Graph tools

 

𝐓𝐨𝐨𝐥𝐬 𝐭𝐨 𝐦𝐚𝐢𝐧𝐥𝐲 𝐯𝐢𝐬𝐮𝐚𝐥𝐢𝐳𝐞 𝐧𝐞𝐭𝐰𝐨𝐫𝐤𝐬:
- Geph - https://gephi.org
- Gephisto- https://lnkd.in/diSp3BWN
- VOSviewer - https://www.vosviewer.com
- Cytoscape - https://cytoscape.org
- Kumu - https://kumu.io
- GraphInsight - https://lnkd.in/d5XnkWJr
- NodeXL - https://nodexl.com
- Orange - https://lnkd.in/dZU8Zx3D
- Graphia - https://graphia.app
- Graphistry - https://www.graphistry.com
- SocNetV - https://socnetv.org
- Tulip - https://lnkd.in/dtc_BD33


𝐍𝐞𝐭𝐰𝐨𝐫𝐤 𝐥𝐢𝐛𝐫𝐚𝐫𝐢𝐞𝐬 𝐢𝐧 𝐏𝐲𝐭𝐡𝐨𝐧:
- networkx - https://lnkd.in/dKCCXjif
- graphviz - https://lnkd.in/dtrTeqRv
- pydot - https://lnkd.in/dA46YZvy
- python-igraph - https://lnkd.in/dCGsRXh2
- pyvis - https://lnkd.in/dVrQ64nN
- ipycytoscape - https://lnkd.in/d-hJjDdG
- pygsp - https://lnkd.in/dS7s-A_v
- graph-tool - https://lnkd.in/dvytUzdu
- nxviz - https://lnkd.in/duHbKGPN
- py2cytoscape - https://lnkd.in/dWUU8TZH
- ipydagred3 - https://lnkd.in/diXgFWMD
- ipysigma - https://lnkd.in/dP55J5et
- Py3Plex - https://lnkd.in/dhwe7f_g
- net wulf - https://lnkd.in/dxrHAm2P
 

Render tools - POV Ray

Compiling

https://github.com/POV-Ray/povray/releases/tag/v3.8.0-beta.2 

configure error: Could not link against boost_

sudo apt-get install libboost-all-dev

Update Gimp

From 2.8 to 2.10 using apt-get

$ sudo add-apt-repository ppa:otto-kesselgulasch/gimp

$ sudo apt-get update

$ sudo apt-get install gimp

 

References:

https://linuxhint.com/install_gimp_210_ubuntu_1804/

ASNetwork : Breaking ambiguity

 

 

[1] Salient Object Detection Driven by Fixation Prediction https://openaccess.thecvf.com/content_cvpr_2018/papers/Wang_Salient_Object_Detection_CVPR_2018_paper.pdf

[2] Action Schema Networks https://ipc2023-learning.github.io/abstracts/asnets.pdf

Volume Fractions

Thesis

[1] Smooth Interface Reconstruction from Volume Fraction Data Using Variational
Techniques and Level Set Methods

https://escholarship.org/content/qt2466j56f/qt2466j56f_noSplash_4c9dcb1c6cacafb1bcdc4a7bab220630.pdf?t=odypru

 

Volume Fractions in Rectangular Grids

Analytical Relations Connecting Linear Interfaces and Volume Fractions in Rectangular Grids
http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.536.848&rep=rep1&type=pdf
[1] Markers - A front-tracking algorithm for accurate representation of surface tension (Zaleski)
https://hal.archives-ouvertes.fr/hal-01445441/document



[2] Level Set Methods (LSM)
[2.1] Tutorial Level Set vs Marching Methods https://math.berkeley.edu/~sethian/2006/Explanations/level_set_explain.html

[2.2-1] Part I (Def) https://wiseodd.github.io/techblog/2016/11/05/levelset-method/
[2.2-2] Part II(Application for segmentation) https://wiseodd.github.io/techblog/2016/11/20/levelset-segmentation/

Deep Gan Applications

Super Resolution

[0] https://replicate.com/collections/super-resolution 

[1] https://replicate.com/nightmareai/real-esrgan  /require github account

[2] https://replicate.com/mv-lab/swin2sr (alternative) 

[3] Nightmare https://www.nightmare-ai.com/playground

Styles

[1] https://replicate.com/collections/ml-makeovers 

Restoration

[1] 5byday https://www.restorephotos.io/restore (based on replicate)

[2] https://replicate.com/collections/image-restoration

[3] https://replicate.com/microsoft/bringing-old-photos-back-to-life

 

Alternatives

[1] https://ai.nero.com/photo-restore

[2] https://www.aiease.ai/app/restore-photo

[3] https://photobooth.online/en-us/photo-restoration/upload

[4] https://www.photorestore.io/restore 

[5] https://jpghd.com/

Frequence space ( Source codes )

References:

[1] Elliptic Harmonics http://www.cs.utah.edu/~jfishbau/advimproc/project3/



Resources:
 0) Discrete Fourier Transform 1D, source code c/c++/java/python and more https://www.nayuki.io/page/how-to-implement-the-discrete-fourier-transform
1) Discret Sine Tranform  https://people.sc.fsu.edu/~jburkardt/cpp_src/sine_transform/sine_transform.html
  1.1) Python version http://www-personal.umich.edu/~mejn/computational-physics/dcst.py

2) Haar Wavelet compression https://people.math.osu.edu/husen.1/teaching/wi2010/572/572.html

3) Fast Fourier Tranform 1d/2d http://www.kurims.kyoto-u.ac.jp/~ooura/fft.html
4) Elliptic Fourier Transform source code python https://github.com/hbldh/pyefd
5) Spatial Elliptical Fourier Descriptors python https://spatial-efd.readthedocs.io/en/latest/raster_link.html 

6) Morphometric in R https://github.com/MomX/Momocs/

Visual Computing

 

 

[1] Definition https://link.springer.com/content/pdf/10.1007/978-3-642-85023-3_1.pdf

Web Screen-Space methods for fluid rendering

 

[1] https://www.babylonjs.com/

Writing

[1]  Writing and Publishing Scientific Papers Image de couverture Series https://books.openbookpublishers.com/10.11647/obp.0235.pdf

AI Surfaces

 

[1] https://dsilvavinicius.github.io/nise/

Geo DataScience

Datasets

[1] Flood Mapping https://ieee-dataport.org/competitions/2024-ieee-grss-data-fusion-contest-flood-rapid-mapping

 

[1] datos https://www.datosabiertos.gob.pe/

[2] lat/long Perú https://github.com/jmcastagnetto/ubigeo-peru-aumentado

[3] variables vivienda y conocimiento https://www.redalyc.org/journal/6357/635767693004/html/

CONCLUSIONES

El conocimiento sobre dengue, las viviendas que presentan depósitos de basura y agua acumulada están relacionadas a los casos de Dengue en los distritos de Luyando y Rupa Rupa, en la provincia de Leoncio Prado. Persisten conductas de riesgo a pesar del adecuado conocimiento sobre la enfermedad. No se encontró asociación con el tipo de vivienda, género, material predominante en las viviendas, tipo de abastecimiento de agua y servicios higiénicos.

 

[4] datos amazonia https://www.dge.gob.pe/sala-situacional-dengue/#grafico27

[5] Mapas Perú .shp https://www.geogpsperu.com/2014/03/base-de-datos-peru-shapefile-shp-minam.html

[6] Información Geoespacial Perú https://www.idep.gob.pe/geovisor/descarga/visor.html

[6] Hidrografía https://data.humdata.org/dataset/hidrografia-de-peru?

   https://data.humdata.org/dataset

[7] Áreas  naturales protegidas https://geo.sernanp.gob.pe/visorsernanp/

[8] Biomasa Brasil https://mapbiomas.org/download

Processing 

[1] plotting maps https://ggplot2-book.org/maps.html

[1.1] https://community.rstudio.com/t/geom-label-with-custom-background-and-color-text/45161

[2] poly2nb https://www.rdocumentation.org/packages/spdep/versions/1.2-8/topics/poly2nb

[3] Indicadores demograficos Perú (teoria) https://www.inei.gob.pe/media/MenuRecursivo/publicaciones_digitales/Est/Lib1743/Libro.pdf

R Installation and more

 

* R installation




$sudo apt install r-base

 

* Package installation

install.packages('readr')

 

* install.packages('sf')

//Configuration failed because libudunits2.so was not found


sudo add-apt-repository ppa:ubuntugis/ubuntugis-unstable
sudo apt-get update
sudo apt-get install libudunits2-dev libgdal-dev libgeos-dev libproj-dev 

* install.packages('dplyr') //dataframe, works with R version >= 3.5

* install.packages('tidyverse') //Contains other packages (dplyr, ggplot2, etc.)  

* install.packages('spdep') //Spatial Dependence: Weighting Schemes, Statistics. A collection of functions to create spatial weights matrix objects from polygon

* install.packages('GGally') //extends 'ggplot2'

 

* install.packages('leaflet') //makes it easy to integrate and control Leaflet maps in R.

* install.packages('coda')

 

* install.packages('CARBayes')

* install.packages('CARBayesdata') 

 

* install.packages('xlsx')  

 

    dependences:

      1) java

      2) sudo apt-get install openjdk-11-jdk

      3) sudo R CMD javareconf    

      4) https://github.com/PCRE2Project/pcre2/releases  

      4.1) compilation https://www.appsloveworld.com/r/100/371/how-to-solve-lpcre2-8-error-while-installing-rjava-package-in-r


* install.packages('readxl')

 

* install.packages('tmap')


 

 

 

References:

[1] rstudio https://linuxconfig.org/rstudio-on-ubuntu-18-04-bionic-beaver-linux

[2] R 3.5 installation on Linux 18 https://rtask.thinkr.fr/installation-of-r-3-5-on-ubuntu-18-04-lts-and-tips-for-spatial-packages

[2] rstudio previous https://docs.posit.co/previous-versions/rstudio/

Latex writing

Highlighting code

[1] Custom C https://tex.stackexchange.com/questions/312789/lstdefinelanguage-cannot-handle-keywords-if-endif

Multi references

\bibliography{paper,references2019}

Soundscape works

 

[1] A pipeline for identification of bird and frog species in tropical soundscape recordings using a convolutional neural network

https://www.sciencedirect.com/science/article/pii/S1574954120300637?via%3Dihub

[2] https://www.frontiersin.org/articles/10.3389/fevo.2021.738537/full

Backtesting

 

[1] popular code https://github.com/kernc/backtesting.py/tree/master/backtesting

[2] https://blog.devgenius.io/algorithmic-trading-backtesting-a-strategy-in-python-3a136be16ece

[3]  https://towardsdatascience.com/backtest-your-trading-strategy-with-only-3-lines-of-python-3859b4a4ab44

Python Genetic Algorithms

 

[1] pyGAD https://github.com/ahmedfgad/GeneticAlgorithmPython

Transformers in Computer Vision

 

[1] Review https://sh-tsang.medium.com/review-vision-transformer-vit-406568603de0

[2] Colab ViT Tutorial https://colab.research.google.com/github/hirotomusiker/schwert_colab_data_storage/blob/master/notebook/Vision_Transformer_Tutorial.ipynb

[3] ViT pytorch https://github.com/lucidrains/vit-pytorch

[4] Vit Keras https://wandb.ai/ayush-thakur/keras_cv_vit/reports/Image-Classification-Using-Vision-Transformer-and-KerasCV--VmlldzozNTE4MzMz

[5] Fine tunning https://huggingface.co/blog/fine-tune-vit

[6] Full material https://github.com/cmhungsteve/Awesome-Transformer-Attention

Watercolor tips

 

Material

[1] https://www.nicoletalle.com/como-elegir-el-mejor-set-de-acuarelas/

Paper

[1] ...

Latex - Format listing environment

minted package 

References:

[1] https://www.overleaf.com/learn/latex/Code_Highlighting_with_minted

Ubuntu 18 OpenGL compilation issues

1) 

In file included from main.cpp:8:0:
gluvi.h:10:10: fatal error: GL/glut.h: No such file or directory
#include <GL/glut.h> // ...when everyone else puts it here?
         ^~~~~~~~~~~

$ sudo apt-get install freeglut3-dev

2)

util.h: In function ‘double randhashd(unsigned int)’:
util.h:259:33: error: ‘UINT_MAX’ was not declared in this scope
{ return randhash(seed)/(double)UINT_MAX; }

#include <climits>

3)


array1.h: In constructor ‘Array1<T>::Array1(long unsigned int, const T*, long unsigned int)’:
array1.h:124:12: error: ‘memcpy’ is not a member of ‘std’
      std::memcpy(data, data_, n*sizeof(T));

#include <cstring>

4) Does not find/recognize libGL

fincahuanaco@pisces:~/DRIVE/Research23/viscosity$ g++ testgl.cpp -lglut -lGLU -L/usr/lib -lGL
/usr/bin/ld: cannot find -lGL
collect2: error: ld returned 1 exit status

#Check symbolic link

$ file /usr/lib/x86_64-linux-gnu/libGL.so 

/usr/lib/x86_64-linux-gnu/libGL.so: broken symbolic link to libGL.so.1.0.0 

 

$ file /usr/lib/x86_64-linux-gnu/libGL.so.1.7.0 #this is right file

/usr/lib/x86_64-linux-gnu/libGL.so.1.7.0: ELF 64-bit LSB shared object, x86-64, version 1 (SYSV), dynamically linked, stripped

#Update libGL link, first go to directory and update

$ cd /usr/lib/x86_64-linux-gnu
$ sudo ln -s libGL.so.1.7.0 libGL.so

#back to source directory and try again

fincahuanaco@pisces:~/DRIVE/Research23/viscosity$ g++ testgl.cpp -lglut -lGLU -lGL            
fincahuanaco@pisces:~/DRIVE/Research23/viscosity$ ./a.out

References:

[1] First OpenGL code http://www.codebind.com/linux-tutorials/install-opengl-ubuntu-linux/

Ubuntu 18: Dark theme

 

$gsettings set org.gnome.desktop.interface gtk-theme 'Adwaita-dark'

References:
[1] https://askubuntu.com/questions/1047604/ubuntu-18-04-missing-global-dark-theme-option-in-gnome-tweak-tool

 

My Wallpapers

 [1] Leopard https://wallhere.com/en/wallpaper/1058505

Graph Neural Network - Step 1

 

References:

[1] Short review https://neptune.ai/blog/graph-neural-network-and-some-of-gnn-applications

[2] Coding GNN https://keras.io/examples/graph/gnn_citations/

[2.1] https://keras.io/examples/graph/gat_node_classification/

AI tools to create videos

[0] Create a Story using chatGPT

[1] Text to speach https://www.speachy.ai  #no includes english/doesnt work

[2] Text and Speach to Video https://invideo.io/

[3] Free Atatars https://www.synthesia.io

Data Visualization tools

 

[1] A new library for LLMs and NNs that provides visual clustering analysis and model interpretability. Super useful.

!pip install arize-phoenix

CG Visualization tools

 

[1] tools https://graphics.tudelft.nl/software/

[2] Surface from fluid in GPU https://github.com/xiaoxiaoyu1872/PostMPS

Latent space

 

References:

[1] https://www.europeanvalley.es/noticias/el-espacio-latente-en-la-ia/

[2] https://rstudio-pubs-static.s3.amazonaws.com/840251_35002e1971484924bc78c24f442e530a.html

Convert Photo in Cartoon

 

 

[1] https://imglarger.com/Cartoonizer

[2] https://vanceai.com/toongineer-cartoonizer/

[3] Prompt image to cartoon https://deepai.org/machine-learning-model/image-editor

[4] https://www.befunky.com/create/photo-to-cartoon/

[5] Head+ [Body models]  https://imagetocartoon.com/ 10/week

[6] 4Adults AI https://metaroids.com/lists/adult-ai-art-tools-that-can-generate-nsfw-ai-images/

WebAssembly

 

[1] Compiling an Existing C Module to WebAssembly

 https://developer.mozilla.org/en-US/docs/WebAssembly/existing_C_to_wasm

Jetson Wifi issues

#Alternative to wpa_supplicant

Creating connection(important don't remove --):

$ nmcli connection add type wifi con-name "myconname" ifname wlan0 ssid "eduroam" -- wifi-sec.key-mgmt wpa-eap 802-1x.eap ttls
 802-1x.phase2-auth mschapv2 802-1x.identity "USERNAME" 

$ sudo --ask nmcli c up myconname 

 

 

$ ls /etc/NetworkManager/system-connections  #show connections

$ cat /etc/NetworkManager/system-connections/myconname #show file connection 

$ nmcli con show myconname  #show connection detailed

Error 1:

password for '802-1x.identity' not given in 'passwd-file' 

Solution 1:

$ vi mypassfile  #add next line with pass value

802-11-wireless-security.psk:mypassvalue

$ nmcli con up <myconname> passwd-file <mypassfile>



References:

[1] Single connection https://www.linuxfordevices.com/tutorials/ubuntu/connect-wifi-terminal-command-line

[2] https://vessokolev.blogspot.com/2018/08/using-nmcli-to-create-8021x-eap-ttls.html

 

 

 

Python - Creating virtual environments

Install pip if it doesn't exist

$curl -O https://bootstrap.pypa.io/get-pip.py

$python3 get-pip.py --user

$python3 -m pip list

$python3 -m pip install tensorflow --no-cache-dir  #for space issue
 

Error during execution of: python3.8 -m venv myenv

Error: Command '['/path/to/desired/env/bin/python3.8', '-Im', 'ensurepip', '--upgrade', '--default-pip']' returned non-zero exit status 1.

Solution: Create a virtual environment using a especific python version

$virtualenv --python=$(which python3.7) envtf4p37

 

Proxy list and tools

 

 

Tools:

[1] https://hidemy.name/en/proxy-checker

[2] Listing proxies by country https://www.proxynova.com/proxy-server-list/country-us

FAPESP Brazil

References

[1] https://fapesp.br/valores/bolsasnopais

Jetson Nano and Tensorflow 2.4 in Python3.6

 

References:

[1] https://qengineering.eu/install-tensorflow-2.4.0-on-jetson-nano.html

[2] Lite https://qengineering.eu/install-tensorflow-2-lite-on-jetson-nano.html

[3] Install bazel https://github.com/jkjung-avt/jetson_nano/blob/master/install_bazel-3.1.0.sh

Linux verify disk activities

 

 

$ sudo apt-get install iotop

$ sudo iotop -a
$ sudo iotop -oPa -d 2  #more specific
 

$ iostat  #activity by sda, sdb, etc.
 

jbd2 is a kernel thread that updates the filesystem journal.

 

References:

[1] Reduce firefox disk access https://gist.github.com/gagarine/5cf8f861abe0dd035b7af19e4f691cd8

[2] Monitoring disk activity(htop) https://askubuntu.com/questions/276669/how-to-monitor-disk-activity

Get create/birth date from files

$ stat wakeup.txt  #get the inode

$ df -h wakeup.txt #get device name sdxy

$ sudo debugfs -R 'stat <586205>' /dev/sda1

Output:

Inode: 586205   Type: regular    Mode:  0664   Flags: 0x80000
Generation: 1277687204    Version: 0x00000000:00000001
User:  1000   Group:  1000   Size: 31
File ACL: 0    Directory ACL: 0
Links: 1   Blockcount: 8
Fragment:  Address: 0    Number: 0    Size: 0
ctime: 0x615eed87:dba39c9c  -- Thu Oct  7 09:52:23 2021
atime: 0x64231159:334e6b48  -- Tue Mar 28 13:10:01 2023
mtime: 0x615eed87:dba39c9c  -- Thu Oct  7 09:52:23 2021
crtime: 0x615eed87:dba39c9c -- Thu Oct  7 09:52:23 2021
Size of extra inode fields: 32

 

References:

[1] https://www.linuxshelltips.com/find-file-creation-date/

[2] https://www.baeldung.com/linux/get-file-creation-date