
find all the nodes which form a specific loop 3 messages
Hi Dmitriy! I am a new user of Dionysus and I met a problem when using the package. from H1 homology group, I can know the birth time and the death time of a loop by using Dionysus, but I don't know h
Hi Dmitriy! I am a new user of Dionysus and I met a problem when using the package. from H1 homology group, I can know the birth time and the death time of a loop by using Dionysus, but I don't know h

By yihangs@...
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Death index 2 messages
Hello, I was wondering if it is possible to obtain the index of the simplex that realises the death of a component? You can output the birth index with pt.data but can you also do this for the death i
Hello, I was wondering if it is possible to obtain the index of the simplex that realises the death of a component? You can output the birth index with pt.data but can you also do this for the death i

By K.A.Garside2@...
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Bottleneck distance is not symmetric 7 messages
Hi Dimitry, I found that the bottleneck distance is not symmetric, although the difference is not significant. import dionysus as d dgm1 = d.Diagram([(8.04545,4.59091), (5.5,4.68182)]) dgm2 = d.Diagra
Hi Dimitry, I found that the bottleneck distance is not symmetric, although the difference is not significant. import dionysus as d dgm1 = d.Diagram([(8.04545,4.59091), (5.5,4.68182)]) dgm2 = d.Diagra

By cai.507@...
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Persistent Homology on highdimensional datasets 7 messages
Hi! I'm new to Dionysus (and to coding in general), so this question may be trivial. I need to compute persistent homology for a high dimensional dataset ( d ~ 1000) embedded in a vector space. I'd on
Hi! I'm new to Dionysus (and to coding in general), so this question may be trivial. I need to compute persistent homology for a high dimensional dataset ( d ~ 1000) embedded in a vector space. I'd on

By Tommaso Salvatori
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dionysus Wasserstein distances 5 messages
Hi Dmitriy, I have a question about computing the Wasserstein distance using Dionysus 2. If either of the the diagrams have a point of multiplicity greater than one, having a death time as inf, the wa
Hi Dmitriy, I have a question about computing the Wasserstein distance using Dionysus 2. If either of the the diagrams have a point of multiplicity greater than one, having a death time as inf, the wa

By Adam Spannaus
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Saving images created with d.plot 3 messages
Greetings, I would like to know if there is a quick way to save the plots generated by the plot_diagram and plot_bars. I know they use matplotlib, and I have tried to modify the file plot.py in the di
Greetings, I would like to know if there is a quick way to save the plots generated by the plot_diagram and plot_bars. I know they use matplotlib, and I have tried to modify the file plot.py in the di

By Xavier Flores
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Computing extended persistence in dionysus2 5 messages
Hello Dmitriy, I am trying to compute extended persistence for graphs using dionysus2. I found in dionysus1 there is a file called 08extendedpersistence.py in the accomapnying examples. But I am not
Hello Dmitriy, I am trying to compute extended persistence for graphs using dionysus2. I found in dionysus1 there is a file called 08extendedpersistence.py in the accomapnying examples. But I am not

By cai.507@...
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Dionysus Install Issues 11 messages
Hello, My name is Jonathan. I'm a senior at UF helping a professor with their research. We would like to use Dionysus' Omnifield persistence but I'm having difficulty getting Dionysus installed. As f
Hello, My name is Jonathan. I'm a senior at UF helping a professor with their research. We would like to use Dionysus' Omnifield persistence but I'm having difficulty getting Dionysus installed. As f

By Jonathan C
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Picking Generators of Homology 6 messages
Hi I have a question about picking generators of homology represented in the barcodes. I understand that the homology generators are equivalence classes of non boundary cycles, so we can only pick a r
Hi I have a question about picking generators of homology represented in the barcodes. I understand that the homology generators are equivalence classes of non boundary cycles, so we can only pick a r

By nukpezah@...
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gpu implementation of persistence computation
Hello, This is maybe not very relevant but I still want to post the question here. Since the major computation of persistence diagram boils down the Gaussian elimination of boundary matrix, should GPU
Hello, This is maybe not very relevant but I still want to post the question here. Since the major computation of persistence diagram boils down the Gaussian elimination of boundary matrix, should GPU

By cai.507@...
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How to know which points form some bar code 7 messages
Hi, For a bar code, is it possible to know which points form this bar code? For example, if I use a distance matrix to create a filtration and then a reduced matrix, then I generate the bar code graph
Hi, For a bar code, is it possible to know which points form this bar code? For example, if I use a distance matrix to create a filtration and then a reduced matrix, then I generate the bar code graph

By
zhanghon@...
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Persistence Diagram of a Graph 4 messages
Hi, If I have a graph with nodes and edges and I know the edge weights, how to think about getting a filtration and hence persistent homology/persistence diagram of this graph. Is it doable in Dionysu
Hi, If I have a graph with nodes and edges and I know the edge weights, how to think about getting a filtration and hence persistent homology/persistence diagram of this graph. Is it doable in Dionysu

By Kowshik Thopalli
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Computing persistence and plotting bar codes 3 messages
Hi Dimitri I have the following code (following your tutorials) for a protein point cloud that I wanted to compute the persistence bar codes. I am very new to persistence homology and python in genera
Hi Dimitri I have the following code (following your tutorials) for a protein point cloud that I wanted to compute the persistence bar codes. I am very new to persistence homology and python in genera

By nukpezah@...
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Pip install error 4 messages
Hi, I tried to pip install Dionysus in an anaconda environment on windows 10 and got the same error that was reported here: https://github.com/mrzv/dionysus/issues/15 . Was this ever resolved? Full ou
Hi, I tried to pip install Dionysus in an anaconda environment on windows 10 and got the same error that was reported here: https://github.com/mrzv/dionysus/issues/15 . Was this ever resolved? Full ou

By rcg54@...
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Computing persistence diagram in parallel 4 messages
Hi Dmitriy, I am trying to compute persistence diagram for different graphs in parallel in python2. I use joblib to do multiprocessing computation. Here is a toy example: def computePD(i): import dion
Hi Dmitriy, I am trying to compute persistence diagram for different graphs in parallel in python2. I use joblib to do multiprocessing computation. Here is a toy example: def computePD(i): import dion

By cai.507@...
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CGAL problem when building diode 4 messages
Hi, I try to build diode on debian (CGAL 4.9), but got the following error (only the first several errors are listed here): #################################### error message ################## In fil
Hi, I try to build diode on debian (CGAL 4.9), but got the following error (only the first several errors are listed here): #################################### error message ################## In fil

By zhuceyonghu123@...
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Bottleneck distances 6 messages
Hi Dimitri, I am having an issue when computing the bottleneck distance between two diagrams. When both persistence diagrams have a point that has inf as its death time, the bottleneck distance seems
Hi Dimitri, I am having an issue when computing the bottleneck distance between two diagrams. When both persistence diagrams have a point that has inf as its death time, the bottleneck distance seems

By Adam Spannaus
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Error Installing via pip on Cloud9/AWS (Ubuntu instance) 6 messages
Hello all. I'm terribly new to a lot of stuff involved here. I'm trying to help a friend get Dionysus up and running using Cloud9 IDE through AWS (Ubuntu instance). I have Python 2.7 installed and tri
Hello all. I'm terribly new to a lot of stuff involved here. I'm trying to help a friend get Dionysus up and running using Cloud9 IDE through AWS (Ubuntu instance). I have Python 2.7 installed and tri

By
E. Noel Brown (SavageDuck)
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Error when building on windows 4 messages
I am building Dionysus on Windows 10 using vcpkg and python 3.6.5. I'm getting a variety of errors that I suspect all have the same cause. Here's an example of the errors I get when building filtratio
I am building Dionysus on Windows 10 using vcpkg and python 3.6.5. I'm getting a variety of errors that I suspect all have the same cause. Here's an example of the errors I get when building filtratio

By
sharsnik@...
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Installation/Compilation problems Dionysus 2 messages
Hello, I tried to install Dionysus 2 with pip and got an output with very internal error messages. Am I doing something wrong? Thank you for your help! All the best Arne Roland
Hello, I tried to install Dionysus 2 with pip and got an output with very internal error messages. Am I doing something wrong? Thank you for your help! All the best Arne Roland

By Arne Roland
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