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Commit 272c17ed authored by Felix's avatar Felix
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fix bugs and rebuild wheel

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kirchhoff/kirchhoff_dual.py → kirchhoff/circuit_dual.py
+ 5
− 6
View file @ 272c17ed
......@@ -3,7 +3,7 @@
# @Email: kramer@mpi-cbg.de
# @Project: go-with-the-flow
# @Last modified by: Felix Kramer
# @Last modified time: 2021-05-23T23:17:43+02:00
# @Last modified time: 2021-05-23T23:55:51+02:00
# @License: MIT
import networkx as nx
......@@ -11,11 +11,10 @@ import numpy as np
import scipy.linalg as lina
import sys
from kirchhoff.kirchhoff_init import *
from kirchhoff.kirchhoff_flow import *
from kirchhoff.kirchhoff_flux import *
import kirchhoff.init_dual
from kirchhoff.circuit_init import *
from kirchhoff.circuit_flow import *
from kirchhoff.circuit_flux import *
import kirchhoff.init_dual as init_dual
def initialize_dual_circuit_from_networkx(input_graph1,input_graph2,e_adj):
......
kirchhoff/kirchhoff_flow.py → kirchhoff/circuit_flow.py
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− 5
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......@@ -3,7 +3,7 @@
# @Email: kramer@mpi-cbg.de
# @Project: go-with-the-flow
# @Last modified by: Felix Kramer
# @Last modified time: 2021-05-23T23:17:20+02:00
# @Last modified time: 2021-05-23T23:56:10+02:00
# @License: MIT
import random as rd
......@@ -11,12 +11,12 @@ import networkx as nx
import numpy as np
import sys
import pandas as pd
# import kirchhoff_init
from kirchhoff.kirchhoff_init import *
from kirchhoff.circuit_init import *
# custom embeddings/architectures
import init_crystal
import init_random
import kirchhoff.init_crystal as init_crystal
import kirchhoff.init_random as init_random
def initialize_flow_circuit_from_networkx(input_graph):
......
kirchhoff/kirchhoff_flux.py → kirchhoff/circuit_flux.py
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− 5
View file @ 272c17ed
......@@ -3,7 +3,7 @@
# @Email: kramer@mpi-cbg.de
# @Project: go-with-the-flow
# @Last modified by: Felix Kramer
# @Last modified time: 2021-05-23T23:17:02+02:00
# @Last modified time: 2021-05-23T23:55:42+02:00
# @License: MIT
import random as rd
......@@ -11,10 +11,10 @@ import networkx as nx
import numpy as np
import sys
import pandas as pd
# import kirchhoff_flow
from kirchhoff.kirchhoff_flow import *
import init_crystal
import init_random
from kirchhoff.circuit_flow import *
import kirchhoff.init_crystal as init_crystal
import kirchhoff.init_random as init_random
def initialize_flux_circuit_from_networkx(input_graph):
......
kirchhoff/kirchhoff_init.py → kirchhoff/circuit_init.py
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File moved
kirchhoff/init_dual.py
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− 1
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......@@ -3,13 +3,14 @@
# @Email: kramer@mpi-cbg.de
# @Project: go-with-the-flow
# @Last modified by: Felix Kramer
# @Last modified time: 2021-05-23T23:17:55+02:00
# @Last modified time: 2021-05-24T00:03:20+02:00
# @License: MIT
import networkx as nx
import numpy as np
import kirchhoff.init_crystal
from scipy.spatial import Voronoi
import kirchhoff.init_crystal as init_crystal
def init_dual_minsurf_graphs(dual_type,num_periods):
......
notebook/test_goflow.ipynb deleted 100644 → 0
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%% Cell type:code id: tags:
``` python
import networkx as nx
import sys
import numpy as np
sys.path.insert(0,'../goflow')
import kirchhoff_init as ki
import pandas as pd
```
%% Cell type:code id: tags:
``` python
n=3
G=nx.grid_graph(( n,n,1))
K = ki.initialize_circuit_from_networkx(G)
```
%% Output
circuit(): initialized and ready for (some) action :)
%% Cell type:code id: tags:
``` python
import kirchhoff_flow as kf
n=3
G=nx.grid_graph(( n,n,1))
K= kf.initialize_flow_circuit_from_networkx(G)
```
%% Output
circuit(): initialized and ready for (some) action :)
%% Cell type:code id: tags:
``` python
K.graph['num_sources']=4
K.set_source_landscape('root_multi',num_sources=2)
```
%% Output
set_source_landscape(): root_multi is set and consistent :)
%% Cell type:code id: tags:
``` python
print(K.nodes['source'])
K.nodes.plot('source','source',kind='scatter')
```
%% Output
0 -1.0
1 -1.0
2 3.5
3 -1.0
4 -1.0
5 3.5
6 -1.0
7 -1.0
8 -1.0
Name: source, dtype: float64
<AxesSubplot:xlabel='source', ylabel='source'>
%% Cell type:code id: tags:
``` python
custom={}
for i,n in enumerate(K.G.nodes()):
if i==0:
custom.update({n:len(K.G.nodes())-1})
else:
custom.update({n:-1})
print(custom)
K.set_source_landscape('root_geometric')
```
%% Output
{0: 8, 1: -1, 2: -1, 3: -1, 4: -1, 5: -1, 6: -1, 7: -1, 8: -1}
set networkx.spring_layout()
set_source_landscape(): root_geometric is set and consistent :)
%% Cell type:code id: tags:
``` python
K.set_plexus_landscape()
```
%% Output
set_plexus_landscape(): root_geometric is set and consistent :)
%% Cell type:code id: tags:
``` python
K.set_source_landscape()
```
%% Output
set_source_landscape(): default is set and consistent :)
%% Cell type:code id: tags:
``` python
```
notebook/test_init_graphs.ipynb
+ 20
− 68
View file @ 272c17ed
%% Cell type:code id: tags:
``` python
import networkx as nx
import numpy as np
import sys
sys.path.insert(0,'../kirchhoff')
import kirchhoff_init as ki
import kirchhoff_flow as kiw
import kirchhoff_flux as kix
import kirchhoff_dual as kid
import kirchhoff
```
%% Cell type:code id: tags:
``` python
import kirchhoff.circuit_init as ki
n=3
G=nx.grid_graph(( n,n,1))
K = ki.initialize_circuit_from_networkx(G)
```
%% Output
circuit(): initialized and ready for (some) action :)
%% Cell type:code id: tags:
``` python
kiw.initialize_circuit_from_networkx(G)
import kirchhoff.circuit_flow as kfc
kfc.initialize_circuit_from_networkx(G)
kfc.initialize_flow_circuit_from_crystal('simple',3)
kfc.initialize_flow_circuit_from_random(random_type='voronoi_volume')
```
%% Output
circuit(): initialized and ready for (some) action :)
<kirchhoff_init.circuit at 0x16367462c48>
%% Cell type:code id: tags:
``` python
kix.initialize_circuit_from_networkx(G)
```
%% Output
circuit(): initialized and ready for (some) action :)
<kirchhoff_init.circuit at 0x1636747bd48>
%% Cell type:code id: tags:
``` python
kiw.initialize_flow_circuit_from_crystal('chain',3)
```
%% Output
circuit(): initialized and ready for (some) action :)
<kirchhoff_flow.flow_circuit at 0x1636748c088>
<kirchhoff.circuit_flow.flow_circuit at 0x1480007a0c8>
%% Cell type:code id: tags:
``` python
kiw.initialize_flow_circuit_from_random(random_type='voronoi_volume')
import kirchhoff.circuit_flux as kfc
kfc.initialize_circuit_from_networkx(G)
kfc.initialize_flow_circuit_from_crystal('simple',3)
kfc.initialize_flow_circuit_from_random(random_type='voronoi_volume')
```
%% Output
circuit(): initialized and ready for (some) action :)
circuit(): initialized and ready for (some) action :)
circuit(): initialized and ready for (some) action :)
<kirchhoff_flow.flow_circuit at 0x16367467288>
<kirchhoff.circuit_flow.flow_circuit at 0x14803149788>
%% Cell type:code id: tags:
``` python
kid.initialize_dual_flux_circuit_from_minsurf('laves',3)
import kirchhoff.circuit_dual as kid
kid.initialize_dual_flux_circuit_from_minsurf('simple',3)
```
%% Output
circuit(): initialized and ready for (some) action :)
circuit(): initialized and ready for (some) action :)
<kirchhoff_dual.dual_circuit at 0x163674ffd48>
<kirchhoff.circuit_dual.dual_circuit at 0x148031ead08>
%% Cell type:code id: tags:
``` python
```
......
notebook/test_initgraph.ipynb deleted 100644 → 0
+ 0
− 84
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%% Cell type:code id: tags:
``` python
import test as cat
import networkx as nx
import matplotlib.pyplot as plt
import cycle_analysis.cycle_tools_coalescence as ctc
import cycle_analysis.test as cat
# generate a dummy graph for testing
# put an edge weight distribution on the system, available are random/gradient/bigradient/nested_square
n=7
G=nx.grid_graph(( n,n,1))
G=cat.generate_pattern(G,'random')
weights=[G.edges[e]['weight'] for e in G.edges()]
pos=nx.get_node_attributes(G,'pos')
# merge all shortest cycles and create merging tree, then calc asymmetry of the tree's branches
T=ctc.coalescence()
minimum_basis=T.construct_networkx_basis(G)
cycle_tree=T.calc_cycle_coalescence(G,minimum_basis)
dict_asymmetry=T.calc_tree_asymmetry()
# plot branching asymmetry in dependence of branching level
x,y=[],[]
for n in dict_asymmetry:
x.append((cycle_tree.nodes[n]['pos'][1]-6)/2.)
y.append(dict_asymmetry[n])
plt.scatter(x,y)
plt.ylabel('asymmetry')
plt.xlabel('branching level')
plt.grid(True)
plt.show()
```
%% Output
%% Cell type:code id: tags:
``` python
```
notebook/test_path_statistics.ipynb deleted 100644 → 0
+ 0
− 74
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%% Cell type:code id: tags:
``` python
import networkx as nx
import numpy as np
import scipy.linalg as snl
```
%% Cell type:code id: tags:
``` python
n=2
G=nx.grid_graph(dim=(n,n,1))
print(nx.info(G))
p=4
adj=nx.adjacency_matrix(G).todense()
adj_p=np.linalg.matrix_power(adj,p)
evs=snl.eigvalsh(adj_p)
print(np.sum(evs))
```
%% Output
Name:
Type: Graph
Number of nodes: 4
Number of edges: 4
Average degree: 2.0000
32.0
%% Cell type:code id: tags:
``` python
```
setup.py
+ 2
− 2
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......@@ -3,7 +3,7 @@
# @Email: kramer@mpi-cbg.de
# @Project: go-with-the-flow
# @Last modified by: Felix Kramer
# @Last modified time: 2021-05-23T23:29:24+02:00
# @Last modified time: 2021-05-24T00:03:32+02:00
# @License: MIT
......@@ -15,7 +15,7 @@ with open("README.md", "r", encoding="utf-8") as fh:
setuptools.setup(
name="kirchhoff", # Replace with your own username
version="0.0.1",
version="0.0.6",
author="felixk1990",
author_email="felixuwekramer@protonmail.com",
description="Collecton of routines for creation and manipulation of Kirchhoff circuits based on resistor-only networks, together with 2D/3D spatial embeddings. ",
......
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