
Extracting boundary chain
2 messages
Dear all, At your recent AATRN talk, Dmitriy, you mention how the standard algorithm outputs a bounding chain; https://youtu.be/DEl6hCcGwag (11:40). Is there a routine in Dionysus for outputting the c
Dear all, At your recent AATRN talk, Dmitriy, you mention how the standard algorithm outputs a bounding chain; https://youtu.be/DEl6hCcGwag (11:40). Is there a routine in Dionysus for outputting the c

By
Botnan, M.B. (Magnus Bakke)
·


Persistence Vineyards in Python
2 messages
Hello Dmitriy, Has there been any update to binding persistence vineyards in python? I am hoping to use persistence vineyards for a few research applications relating to brain network dynamics, and wa
Hello Dmitriy, Has there been any update to binding persistence vineyards in python? I am hoping to use persistence vineyards for a few research applications relating to brain network dynamics, and wa

By
katrina.prantzalos@...
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Distance matrix vineyard
4 messages
Hi Dmitriy, I would like to look at the vineyard of a time varying point cloud obtained from a distance matrix but I am unsure about the correct input data format and whether the plvineyard function
Hi Dmitriy, I would like to look at the vineyard of a time varying point cloud obtained from a distance matrix but I am unsure about the correct input data format and whether the plvineyard function

By
K.A.Garside2@...
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Save and reload objects
6 messages
Hi Dmitriy, I was wondering if it possible to save the d.fill_rips and the d.homology_persistence objects and reload them later on so as not to recompute them? I was trying to pickle them but was runn
Hi Dmitriy, I was wondering if it possible to save the d.fill_rips and the d.homology_persistence objects and reload them later on so as not to recompute them? I was trying to pickle them but was runn

By
jonathan nukpezah
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Installing Dionysus 2
3 messages
Hi, Dmitriy! I'm so sorry to ask this, but I'm a beginner in programming and I don't have enough experience in installing things. However I strongly intend to do some persistently homological stuff wi
Hi, Dmitriy! I'm so sorry to ask this, but I'm a beginner in programming and I don't have enough experience in installing things. However I strongly intend to do some persistently homological stuff wi

By
Artem
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Store cohomology output as pandas dataframe
4 messages
Hi Dimitry, I'm using Dionysus 2 in python and I'm trying to find what the quickest way is to convert a persistence diagram into a pandas DataFrame. My current code looks like this: import numpy as np
Hi Dimitry, I'm using Dionysus 2 in python and I'm trying to find what the quickest way is to convert a persistence diagram into a pandas DataFrame. My current code looks like this: import numpy as np

By
Shael Brown
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Enriched Barcodes
3 messages
Hi I'm trying to implement and integrate this work: https://epubs.siam.org/doi/epdf/10.1137/19M1272226 found in this repository: https://github.com/GWWEI/EnrichedBarcode/blob/master/enriched_ph/Enrich
Hi I'm trying to implement and integrate this work: https://epubs.siam.org/doi/epdf/10.1137/19M1272226 found in this repository: https://github.com/GWWEI/EnrichedBarcode/blob/master/enriched_ph/Enrich

By
Tyler Kolody
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hi Dmitriy Morozov .sorry,I got a question
3 messages
i use d.zigzag_homology_persistence to compute zigzag persistence,and the input completeGVRips is 32644 Simplices and the related in and out time and the G_dgms is #Dimension: 0 Dimension: 1 #dgm Diag
i use d.zigzag_homology_persistence to compute zigzag persistence,and the input completeGVRips is 32644 Simplices and the related in and out time and the G_dgms is #Dimension: 0 Dimension: 1 #dgm Diag

By
timemachinezym@...
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Persistent diagrams for point clouds
10 messages
Hello, This may be a somewhat basic question but I'm a bit stumped. How would I go about using Dionysus2 to generate a persistence diagram from a point cloud stored in numpy array? I tried the followi
Hello, This may be a somewhat basic question but I'm a bit stumped. How would I go about using Dionysus2 to generate a persistence diagram from a point cloud stored in numpy array? I tried the followi

By
chinenye.onwuzurike@...
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Runtime error when computing persistence diagram
12 messages
Hi Dimitriy, I have been used Dionysus to compute the persistence diagram for a long time. But recently I encounter a strange runtime error. Here is a small example that is able to reproduce the error
Hi Dimitriy, I have been used Dionysus to compute the persistence diagram for a long time. But recently I encounter a strange runtime error. Here is a small example that is able to reproduce the error

By
cai.507@...
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Installation of Dionysus on Windows
2 messages
Hi Could you please help me with the problem that the Cmake cannot find Boost_INCLUDE_DIR during the installation of the Dionysus. Thank you for your help. Best regards Vincent Sent from Mail for Wind
Hi Could you please help me with the problem that the Cmake cannot find Boost_INCLUDE_DIR during the installation of the Dionysus. Thank you for your help. Best regards Vincent Sent from Mail for Wind

By
Yanzhi Guo
·


Citations to Dionysus 2
4 messages
Hi all, I am working on a paper now that uses Dionysus 2. Does anyone know the proper citation to Dionysus 2? Is there a paper published that we can cite? Best, Pierre
Hi all, I am working on a paper now that uses Dionysus 2. Does anyone know the proper citation to Dionysus 2? Is there a paper published that we can cite? Best, Pierre

By
Pierre Christian
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If there is a way to get a better generator?
3 messages
Sorry to trouble, I am now using zigzag persistence to compute representative cycles of a rips complex but seems the generator is not what I want. For example see the data above, for 1cycles I want a
Sorry to trouble, I am now using zigzag persistence to compute representative cycles of a rips complex but seems the generator is not what I want. For example see the data above, for 1cycles I want a

By
Chunhui Shao
·


Interval of alive component for a simplex
3 messages
Hi Dmitriy, Is there a quick way using Dionysus to find out the interval in which a given simplex exists as part of an alive component? For example, say the 1simplex <a,b> joins the filtration at lev
Hi Dmitriy, Is there a quick way using Dionysus to find out the interval in which a given simplex exists as part of an alive component? For example, say the 1simplex <a,b> joins the filtration at lev

By
K.A.Garside2@...
·


Reduction matrix
5 messages
Hi all, Is there a way to get the reduction matrix for the boundary matrix? To be precise, let D be the boundary matrix. With the column reduction, we obtain DV=R. I wonder if there is a function to o
Hi all, Is there a way to get the reduction matrix for the boundary matrix? To be precise, let D be the boundary matrix. With the column reduction, we obtain DV=R. I wonder if there is a function to o

By
zhouling0903@...
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Installation problem on Windows and Mac
2 messages
You should search this forum for previous discussions of installation on Windows. The specific problem you are seeing is that you don't have C/C++ compilers installed, or at least CMake is not finding
You should search this forum for previous discussions of installation on Windows. The specific problem you are seeing is that you don't have C/C++ compilers installed, or at least CMake is not finding

By
zhouling0903@...
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Install problem
2 messages
hello.My pathon verion is ,my boost version is 1.7.0,i have installed mingGW8.10,and when i follow the process on this link https://groups.io/g/dionysus/topic/build_under_windows/32045298?p=,,,20,0,0,
hello.My pathon verion is ,my boost version is 1.7.0,i have installed mingGW8.10,and when i follow the process on this link https://groups.io/g/dionysus/topic/build_under_windows/32045298?p=,,,20,0,0,

By
jingsong sun
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i can use it.Why helphelphelp!!urgent!!
3 messages
hello. Now i have a problem about my project.It is urgent.And i want to ask you and look for your help. I have try the package of the dionysus, i mkdir cd cmake and make.And then i copy the folder in
hello. Now i have a problem about my project.It is urgent.And i want to ask you and look for your help. I have try the package of the dionysus, i mkdir cd cmake and make.And then i copy the folder in

By
jingsong sun
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Easy(?) conceptual question on finding the diameter of a circle with dionysus
6 messages
Hi all, I am very new to topological data analysis and dionysus. To test my understanding, I am doing the following exercise: 1) Create a data cloud that is a perfect circle with diameter 1 2) Plot th
Hi all, I am very new to topological data analysis and dionysus. To test my understanding, I am doing the following exercise: 1) Create a data cloud that is a perfect circle with diameter 1 2) Plot th

By
Pierre Christian
·


Installation Problem on Linux
7 messages
Hi, I've tried to install Dionysis (latest version) with pip on Ubuntu (18.04). I have multiple Python versions available, and I have first downloaded Boost, and built it specifying Python version. Al
Hi, I've tried to install Dionysis (latest version) with pip on Ubuntu (18.04). I have multiple Python versions available, and I have first downloaded Boost, and built it specifying Python version. Al

By
eva.breznik91@...
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