= make_scriptF =

||Category B||Version 3.0||

== Description ==

This program generates the run script and .INN files required for batch processing using [[lithos]]. You must also generate a seed file containing the required [[lithos]] commands.

[[make_scriptF]] is a generic script maker for batch lithos processing tasks. You specify the set of landmarks to process in [[make_script.in]] and the sequence of commands to process in [[make_scriptF.seed]].

[[make_scriptF]] generates the .INN files and run scripts to batch process the landmarks, and generates .OOT files and saves display files during processing for user inspection.

 /!\ You should test the command sequence in [[lithos]] before running the script generated by [[make_scriptF]].

=== Required Files ===

'''input file''':
 * [[make_script.in]] - Text file containing the names of landmarks to be processed. 
'''seed file''':
 * [[make_scriptF.seed]] - Text file containing the [[lithos]] option commands intended during batch processing.
'''processed files''':
 * [[TESTFILES]]/ - Directory in which to store copies of LMRK_DISPLAY1.pgm (output by [[lithos]]) for each landmark.
 * [[TESTFILES1]]/ - Directory in which to store copies of tmpl.pgm (output by [[lithos]]) for each landmark.

 /!\ [[lithos]] requires a number of directories and files. Refer to [[lithos]] for more information.

=== Output Files ===

'''make_scriptF outputs''':
 * run_script.b - Run script for batch processing.
 * .INN files - [[lithos]] command seed file for each landmark.
 * rem_script.b - Script for removal of temporary files (working directory clean-up).
'''run_script.b outputs''':
 * .OOT files - standard output from [[lithos]] for each landmark.
'''processed files outputs''': 
 * [[TESTFILES]]/ - A copy of LMRK_DISPLAY1.pgm (output by [[lithos]]) is saved for each landmark.
 * [[TESTFILES1]]/ - A copy of tmpl.pgm (output by [[lithos]]) is saved for each landmark.
 * [[SUMFILES]]/ - S/C and camera information are updated by [[lithos]] if image shifts occur.
 * [[LMKFILES]]/ - LMKFILES for each landmark are updated by [[lithos]].
 * [[MAPFILES]]/ - MAPFILES for each landmark are updated by [[lithos]].

 /!\ Several information text and display files in the working directory are modified by [[lithos]]. Refer to the entries for those files for more information.

== User Warnings ==
 /!\ The [[make_scriptF.seed]] file must start with a set of commands which deal with the [[lithos]] ''Check for more images? y[n]'' option sequence.

 /!\ The [[make_scriptF.seed]] file must end with the [[lithos]] quit command, '''q''', and the end-of-file identifier, '''END'''.

 /!\ You should test the [[make_scriptF.seed]] [[lithos]] command sequence before running the script generated by '''make_scriptF'''.

== Using make_scriptF ==
=== 1. Create Input Files ===

Here is a sample [[make_script.in]] file (see that entry for further information):

{{{
EE0001
EE0002
EE0003
END
}}}

[[lithos]] expects a sequence of start and end commands which must be contained in the seed file before and after the processing commands.

Here is an annotated sample '''make_scriptF.seed''' file.  The required start and end command sequences are explained below.

{{{
# Seed file to attach map to overlapping maps
#start commands
n                                                 <- don't check for more images
n                                                 <- don't include a single image
#processing commands
o
RECENT
y
1
o
RECENT
n
3
y
1, 3, 5 w
i
RECENT
n
n
v
1
u
1
o
RECENT
n
1
#end command
q                                                 <- quit
#end-of-file identifier
END                                               <- end-of-file
}}}

==== Start Commands ====

The .INN file starts with the command '''i''': input landmark, and the landmark name. [[lithos]] then asks you whether to check for more images. The following samples show the prompts and responses for both 'y' and 'n' responses to this prompt:

{{{
 Check for more images? y[n]
n
 Include a single image? y[n]
n
}}}

{{{
 Check for more images? y[n]
y

 Enter fractional width (0=center).
.5

 Reject invisibles? y[n]
n
}}}

When you create the '''make_scriptF.seed''' file, you must start with a sequence that deals with this set of options.  In the sample, the Start Commands lines are annotated to indicate these responses.

==== End Command ====

[[make_scriptF]] expects you to quit [[lithos]] on completion of each landmark. The '''make_scriptF.seed''' file must contain the quit command '''q''' on the second-to-last-line.

==== End-Of-File Identifier ====

[[make_scriptF]] expects the seed file to end with the end-of-file identifier, '''END'''. Any commands following this will not be appended to the .INN file.

==== Comments ====

Use '''#''' at the beginning of any comment line you want to include. [[make_scriptF]] does not append these to the .INN file.

=== 2. Run make_scriptF ===

'''make_scriptF''' generates a .INN file for each landmark listed in [[make_script.in]]. 

Here is a sample .INN file for landmark '''EE0001.INN''':

{{{
i
EE0001
n                   
n                   
o                   
RECENT              
y                   
1                   
o                   
RECENT              
n                   
3                   
y                   
1, 3, 5 w           
i                   
RECENT              
n                   
n                   
v                   
1                   
u                   
1                   
o                   
RECENT              
n                   
1                   
q                   
}}}

The first two lines of the .INN file load the next landmark into [[lithos]]. The remainder of the .INN file lists the [[lithos]] commands contained in [[make_scriptF.seed]].

'''make_scriptF''' also generates the '''run_script.b''' script, which looks like this:

{{{
rm -f EE0001.OOT
/usr/local/bin/LITHOS < EE0001.INN > EE0001.OOT
cp LMRK_DISPLAY1.pgm ./TESTFILES/EE0001.pgm
cp tmpl.pgm ./TESTFILES1/EE0001.pgm
rm -f EE0002.OOT
/usr/local/bin/LITHOS < EE0002.INN > EE0002.OOT
cp LMRK_DISPLAY1.pgm ./TESTFILES/EE0002.pgm
cp tmpl.pgm ./TESTFILES1/EE0002.pgm
rm -f EE0003.OOT
/usr/local/bin/LITHOS < EE0003.INN > EE0003.OOT
cp LMRK_DISPLAY1.pgm ./TESTFILES/EE0003.pgm
cp tmpl.pgm ./TESTFILES1/EE0003.pgm
}}}

=== 3. Execute the Run Script ===

Here is a sample command line for running '''run_script.b''':
{{{
sh run_script.b
}}}

You can also run this in the background using this command line: 
{{{
nohup sh run_script.b &
}}}

The [[lithos]] standard output for each image is captured in the .OOT files. The LMRKDISPLAY1.pgm and tmpl.pgm files output by [[lithos]] are copied once a landmark has been processed. These are stored under the landmark's name in [[TESTFILES]]/ and [[TESTFILES1]]/ respectively.

=== 4. Quality Check the New Maplets ===

You must review the .OOT files to determine the success of the tiling process.

=== 5. Clean Working Directory ===

You can use '''rem_script.b''' to clean out the directory of '''make_scriptF''' working files once tiling is complete and you have quality checked the resulting suite of maplets. 

Here is a sample '''rem_script.b''' file:

{{{
rm -f *.INN
rm -f *.OOT
rm -f run_script*
}}}

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''(Compiled by DL)''

CategoryPrograms