GMatch4py issueshttps://gitlab.irstea.fr/jacques.fize/GMatch4py/-/issues2018-09-17T23:40:22+02:00https://gitlab.irstea.fr/jacques.fize/GMatch4py/-/issues/2Fresh Install doesn't work2018-09-17T23:40:22+02:00Fize JacquesFresh Install doesn't work*Created by: daubin427*
Hello!
I'd love to try this out, but the installation appears to be broken. Using Ubuntu18.04 I
1. git clone https://github.com/Jacobe2169/GMatch4py.git
2. cd to GMatch4py
3. sudo python3 setup.py inst...*Created by: daubin427*
Hello!
I'd love to try this out, but the installation appears to be broken. Using Ubuntu18.04 I
1. git clone https://github.com/Jacobe2169/GMatch4py.git
2. cd to GMatch4py
3. sudo python3 setup.py install
4. All is well
I build a simple setup.py to test:
```
from distutils.core import setup
from Cython.Build import cythonize
setup(
ext_modules = cythonize("simpleGmatch4py.pyx")
)
```
I create a simpleGmatch4py.pyx:
```
# Gmatch4py use networkx graph
import networkx as nx
# import the GED using the munkres algorithm
import gmatch4py as gm
g1=nx.complete_bipartite_graph(5,4)
g2=nx.complete_bipartite_graph(6,4)
ged=gm.GraphEditDistance(1,1,1,1) # all edit costs are equal to 1
result=ged.compare([g1,g2],None)
print(result)
print("Hello")
```
I build inplace:
`python3 setup.py build_ext --inplace`
I then try to run it and get an error:
```
python3
>>import simpleGmatch4py
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "simpleGmatch4py.pyx", line 4, in init simpleGmatch4py
import gmatch4py as gm
File "/usr/local/lib/python3.6/dist-packages/gmatch4py/__init__.py", line 4, in <module>
from .ged.graph_edit_dist import *
File "gmatch4py/ged/graph_edit_dist.pyx", line 1, in init GMatch4py.gmatch4py.ged.graph_edit_dist
ModuleNotFoundError: No module named 'GMatch4py'
```
Please help :)https://gitlab.irstea.fr/jacques.fize/GMatch4py/-/issues/3Issue with install with sudo2019-03-05T02:07:10+01:00Fize JacquesIssue with install with sudo*Created by: daubin427*
Hello,
I did a fresh install on an Ubuntu 18.04.1 virtual machine. If I follow the steps in the readme all is fine to install. However when I run an example, I get this output:
1. git clone https:/...*Created by: daubin427*
Hello,
I did a fresh install on an Ubuntu 18.04.1 virtual machine. If I follow the steps in the readme all is fine to install. However when I run an example, I get this output:
1. git clone https://github.com/Jacobe2169/GMatch4py.git
2. cd to GMatch4py
3. sudo python3 setup.py install
4. All is well
I build a simple setup.py to test:
from distutils.core import setup
from Cython.Build import cythonize
setup(
ext_modules = cythonize("simpleGmatch4py.pyx")
)
I create a simpleGmatch4py.pyx:
# Gmatch4py use networkx graph
import networkx as nx
# import the GED using the munkres algorithm
import gmatch4py as gm
g1=nx.complete_bipartite_graph(5,4)
g2=nx.complete_bipartite_graph(6,4)
ged=gm.GraphEditDistance(1,1,1,1) # all edit costs are equal to 1
result=ged.compare([g1,g2],None)
print(result)
print("Done")
I build inplace:
python3 setup.py build_ext --inplace
I then try to run it and get an error:
python3
>>import simpleGmatch4py
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "simpleGmatch4py.pyx", line 4, in init simpleGmatch4py
import gmatch4py as gm
File "/usr/local/lib/python3.6/dist-packages/gmatch4py/__init__.py", line 4, in <module>
from .ged.graph_edit_dist import *
File "gmatch4py/ged/graph_edit_dist.pyx", line 1, in init GMatch4py.gmatch4py.ged.graph_edit_dist
ModuleNotFoundError: No module named 'GMatch4py'
This error is similar to Issue #2. In Issue #2 the virtualenv method works perfectly.
Digging further, If I do the additional steps:
1. pip3 install numpy networkx scikit-learn ipython cython scipy (Note no sudo here)
2. python3 setup.py install (Note no sudo here)
A. Errors installing in to /usr/local/lib/python3.6/dist-packages
3. sudo chmod -R 777 /usr/local/lib/python3.6/dist-packages/gmatch4py
4. python3 setup.py install (Note no sudo here)
5. Rerun the test above and it works perfectly
[[ 0. 14.]
[10. 0.]]
Done
While I do get it to work, it is not install/working as expected. I hope these details help.
Thank you again for your amazing work! :)https://gitlab.irstea.fr/jacques.fize/GMatch4py/-/issues/6Deepwalk is a node embedding algorithm.2019-03-08T10:55:03+01:00Fize JacquesDeepwalk is a node embedding algorithm.*Created by: benedekrozemberczki*
Deepwalk is a node embedding algorithm (graph embedding ≠ node embedding). As each run of a node embedding can be rotated with an orthogonal rotation matrix doing any sort of comparison of two node embe...*Created by: benedekrozemberczki*
Deepwalk is a node embedding algorithm (graph embedding ≠ node embedding). As each run of a node embedding can be rotated with an orthogonal rotation matrix doing any sort of comparison of two node embedding is totally meaningless. I am also somewhat surprised to see large blocks of code from my graph2vec repository.https://gitlab.irstea.fr/jacques.fize/GMatch4py/-/issues/4warning: libstdc++ is deprecated; move to libc++ with a minimum deployment ta...2019-03-05T02:07:33+01:00Fize Jacqueswarning: libstdc++ is deprecated; move to libc++ with a minimum deployment target of OS X 10.9 [-Wdeprecated]*Created by: verazuo*
Hi, When I executed this command `sudo python3 setup.py install`, I encountered the following error.
```
veradeMacBook-Pro:GMatch4py vera$ sudo python3 setup.py install
Password:
gmatch4py/kernels/weisfeiler_l...*Created by: verazuo*
Hi, When I executed this command `sudo python3 setup.py install`, I encountered the following error.
```
veradeMacBook-Pro:GMatch4py vera$ sudo python3 setup.py install
Password:
gmatch4py/kernels/weisfeiler_lehman.pyx: cannot find cimported module '..base'
gmatch4py/vertex_ranking.pyx: cannot find cimported module '.base'
gmatch4py/vertex_edge_overlap.pyx: cannot find cimported module '.base'
gmatch4py/mcs.pyx: cannot find cimported module '.base'
gmatch4py/bag_of_cliques.pyx: cannot find cimported module '.base'
gmatch4py/bon.pyx: cannot find cimported module '.base'
gmatch4py/jaccard.pyx: cannot find cimported module '.base'
gmatch4py/ged/graph_edit_dist.pyx: cannot find cimported module '.abstract_graph_edit_dist'
gmatch4py/ged/graph_edit_dist.pyx: cannot find cimported module '..base'
gmatch4py/ged/graph_edit_dist.pxd: cannot find cimported module '.abstract_graph_edit_dist'
gmatch4py/ged/bipartite_graph_matching_2.pyx: cannot find cimported module '..base'
gmatch4py/ged/greedy_edit_distance.pyx: cannot find cimported module '.graph_edit_dist'
gmatch4py/ged/hausdorff_edit_distance.pyx: cannot find cimported module '..base'
gmatch4py/ged/abstract_graph_edit_dist.pyx: cannot find cimported module '..base'
gmatch4py/ged/abstract_graph_edit_dist.pxd: cannot find cimported module '..base'
/anaconda3/lib/python3.7/distutils/dist.py:274: UserWarning: Unknown distribution option: 'long_description_content_type'
warnings.warn(msg)
/anaconda3/lib/python3.7/distutils/dist.py:274: UserWarning: Unknown distribution option: 'setup_requires'
warnings.warn(msg)
/anaconda3/lib/python3.7/distutils/dist.py:274: UserWarning: Unknown distribution option: 'install_requires'
warnings.warn(msg)
running install
running build
running build_py
creating build/lib.macosx-10.7-x86_64-3.7
creating build/lib.macosx-10.7-x86_64-3.7/gmatch4py
copying gmatch4py/__init__.py -> build/lib.macosx-10.7-x86_64-3.7/gmatch4py
creating build/lib.macosx-10.7-x86_64-3.7/gmatch4py/helpers
copying gmatch4py/helpers/__init__.py -> build/lib.macosx-10.7-x86_64-3.7/gmatch4py/helpers
running build_ext
building 'gmatch4py.kernels.random_walk_kernel' extension
creating build/temp.macosx-10.7-x86_64-3.7
creating build/temp.macosx-10.7-x86_64-3.7/gmatch4py
creating build/temp.macosx-10.7-x86_64-3.7/gmatch4py/kernels
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/anaconda3/include -arch x86_64 -I/anaconda3/include -arch x86_64 -I/anaconda3/lib/python3.7/site-packages/numpy/core/include -I/anaconda3/include/python3.7m -c gmatch4py/kernels/random_walk_kernel.cpp -o build/temp.macosx-10.7-x86_64-3.7/gmatch4py/kernels/random_walk_kernel.o
warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the
libc++ standard library instead [-Wstdlibcxx-not-found]
1 warning generated.
creating build/lib.macosx-10.7-x86_64-3.7/gmatch4py/kernels
g++ -bundle -undefined dynamic_lookup -L/anaconda3/lib -arch x86_64 -L/anaconda3/lib -arch x86_64 -arch x86_64 build/temp.macosx-10.7-x86_64-3.7/gmatch4py/kernels/random_walk_kernel.o -o build/lib.macosx-10.7-x86_64-3.7/gmatch4py/kernels/random_walk_kernel.cpython-37m-darwin.so
clang: warning: libstdc++ is deprecated; move to libc++ with a minimum deployment target of OS X 10.9 [-Wdeprecated]
ld: library not found for -lstdc++
clang: error: linker command failed with exit code 1 (use -v to see invocation)
error: command 'g++' failed with exit status 1
```
My env is in anaconda python3.6, Mac 10.14(Mojave)
https://gitlab.irstea.fr/jacques.fize/GMatch4py/-/issues/8HED returns 02019-05-02T10:25:42+02:00Fize JacquesHED returns 0*Created by: computerquest*
I have a bunch of graphs I know to be unique, and when I calculate GED using GraphEditDistance it returns non-zero values as expected. However when using HED instead of GraphEditDistance, it outputs only 0.
...*Created by: computerquest*
I have a bunch of graphs I know to be unique, and when I calculate GED using GraphEditDistance it returns non-zero values as expected. However when using HED instead of GraphEditDistance, it outputs only 0.
````
ged = gm.HED(1, 1, 1, 1)
result = ged.compare(all_graph, None)
print(*result)
````
Is my code wrong or is there an issue with the library?https://gitlab.irstea.fr/jacques.fize/GMatch4py/-/issues/9 can i use a edge image as a input to Hausdorff ?2019-05-09T20:10:00+02:00Fize Jacques can i use a edge image as a input to Hausdorff ?*Created by: 2018hello*
Hi can i use a edge image as a input to Hausdorff ?
Thank you !*Created by: 2018hello*
Hi can i use a edge image as a input to Hausdorff ?
Thank you !https://gitlab.irstea.fr/jacques.fize/GMatch4py/-/issues/1Usage documentation?2019-07-12T08:10:15+02:00Fize JacquesUsage documentation?*Created by: bojan2110*
Hi!
Thanks for sharing this project! It would be really nice if we can get at least some simple examples of how to use it?
I am mostly interested in testing graph distances with edit distance, but fail to...*Created by: bojan2110*
Hi!
Thanks for sharing this project! It would be really nice if we can get at least some simple examples of how to use it?
I am mostly interested in testing graph distances with edit distance, but fail to produce an working example.
Regards
Bojanhttps://gitlab.irstea.fr/jacques.fize/GMatch4py/-/issues/7Edit Path2019-08-23T17:38:19+02:00Fize JacquesEdit Path*Created by: safreita1*
Is it possible to get the edit path (not just the distance) between two graphs for any of the graph edit algorithms?*Created by: safreita1*
Is it possible to get the edit path (not just the distance) between two graphs for any of the graph edit algorithms?https://gitlab.irstea.fr/jacques.fize/GMatch4py/-/issues/12Installation error2019-08-09T13:15:36+02:00Fize JacquesInstallation error*Created by: Sultan91*
After running `python setup.py install `:
Terminal prompted with the following error:
`gmatch4py/mcs.cpp:27:20: fatal error: Python.h: No such file or directory
compilation terminated.
error: command 'x86_64-l...*Created by: Sultan91*
After running `python setup.py install `:
Terminal prompted with the following error:
`gmatch4py/mcs.cpp:27:20: fatal error: Python.h: No such file or directory
compilation terminated.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
`https://gitlab.irstea.fr/jacques.fize/GMatch4py/-/issues/11GMatch4py accuracy for graph edit distance2019-08-20T13:00:11+02:00Fize JacquesGMatch4py accuracy for graph edit distance*Created by: ffaez*
Hi,
I have a simple code to compare the computed graph edit distance with GMatch4py and also the graph_edit_distance function in networkx.
my code is as follows:
```import gmatch4py as gm
g1=nx.complete_graph(3...*Created by: ffaez*
Hi,
I have a simple code to compare the computed graph edit distance with GMatch4py and also the graph_edit_distance function in networkx.
my code is as follows:
```import gmatch4py as gm
g1=nx.complete_graph(3)
g2=nx.complete_graph(4)
ged=gm.GraphEditDistance(1,1,1,1) # all edit costs are equal to 1
result=ged.compare([g1,g2],None)
print("GMatch4py output:\n", result)
print("networkx output:\n", nx.graph_edit_distance(g1,g2))
```
and the results are:
```
GMatch4py output:
[[0. 7.]
[7. 0.]]
networkx output:
4.0
```
Would you please tell me what does each element of the output matrix of GMatch4py mean? Is 7 the edit distance computed by GMatch4py while the exact edit distance is 4? Is the performance and accuracy of GMatchpy low even for very small graphs or it is just an understanding mistake made by me?
Regardshttps://gitlab.irstea.fr/jacques.fize/GMatch4py/-/issues/13Citiation2019-08-26T18:13:53+02:00Fize JacquesCitiation*Created by: UTpH*
What would be the citation for the following algorithm implemented in this library?
https://github.com/Jacobe2169/GMatch4py/blob/master/gmatch4py/ged/graph_edit_dist.pyx
Thanks!*Created by: UTpH*
What would be the citation for the following algorithm implemented in this library?
https://github.com/Jacobe2169/GMatch4py/blob/master/gmatch4py/ged/graph_edit_dist.pyx
Thanks!https://gitlab.irstea.fr/jacques.fize/GMatch4py/-/issues/14Quick question: Do not quite understand simple output2019-09-05T04:03:23+02:00Fize JacquesQuick question: Do not quite understand simple output*Created by: davidlee321*
This simple example shows a different edit distance compared to networkX's GED. Would be great if someone could help me understand the difference. From my understanding of GED, the edit distance should be 1, no...*Created by: davidlee321*
This simple example shows a different edit distance compared to networkX's GED. Would be great if someone could help me understand the difference. From my understanding of GED, the edit distance should be 1, not 2.
```python
import networkx
import gmatch4py as gm
g1=nx.complete_bipartite_graph(2,3)
g2=nx.complete_bipartite_graph(2,3)
g2.add_edge(0, 1)
adj=[(v, neighbors) for v, neighbors in g1.adjacency()]
print(adj)
adj=[(v, neighbors) for v, neighbors in g2.adjacency()]
print(adj)
ged=gm.GraphEditDistance(1,1,1,1) # all edit costs are equal to 1
result=ged.compare([g1,g2],None)
print(result)
```
```bash
[(0, {2: {}, 3: {}, 4: {}}), (1, {2: {}, 3: {}, 4: {}}), (2, {0: {}, 1: {}}), (3, {0: {}, 1: {}}), (4, {0: {}, 1: {}})]
[(0, {2: {}, 3: {}, 4: {}, 1: {}}), (1, {2: {}, 3: {}, 4: {}, 0: {}}), (2, {0: {}, 1: {}}), (3, {0: {}, 1: {}}), (4, {0: {}, 1: {}})]
[[0. 2.]
[2. 0.]]
```
```python
ged_nx = nx.graph_edit_distance(g1, g2)
print(ged_nx)
```
```bash
1.0
```https://gitlab.irstea.fr/jacques.fize/GMatch4py/-/issues/10Importing Cython 'munkres' module2019-05-02T10:25:18+02:00Fize JacquesImporting Cython 'munkres' module*Created by: emmanuelasso*
Hi. When I import gmatch4py there is a warning: for optimal results, the Cython 'munkres' module must be installed. But when entering the given url this is totally deprecated and it is impossible to install. H...*Created by: emmanuelasso*
Hi. When I import gmatch4py there is a warning: for optimal results, the Cython 'munkres' module must be installed. But when entering the given url this is totally deprecated and it is impossible to install. How much does this affect the operation of gmatch4py?