LinuxShort

Usefull short commands

Kill a process tree

When some script is started from a command line in a for-loop and a process tree is made, one should find the parent process and its PID and then simply kill it:

   $ pstree username -p 
   sshd(19953)---bash(19954)---bash(22238)---idl(22323)-+-{idl}(22326)
                                                        |-{idl}(22327)
                                                        |-{idl}(22328)
                                                        `-{idl}(22329) 
   sshd(20096)---bash(20097)
   sshd(20762)---bash(20763)
   sshd(21087)---bash(21088)-+-grep(21309)
                             `-top(21308)
   sshd(21736)---bash(21737)
   sshd(21780)---bash(21781)---pstree(22331)

Or if this tree is to long, one should grep the program (here:idl) with: $ pstree usrname -p | grep idl

   $ kill 19953  
   $ pstree username -p  
   sshd(20096)---bash(20097)
   sshd(20762)---bash(20763)
   sshd(21087)---bash(21088)-+-grep(21309)
                             `-top(21308)
   sshd(21736)---bash(21737)
   sshd(21780)---bash(21781)---pstree(22332)

Change sth inside file

  sed -i s/'\-9999'/'NaN'/g filename 

This will change -9999 with NaN inside a file, without making some tmp file in between.

Print rotated picture

  lp -o media=a4 -o orientation-requested=4 -o fitplot figure.ps

Print in fixed width format with awk

 echo $a $b $c |  awk '{for (i=1; i<=NF; i++) printf("%-20s ",$i);printf ("\n")}' > outfile.dat

where strings a,b,c may be entire lines.

Make a small size pdf out of several pdfs

 gs -sDEVICE=pdfwrite -q -dNOPAUSE -dBATCH -sOutputFile=MajorFile.pdf SmallFiles*.pdf 

Combined files can ba a mix of .pdf .ps and .eps files and output file can be a .ps also

Cut a portion of a pdf file saving resolution and sharpness

 gs -g2700x3500 -sOUTPUTFILE=output.pdf -sDEVICE=pdfwrite -dBATCH -c "<< /PageOffset [-30 -120] >> setpagedevice" -f input.pdf

Where [-30 -120] means - shift the content of the old image to its left corner by (x,y)=(30,120) pixels (change the origin of the image) and 2700x3500 are the dimensions of the new image. Be careful - input.pdf should be a single page.

Make a series of single-page EPS files from various inputs

 gs -sDEVICE=epswrite -q -dNOPAUSE -dBATCH -dSAFER -sOutputFile=p%08d.eps 5page-first.pdf 7page-second.ps 1page-third.eps 

The resulting files will be nicely named as p00000001.eps .... p00000013.eps

Cut a portion of a .pdf file

Make a script named boundingBox.sh:

 gs                          \
  -q                         \
  -dBATCH                    \
  -dNOPAUSE                  \
  -sDEVICE=bbox              \
  -dLastPage=1               \
   $1 \
 2>&1                        \
 | grep %%BoundingBox

Call the script from the line with file_name as input:

./boundingBox.sh file.pdf 

The result will be sth. like: %%BoundingBox: 42 510 305 746, where lower left img coords = (42,510) and upper right = (305,746). Finaly, to cut a box 305-42=263 px wide and 746-510=236 high, excluding 42 pixels from the left and 510 pixels from the bottom, make a script crop.sh:

 gs                                                      \
   -o out.png                                            \
   -sDEVICE=pngalpha                                     \
   -g$2x$3                                             \
   -dLastPage=1                                          \
   -c "<</Install {$4 $5 translate}>> setpagedevice" \
   -f $1 

where $1x$2=width x height and $4 $5 are the portion excluded from the left and bootom. In this example:

 ./crop.sh file.pdf 263 236 -42 -510

To make .pdf out try:

gs -o out.pdf -sDEVICE=pdfwrite -c "[/CropBox [42 510 305 746] /PAGES pdfmark" -f file.eps

Extract particula pages from pdf file

 #!/bin/sh
 #
 # pdfsplit [input.pdf] [first_page] [last_page] [output.pdf] 
 #
 # Example: pdfsplit big_file.pdf 10 20 pages_ten_to_twenty.pdf
 #
 # written by: Westley Weimer, Wed Mar 19 17:58:09 EDT 2008
 #
 # The trick: ghostscript (gs) will do PDF splitting for you, it's just not
 # obvious and the required defines are not listed in the manual page. 

 if [ $# -lt 4 ] 
 then
         echo "Usage: pdfsplit input.pdf first_page last_page output.pdf"
         exit 1
 fi
 gs -dNOPAUSE -dQUIET -dBATCH -sOutputFile="$4" -dFirstPage=$2 -dLastPage=$3 -sDEVICE=pdfwrite "$1"

Convert eps to jpg using native gs

 gs -sDEVICE=jpeg -q -dJPEGQ=100 -dNOPAUSE -dBATCH -dSAFER -r100 -sOutputFile=image.jpg image.eps # -r100 should be changed to -r50 for denser image 

Convert (e)ps to png or gif

name="imgName"; figdir="/home/..../Figures"; text="my image"
1. convert $name.ps -depth 8 -alpha off -density 600 
2. convert $name.ps -depth 8 -alpha off -density 600 ${figdir}/${name}_large.gif 
3. convert $name.ps -depth 8 -alpha off -density 600 -resize 320x240 ${figdir}/${name}_large.gif
4. convert $name.ps -depth 8 -alpha off -density 600 -gravity Southeast -font helvetica -pointsize 75 \ 
-draw "text 150,100 '$text'" ${figdir}/${name}_large.gif

1. Resulting image will be named as .eps and will end up at the same place.

2. Resulting image will be named imgName_large.gif and will be placed in \$figdir.

3. Additionally, image can be resized in the same step.

4. Put text into image

Resize image

 mogrify -trim -resize 70% image.jpg   # or -resize 800x600 for fixed width

Screen command

 screen -S name # name a screen
 screen -ls # list all screens (those named will be easily read)
 Ctrl+a+d # detach screen
 screen -r name # attach to a screen
 screen -S name -X quit # kill detached screen and return to a terminal
 ls -laR /var/run/screen/ # lists when the screens start running

Several images into one

 montage img1.png img2.png img3.png img4.png img5.png img6.png -tile 2x3  -frame 2  -geometry +0+0 out.png 

Animation on .gif images

 convert -delay 50 img1.gif img2.gif -loop 0 anim.gif

Some cool stuff

• Very nice themes for Ubuntu 10.04

   sudo add-apt-repository ppa:bisigi
   sudo aptitude update
   sudo aptitude install bisigi-themes

• Convert youtube .flv to .mp3 (FORUM)

  sudo apt-get install youtube-dl
  sudo youtube-dl -U
  sudo youtube-dl -U
  sudo apt-get install ffmpeg libavcodec-unstripped-52
  sudo apt-get install ubuntu-restricted-extras 
  # Example:
  youtube-dl http://www.youtube.com/watch?v=Md7IhGYKncs
  ffmpeg -i Md7IhGYKncs.flv -acodec libmp3lame -ab 128 indiana.mp3

Install IRAF in Ubuntu 16 with Anaconda

Source: https://www.anaconda.com/download/#_unix

First install the following libs:

  sudo apt-get install libc6:i386 libz1:i386 libncurses5:i386 libbz2-1.0:i386 libuuid1:i386 libxcb1:i386 
  sudo apt-get install libxmu-dev:i386

Then download Anaconda from https://www.continuum.io/downloads

  cd /home/<user_name>/
  bash Anaconda2-4.4.0-Linux-x86_64.sh
  conda config --add channels http://ssb.stsci.edu/astroconda
  conda create -n iraf python=2.7 iraf-all pyraf-all stsci
  source activate iraf
  mkiraf
  <set to xgterm>
  cl
  ...
  source deactivate iraf
     

Pyraf also works in a standard way...