C2110 UNIX and programming 7th lesson -1C2110
UNIX and programming
Petr Kulhánek, Jakub Štěpán
kulhanek@chemi.muni.cz
National Centre for Biomolecular Research, Faculty of Science
Masaryk University, Kotlářská 2, CZ-61137 Brno
CZ.1.07/2.2.00/15.0233
7th Lesson
C2110 UNIX and programming 7th lesson -2-
Contents
 Scripts
• Scripting in Bash
• Cycle using for and for in
 ImageMagic
• Image conversions
• Commands convert, display
 Commands for names and paths processing
• dirname, basename
C2110 UNIX and programming 7th lesson -3-
Scripts
 Scripting in Bash
 How to write scripts
 Cycle using for
C2110 UNIX and programming 7th lesson -4Script
in Bash
#!/bin/bash
# this is comment
echo 'This is script in Bash!'
echo "Directory content `pwd` is:"
ls # print directory contents
A=6 # set variable A value
echo "Variable A value is $A"
echo "first command"; echo "second command"
./mycommand first_argument second_argument \
third_argument
Commandprocessingorder
• empty lines are ignored
• text behind symbol # is ignored (used to make comments)
• multiple commands can be on one line, commands are then separated by semicolon ;
• one command may be written on multiple lines using backslash \
New line
follows
C2110 UNIX and programming 7th lesson -5Running
Bash scripts
1) Indirect run
We run language interpreter and as a parameter we give script name.
$ bash my_bash_script
Script does not need x (executable) permission.
2) Direct run
We run directly script (shell runs interpreter automatically).
$ chmod u+x my_bash_script
$./my_bash_script
Script needs permission x (executable) and interpreter (script file).
#!/bin/bash
echo 'This is script in Bash interpreter!'
C2110 UNIX and programming 7th lesson -6Cycle
using for
for((initialization;condition;change))
do
command1
...
done
for((initialization;condition;change)); do
command1
...
done
Compact form:
Cycle (loop) is control structure, that repeatedly processes set of commands. Repeats are
done until condition is fulfilled.
provede se před spuštěním cyklu
(inicializace počítadla)
If condition is true, commands command1
etc. are processed.
Actualization of counting
variable after commands
processing
C2110 UNIX and programming 7th lesson -7Cycle
using for, example
for((I=1;I <= 10;I++)); do
echo $I
done
for((I=10;I >= 1;I--)); do
echo $I
done
Write numbers 10 to 1Write numbers 1 to 10
Condition:
If variable may be interpreted as number,
following operators can be used:
!= not equal
== equal
< lower
<= lower or equal
> greater
>= greater or equal
Initialization variable assignment is same as
Bash variable assignment.
Variable I has counting role.
Change:
If variable may be interpreted as number,
then following arithmetic operators may be
used:
++ increments variable value by one
-- decrements variable value by one
To be continued ....
C2110 UNIX and programming 7th lesson -8Cycle
using for, count change
If variable may be interpreted as number, then following arithmetic operators may be used:
++ increments variable value by one
A++
-- decrements variable value by one
A--
+ adds two values
A=5 + 6
A=A + 1
- subtracts two values
A=5 - 6
A=A – 1
* multiplies two values
A=5 * 6
A=A * 1
/ divides two values (integer division)
A=5 / 6
A=A / 1
+= adds value to variable
A+=3
A+=B
-= subtracts value from variable
A-=3
A-=B
*= multiplies variable by value
A*=3
A*=B
/= divides variable by value
A/=3
A/=B
A=A+3
C2110 UNIX and programming 7th lesson -9Cycle
and variables
A=$A + 1
A = $A + 1
A=A + 1
A = A + 1
Count change:
A=1
A = 1
Count initialization:
A <= 10
$A <= 10
Condition:
It is possible to use space between symbol =,
variable name and value.
It is optional to use operator $ for access to
variable value (not needed).
Correct syntaxes
for((I=1;I <= 10;I++)); do
echo $I
done
Benevolent syntax is only in cycle
definition.
Here operator is compulsory to access variable
value.
C2110 UNIX and programming 7th lesson -10-
Exercise
1. Write script, that writes path to current directory and its contexts.
2. Write ten symbols A, each to separate line.
3. Write ten symbols A all on same line (echo –n and manual page).
4. Write script, that prints even numbers from 2 to 100.
5. Write script, that prints power 2n for n from 0 to 32.
Reccomendation:
Solve each task in separate directory. Number your directories (for
example):
task01
task02
etc.
C2110 UNIX and programming 7th lesson -11Nested
cycle
Cycle control structures may be nested.
for((I=1;I <= 10;I++)); do
for((J=1;J <= 10;J++)); do
echo "$I $J"
done
done
Outer cycle
Inner cycle
for((I=1;I <= 10;I++)); do
for((J=1;J <= I;J++)); do
echo "$I $J"
done
done
Count of outer cycle may
influence behavior of inner cycle.
C2110 UNIX and programming 7th lesson -12-
Exercise
1. Compare function of nested cycles shown on previous page.
2. Write script, that print ten times ten symbols (of your choice) on line.
3. Write script, that print one symbol on first line, two symbols on second line,
etc. Write ten lines in this way.
4. Change previous script, so that it print 15 times 6 symbols on one line.
5. Find out why it is advantageous to use variables in control structures.
NUMBER=10
for((I=1;I <= NUMBER;I++));
do
echo $I
done
Values in control structures should be given by variables.
for((I=1;I <= 10;I++)); do
echo $I
done
Worse solution
C2110 UNIX and programming 7th lesson -13Image
Magic
 Image conversion
http://www.imagemagick.org
(documentation, tutorials, source code)
C2110 UNIX and programming 7th lesson -14-
Commands
animate, compare, composite, conjure, convert, display, identify, import, mogrify, montage,
stream
Overview:
Most important commands:
display show image or image sequence on screen
convert converts image between formats, including operations like size
change, crop, etc.
Detail description is accessible in manual pages or web pages of
Image Magic.
Examples:
$ convert input.eps output.png
convert image from postscript format to PNG format
High quality for publications:
$ convert -density 300x300 input.eps -units PixelsPerInch \
-density 300 -background white -flatten output.png
C2110 UNIX and programming 7th lesson -15-
Scripts
 Cycle using for in
C2110 UNIX and programming 7th lesson -16Cycle
using for ... in ...
for VAR in LIST
do
command1 $VAR
...
done
for VAR in LIST; do
command1 $VAR
...
done
Compact syntax:
Commands in block do/done (command1, …) are processed for each item in list LIST. In
each loop iteration variable VAR contains actual item from list LIST.
C2110 UNIX and programming 7th lesson -17Cycle
using for ... in ..., lists
for A in a b c; do
echo $A
done
Cycle is done three times, printing symbols a, b, c
consequently.
Lists of items may be created by program (using backward aphostrophes).
for A in `ls *.eps`; do
./process_file $A
done
Command process_file is processed for each
file with extension .eps that is in current
working directory.
C2110 UNIX and programming 7th lesson -18Commands
for paths and
names processing
 dirname
 basename
C2110 UNIX and programming 7th lesson -19Commands
for name and path proc
dirname extracts directory name from full path
basename extracts file name from full path
Example:
$ basename /home/kulhanek/pokus.txt
pokus.txt
$ basename pokus.txt
pokus.txt
$ basename /home/kulhanek/pokus.txt .txt
pokus
$ dirname /home/kulhanek/pokus.txt
/home/kulhanek
$ dirname pokus.txt
.
Commands dirname and basename process paths without checking if file exists.
C2110 UNIX and programming 7th lesson -20-
Exercise
1. Create directory images
2. Copy files with extension .eps from /home/kulhanek/Data/Snapshots/ to
directory images.
3. Write script, that prints file names, that contain directory images in
following format:
Directory images contain file: file1.eps
Directory images contain file: file2.eps
1. Write script that, convert files from format eps in directory images to
format png.
2. Make sure by command display, that conversion was processed correctly.