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Introduction To Linux & IDL: Chia-Hsien Lin

This document introduces Linux, IDL, and some exercises for image processing. It discusses how to connect to Linux remotely, transfer files, and navigate directories. It also covers basic IDL commands, data types, plotting, and programming structures. Exercises demonstrate how to filter an image, crop a region of interest, and convert a 2D image into a 3D array stack.

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Merlin Mendoza
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41 views12 pages

Introduction To Linux & IDL: Chia-Hsien Lin

This document introduces Linux, IDL, and some exercises for image processing. It discusses how to connect to Linux remotely, transfer files, and navigate directories. It also covers basic IDL commands, data types, plotting, and programming structures. Exercises demonstrate how to filter an image, crop a region of interest, and convert a 2D image into a 3D array stack.

Uploaded by

Merlin Mendoza
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
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Introduction to Linux & IDL

Chia-Hsien Lin

2021 Spring (1092)

Chia-Hsien Lin Introduction to Linux & IDL 2021 Spring (1092) 1 / 12


Linux
Remote connection (IP: 140.115.120.39 port 77) (IP: 192.168.1.105 port 10000)
I Two ways for remote connection from Windows:
F mobaXterm: can do ssh and sftp
https://mobaxterm.mobatek.net/download-home-edition.html
F Xmin and putty: can only do ssh
http://www.geo.mtu.edu/geoschem/docs/putty install.html
I Connection steps:
1 use mobaXterm to connect to tiny
2 use ssh to connect to project2
transfer files:
I from project2 to your computer:
1 put the files to tiny:
sftp -P77 tiny@192.168.1.100
and then put the files
2 drag the files from the mobaxterm side column to your computer
I from your computer to project2:
1 drag the files from your computer to the mobaxterm side column
2 put the files to project2:
sftp -P10000 stdent01@192.168.1.105
and then put the files

Chia-Hsien Lin Introduction to Linux & IDL 2021 Spring (1092) 2 / 12


Linux

A good on-line guide for Linux: http://linux.vbird.org/


directory operation:
commands to do the following operations on directory:
I to create a new directory:mkdir;
I to go to a directory: cd;
I to move a directory mv);
I to remove a directory (The directory must be empty) rmdir;
I to copy an entire directory cp -rf;
I to check content: ls
file operation: create, edit, move, copy

Chia-Hsien Lin Introduction to Linux & IDL 2021 Spring (1092) 3 / 12


Linux

path:
I The symbol / at the beginning of a path means the root directory
e.g., cd / means go to the root directory
cd /home means go to a directory called home which is below the root
directory
I The symbol / is also used to separate mother directory and its
subordinate directory
e.g., cd /user/local means go to a directory local which is under
the directory user which is under the root directory
I go to a directory below the current directory:
I go back to a directory above the current directory
I return to your home directory: simply type cd and enter
I the symbol ∼ represents your home directory
I the symbol .. represents the mother directory of the current one
I the symbol . represents the current directory

Chia-Hsien Lin Introduction to Linux & IDL 2021 Spring (1092) 4 / 12


IDL

We will be using SSWIDL, which is IDL plus special packages designed to


process solar data.
On-line IDL course:
http://www.astro.ufl.edu/∼warner/IDL5220/
Helpful on-line IDL guide and help pages:
A Guide to IDL for Astronomers’ (U Virginia)
http://www.astro.virginia.edu/class/oconnell/astr511/IDLguide.html
Coyote’s Guide to IDL Programming:
www.idlcoyote.com

Chia-Hsien Lin Introduction to Linux & IDL 2021 Spring (1092) 5 / 12


IDL basics

command syntax: <command>, <inputs>, <keywords>


compilation: .r <procedure name>
program format: (IDL programs: ***.pro)
Three types of IDL programs:
I procedure:
pro name of program, [list of input and output variables, keywords]
; comment lines are marked by ; in the beginning of the line
content (a collection of IDL commands)
end
I script:
lines of commands
end
I function:
function name of program, [list of input variables, keywords]
content of the funcion
end

Chia-Hsien Lin Introduction to Linux & IDL 2021 Spring (1092) 6 / 12


IDL basics

How to look for help


I standard IDL command/procedures: ?name of procedure
I SSWIDL command/procedures: xdoc
I Use keyword: tftd, keyword
Command to type whenever you get error messages: retall
save your stuff:
save, [variables you want to save], filename, /compress

Chia-Hsien Lin Introduction to Linux & IDL 2021 Spring (1092) 7 / 12


How to save something in IDL?
save it as an IDL save file:
save, <variable names>, description=description, $
filename=’<your filename>’, /compress
I how to restore an IDL save file:

restore,filename=’<your filename>’

save it as a FITS file:


writefits, filename=’<your filename>’, <variable name>
I how to read a FITS file in IDL:

<variable name> = readfits(’<your filename>’)

save it as a generic file


savegen, <variable names>, file=’<your filename>’, $
names = names, text = text
I how to restore an IDL generic file

restgen, <variable names>, file=’<your filename>’

Chia-Hsien Lin Introduction to Linux & IDL 2021 Spring (1092) 8 / 12


IDL basics

data types
How to create arrays of different data types:
intarr,fltarr,strarr,dblarr,indgen
Loops (for ... endfor), selections (if ... endif)
Output plots to a postscript file

Chia-Hsien Lin Introduction to Linux & IDL 2021 Spring (1092) 9 / 12


Exercises

Image Filtering
1 read one image

2 filter out the pixels with intensity < some threshold:


Set their intensity fo NAN
a=where(abs(img lt thresh))
b=array indices(img, a)
img[b[0,*], b[1,*]] = !VALUES.F NAN

3 plot the filtered image


plot image, img

Chia-Hsien Lin Introduction to Linux & IDL 2021 Spring (1092) 10 / 12


Exercises

Image Cropping
1 read one image

2 cut a region of interest:


xrange: xl to xr
yrange: yl to yu
img2 = image[xl:xr, yl:yu]

3 plot the cropped region


plot image, img2

Chia-Hsien Lin Introduction to Linux & IDL 2021 Spring (1092) 11 / 12


Exercises
2D image → 3D array
1 create an empty 3D array
Nx = xr-xl+1 & Ny = yu - yl + 1 & Nf =
imgarr = fltarr(Nx, Ny, Nf)

2 Use a for loop to do the following:


for i=0, Nf-1 do begin
1 read in each image from a list of images
2 cut a region of interest (must be of same size)
img2 = image[xl:xr, yl:yu]
3 put the cropped region in the 3D array sequentially
imgarr[*,*,i] = img2
endfor

Chia-Hsien Lin Introduction to Linux & IDL 2021 Spring (1092) 12 / 12

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