runstanton.shell.script

#!/bin/bash
#######################################################################
## A script that runs stanton combined with a little script to 		 ##
## extract a bunch of numbers between two lines, place all numbers 	 ##
## in each group onto a single line, then save it to a file and then ##                                                       ##
## plot it                                                           ##
## Also, numbers from a single line with certain key word are saved  ##
## to a file.                                                        ##
#######################################################################
## Example of running, with stantoninput.dat as the input 		     ##
##   ./extraction.shell.script stantoninput.dat 					 ##
##                                                                   ##
## or, with specific output file names:                              ##
##   ./runstanton.shell.script stantoninput.dat stantonoutput.dat 	 ##
##    file1.dat file2.dat										     ##
#######################################################################

########## Stanton part  ##########################################
##########Input & output of stanton################################
	
stantoninput=$1
stantonoutput=$2

rm -r stantonoutput.dat

# if no input is given, print help and exit
	if [ $# == 0 ] ; then
		echo -e "please enter .dat file name, for example:\n    ./extraction.shell.script stantoninput.dat " ;
		echo -e "or to use specific output names:\n    ./extraction.shell.script stantoninput.dat stantonoutput.dat file.a.txt file.b.txt"
	exit; fi 

	if [ -z "$stantonoutput" ] ; then stantonoutput=output/stantonoutput.dat ; fi

####### Running stanton ###############################################
./bin/stanton_emil  <<  EOF
$stantoninput
$stantonoutput
EOF

###################################################################
### INPUT & OUTPUT ###
######################

	# the input file from the stantonprogram
	#input=$2

	# the output file names, optional
	output1=$3
	output2=$4

	# if no input is given, print help and exit
	if [ $# == 0 ] ; then
		echo -e "please enter .dat file name, for example:\n    ./extraction.shell.script stantoninput.dat " ;
		echo -e "or to use specific output names:\n    ./extraction.shell.script stantoninput.dat stantonoutput.dat file.a.txt file.b.txt"
	exit; fi

	# if no names are given, use some default names
	if [ -z "$output1" ] ; then output1=output/lots_of_numbers.txt ; fi
	if [ -z "$output2" ] ; then output2=output/neutron_energies.txt ; fi
	###################################################################
	
	
	### Extractionpart ################################################


	###################################################################
	### PART 1 ###
	##############

	# phrases to search for
	key_word_1="NOTE  FIRST"
	key_word_2="SCINTILLATOR"  #removed 1Cylindrical from keyword2

	# search for the phrases, keep whatever is inbetween them
	sed -rn "/$key_word_1/,/$key_word_2/{ /$key_word_1|$key_word_2/!p }" $stantonoutput > temp.$$.txt

	# replace all blank lines with the word 'hej'
	sed 's/^$/hej/' temp.$$.txt > blah.$$.txt

	# replace all new lines with a space
	sed ':a;N;$!ba;s/\n/ /g' blah.$$.txt > bleh.$$.txt

	# replace all instances of 'hej' with a new line, and more than one space with just one space
	sed -e 's/hej/\n/g' -e 's/[ \t]\+/ /g' bleh.$$.txt > bloo.$$.txt

	# remove any spaces from the front of lines
	sed 's/^[ \t]*//' bloo.$$.txt > blop.$$.txt

	# still can't get rid of first empty line!! remove it here in a silly way...
	# final output is saved to a text file
	tail --lines=+2 blop.$$.txt > $output1

	# remove temporary files
	rm bleh.$$.txt
	rm blah.$$.txt
	rm bloo.$$.txt
	rm blop.$$.txt
	rm temp.$$.txt
	###################################################################


	###################################################################
	### PART 2 ###
	##############
	## Another word to search for
	key_word_3="BINW"

	# look for this word and save whatever is in column 6
	# output is saved to a text file
	grep $key_word_3 $stantonoutput | awk '{print $6}' > $output2
	###################################################################
	
	########Calling root ##############################################
	
		
	##Calling root in a new terminal (not working)
	##gnome-terminal -x bash -c "	root -l  'plotmod.cxx('\"$output1\"', '\"$output2\"')';bash" opens root in a new terminal
	
	root -l  'scr/plotmod.cxx('\"$output1\"', '\"$output2\"')'  #-b added to the root will prevent any graphics -q will kill root
		
	exit;