3D Cell Viewer

Tools online
http://www.allencell.org/3d-cell-viewer.html

Linux Drive Series/C210

Auxiliary Commands
$ journalctl
$ systemctl
$ alsactl

$ lsof | grep pcm  #still using
$ lsmod | grep snd #modules

$ sudo apt-get remove pulseaudio
$ sudo apt-get remove alsa
$ sudo apt-get install alsa


$ lspci 
Audio device: Intel Corporation 7 Series/C210 Series Chipset Family High Definition Audio Controller

$ lspci -v | grep Audio

$ sudo modprobe snd-hda-intel
modprobe: ERROR: ../libkmod/libkmod.c:586 kmod_search_moddep() could not open moddep file '/lib/modules/4.10.0-37-generic/modules.dep.bin'
modprobe: FATAL: Module snd-hda-intel not found in directory /lib/modules/4.10.0-37-generic

$ vi /etc/modprobe.d/alsa-base.conf  #for verify



*When is right installed
$ cat /proc/asound/card0/codec* | grep Codec
Codec: Realtek ALC887

$ cat /proc/asound/cards
 0 [Intel                ]: HDA-Intel - HDA Intel
 1 [NVidia            ]: HDA-Intel - HDA NVidia
 2 [U0x46d0x825 ]: USB-Audio - USB Device 0x46d:0x825

Upgrade
[*] https://wiki.ubuntu.com/Audio/UpgradingAlsa/DKMS
$ rm -r ~/.config/pulse;
$ pulseaudio -k



Note: try to select previous  version on grub

References
 [1] https://help.ubuntu.com/community/HdaIntelSoundHowto
 [2] https://askubuntu.com/questions/508692/intel-corporation-7-series-c210-series-isnt-being-detected-by-any-module
 

Lecture about SoundScape

Acoustic scenes, Acoustic events and Feature aggregation

D-CASE2013

Environment sound recognition using short-time feature aggregation
https://link.springer.com/article/10.1007/s10844-017-0481-4

Task of segmentation
  Speech recognition
  Musical information retrieval(MIR)
  Environment sound
  Survillance
  Index of video content
Task of acoustic events classification
  Statistic large set of features and K-NN
  Feature agregation (Bag of feaures)
  HMM/GMM(better for segementation and annotation for small scales)
  Deep learning
  Blind segmentation and SVM


Recurrence quantification analysis(RQA), RQA Features
Short Time Fourier Transform (STFT)

Lectures Neural Networks

Colour and Texture, but fail for shape.

Generative Adversarial Networks
https://arxiv.org/pdf/1406.2661.pdf

Unpaired Image-to-Image Translation using Cycle-Consistent Adversarial Networks https://junyanz.github.io/CycleGAN/

Eigen linear algebra library

Home http://eigen.tuxfamily.org
Examples https://eigen.tuxfamily.org/dox/group__TutorialLinearAlgebra.html

PDF Tools & Editors

PDF Annotator

[1] online/free/for signatures https://www.pdfescape.com/

PDF Tools 

$sudo apt-get install pdftk

$pdftk A.pdf cat 1-9 26-end output B.pdf # keep pages 1-9 and 26-end of the original file

$pdftk file1.pdf file2.pdf file3.pdf cat output newfile.pdf #join

$convert file1.pdf file2.pdf file3.pdf output.pdf #reduce resolution

$sudo apt-get install pdfmod #remove pages, works with A4

$sudo apt-get install pdfshuffler #remove pages, works with beamer too

PDF Editors

[1] Master PDF Editor http://code-industry.net/
[2] Fonst http://linuxg.net/how-to-install-master-pdf-editor-1-9-on-ubuntu-linux-mint-debian-fedora-opensuse-and-many-other-linux-systems/

[3] xournal, is possible add notes and free text, and [3] have other edition tools.
http://kuboosoft.blogspot.com/2012/07/5-editores-de-pdf-para-linux.html  
 
[4] Extract images from PDF online
http://pdfaid.com/ExtractImages.aspx

[5] How to extract part https://askubuntu.com/questions/221962/how-can-i-extract-a-page-range-a-part-of-a-pdf

OpenCV2 in Python for Windows

1.   Below Python packages are to be downloaded and installed to their default locations.
  Python-2.7.x.
  Numpy.
  Matplotlib (Optional).
2.    Install all packages into their default locations. Python will be installed to C:/Python27/.
3.    After installation, open Python IDLE. Enter import numpy and make sure Numpy is working fine.
4.    Download latest OpenCV release from sourceforge site and double-click to extract it.
5.    Goto opencv/build/python/2.7
       Copy cv2.pyd to C:/Python27/lib/site-packages.
6.  Test
>>> import cv2
>>> print cv2.__version__

Compiling Windows C++ Project in Linux (wavelet rasterization)

Josiah Manson Codes translate to GNU

Source code:
[*] Windows http://josiahmanson.com/research/wavelet_rasterization/supplemental/wavelet_raster.zip



g++ vect.cpp timer.cpp raster_poly.cpp get_font.cpp global.cpp insert_bez2.cpp insert_line.cpp vect.cpp save.cpp write_grid.cpp main.cpp -Wall -Wextra  -I/usr/include/freetype2 -lfreetype -lpthread -lm -o gnurasterize

_aligned_malloc

void *aligned_alloc(size_t alignment, size_t size);
//Since the question was asked, a new function was standardized by C11
[*] http://en.cppreference.com/w/cpp/memory/c/aligned_alloc
mkdir

#include <sys/types.h>
#include <sys/stat.h>
int result = mkdir("/home/me/test.txt", 0777);

__forceline
[*] https://stackoverflow.com/questions/8897791/how-to-define-forceinline-inline



__declspec

[*] http://gcc.gnu.org/wiki/Visibility
[*] https://stackoverflow.com/questions/2164827/explicitly-exporting-shared-library-functions-in-linux


Time
[*] https://stackoverflow.com/questions/2418157/ubuntu-linux-c-error-undefined-reference-to-clock-gettime-and-clock-settim

Freetype
$ sudo apt-get install libfreetype6-dev
$ g++ ... -I/usr/include/freetype2 -lfreetype

Change FreeImage by PPM
[*] pngwriter https://github.com/pngwriter/pngwriter

[1] PPM Specification http://paulbourke.net/dataformats/ppm/
[2] C/C++ Create PPM File https://rosettacode.org/wiki/Bitmap/Write_a_PPM_file

Related
[1] https://stackoverflow.com/questions/2033997/how-to-compile-for-windows-on-linux-with-gcc-g

Wavelet rasterization

Lectures
[1]
[2]
[3] http://faculty.cs.tamu.edu/schaefer/research/index.html

Geometry Processing Resources

Courses:
[1] http://www.hao-li.com/Hao_Li/Hao_Li_-_teaching_%5BCSCI_599__Digital_Geometry_Processing_SS_2015%5D.html
[2] Generating 3D models from: medical images http://www.banterle.com/francesco/courses/2017/be_3drec/
[3] Haar Wavelet (Computer Graphics Course) http://www.faculty.jacobs-university.de/llinsen/teaching/320491.htm More content about lectures and projects and others.


Tools
[1] http://download.slicer.org/
[2] Molecular Modeling http://www.cgl.ucsf.edu/chimera/

Love Equations

https://www.wolframalpha.com

1) plot x^2 + ( 5y/4 - sqrt(abs(x)))^2 = 1
2) plot x^2 + ( y - sqrt(abs(x)))^2 = 2
3) plot x^2 + ( y - (abs(x))^(1/3) )^2 = 1
4) plot (x^2 + y^2 -1)^3 -x^2y^3 = 0

Installing Tensor Flow (Problems)

Main guide
https://www.tensorflow.org/install/install_sources

Cannot find bazel. Please install bazel.
Solution https://docs.bazel.build/versions/master/install-ubuntu.html

Monitoring Nvidia card

$watch -n 1 nvidia-smi #to obtain continuous updates without filling the terminal with output

$sudo pip install gpustat
$gpustat
 
$sudo pip install glances
$sudo pip install glances[gpu]
$glances

Resources:
[1] Cuda 7.5 http://developer.download.nvidia.com/compute/cuda/7.5/Prod/local_installers/cuda_7.5.18_linux.run
[2] Install Cuda 7.5 http://www.r-tutor.com/gpu-computing/cuda-installation/cuda7.5-ubuntu

Vertex Smooth

Resources:
[1] http://www.stat.wisc.edu/~mchung/papers/HBM2001/HBM2001diffusion.html

[2] http://www.stat.wisc.edu/~mchung/papers/HBM2001/chung.2001.OHBM.pdf
[3] http://www.stat.wisc.edu/~mchung/papers/HBM2001/chung.2001.OHBMposter.pdf

[4] http://docs.salome-platform.org/5/smesh/user/smoothing_page.html
[5] https://www.youtube.com/watch?v=TQcS2q_rAHQ
     https://i.ytimg.com/vi/TQcS2q_rAHQ/maxresdefault.jpg
[6] http://grasshopperprimer.com/en/1-foundations/1-5/1_surface-geometry.html

HPC - High Performance Computing

[1] SLURM https://www.hpc.cam.ac.uk/using-clusters/running-jobs

[2] Module

Latex Desing

Resources
[1] Draw Complex Networks https://github.com/hackl/tikz-network/

Execute VTK Samples on ubuntu

VTK5.10
$locate vtkXOpenGLRenderWindow.cxx
$gedit  ... vtkXOpenGLRenderWindow.cxx
Uncomment next line
#define GLX_GLXEXT_LEGACY

$ CC=/usr/bin/gcc-5 CXX=/usr/bin/g++-5 cmake ..


cmake -DVTK_DIR=/home/DRIVE/Backup2018/Downloads2017/tools2/VTK5.10.1/build .

VTK7.1
$cmake -DVTK_DIR=/home/DRIVE/Downloads/tools/VTK7.1/build .

Resources
[1] How to write in vtk format https://github.com/arborworkflows/Visomics/blob/master/Base/voIOManager.cpp
[2] https://vtk.org/download/

Computer Graphics - Grid Structures

$sudo apt-get install freeglut3-dev
$sudo apt-get install libxmu-dev
$make

Resource:
[1] corner table exercice https://www.cc.gatech.edu/~lena007/cs4451_p2/corner_tab.html

Books online repositories

Library Genesis

Resources:
[0] Main reference https://en.wikipedia.org/wiki/Library_Genesis
      http://93.174.95.27/ 
[1] Mathematic, Biology and others https://libgen.pw (*)
[2] Mathematic and others http://libgen.io (*)
[3] http://gen.lib.rus.ec/
[4] zlibrary https://b-ok.org/ 
[5] sci-hub.tw
[6] https://whereisscihub.now.sh/
[7] Art books https://www.artubook.com (*)

(*) My favorite list


https://marcusnunes.me/posts/livros-gratuitos-da-springer/

Español

'A ver' y 'haber' se pronuncian de la misma forma, pero es habitual confundirlas y utilizarlas de manera incorrecta a la hora de escribir. Por eso, a continuación procedemos a distinguirlas tal y como marca la Real Academia Española (RAE):


A ver: Se trata de la secuencia constituida por la preposición a y el infinitivo verbal ver. Se utiliza en los siguientes casos:
        Para pedir al interloculor que nos deje ver algo: - Mira mi coche. - ¿A ver?
        Para dejar claro una cierta expectación: A ver cuándo viene la ayuda.
        Para llamar la atención sobre algo: A ver, ¿por qué no no vinisteis ayer a casa?
        En los casos en los que equivale a 'claro' o 'naturalmente': ¡A ver! Estaremos allí sin falta.
        En los casos que lleva delante la conjunción si, expresa, bien expectación, curiosidad o interés, a veces también un reto; otras temor o sospecha; y deseo o mandato: ¡A ver si me traes lo que te he pedido!

Haber: Puede tratarse de un verbo o un sustantivo:
        Como verbo se emplea como auxiliar seguido de un participio, para formar los infinitivos compuestos de la conjugación: Debe haber faltado a clase.
        También como verbo se emplea como infinitivo del impersonal que indica la presencia o existencia de lo designado por el sustantivo que lo acompaña: En su casa debe haber mucho dinero.
        Como sustantivo masculino su significado es "conjunto de bienes o caudales de una persona": En su haber contaba con muchos títulos.

Create Partition and Format for Fix HD

$sudo fdisk /dev/sdb #commands d, n, w

$sudo mkntfs /dev/sdb1

$mkfs.ntfs -f /dev/sdb1 

$dmesg | grep sd

$sudo lshw -C disk