+	journal={PLoS Computational Biology},
+	year={2014},
+	volume={10},
+	url={}
+}
+
+@article{Jensen2014HumanBO,
+	title={Human Brain Oscillations: From Physiological Mechanisms to Analysis and Cognition},
+	author={Ole Jensen and Eelke Spaak and Johanna M. Zumer},
+	journal={Magnetoencephalography},
+	year={2014},
+	url={}
+}
+
+@article{Lowet2015InputDependentFM,
+	title={Input-Dependent Frequency Modulation of Cortical Gamma Oscillations Shapes Spatial Synchronization and Enables Phase Coding},
+	author={Eric Lowet and M. Roberts and Avgis Hadjipapas and Alina Peter and Jan van der Eerden and Peter de Weerd},
+	journal={PLoS Computational Biology},
+	year={2015},
+	volume={11},
+	url={}
+}

examples/Simulate1Layer.py

@@ -10,17 +10,19 @@ import numpy as np
 from neuropercolation import Simulate1Layer
 
 #eps_space = np.linspace(0.005,0.5,100)
-eps_space = np.linspace(0.135,0.15,4)
+eps_space = np.linspace(0.01,0.5,50)
+stp = 1000100
 
-for dim in [49,100]:
+for dim in range(11,21,2):
     for eps in eps_space:
         eps = round(eps,3)
-        Simulate2Layers(dim,
+        Simulate1Layer(dim,
                        eps,
-                       res=2,
+                       steps=stp,
-                       path=f'/cloud/Public/_data/neuropercolation/1lay/steps=100000/dim={dim:02}/',
+                       init = 0,
-                       #draw=None
+                       draw=None,
-                       ).run(evolutions_per_second=30,
+                       res=6,
-                             last_evolution_step=100000,
+                       save='all',
-                             save_states=False)
+                       path=f'/cloud/Public/_data/neuropercolation/1lay/steps={stp}/dim={dim:02}/',
-        print(f'Done eps={eps:.3f} with dim={dim} at {datetime.now()}')
+                       )
+        print(f'Done eps={eps:.3f} with dim={dim} at {datetime.now()}')

examples/Simulate2Layers.py

@@ -8,30 +8,20 @@ Created on Fri Aug 18 19:05:04 2023
 
 from datetime import datetime
 import numpy as np
-from neuropercolation import Simulate2Layers, Simulate4Layers
+from neuropercolation import Simulate2Layers
 
 eps_space = np.linspace(0.005,0.5,100)
 #eps_space = np.linspace(0.135,0.15,4)
 
-for dim in [8]:
+dims=list(range(21,27,2))
-    for eps in eps_space:
+for dim in [101]:
-        eps = round(eps,3)
+    for eps in [0.15]:
-        sim = Simulate4Layers(dim,
-                       eps,
-                       steps=100100,
-                       draw=None,
-                       save='all',
-                       path=f'/cloud/Public/_data/neuropercolation/4lay/steps=100100/dim={dim:02}/',
-                       )
-        print(f'Done eps={eps:.3f} with dim={dim} at {datetime.now()}')
-    
-    for eps in eps_space:
         eps = round(eps,3)
         sim = Simulate2Layers(dim,
                        eps,
                        steps=100100,
-                       draw=None,
+                       draw='pygame',
                        save='all',
                        path=f'/cloud/Public/_data/neuropercolation/2lay/steps=100100/dim={dim:02}/',
                        )
-        print(f'Done eps={eps:.3f} with dim={dim} at {datetime.now()}')
+        print(f'Done eps={eps:.3f} with dim={dim} at {datetime.now()}')

examples/Simulate4Layers.py

@@ -6,29 +6,53 @@ Created on Fri Aug 18 19:05:04 2023
 @author: astral
 """
 
+import os
 from datetime import datetime
 import numpy as np
 from neuropercolation import Simulate4Layers
 
+def new_folder(path):
+    if not os.path.exists(path):
+        os.makedirs(path)
+
 eps_space = np.linspace(0.005,0.5,100)
 #eps_space = np.linspace(0.135,0.15,4)
 
 stp = 1000100
+dims = range(9,10)
+batches = 1
 
-for batch in range(5):
+path = f'/cloud/Public/_data/neuropercolation/4lay/cons=27-knight_steps=1000100_diares/dim=09/batch=0/'
-    for dim in [8]:
+
-        for eps in eps_space[1:41:2]:
+for dim in dims:
+    con_gap = 3
+    cons = [(n,(2*n+m)%dim) for n in range(dim) for m in range(0,dim-2,con_gap)]
+    dimpath = path + f'dim={dim:02}_cons={len(cons)}/'
+    
+    max_bat=0
+    # for file in os.listdir(dimpath):
+    #     f = os.path.join(dimpath, file)
+    #     if not os.path.isfile(f):
+    #         bat = file.replace('batch=','')
+    #         if bat != file and int(bat)+1 > max_bat:
+    #             max_bat = int(bat)+1
+    
+    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]):
             eps = round(eps,3)
-            cons = [(n,(n+m)%dim) for n in range(dim) for m in [0,int(dim/2)]]
             initstate = [[0,0],[0,0]]
             sim = Simulate4Layers(dim,
                            eps,
                            coupling=cons,
                            init=initstate,
                            steps=stp,
+                           noeffect=-1,
+                           #fps=20,
                            draw=None,
-                           res=2,
+                           res=6,
-                           save='simple',
+                           save='all',
-                           path=f'/cloud/Public/_data/neuropercolation/4lay/cons={len(cons)}-2diag_steps={stp}/dim={dim:02}/batch={batch}/',
+                           path=path,
                            )
             print(f'Done eps={eps:.3f} with dim={dim} at {datetime.now()}')

neuropercolation/automaton.py

@@ -92,7 +92,7 @@ class Neurolattice(CellularAutomatonCreator, abc.ABC):
         self.epsilon = eps
         
     def init_cell_state(self, coord):  # pylint: disable=no-self-use
-        return DEAD
+        return [self.init]
 
     def get_cells(self):
         return self._current_state
@@ -195,7 +195,8 @@ class Neuropercolation(CellularAutomatonCreator, abc.ABC):
         for coord, old, new in zip(this_state.keys(), this_state.values(), next_state.values()):
             coord_c = tuple([*coord[:2],int(1-coord[2])])
             old_c = this_state[coord_c]
-            new_state = evolution_rule(old.state.copy(), old_c.state.copy(), [n.state[0] for n in old.neighbors], coord[2], coord_c[2]) #inverse the inhibitory layer's action
+            new_state = evolution_rule(old.state.copy(), old_c.state.copy(), [n.state[0] for n in old.neighbors], coord[2], coord_c[2])
+            #inverse the inhibitory layer's action
             
             evolve_cell(old, new, new_state)
         
@@ -233,16 +234,25 @@ class Neuropercolation(CellularAutomatonCreator, abc.ABC):
         
 class NeuropercolationCoupled(CellularAutomatonCreator, abc.ABC):
     
-    def __init__(self, dim, eps, coupling=[], init=[[0,0],[0,0]], *args, **kwargs):
+    def __init__(self, dim, eps, coupling=[], init=[[0,0],[0,0]], noeffect=-1, *args, **kwargs):
         super().__init__(dimension=[dim, dim, 2, 2],
                          init=init,
                          neighborhood=VonNeumannNeighborhood(EdgeRule.FIRST_AND_LAST_CELL_OF_DIMENSION_ARE_NEIGHBORS))
         self._evolution_step = 0
         self.epsilon = eps
         self.coupling = coupling
+        self.noeffect = noeffect
         
     def init_cell_state(self, coord):  # pylint: disable=no-self-use
-        return [self.init[coord[3]][coord[2]]]
+        if type(self.init) is list:
+            return [self.init[coord[3]][coord[2]]]
+        elif type(self.init) is str:
+            self.init = self.init.translate(str.maketrans('', '', '.-='))
+            dim = self._dimension[0]
+            assert len(self.init)==4*dim**2
+            coordval = [1, dim, dim**2, 2*dim**2]
+            digit = sum([coord[i]*coordval[i] for i in range(4)])
+            return [int(self.init[digit])]
     
     def get_cells(self):
         return self._current_state
@@ -277,11 +287,14 @@ class NeuropercolationCoupled(CellularAutomatonCreator, abc.ABC):
             if coord[:2] in self.coupling:
                 coord_c = tuple([*coord[:2],coord[2],int(1-coord[3])])
                 old_c = this_state[coord_c]
-                new_state = evolution_rule(old.state.copy(), old_c.state.copy(), [n.state[0] for n in old.neighbors], 0)
+                new_state = evolution_rule(old.state.copy(), old_c.state.copy(), [n.state[0] for n in old.neighbors], 0) \
+                    if self.noeffect<self._evolution_step \
+                    else evolution_rule(old.state.copy(), old_c.state.copy(), [n.state[0] for n in old.neighbors], 'disabled')
             else:
                 coord_c = tuple([*coord[:2],int(1-coord[2]),coord[3]])
                 old_c = this_state[coord_c]
-                new_state = evolution_rule(old.state.copy(), old_c.state.copy(), [n.state[0] for n in old.neighbors], coord_c[2]) #inverse the inhibitory layer's action
+                new_state = evolution_rule(old.state.copy(), old_c.state.copy(), [n.state[0] for n in old.neighbors], coord_c[2])
+                #inverse the inhibitory layer's action
                 
             evolve_cell(old, new, new_state)
 
@@ -295,20 +308,25 @@ class NeuropercolationCoupled(CellularAutomatonCreator, abc.ABC):
         new_cell_state = last_cell_state
         if other_layer==0:
             alive_neighbours = sum(neighbors_last_states)+link_last_state[0] # adjust for excitatory link cells
-        else:
+        elif other_layer==1:
             alive_neighbours = sum(neighbors_last_states)+(1-link_last_state[0]) # adjust for inhibitory link cells
+        else:
+            alive_neighbours = sum(neighbors_last_states)+0.5
         
         CASE = (random.random()>=self.epsilon)
-        if alive_neighbours > 2:
+        if alive_neighbours > 2.5:
             if CASE:
                 new_cell_state = ALIVE
             else:
                 new_cell_state = DEAD
+        elif alive_neighbours < 2.5:
+            if CASE:
+                new_cell_state = DEAD
+            else:
+                new_cell_state = ALIVE
         else:
-            if CASE:
+            new_cell_state = [int(random.random()>=0.5)]
-                new_cell_state = DEAD
+            
-            else:
-                new_cell_state = ALIVE
         return new_cell_state
     
     def count_channels(self):

neuropercolation/display.py

@@ -148,7 +148,7 @@ class Simulate1Layer:
             self._append_activation()
         
     def _append_all(self):
-        automaton_state = [[0 for n in range(self.__dimension)] for m in range(self.__dimension)]
+        automaton_state = [[0 for n in range(self.__dimension)] for l in range(self.__dimension)]
         activation = 0
         for coord, cell in self._cellular_automaton._current_state.items():
             x,y = coord
@@ -321,7 +321,7 @@ class Simulate2Layers:
             self.__channel_list.append(self._cellular_automaton.count_channels())
         
     def _append_all(self):
-        automaton_state = [[[0 for n in range(self.__dimension)] for m in range(self.__dimension)] for l in range(2)]
+        automaton_state = [[[0 for n in range(self.__dimension)] for l in range(self.__dimension)] for k in range(2)]
         activation = [0]*2
         for coord, cell in self._cellular_automaton._current_state.items():
             x,y,l = coord
@@ -424,6 +424,7 @@ class Simulate4Layers:
                  eps,
                  coupling=[],
                  init=[[0,0],[0,0]],
+                 noeffect=-1,
                  steps=100,
                  draw='pygame',
                  res=4,
@@ -442,11 +443,12 @@ class Simulate4Layers:
         :param state_to_color_cb:   A callback to define the draw color of CA states (default: red for states != 0)
         """
         super().__init__(*args, **kwargs)
-        self._cellular_automaton = NeuropercolationCoupled(dim,eps,coupling,init)
+        self._cellular_automaton = NeuropercolationCoupled(dim,eps,coupling,init,noeffect)
         self.__active = True
         self.__cell_size = [res,res]
         self.__dimension = dim
         self.__epsilon = eps
+        self.__coupling = coupling
         self.__gridside = dim*res
         self.__samegap = 10
         self.__othergap = 20
@@ -499,18 +501,22 @@ class Simulate4Layers:
                     except:
                         print('Failed to quit pygame')
                 
+    def _activations(self):
+        return self.__activation_list
     
-            
+    def _channels(self):
+        return self.__channel_list
+             
     
     def _track(self):
         if self.__save == 'all':
             self._append_all()
-        elif self.__save == 'simple':
+        else:
             self._append_activation()
             self.__channel_list.append(self._cellular_automaton.count_channels())
 
     def _append_all(self):
-        automaton_state = [[[[0 for n in range(self.__dimension)] for m in range(self.__dimension)] for l in range(2)] for k in range(2)]
+        automaton_state = [[[[0 for n in range(self.__dimension)] for l in range(self.__dimension)] for k in range(2)] for j in range(2)]
         activation = [[0,0],[0,0]]
         for coord, cell in self._cellular_automaton._current_state.items():
             x,y,l,o = coord
@@ -545,7 +551,9 @@ class Simulate4Layers:
     def _save_all(self):
         if not os.path.exists(self.__path):
             os.makedirs(self.__path)
-            
+        
+        with open(self.__path+f"eps={round(self.__epsilon,3):.3f}_coupling.txt", 'w', encoding='utf-8') as f:
+            json.dump(self.__coupling, f, indent=1)
         with open(self.__path+f"eps={round(self.__epsilon,3):.3f}_states.txt", 'w', encoding='utf-8') as f:
             json.dump(self.__state_list, f, indent=1)
         with open(self.__path+f"eps={round(self.__epsilon,3):.3f}_activation.txt", 'w', encoding='utf-8') as f:
@@ -557,6 +565,8 @@ class Simulate4Layers:
         if not os.path.exists(self.__path):
             os.makedirs(self.__path)
             
+        with open(self.__path+f"eps={round(self.__epsilon,3):.3f}_coupling.txt", 'w', encoding='utf-8') as f:
+            json.dump(self.__coupling, f, indent=1)
         with open(self.__path+f"eps={round(self.__epsilon,3):.3f}_activation.txt", 'w', encoding='utf-8') as f:
             json.dump(self.__activation_list, f, indent=1)
         with open(self.__path+f"eps={round(self.__epsilon,3):.3f}_channels.txt", 'w', encoding='utf-8') as f: