SST

The Swedish 1-m Solar Telescope (SST) is a refracting solar telescope at Roque de los Muchachos Observatory, La Palma in the Canary Islands. The SST is capable of providing high-quality time series of spectrally resolved photospheric and chromospheric diagnostics that under excellent seeing conditions reach the diffraction limit of 0.1" over the full arcmin^2 FOV. Furthermore, the versatile CRISP instrument can provide spectro-polarimetric data that enable measurement of the magnetic field topology. In addition, the tunable filter system CHROMIS, installed in 2016, can simultaneously provide narrowband filtergrams at several wavelengths in the core of the Ca II K line (Extracted from Rouppe et al. (2020)).

SST literature

Data analysis

This is a brief documentation to analyze SST data. In case of using IDL, it is necessary to have SSWIDL to use CRISPEX, and to clone the DNS in order to read SST cubes. For Python users, you need to install Helita.

IDL users

Within a folder with reduced SST observations, run SSWIDL.

Then create a string list with the names of the cube files within that folder. To that en\ d, type 

fcube, f

That will give you an array f of files that can be fcubes (floating-point cubes) or\ icubes (integer cubes).

The following step is, e.g., to read the first cube of the list by writting 

cube=lp_read(f(0),header=header)
You can also run a CRISPEX session by doing the following. Let's assume your list contain\ s the following files: 
 0 nb_6563_08:05:00_aligned_3950_2017-05-25T08:07:37.icube
 1 nb_6563_08:05:00_aligned_3950_2017-05-25T08:07:37_sp.icube
 2 hmimag_2017-05-25T08:07:37_aligned_3950_2017-05-25T08:07:37.fcube
so, 
crispex, f[0], f[1], refcube=f[2]
will start a CRISPEX session using the Halpha data together with an HMI magnetogram as re\ ference. Please remind that the first file has to be an image file and the second file has to be a sp (spectral) file. They are\ actually the same array, but ordered differently.

Python

To read SST data using Helita, you need to import lp, which contains all the routines to manipulate SST cubes. 

import numpy as np
from helita.io import lp
import matplotlib.pyplot as plt

file   = "nb_6563_08:05:00_aligned_3950_2017-05-25T08:07:37.icube"
header = lp.getheader(file)
data   = lp.getdata(file)
the data will have (nx,ny, nt*nw) dimensions, where 
nx   = header[0][0]
ny   = header[0][1]
ntnw = header[0][2]
are the x, y, time and lambda dimensions. Knowing how many scans and how many spectral positions are contained in the observation, you can reshape the data, e.g., and plot the image: 
nt  = 240
nw  = 32
data  = data.reshape((nx, ny, nt, nw))
plt.imshow(data[:,::-1,180,5].T,cmap="Greys_r")
plt.show()

SST Campaigns

This documentation is not longer going to be updated since now we have a dedicated github webpage for SST with a detailed wiki: SST

Quicklook storage

ITA has now a very basic web server with the purpose of providing simple access to files ment for temporary viewing - like quicklook movies. We can put the SST quicklook movies at 

/mn/stornext/d18/lapalma/quicklook/

which will then appear under http://tsih3.uio.no/lapalma/

Scripts

Here you can find a list of useful scripts that may help you (to see the code block, just click in the name). If you have the DNS package, all these scripts are within the scripts folder:

Transfer all the CRISP and CHROMIS quicklook files from SST transport1 to Oslo: 

#!/bin/bash

#------------------------------------------------------------------------------------------
# DATE
default_date=`date +"%Y.%m.%d"`
read -p "Enter date with format YYYY.MM.DD ($default_date): " userdate
: "${userdate:=$default_date}"
year=${userdate:0:4}
month=${userdate:5:2}
day=${userdate:8:2}
#------------------------------------------------------------------------------------------

#------------------------------------------------------------------------------------------
# LOCATION OF THE QUICKLOOK MOVIES
crisp_folder="/scratch/obs/$userdate/CRISP/quicklook/"
chromis_folder="/scratch/obs/$userdate/CHROMIS/quicklook/"
echo "Preparing to transfer quicklook files from the following folders: "
echo $crisp_folder
echo $chromis_folder
#------------------------------------------------------------------------------------------

#------------------------------------------------------------------------------------------
# OSLO DESTINATION
default_folder="/mn/stornext/d18/lapalma/quicklook/$year/$year-$month-$day/"
read -p "Enter destination at ITA ($default_folder): " ita_folder
: "${ita_folder:=$default_folder}"
#------------------------------------------------------------------------------------------

#------------------------------------------------------------------------------------------
# OSLO USER
default_user=desiveri
read -p "Enter your UiO username ($default_user): " username
: "${username:=$default_user}"
#------------------------------------------------------------------------------------------

#------------------------------------------------------------------------------------------
# RSYNC TO OSLO
rsync -avzP \
      --prune-empty-dirs \
      $crisp_folder $chromis_folder \
      --rsync-path="mkdir -p $ita_folder && rsync" \
      $username@tsih.uio.no:$ita_folder
#------------------------------------------------------------------------------------------


Combine CHROMIS quicklook movies and images: 

#!/bin/bash
quickfile1=$1
quickfile2=$2
image_format=.jpg
movie_format=.mov

temp=*$quickfile1*$image_format
header=$( echo $temp | sed -e 's/\(quick_...................\).*/\1/')
image=$header"${jj//:}"$image_format 
movie=$header"${jj//:}"$movie_format
ysize=$(ffprobe -v error -select_streams v:0 -show_entries stream=height -of csv=s=x:p=0 *$quickfile1*$image_format)

echo "---------------------------------------------------------------------"
echo "Creating $image"
ffmpeg -i *$quickfile1*$image_format -i \
          *$quickfile2*$image_format    \
      -q:v 1 -filter_complex vstack=inputs=2 $image \
   -hide_banner -loglevel error
echo "---------------------------------------------------------------------"
echo "Creating $movie"
ffmpeg -i *$quickfile1*$movie_format -i \
          *$quickfile2*$movie_format    \
          -filter_complex vstack=inputs=2 \
          $movie \
   -hide_banner -loglevel error


Combine CRISP quicklook movies and images: 

#!/bin/bash
quickfile1=$1
quickfile2=$2
quickfile3=$3
image_format=.jpg
movie_format=.mov

temp=*$quickfile1*$image_format
header=$( echo $temp | sed -e 's/\(quick_...................\).*/\1/')
image=$header"${jj//:}"$image_format 
movie=$header"${jj//:}"$movie_format
echo "---------------------------------------------------------------------"
echo "Creating $image"
ffmpeg -i *$quickfile1*$image_format -i \
          *$quickfile2*$image_format -i \
          *$quickfile3*$image_format      \
          -q:v 1 -filter_complex hstack=inputs=3 $image \
   -hide_banner -loglevel error
echo "---------------------------------------------------------------------"
echo "Creating $movie"
ffmpeg -i *$quickfile1*$movie_format -i \
          *$quickfile2*$movie_format -i \
          *$quickfile3*$movie_format      \
          -filter_complex hstack=inputs=3 $movie \
   -hide_banner -loglevel error


Transform from pdf to png:

To use this script is necessary to install 

 brew install poppler
which contains the main command to use (pdftoppm). Note that the instalation takes a while. After that, you can use the following script which will transform all the pdf file in the folder and subfolders to png files. 
#!/bin/bash

echo "-------------------------------------------------"
echo "Transforming from pdf to png the following files:"
filelist=`find . -type f -name '*.pdf'`
for ii in ${filelist}; do
    echo $ii
    pdftoppm $ii $ii -png
done


See list of dates with avaialable quicklook files at ITA: 

#!/bin/bash                                                                                                                    
for year in $(curl -s http://tsih3.uio.no/lapalma/ |
                  grep '\[DIR\]' |
                  sed 's/.*href="//' |
                  sed 's/".*//'
             ); do
    echo "---------------------------"
    echo $year
    echo "---------------------------"
    for date in $(curl -s http://tsih3.uio.no/lapalma/$year |
                      grep '\[DIR\]' |
                      sed 's/.*href="//' |
                      sed 's/".*//'); do
        echo $date
    done
done


Download quicklook movies from ITA by date: 

#!/bin/bash
web="http://tsih3.uio.no/lapalma/"
input=$1

if [ ${#input} -eq 0 ]
then
    folder=$web
    read -p "Do you want to download all the available movies from "$folder" [y/n]: " yn
    case $yn in
 [Yy]* ) wget -c -r -l 3 -q --show-progress --cut-dirs=1 -nH --no-parent --reject="index.html*" $folder;;
 [Nn]* ) break;;
    esac           
fi

if [ ${#input} -eq 4 ]
then
    folder=$web$input"/"
    wget -c -r -l 2 -q --show-progress --cut-dirs=1 -nH --no-parent --reject="index.html*" $folder
fi

if [ ${#input} -eq 7 ]
then
    temp=(${input//-/ })
    year=${temp[0]}
    folder=$web$year"/"
    echo $folder
    echo  ${input}*
    for date in $(curl -s $folder |
                      grep '\[DIR\]' |
                      sed 's/.*href="//' |
                      sed 's/".*//'); do
 if [[ "$date" == "$input"* ]]; then
     echo $date
     wget -c -r -l 2 -q --show-progress --cut-dirs=1 -nH --no-parent --reject="index.html*" $folder"/"$date
 fi
    done
fi

if [ ${#input} -eq 10 ]
then
    temp=(${input//-/ })
    year=${temp[0]}
    folder=$web$year"/"$input"/"
    wget -c -r -l 2 -q --show-progress --cut-dirs=1 -nH --no-parent --reject="index.html*" $folder
fi


Extract IRIS SAA times for the SST log:

This scripts extracts the IRIS SAA times and copy them in your clipboard on MacOs systems. 

#!/bin/bash
###########################################################################################################
# IRIS_SAA 
#
# This scripts automatically extracts the IRIS SAA times of the current day.
# This information is located within TIM in https://iris.lmsal.com/health-safety/timeline/
# After extracting them, the script copies them in your clipboard,
# so you can paste the IRIS SAA times in the SST Github wiki.
#
# NOTE: Please note that for weekends, the script will provide the SAA dates
# for Saturday, Sunday and Monday in a single block.
#
# Current version is designed for MacOs systems.
# For Linux, define the following alias (if you have X installed):
#     alias pbcopy='xsel --clipboard --input'
#     alias pbpaste='xsel --clipboard --output'
# or in case you use xclip:
#     alias pbcopy='xclip -selection clipboard'
#     alias pbpaste='xclip -selection clipboard -o'
#
#
# You should obtain in your clipboard a result with the following format:
#
# > 07:xx - 08:xx IRIS in SAA
# > 08:xx - 09:xx IRIS in SAA     
# > 09:xx - 09:xx IRIS in SAA     
# > 10:xx - 11:xx IRIS in SAA     
#
# v1.0: 2022-06-28. Daniel Nobrega-Siverio: desiveri@astro.uio.no
#
###########################################################################################################

# IRIS TIM Webpage
web="https://iris.lmsal.com/health-safety/timeline/iris_tim_archive"
# Current day
year=`date +"%Y"`
month=`date +"%m"`
day=`date +"%d"` 
web=$web"/"$year"/"$month"/"$day"/" 

# It looks for all the available versions of the TIM.
# It extracts them and it takes the name of the latest version: 
iris_tim=`curl -s $web | grep ".txt" | sed 's/.*timeline_//' | sed 's/\.txt.*//' | sort -nr | head -1`

# It greeps for the initial (SAAI) and ending (SAAO) times within the webpage,
# creating two temporary files that store that information.
web=$web"iris_tim_"$iris_tim
echo "Getting IRIS SAA from: "$web
curl -s $web | grep SAAI | awk '{print $2}' | sed -e 's/\(:..\).*/\1/' | sed -e 's/^/> /' > saai.txt
curl -s $web | grep SAAO | awk '{print $2}' | sed 's/\(:..\).*/\1/' | sed -e 's/$/ IRIS in SAA/' > saao.txt
# It puts together the SAAI and SAAO times for the Markdown wiki, and removes the temporary files
paste -d "~" saai.txt saao.txt | sed 's/~/ - /' | pbcopy -selection c
rm saai.txt
rm saao.txt
The script automatically finds the timeline for the current day within TIM in the following webpage (Please note that for weekends, the TIM link will provide the SAA dates for Saturday, Sunday and Monday): [IRIS_SAA](https://iris.lmsal.com/health-safety/timeline/) For Linux, if you have X installed you may define an equivalent to pbcopy from MacOS in this way : 
alias pbcopy='xsel --clipboard --input'
alias pbpaste='xsel --clipboard --output'
or with xclip: 
alias pbcopy='xclip -selection clipboard'
alias pbpaste='xclip -selection clipboard -o'


SST computers

It is possible to login into the SST related computers to transfer files and to make the quicklook movies. To that end, type: ssh obs@royac6.royac.iac.es

It will require a password that observers should know. Then you can type, e.g., ssh -X obs@transport1 to login into the transport1 machine.