# THIS IS A COMMAND FILE TO MAKE 3 TOMOGRAM SAMPLES
#
####CreatedVersion#### 3.8.25
# 
# The sample aligned stacks will each be 60 pixels in Y
# The sample tomograms will have 10 slices
# To get more slices in the samples, change "sampletilt 25 34" by
# decreasing 25 and increasing 34 by equal amounts, up to 0 and 59
#
# THESE ARE COMMANDS TO MAKE AN ALIGNED STACK FROM THE ORIGINAL STACK
#
####CreatedVersion#### 3.10.23
#
# It assumes that the views are in order in the image stack
#  
# The -size argument should be ,, for the full area or specify the desired 
# size (e.g.: ,10)
#
# The -offset argument should be 0,0 for no offset, 0,300 to take an area
# 300 pixels above the center, etc.
#
$newstack -taper 1,0   -size ,60 -offset 0,0 -xf WTI042413_1series4.xf WTI042413_1series4.st WTI042413_1series4.ali -image 2 -distort 33kGIF_nos.idf 

$sampletilt 25 34 898 WTI042413_1series4 mid.rec tilt.com
# THESE ARE COMMANDS TO MAKE AN ALIGNED STACK FROM THE ORIGINAL STACK
#
####CreatedVersion#### 3.10.23
#
# It assumes that the views are in order in the image stack
#  
# The -size argument should be ,, for the full area or specify the desired 
# size (e.g.: ,10)
#
# The -offset argument should be 0,0 for no offset, 0,300 to take an area
# 300 pixels above the center, etc.
#
$newstack -taper 1,0   -size ,60 -offset 0,678 -xf WTI042413_1series4.xf WTI042413_1series4.st WTI042413_1series4.ali -image 2 -distort 33kGIF_nos.idf 

$sampletilt 25 34 1576 WTI042413_1series4 top.rec tilt.com
# THESE ARE COMMANDS TO MAKE AN ALIGNED STACK FROM THE ORIGINAL STACK
#
####CreatedVersion#### 3.10.23
#
# It assumes that the views are in order in the image stack
#  
# The -size argument should be ,, for the full area or specify the desired 
# size (e.g.: ,10)
#
# The -offset argument should be 0,0 for no offset, 0,300 to take an area
# 300 pixels above the center, etc.
#
$newstack -taper 1,0   -size ,60 -offset 0,-678 -xf WTI042413_1series4.xf WTI042413_1series4.st WTI042413_1series4.ali -image 2 -distort 33kGIF_nos.idf 

$sampletilt 25 34 220 WTI042413_1series4 bot.rec tilt.com
$if (-e ./savework) ./savework