bash console GUI popup notification

The following script allows for GUI popup display for Ubuntu and the likes:

#!/bin/bash

# basic script to display a GUI popup box
# requires libnotify-bin (for command notify-send)
notify-send -t 4000 "Take a look at the console !" $(eval pwd)"\n"`date +%Y/%m/%d-%H:%M:%S`

c++ change pointer passed as argument

To change the pointer passed in argument you need something like this:

void foo(int **ptr) //pointer to pointer
{
    *ptr = new int[10]; //just for example, use RAII in a real world
}

or

void bar(int *& ptr) //reference to pointer (a bit confusing look)
{
    ptr = new int[10];
}

Original thread:  http://stackoverflow.com/questions/11842416/function-does-not-change-passed-pointer-c

C++ headers and sources, templates

Original thread:  http://stackoverflow.com/questions/23962044/multiple-definition-of-first-defined-here-in-the-same-line-in-a-data-struc



If I understand you correctly, you are doing things like this:

// C.h

class C
{
   void f(); // declaration of f; ok to include in many modules
};

// definition of f; must not exist in more than one module
void C::f()
{
}

That doesn't work because the definition of f() will wind up in every module that includes C.h, leading to exactly the linker error you describe. You can fix this by either marking f() as inline, or by moving the definition of f() to a separate cpp file.
There is one special case where this is allowed, and that's when f() is a template (either directly or because C is a template). In that case, the definition must be in the header so the compiler can know how to instantiate it for whatever type(s) you specify. This does make life difficult for the linker since you can and often do end up with the sorts of redundant definitions that would normally be errors (e.g if you use f() in more than one module). Special behavior is needed to handle this.
Incidentally, the reason things work when you move the function bodies inside the class definition is because that has the effect of making them implicitly inline.

git graphical diff

One can use the "git difftool" command, which has direct knowledge of many diffing tools, including meld.
By default it always asks for which diffing tool to use (and defaults to 'meld' on my box), but you can automate the choice with configuration variables. See "git help difftool" for details.

Src: http://blog.deadlypenguin.com/blog/2011/05/03/using-meld-with-git-diff/
see "comments" sections

CUDA_VISIBLE_DEVICES – Masking GPUs

Src: http://acceleware.com/blog/cudavisibledevices-masking-gpus

Does your CUDA application need to target a specific GPU? If you are writing GPU enabled code, you would typically use a device query to select the desired GPUs. However, a quick and easy solution for testing is to use the environment variable CUDA_VISIBLE_DEVICES to restrict the devices that your CUDA application sees. This can be useful if you are attempting to share resources on a node or you want your GPU enabled executable to target a specific GPU.

Environment Variable Syntax	Results
CUDA_VISIBLE_DEVICES=1	Only device 1 will be seen
CUDA_VISIBLE_DEVICES=0,1	Devices 0 and 1 will be visible
CUDA_VISIBLE_DEVICES=”0,1”	Same as above, quotation marks are optional
CUDA_VISIBLE_DEVICES=0,2,3	Devices 0, 2, 3 will be visible; device 1 is masked

CUDA will enumerate the visible devices starting at zero. In the last case, devices 0, 2, 3 will appear as devices 0, 1, 2. If you change the order of the string to “2,3,0”, devices 2,3,0 will be enumerated as 0,1,2 respectively. If CUDA_VISIBLE_DEVICES is set to a device that does not exist, all devices will be masked. You can specify a mix of valid and invalid device numbers. All devices before the invalid value will be enumerated, while all devices after the invalid value will be masked.
To determine the device ID for the available hardware in your system, you can run NVIDIA’s deviceQuery executable included in the CUDA SDK. Happy programming!

Nvidia Visual Profiler (NVVP) version 7.5 crashes on new session on Ubuntu

Original thread: http://stackoverflow.com/questions/26436009/eclipse-luna-crashes-on-new-project-in-ubuntu

Extracted Solution:

According to comment 20 in this bug report: https://bugs.eclipse.org/bugs/show_bug.cgi?id=440660#c20

This seems to be a bug in GTK according to https://bugs.launchpad.net/ubuntu/+source/gtk2-engines-oxygen/+bug/1242801 (there a similar problem for Meld was reported).
Another workaround mentioned there is for Oxygen, edit the normally already existing file /usr/share/themes/oxygen-gtk/gtk-2.0/gtkrc and change

`GtkComboBox::appears-as-list = 1`

into

`GtkComboBox::appears-as-list = 0`

This workaround is working for me.

LD cannot find library because of version numbering

It is Debian convention to separate shared libraries into their runtime components (libmagic1: /usr/lib/libmagic.so.1 → libmagic.so.1.0.0) and their development components (libmagic-dev: /usr/lib/libmagic.so → …).
Because the library's soname is libmagic.so.1, that's the string that gets embedded into the executable so that's the file that is loaded when the executable is run.
However, because the library is specified as -lmagic to the linker, it looks for libmagic.so, which is why it is needed for development.
See Diego E. Pettenò: Linkers and names for details on how this all works on Linux.

---

In short, you should apt-get install libmagic-dev.
This will not only give you libmagic.so but also other files necessary for compiling like /usr/include/magic.h.

src: http://stackoverflow.com/questions/335928/ld-cannot-find-an-existing-library

How to install Skype on Kubuntu 14.04

open muon
if you are in muon discover go to "sources">"configure sources"
check all on the Kubuntu software tab
then click the "other software"tab and make sure "canonical partners" is checked.
close muon
and back at the konsole:

sudo apt-get update

sudo apt-get install skype

Src: http://community.skype.com/t5/Linux-archive/How-to-install-Skype-for-Kubuntu-14-04/td-p/3602591 

Imagemagick in bash, resize images

The following command will resize an image to a height of 100:

convert example.png -resize x100 example.png

 Src: http://www.howtogeek.com/109369/how-to-quickly-resize-convert-modify-images-from-the-linux-terminal/

Latex Temporarily disable superscript in citation

The following example changes \setcitestyle locally and puts it in macro \citen. \setcitestyle of package natbib (2010/09/13 8.31b) contains a space right at the beginning of the macro definition by an uncommented end of line, the trick with \romannumeral removes this space.

\documentclass{article}
\usepackage[square]{natbib}
\setcitestyle{super}

\newcommand*{\citen}[1]{%
  \begingroup
    \romannumeral-`\x % remove space at the beginning of \setcitestyle
    \setcitestyle{numbers}%
    \cite{#1}%
  \endgroup   
}

\begin{document}
Package \textsf{accsupp}\cite{oberdiek:accsupp}.
This figure is reproduce from reference~\citen{oberdiek:zref}.
\bibliographystyle{plainnat}
\raggedright
\bibliography{oberdiek-bundle}
\end{document}

Inside moving arguments (e.g., \caption) macro \citen can be protected using \protect or by using \DeclareRobustCommand for the definition:

\newcommand*{\citen}{}% generate error, if `\citen` is already in use
\DeclareRobustCommand*{\citen}[1]{%
  \begingroup
    \romannumeral-`\x % remove space at the beginning of \setcitestyle
    \setcitestyle{numbers}%
    \cite{#1}%
  \endgroup
}

Source: http://tex.stackexchange.com/questions/94178/temporarily-disable-superscript-in-citation

bash split pdf

$ sudo apt-get update
$ sudo apt-get install pdftk

EDIT: since pdftk became deprecated, do:

sudo snap install pdftk

Then, to make a new pdf with just pages 1, 2, 4, and 5 from the old pdf, do this:

$ pdftk myoldfile.pdf cat 1 2 4 5 output mynewfile.pdf

Note that cat and output are special pdftk keywords. cat specifies the operation to perform on the input file. output signals that what follows is the name of the output pdf file.
You can specify page ranges like this:

$ pdftk myoldfile.pdf cat 1-2 4-5 output mynewfile.pdf 

http://linuxcommando.blogspot.ca/2013/02/splitting-up-is-easy-for-pdf-file.html 

Find LaTeX multiply-defined labels

perl -nE 'say $1 if /(\\label[^}]*})/' *.tex | sort | uniq -c | sort -n

 http://www.mawode.com/blog/blog/2012/03/21/finding-duplicate-latex-labels/

MATLAB uniform ticks (uniformticks) and printing

The following script can make the axes nicer. Example:

%% render uniform ticks digits on Y axis
function uniformticks_y(deci) ; % input number of decimals as string
command = ['%0.' mat2str(deci) 'f|'] ;
ticks = get(gca, 'Ytick') ;
set(gca, 'YTickLabel', sprintf(command, ticks));

However, changing the graph manually in the GUI can upset the nice axes settings. Simply rerun the script from the console without closing the graphs.

convert graph image to text data

To convert a screenshot, photo or scan of a graph or plot to a text data table, use this software:

Engauge Digitizer

http://sourceforge.net/projects/digitizer/?source=navbar

bash copy a directory recursively, excluding some directory or file name

rsync -av --progress sourcefolder /destinationfolder --exclude thefilenametoexclude

rsync -av --progress sourcefolder /destinationfolder --exclude thefoldertoexclude

NOTE: if the filename or directory appear multiple times, they will be excluded multiple times

Src:http://stackoverflow.com/questions/4585929/how-to-use-cp-command-to-exclude-a-specific-directory 

Latex / Bibtex rename Bibliography / references section when using babel

\addto\captionsenglish{\renewcommand{\refname}{Newname}} %% for babel

Kubuntu 12.04 wifi before logon

Check both boxes in network manger to get wifi running before login:
connect automatically & system connection

bash config files

For this task, you don't have to write fat parser routines (unless you want it 100% secure or you want a special file syntax) - you can use Bash's source command. The file to be sourced should be formated in key="value" format, otherwise bash will try to interpret commands:

#!/bin/bash
echo "Reading config...." >&2
source /etc/cool.cfg
echo "Config for the username: $cool_username" >&2
echo "Config for the target host: $cool_host" >&2

So, where do these variables come from? If everything works fine, they are defined in /etc/cool.cfg which is a file that's sourced into the current script or shell. Note that this is not the same as executing this file as a script! The sourced file most likely contains something like:

cool_username="guest"
cool_host="foo.example.com"

These are normal statements understood by Bash, nothing special to do. Of course (and that is a big disadvantage under normal circumstances) the sourced file can contain everything that Bash understands, including evil code!
Src/more: http://wiki.bash-hackers.org/howto/conffile

Subversion 1.7 on Ubuntu 12.04

there’s an official Subversion PPA on Launchpad, so for Ubuntu 12.04 all you have to do is add the following couple lines to your /etc/apt/sources.list file:

deb http://ppa.launchpad.net/svn/ppa/ubuntu precise main 
deb-src http://ppa.launchpad.net/svn/ppa/ubuntu precise main 

 To configure APT to trust this repository's signing key, run script from the page
https://launchpad.net/~svn/+archive/ubuntu/ppa

And upgrade Subversion to its latest version with apt-get:

sudo apt-get update
sudo apt-get install subversion

Source: https://kovshenin.com/2013/subversion-1-7-on-ubuntu-12-04/ 

Obtain the number of CPUs / cores in Linux / bash

grep -c ^processor /proc/cpuinfo 

Src:http://stackoverflow.com/questions/6481005/obtain-the-number-of-cpus-cores-in-linux 

Inkscape - change the color of markers

How do I change the color of markers (e.g., arrow ends)?

By default, markers are black. You can change their color to match the color of the stroke of the object they are applied to by enabling an effect: Extensions > Modify Path > Color Markers to Match Stroke. 

http://wiki.inkscape.org/wiki/index.php/Frequently_asked_questions#How_do_I_change_the_color_of_markers_.28e.g..2C_arrow_ends.29.3F

Adding alpha (transparent) background to jpeg images, logos

- Some posters, powerpoints, have non-white backgrounds. Company logos with transparency look nicer on these. However, sometimes logos are only available in the jpeg format.

- Tools like GIMP/KolourPaint will easily flood-fill the white as alpha, except for the closed figures like "O,e" letters. This can be done by hand, than the result saved as png with alpha channel.

- However, jpeg images are full of shades of white, so the result can be very messy sometimes.

- Solution: use advanced software such as ImageJ, to change the contrast so any intensity value say, above 250/255, will be brought to 255. Then automatic flood-fill of the other software programs will be a lot more efficient.

Note: as of 03/2015, ImageJ does not natively support the alpha channel, so other paint software is still required to finish the job.

bash merge multiple pdf files

A) Using mutool

apt-get install mupdf-tools

mutool merge [options] file1 [pages] file2 [pages] ...

Options:

-o output

The output filename.

-O options

See mutool create for details on this option. 

 

Source: https://mupdf.com/docs/manual-mutool-merge.html

B) Using pdfunite. If needed, install poppler package

example uses:

pdfunite in-1.pdf in-2.pdf in-n.pdf out.pdf

pdfunite *.pdf out.pdf

Src:http://stackoverflow.com/questions/2507766/merge-convert-multiple-pdf-files-into-one-pdf

bibtex medphys aapm enquote error

- when using the custom home-brew style medphys.bst
- after pasting the pre-compiled bibliography
- if the compilation crashes and says, \enqoute() already defined,
- you simply forgot to comment out \bibliographystyle(medphys)

convert bunch of images to video using ffmpeg

sample code:

avconv -framerate 7 -i img%03d.png -qscale 1 -c:v libx264 -pix_fmt yuv420p out.mp4

-use avconv, cause ffmpeg command is deprecated
-framerate is the desired visual result in fps units, can be a fraction like 1/5
-i is the regexp to retrieve pics
-qscale is quality: 1 for best, 31 for worst
-c:v is the video codec
-pix_fmt is the color space setting, yuv240p is the most portable
NOTE: the order of the arguments is important: some come before -i, some after -i


Src: https://trac.ffmpeg.org/wiki/Create%20a%20video%20slideshow%20from%20images

keywords: video, mpg, mpeg, mp4, movie, film

install ffmpeg video tool

sudo apt-get install ffmpeg

sudo apt-get install libavcodec-extra-53
sudo apt-get install libavcodec-extra57

Src: http://ubuntuforums.org/showthread.php?t=200562
keywords: video, mpg, mpeg, mp4, movie, film 

makebst \enquote command error

The makebst program can crete custom commands within .bbl files.
If such a command, like \enquote{} is giving a compilation error,

try to delete the temporary (non-source) files and recompile the .tex

SVN diff

The difference between working copy and HEAD; the changes which would need to be made to what is now in the repository (HEAD), to produce your working copy:

svn diff -r HEAD --old=

Of possible interest, the difference between BASE and HEAD; changes that have been checked into the repository since you last updated working copy:

svn diff -r BASE:HEAD 

And of course the difference between BASE and working copy; the changes you have made since you last updated working copy:

svn diff 

There are three versions being discussed: BASE, working copy, and HEAD.

• BASE: as last checked out / updated. What working copy would revert to after using svn revert
• working copy: local modifications to which has been checked out / updated as recently as BASE
• HEAD: latest modifications in repository. Equivalent to BASE iff no changes have been committed since was checked out / updated as working copy.

 Src: http://stackoverflow.com/questions/3773345/check-diff-against-file-on-the-server

ImageJ 3DViewer - maximize image resolution

To maximize resolution for 3DViewer, set resampling factor to 1

Bash set variable to command output

In addition to the backticks, you can use $(), which I find easier to read, and allows for nesting.

OUTPUT="$(ls -1)"
echo "${OUTPUT}"

Quoting (") does matter to preserve multi-line values.

Src: http://stackoverflow.com/questions/4651437/how-to-set-a-bash-variable-equal-to-the-output-from-a-command

Matlab new page size scraps plot axis markers

-Run a script to generate only one plot
-Change page size in print preview / export setup
-Run the uniformticks script (x-axis shown here):

%% render uniform ticks digits on X axis
% input: number of decimals after decimal point
function uniformticks_x(deci) ;

command = ['%0.' mat2str(deci) 'f|'] ;
ticks = get(gca, 'Xtick') ;
set(gca, 'XTickLabel', sprintf(command, ticks));

Ubuntu Matlab Plot Fonts

That was the elusive information we needed: I looked at my 11.04 that worked (I was the OP on the other thread) and compared font paths. What you need to install is:

xfonts-100dpi and
xfonts-75dpi

logout and log back in again and you should be away laughing! (worked for me on a fresh install)


Src: http://ubuntuforums.org/showthread.php?t=1762805

bash: Simple way to move files only from one location to another

In the case you have many files to move, and your folder tree has nothing special, use

mv ./*.* destination_path

This will also move directories containing a dot in the name and will ignore files without extensions...quick hack

UNIX Local machine MAC address

$ ifconfig

look for the entry for HWaddr,
6 groups of 2 hex characters

ubuntu teamviewer black screen after unlock

In case after an unlock, the screen keeps dimming to black ...

Radical solution: System settings, Display, screensaver, disable sreensaver.

"May work" solution:

simply go to System settings, Display, screensaver, click anywhere in the application and exit. This will somehow update the config files and prevent further blinking during this session.

also, try to change the connection settings on the "controlling" machine:
tick "enable black screen if partner input is deactivated"

LaTeX Labels for figures

When a label is declared within a float environment, the \ref{...} will return the respective fig/table number, but it must occur after the caption. When declared outside, it will give the section number. To be completely safe, the label for any picture or table can go within the \caption{} command, as in

\caption{Close-up of a gull\label{fig:gull}} 

Source: http://en.wikibooks.org/wiki/LaTeX/Labels_and_Cross-referencing 

update Adobe Flash Player in Kubuntu

You should just install the latest version from the Ubuntu repositories. It is a lot easier and normally they keep this one up-to-date with new Linux Flash releases.
To install it run the command

sudo apt-get install flashplugin-installer

Src: http://askubuntu.com/questions/463295/how-to-update-adobe-flash-player-in-kubuntu-latest-update