make_scriptF
(Compiled by DL)
Purpose: Generates the run script and .INN files required for batch processing using lithos. The user generates a seed file containing the required lithos commands.
make_scriptF is a generic script maker for batch lithos processing tasks. The set of landmarks to process is specified by the user via make_script.in and the sequence of commands to process is specified by the user via make_scriptF.seed. make_scriptF generates the .INN files and run scripts to batch process the landmarks, and generates .OOT files and saves image files during processing for user inspection. The user should test the command sequence in lithos before running the script generated by make_scriptF.
Requires
make_script.in - text file containing the names of landmarks to be processed.
make_scriptF.seed - text file containing the lithos option commands intended during batch processing.
are TESTIFIES/ TESTILFES1/ directories required? or will they be written?
NB: lithos requires a number of directories and files - refer to relevant guide for details.
Output
make_scriptF outputs:
- run_script.b - run script for batch processing.
.INN files - lithos command seed file for each landmark.
- rem_script.b - run script to clean out the directory of make_scriptF working files once batch processing is complete and the user has quality checked the updated maplets.
run_script.b outputs:
.OOT files - standard output from lithos for each landmark.
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.
a number of information text and display files in the working directory are modified by lithos; please refer to the relevant guide for details.
Using make_scriptF
Create Input Files
Example make_script.in file (see make_scriptT.in for further details):
Example make_scriptF.seed file (see make_scriptF.seed for further details):
must the seed file end in lithos quit commands?
Run make_scriptF
make_scriptF generates a .INN file for each landmark listed in make_script.in. The first two lines of the .INN file (see below) load the next landmark into lithos. The remainder of the .INN file comprises a copy of the lithos commands contained in make_scriptF.seed.
Example 001.INN file:
make_scriptF also generates the run script - run_script.b:
Execute Run Script
sh run_script.b
or in the background:
nohup sh run_script.b &
The lithos standard output for each image is captured in the .OOT files, and the LMRKDISPLAY1.pgm and temple.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.
Quality Check New Maplets
The user must review the .OOT files to ascertain the success of the tiling process.
Clean Working Directory
rem_script.b can be used to clean out the directory of make_scriptT working files once tiling is complete and user has quality checked the resulting suite of maplets:
rm -f *.INN rm -f *.OOT rm -f run_script*