# 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#### 4.6.18
#
# 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 -StandardInput
InputFile	MTEg5series6D.st
OutputFile	MTEg5series6D.ali
TransformFile	MTEg5series6D.xf
SizeToOutputInXandY	,60
OffsetsInXandY	 0,0
#DistortionField	.idf
ImagesAreBinned	1
#GradientFile	MTEg5series6D.maggrad
$sampletilt 25 34 1506 MTEg5series6D mid.rec tilt.com
# THESE ARE COMMANDS TO MAKE AN ALIGNED STACK FROM THE ORIGINAL STACK
#
####CreatedVersion#### 4.6.18
#
# 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 -StandardInput
InputFile	MTEg5series6D.st
OutputFile	MTEg5series6D.ali
TransformFile	MTEg5series6D.xf
SizeToOutputInXandY	,60
OffsetsInXandY	 0,1042
#DistortionField	.idf
ImagesAreBinned	1
#GradientFile	MTEg5series6D.maggrad
$sampletilt 25 34 2548 MTEg5series6D top.rec tilt.com
# THESE ARE COMMANDS TO MAKE AN ALIGNED STACK FROM THE ORIGINAL STACK
#
####CreatedVersion#### 4.6.18
#
# 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 -StandardInput
InputFile	MTEg5series6D.st
OutputFile	MTEg5series6D.ali
TransformFile	MTEg5series6D.xf
SizeToOutputInXandY	,60
OffsetsInXandY	 0,-1042
#DistortionField	.idf
ImagesAreBinned	1
#GradientFile	MTEg5series6D.maggrad
$sampletilt 25 34 464 MTEg5series6D bot.rec tilt.com
$if (-e ./savework) ./savework