= make_scriptP =
(Compiled by DL)

'''Purpose:''' Generates the run script and .INN files required to iterate maplets using [[lithosP]].

=== Requires ===
 * [[make_script.in]] - text file containing a list of the landmarks to be processed, appended with the end-of-file identifier, 'END'.
 * [[make_scriptP.seed]] - test file containing the [[lithosP]] option commands for iterating each maplet.
 * [[INIT_LITHOS]] - make_scriptP reads the USRMX (maximum number of core processors) value.
 * TESTFILES1/ - Directory in which to store copies of LMRK_DISPLAY.pgm (output by [[lithosP]]) for each landmark.

NB: [[lithosP]] requires a number of directories and files - refer to relevant guide.

=== Output ===
make_scriptP outputs:
 * run.sh - controlling run script for batch maplet iteration using parallel processing;
  * run script for each core processor:
   * run_script01.b
   * run_script02.b
   * etc ...
 * .INN files - [[lithosP]] seed file for each maplet.
 * rem_script.b - script for removal of temporary files (working directory clean-up).
run_script''nn''.b outputs:
 * .OOT files - standard output from [[lithosP]] for each landmark.
 * TESTFILES/ - a copy of LMRK_DISPLAY.pgm (output by [[lithosP]]) is saved for each landmark;
 * [[SUMFILES]]/ - S/C and camera information are updated by [[lithosP]] as image shifts are accepted. New landmarks and limb fits are added to the SUMFILEs;
 * [[LMKFILES]]/ - LMKFILES are updated by [[lithosP]].
 * [[MAPFILES]]/ - MAPFILES are updated by [[lithosP]].
 * a number of information text and display files in the working directory are modified by [[lithosP]]; please refer to the relevant guide for details.

== Using make_scriptP ==

For guidance with iteration procedures, refer to the 'How-To': [[Standard_iteration]].

=== Create Input Files ===

The make_script.in file comprises the list of landmark names for the landmarks which should be processed. It is standard procedure to ensure that the list is ordered by:
 * highest-to-lowest maplet ground sample distance;
 * name (region identifier (e.g.: ''FF''), unique numeric identifier (e.g.: ''0001'');
and the user should ensure that duplicate entries do not exist. The program [[duplicates]] can be used to generate the make_script.in file. 

Example '''make_script.in''' file:
{{{
EE0001
EE0002
EE0003
  etc...
END
}}}

Example '''make_scriptP.seed''' file (see [[make_scriptP.seed]] for further details):
{{{
# This script performs two maplet iterations in parallel mode. 
# It reinitializes slope and albedo.
# It recomputes maplet overlaps.
# It recomputes limb fits.
# It recomputes central maplet vector.
# Topography determination from slopes is conditioned by:
#   Initial topography, 
#   Overlapping topography, 
#   Shadowing, 
#   Differential stereo, 
#   Limb heghts. 
# Dataless area slopes are set from the shape model.
#
# The script hides most of the screen output.  In order to obtain the 
# full display replace H* by #H*.
#
# Modified 2011_12_31.  Header and comments added.
# Modified 2014_02_26.  Hide screen output added.
#
H*
x
.025
#
# Initialize slope and albedo.
#
a
y
y
#
# Begin first iteration.
#
0
40
1
0
1
n
0
y
u
0
40
#
# Begin topo determination.
#
2
8                fill no data with shape slope
2                condition with existing topo
.01
7                condition with shadows
.025
1                condition with overlapping maps
4                condition with limbs
1, 2.5, 3  
6                condition with differential stereo
y
0                begin integration
.025
15
0
u
1
0
2
n
0
y
1
0
1
n
0
y
u
#
# Begin second iteration.
#
0
40
1
0
1
n
0
y
u
0
40
#
# Begin topo determination.
#
2
8
2
.01
7
.025
1
4
1, 2.5, 3  
6
y
0
.025
15
0
u
1
0
2
n
0
y
H*
1
0
1
n
0
y
H*
u
#
# Begin overlaps and limb fits.
#
o
RECENT
y
1
o
RECENT
n
3
y
1, 3, 5 
#
# Central vector determination.
#
v
RECENT              
q
END
}}}

== Run make_scriptP ==

make_scriptP generates a .INN file for each maplet. The first three lines of the .INN file (see below) supply a processor identifier (e.g.: ''01''), and load the landmark in [[lithosP]]. The remainder of the .INN file comprises a copy of the [[lithosP]] commands contained in [[make_scriptP.seed]].

Example '''EE0001.INN''' file:

{{{
01
i
EE0001
H*                  
x                   
.025                
0                   
40                                                                            
etc ...
}}}

make_scriptP also generates the controller run script - '''run.sh''':

{{{
 chmod +x run_script01.b
 chmod +x run_script02.b
   etc ...

 cd SHAPEFILES
 chmod +w SHAPE.TXT
 cp SHAPE.TXT TSHP01.TXT
 cp SHAPE.TXT TSHP02.TXT
   etc ...
 chmod -w SHAPE.TXT
 cd ..

 ./run_script01.b &
 ./run_script02.b &
   etc ...
}}}

and the run scripts: '''run_script01.b'''; '''run_script02.b'''; etc.:
{{{
rm -f EE0001.OOT
/usr/local/bin/LITHOSP < EE0001.INN > EE0001.OOT
cp LMRK_DISPLAY01.pgm TESTFILES1/EE0001.pgm
rm -f EE0007.OOT
/usr/local/bin/LITHOSP < EE0007.INN > EE0007.OOT
cp LMRK_DISPLAY01.pgm TESTFILES1/EE0007.pgm
rm -f EE0013.OOT
  etc ...
}}}

== Conduct Standard Iteration ==

{{{
sh run.sh
}}}

or in the background: 
{{{
nohup sh run.sh &
}}}

The [[lithosP]] standard output for each image is captured in the .OOT files. 

== Quality Check Iterated Maplets ==

The user must review the .OOT files to ascertain the success of the iteration process, problem landmarks can be detected using the utility program [[find_nofitP]], refer to relevant guide for further details.

== Clean Working Directory ==

rem_script.b can be used to clean out the directory of make_scriptP working files once iteration is complete and user has quality checked the iterated maplets:

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

== User Warnings ==
 * The user must ensure that the correct number of core processors is set for USRMX, a variable contained in [[INIT_LITHOS]], refer to relevant guide for further details.