4SM help

See you on 4SM blog
HowTo Command Line

4SM COMMAND LINE ARGUMENTS:
get this help by entering "4SM...-h" at the prompt

STATUS: the environment arguments specify shallow water work environment
MODULE: the module arguments specify the action to be taken (one only enabled at a time)

Enable/Disable

DISABLE: to disable an argument set it to @-.....
- -Calibrate.......... is enabled
- -calibrate is disabled or @Calibrate is disabled
DISABLE: to disable a sub_argument, set it to -...../@.../...

nice

nice -20 assigns a low priority to your process, so that you can do other things while modeling proceeds.
remove it or set nice to a higher value up to 0,
- if you want to expedite the process
- this sucks more computing power, though

antislashes in the command line

nice -20 ./4SM.4.08 -Process/nosu -Origin/Tarawa_Kiribati -DB/tarawa-subset/27_1_0_0/3_1/650_600/718.079_169.221/1_1 -Mis/Tarawa/Kiribati/Spot/XS/NA/UTM_19_008/0.02_0.02/01_JAN_1986 -MakePIX -Import/data*tarawa-full/dbnc_3_0_0_0/R1630_L1860/Origin_709.049_182.231_0_0/chIn1,3/chOut1,3/import.shp -AutoCAL/NIRmax255/mBPL4/NoSmooth

the commandline is a long string of arguments separated by spaces
- this is a pain in the texteditor
in order to achieve a comfortable display,
- split your command line as appropriate,
and place one antislash at the end of each sub-line

To get HELP
* Try it now *

use a '*' character, before the first slash: -......*/......
to get help on any of the command line arguments,
like
.... -Process*
or
.... -Model* ....
or
.... -MakePIX*

Status arguments

-Ubuntu ....................to save a list of installed programs in ~/Software/Linux_software/dpkg/selections.txt
-Process.................... free comment to make a note of processing date
-DB.............................specifics of the PCIDSK database
-CZ.............................specifics of the PCIDSK Combined Depth database
-Origin........................these_are_free_comments
-Mis............................image metadata
-URL.................................../////......your URL address for mirror copy of the 4SM website on your machine
-Call..........................your favourite tools
-LK............................to provide a required commandline licensekey
-CK...........................to get a ciphered required commandline licensekey
-LE............................to get a free commandline licensekey
-WL...........................wavelengths
-CP...........................calibration pixels on BPL curvBPL
-M.............................bands to be used for modeling: usebj[c]
-Lm..........................radiance minimum thresholds (BOA)
-LS......................... saturation radiances
-LsT.........................minimum radiance
-LsM.........................at-sensor Maximum radiance (TOA)
-Lsw..........................at-sensor radiance (TOA) over optically deep water
-Lw...........................water leaving reflectance (BOA): Lsw=La+Lw
-SCL........................max_radiance for 16_to_8_bits scaling (TOA)
-ST...........................manual stretching factors for Flight_22
-KK..........................optical calibration parameters
-Z.............................details for computing Z
-B.............................details for computing B
-Smooth..................smoothing options
-LL...........................options for screen display of message
-Tc ................Calibration using textfile database_cm0.txt describing the CurvBPL (LsM2 LsM1)
-Tp ...............Calibration using textfile database_pm0.txt describing the PanBPL (LsM2 LsM1)

-E..............................sub-window for modeling or extraction of data
-DD...........................extraction pixel for displaying detailed modeling results
-D..............................extraction series of pixels for displaying modeling results
-d.............................extraction window for displaying modeling results

Module arguments

-MakePIX......................................................create a database.pix with all required channels
-Import..........................................................import raw data
-AutoCAL......................................................for a fully automatic calibration
-Recode........................................................recode from InChannel to OutChannel
-Deglint.........................................................Deglinter
-Extract.........................................................Extractor
-Calibrate......................................................Calibrator
-Model....................................... ...................Modeler
-RegressZZ.................................................. linear regression of depth results against seatruth depths
-ProfileZZ......................................................plot a profile of computed and sea-truth depth vs distance
-ProfileAB.....................................................plot a profile of depth vs distance
-Classify........................................................bottom type classification
-DN................................................................extraction pixel's DN values
-Archive........................................................archive the directory
-Zip.................................................................prepare zipfile 4sm_tutorial...zip

OPTIONAL ARGUMENTS (don't bother, mostly outdated)

-VD (NDVI) ou -VP (PVI)............Vegetation index option and #band Green et Red
or -VR (RGB)...................Option for colorisation of dryland
or -VG.........................Dryland coded at 222 all over
-BSc1/c2/c3/c4/cred/cgreen/cblue/CoefBSC to generate imageBS enhanced c1ac2
(ocean at c3, land at c4); RGBbands for imageBSC
-D or d Calib: Screen display: D for detail, d for summary
-Drow/lin or Drow1/RowM/lin1/linN for extraction and modeling detailed display
-drow/lin or drow1/RowM/lin1/linN for extraction and modeling summary display
-DNrow/lin display spectral radiances of pixel then quit
-Erow1/RowM/line1/linN coordinates of extraction window
-ArowC/linC/altC/fov/scaleAP/dpi....Parameters of aerial viewing
-R ou RE to generate imageR
-RfileName.txt to compute linear regression from two-columns XY textfile
-XbB/minb/maxb/bG/ming/maxg/bR/minr/maxr Linearization/Enhancement==>CC of RGB bands
-XL Calibration: to read pixel selection from DataBase.gli instead of running a selection
-QLbR/bG/bB/nbCol[/minr/maxr/ming/maxg/minb/maxb] Make (Linear) RGB composite of bR, bG, bB
-VClabel1/.../labeln Compute vector Z_contour_lines using masks of ZC.pix (ch1=imageZ) -M(m)ap g/sP/950/2700/280/1000/ZoneA/14_BSC/18_Z/19_B.......(not operational).......Mapper
-MapG/sP/740.7/2703.2/0.2/0.1/Zone_G/14_HEB/15_Z/17_B/18_BSC.......................Mapper
-ForMap/A4L/BSC/Z/ZoneA.......................................................................options for Mapper
-Q(q)uanti /HER/3/2/1/10/14/255/0.7 options for Quanti (not operational)
-V(v)ector ..........................for vectorization of depth contour lines (not operational)

CODES for imageB : see legend
1 to 200 saturated at 201; 202 if Y12>Y12Max

CODES for imageZ

1to95 Z in decimeters (exp: 25=2.5 m)
110to199 Z in 100+Z meters (exp: 125=25 m)
211 foreshore uncovered by tide correction
212to219 non vegetated dryland pixels
220to229 vegetated dryland pixels
237 if Y12>Y12Max

CODES for mask mSE: see legend

1............shallow..........poor data, shall be excluded from calibration data
2............shallow..........quality data: default
3 to 20...shallow..........quality data: available for ROIs (masks)
21..........mSOIL
22-23.....Glint targets
230.........Green vegetated or shallow forced at 216+brown
231.........darkGreen SHADOW on land forced at 231
232.........darkBlue wave breakers landside forced at 233
233.........lightBlue WAVE BREAKERS oceanside forced at 233
234.........White CLOUD/shadow forced at 234
235.........darkGreen lump of haze disables NIR band
236.........Wine dark lagoon bottom forced at LBref[2]
237.........Ochre non-vegetated forced at 219+green
238.........Salmon bright lagoon bottom forced at 238
239.........lightBlue NODATA forced at 239
240.........deep Blue DEEP WATER shallow area forced at 240
241.........Pink area excluded from volume statistics
242.........Blue LAKE/POOL on land forced at 242
243.........Violet vegetated or shallow forced at 212+grey
244.........Pink enable NEGATIVE-CONTRAST: sets Lmin at CN[i]
245.........Blue Lmin multiplies LMinprogressif by 3
246.........Yellow dry -> shallow forced at 0.1 metre
247.........Black AIRSTRIP forced at black 247
248.........Land area
249.........White Bad_Data forced at white 249

How to Command Line

4SM Command Line Syntax

The 4SM command line is stored in an executable text file
which is called image_name.sh.
It must be made executable.
I use gedit in LINUX/GNOME as my text editor: "gedit myimage.sh &".

For a 3-bands image, see tarawa_subset.sh
For a 4-bands image, see tmnov.sh
For a 17 bands image, see mb4.sh

Structure of a 4SM command line

The command line script starts as follows: nice -20 ./4SM...
nice -20 is not really part of it: it is used to set a very low priority level.
- nice -0 would be an average level.
The command line is a long and complex character string
- which starts with the name of the executable code like ./4SM.7.11
This string is composed of many arguments.
With the exception of the executable code name (e.g. 4SM) in the first argument,
- each following argument starts with a "-" character.
Each argument is a complex string of characters
- which is decoded at the start of the execution.

Law and order : layout of the Command Line

One argument per line is best
Arrange your display using antislashes "": see mb4.sh

Enabling/disabling an argument in the command line

To disable an argument, start it with a " @ " character.
- @-Lsw/66.00/17.00/11.00/006.0 this argument is disabled.
To enable it again, remove the "@" character.
- -Lsw/66.00/17.00/11.00/006.0 this argument is enabled.

Some arguments MUST not be disabled: they must start either by an Uppercase or by a Lowercase.
If they are missing 4SM shall complain

-D(d)eglint
- -Deglint... runs the Deglinter module,
- -deglint...ensures that the glint parameters are available and shall be enforced.
- @deglint... or @Deglint... disables deglinting altogether
-E(e)xtract
- -Extract... runs the Extractor module,
- -extract...ensures that the extraction parameters are available.
-M(m)odel
- -Model... runs the Modeler module,
- -model...ensures that the mask specification is available.
-C(c)lassify
- -Classify... runs the Cassifier
- -classify... provides the classification parameters

An argument overwrites the previous one

The sequence -Lsw66/17/11/6 -Lsw67/16/11/6 will retain the second -Lsw67/16/11/6
The only exception is the -CP argument:
- the following sequence
- -CP105.00/30.00/15.00/06.00 -CP082.00/21.00/12.00/06.00 (...)
- describes a sequence of two (or more) distinct calibration pixels.

Enabling/Disabling a command line in the script, and the exit instruction

The command line script starts as follows: nice -20 4SM...
A script may contain several command lines
All command lines which are enabled are executed in sequence
To prevent that, a command line can be disabled as follows: #nice -20 4SM...
To enable it again, remove the # .
Alternately, one can place an " exit " instruction as appropriate.

Several command lines in one single script

A bash script may contain an great number of command lines: see tarawa_subset.sh
Those commandlines which are enabled are executed in sequence, until an "exit" instruction is eventually encountered.