ACRIST Tools

Forward Model Utilities :

NOTE: all the parameters appearing between brackets [] below are optional, the corresponding default value that is used is specified with the parameter. The arrows <name> show that a value/name must be given. The "%s" symbols follow the convention used by C-language function printf().

• AddTrhowToMom_new
• AddThrowToMom
• merisConv
• MomToMerss
• momNodes
• oceanTdsMom
• SimulMeris
• solflux
• RefModel
• TOAModel
• AerosolTau
• AbsorptionBands



---

AddTrhowToMom_new :  produces a TOA reflectance map integrating an atmospheric signal (files archived on CDROM) and a maritime signal and, if asked, a map of marine reflectances ; the output files follow the MOM format. For these data to be processed through the prototype using the pixel-to-pixel mode, they must be thenafter be translated using the momNodes tool.

NOTE: This tool is now obsolete, please use TOAModel instead.

 Syntax :  AddTrhowToMom_new [-C %s] [-s %s] [-y %s] [-press %g] [-ozone %g] [-wvap %g] [-W %g] [-m %d] [-o] [-p] [-r] [-ffq %s] [-fiq %s] [-fk %s] [-fr %s] [-fg %s] [-fi %s] [-fw %s] [-in %s] [-out %s] [-outr %s] [-tl %d] [-fo %s] [-fs %s]  %s

 [-C 0.3]                                              : chlorophyll (mg.m-3)
 [-s 0.0]                                               : suspended matter (g.m-3)
 [-y 0.0]                                               : yellow substance absorption at 440nm(m-1)
 [-press 1013.25]                                 : atmosphere pressure (hPa)
 [-ozone 350.]                                      : ozone (DU)
 [-wvap 0.]                                           : water vapour (g.cm-2)
 [-W 0.]                                                : wind speed (m.s-1)
 [-m 0]                                                  : reflectance model
              0: bb/a, RMD 1.0, K formula
              1: bb/a, RMD 1.0, absorption
              2: bb/a, RMD 1.2, K formula
              3: bb/a, RMD 1.2, absorption
 NOTE: the following models require different f/Q tables !
              4: bb/c, RMD 1.0, K formula
              5: bb/c, RMD 1.0, absorption
              6: bb/c, RMD 1.2, K formula
              7: bb/c, RMD 1.2, absorption
              8: PML tabulated
 [-o]                                                      : old model (equivalent to -m 1)
 [-p]                                                      : pml model (equivalent to -m 8)
 [-r]                                                       : switch to output reflectance file
 [-ffq /megs_test/validation/tools/OceanModel/f_upon_Q.dat.MOM]    : f/Q table file
 [-fiq /megs_test/validation/tools/OceanModel/INDEX_FoverQ]          : f/Q index file
 [-fk /megs_test/validation/tools/OceanModel/TAB_COEFS_KD]       : Kd coefficients file
 [-fr /megs_test/validation/tools/OceanModel/TAB_RGOTH]               : R gothic file
 [-fg /megs_test/validation/tools/OceanModel/GOP.txt]                        : water IOP file
 [-fi /megs_test/validation/tools/OceanModel/IOP_H.txt]                      : water IOP file
 [-fw /megs_test/validation/tools/OceanModel/IOP.dat]                        : water reflectance file
 [-in %s]                                                                                              : input file
 [-out %s]                                                                                            : output file
 [-outr %s]                                                                                           : out. reflectance file
 [-tl 0]                                                                                                  : trace level
 [-fo /megs_test/validation/tools/OceanModel/OPTICAL_THICKNESSES_MOM]: optical thickness file
 [-fs /megs_test/validation/tools/OceanModel/STANDARDS]              : standards file
  %s                                                                                                    : input file

Results:
          The atmospheric reflectances are saved in the file specified w/ the -out option.
          The surface reflectances are saved in the file specified w/ the -outr option.

Notes : 1) this tool needs look-up-tables stored in the following files :

        . INDEX_FoverQ
        . OPTICAL_THICKNESSES_MOM
        . STANDARDS
        . TAB_COEFS_KD
        . TAB_RGOTH
        . f_upon_Q.dat.MOM

2) the C-code must be linked w/ the refpml.c source code!!!


(installed under /megs_test/validation/tools)

---

AddTrhowToMom :  adds a maritime TOA signal to MOM atmospheric reflectances (stored on CDROM).

NOTE: This tool is now obsolete, please use TOAModel instead.


Syntax : AddTrhowToMom   <MOM file> <Chl> <spm> <ys extinction> [-o|-p] [-r] < parameters

 <MOM file> : file containing atmospheric reflectances
 <Chl> : Chlorophyll concentration (mg/m-3) to simulate
 <spm> : Suspended Particulate Matter (mg/l) to simulate
 <ys extinction> : Yellow substance absorption to simulate
 -o    : activates the reference model (using the water absorption values given by Hale&Query)
 -p    : activates the PML model ; chl=ys=0, no wind
 -r    : creates a file w/ surface reflectance values
 parameters : file holding 3 lines
        Psurf : surface pressure
        UO3   : integrated ozone content
        Wind speed : surface wind speed (m/s)

You may also enter the 3 parameters on the keyboard!!!

Results:
The atmospheric reflectances are stored in the file whose name is constructed as follows:
<MOM file>_C<Chl>_S<spm>_Y<ys extinction>

The surface reflectances are stored in the file whose name is constructed as follows:
<MOM file>_C<Chl>_S<spm>_Y<ys extinction>_rhow

Notes : 1) this tool needs look-up-tables stored in the following files :
        . INDEX_FoverQ
        . OPTICAL_THICKNESSES_MOM
        . STANDARDS
        . TAB_COEFS_KD
        . TAB_RGOTH
        . f_upon_Q.dat.MOM

2) the C-code must be linked w/ the refpml.c source code!!!


(installed under /megs_test/validation/tools)

---

merisConv: produces a file following the MERSS maps format from a MERIS Level 1 or Level 2 product - this tool allows to compare the results of the L1b MEGS processing with the original MERSS inputs. You can therefore :
• from a L1b product generate a TOA radiance map.
• from a L2 product generate a water leaving reflectance or chlorophyll map.

Syntax : merisConv %c %s [-t %s] [%s]
 
-c %s   : product key - specifies the input product file (3 : L1RR ; 4 : L2RR ; A : L1FR ; B : L2FR)
-s %s   : product name - input filename
[-t %s]  : output type - if set, should be followed by the favored output map
                   Otherwise the following generic keywords may be used:
                        ltmub : TOA radiance(only keyword allowed for L1b data)
                        reflec : surface reflectance (default keyword for L2 data)
                        chloro : Chlorophyll 1
[%s]: output file name - if set, should be followed by the output map file
                   Otherwise the following filenames will be used:
                        ltmub.iom : TOA radiance file;
                        reflec.iom : reflectance file;
                        chloro.iom : chlorophyll file.
Notes :
1) input flags are taken into account during the processing as follows:
• "invalid" or "duplicate" pixels are not copied. Therefore, from a Reduced Resolution product a map compatible w/ the Reduced Resolution MEGS processing w/ 905 columns is rebuild; for the Full Resolution mode this is less interesting as there can be no matching with the MERIS cameras.
• the "land" (L1b) pixels are preserved as such in the radiance/reflectance TOA map;
• the "land" or "cloud" (L2) pixels are preserved as such in the reflectance/chlorophyll map.


(installed under /u7/fm/megs2/lv2show; not up to date ! )

 

---

MomToMerss: generates, from a MOM file with either radiance or reflectance values, a file compatible w/ MERSS (ltmub.txt file to import in MERSS to translate it into a ltmub.iom file)
 
Syntax : MomToMerss -g %s -p %s [-tl %d] [-x %d] [-nw %d] [-nz %d] [-nd %d] [-L] [-R] [-xcl %d] [-ycl %d] [-wcl %d] [-hcl %d] [-rcl %lf] -mom %s {%s}
 
Options used for data flow checking
    [-tl 0] : trace level: 0: none, 1: main events, 2: detailed

Options used for configuring input/output
    -g %s   : geometry file (geomap.txt)
    -p %s   : output radiance file (ltmub.txt)

Options used for the radiance model
    [-x 0]  : repeat factor (number of MERSS frames - or MEGS frames - using the same MOM file)
    [-L]    : radiance input
    [-R]    : reflectance input

-mom %s : MOM simulations file name (1 single filename or a list of space delimited MOM filenames)
Note : even if input data may be reflectances or radiances, the output data are always radiances.

Options used for the cloud model
    [-xcl -1] : index of the cloud window first column (starting from 0, East to West)
    [-ycl -1] : index of the cloud window first line (starting from 0, North to South)
    NOThe cloud window exists only if both -xcl and -ycl are >= 0.
    [-wcl -1] : width of the cloud window (if set to -1 then window extends to the west edge of the image)
    [-hcl -1] : height of the cloud window (if set to -1 then window extends to the bottom edge of the image)
    [-rcl 0.7] : reflectance of the cloud (the cloud is a white surface)


(installed under /megs_test/validation/tools; Last Modified: 12/11/1999)

---

momNodes :  creates a file compatible with the MEGS pixel-to-pixel mode using both a MOM file and a 3-column ASCII file giving the 3 angles for each pixel (using coordinates relative to the MOM grid or actual values in degrees).
 
Syntax :  momNodes [-R|-s] [-csv] [-a] -mom <mom file> [-in <input file>] [-out <output file>] [-P <pression>] [-O <ozone>] [-Wu <wind_u>] [-Wv <wind_v>] [-tl]
[-R | -s] :  if -R is set then TOA radiances are computed
if -s is set surface reflectances are computed
[-csv] :   switch to output data in CSV format w/ a semi-column delimiter
[-a] :        when set, interpolation from angles is performed
-mom :   MOM input file
[-in] :      3 column space delimited file holding theta-s, theta-v, delta_phi angle coordinates
wrt MOM grid for which MOM data is to be retrieved ;
angles may be given in degrees but then the -a switch needs to be set.
[-out] :   output file compatible w/ MEGS pixel to pixel input file format
[-P] :      pressure value in hPa inserted in MEGS pixel to pixel input file
[-O] :     ozone inserted in MEGS pixel to pixel input file
[-Wu] :  zonal wind in m/s inserted in MEGS pixel to pixel input file
[-Wv] :  meridional wind in m/s inserted in MEGS pixel to pixel input file
[-tl] :      trace level


(installed under /megs_test/validation/tools )

---

oceanTdsMom: produces from one/multiple MOM file (with either reflectance or radiance values) a MERIS L1b product.In addition to the input MOM file, a L1b product file is also needed; this L1b product will be used as a skeleton: the header (MPH, SPH, SQADS) will be used, together w/ certain GADS, the flags, the annotations and the geometry. Only the radiances will be modified by interpolating the MOM data on the geometry of the L1b product. If the MOM file holds reflectance values instead of radiance values than the solar flux values held in the L1b product will be used to translate them into radiance values.
 

Syntax : oceanTdsMom -m %s -p %s [-tl %d] [-r %d] [-x %d] [-loop] [-L] [-R] [-kwl %s] [-kts %s] [-ktv %s] [-kdf %s] [-klu %s] [-fanal %s] [-fbk %s] -mom %s {%s}

Options for checking the data flow:
[-tl 0] : trace level (0: no tracing, 1: major steps, 2: +each frame, 3: +each band)

Options for Input/Output configuration:
-m %s   : model file - input L1b skeleton filename (compulsory)
-p %s   : product name -output filename (compulsory)
 [-r 0]  : resolution (0 : reduced, 1: full)

Options for the radiance model:
 [-x 0]  : repeat factor - number of consecutive frames for which the ame MOM file will be used
 [-loop] : MOM loop switch - if set, then the tool loops on the given MOM files (otherwise, the last MOM file is used for the remaining frames of the L1b product)
 [-L]    : radiance input - is set, then the MOM data should give radiances (LU);
 [-R]    : reflectance input (default) - if set, then the MOM data should give reflectances (ASCII MOM file) or BRDF (NetCDF MOM file). These values are multiplied by [1/p].F0.cos(qs) to compute the radiances (in LU) that are eventually written in the L1b output file. The solar flux and the sun zenith angle qs are retrieved from the L1b product skeleton.
 [-fbk %s] : backup spectrum file- name of the ASCII file giving the reflectance spectrum to be used if the MOM spectrum is incomplete.

 

The format of the file is as follows : one line per wavelength, <wavelength> <reflectance>. The algorithm follows the steps : is the MERIS band in the MOM file ?     yes: use the MOM value     no: is there a backup spectrum ?         oui: use the closest value in the backup spectrum          non: use the closest value in the MOM file

 -mom %s {%s} : MOM filename or list of MOM files to use. If the name is preceded by a '@' character then it is recognized as the name of a list of MOM files (ASCII file w/ one file per line); therefore, an unlimited number of MOM filenames may be provided - each file may have its own format but the -R or -L option is applicable to all.
 
 
 

Both ASCII and netCDF MOM formats are recognized. The ASCII MOM file is automatically analyzed with an awk script - the name of this awk script may be specified using the -fanal option. If the -L option is set then data are interpreted as radiances (in LU); otherwise they are interpreted as reflectances r = p. L/ (F0. cosqs) (dimensionless).  The NetCDF MOM format is self-describing but must hold the following variables: WVL wavelengths values (in nm) . The name may be specified w/ the -kwl option.  SLR_ZNT sun zenith angle qsvalues (in degrees), The name may be specified w/ the -kts option.  PRP_ZNT_ATM viewing zenith angle qv values (in degrees). The name may be specified w/ the -ktv option.  AZM_DFF azimuth difference angle Dfvalues (in degrees). The name may be specified w/ the -kdf option.  L_UP_ATM array. If the -L option is set, then data are interpreted as radiances (in LU); otherwise as BRDF = L / (F0. cos qs) (in sr-1). The name may be specified w/ the -klu option.

Options for reading the MOM file:
 [-kwl WVL] : (NetCDF) name of the wavelength variable (see above)
 [-kts SLR_ZNT ] : (NetCDF) name of the sun zenith angle q_s variable
 [-ktv PRP_ZNT_ATM ] : (NetCDF) name of the viewing zenith angle q_v variable
 [-kdf AZM_DFF ] : (NetCDF) name of the azimuth difference angle Df variable
 [-klu L_UP_ATM] : (NetCDF) name of the BRDF variable
 [-fanal /megs_test/validation/tools/AnalyseMom.awk] : name of the ASCII MOM analyzing program
 

Example

        oceanTdsMom -m l1_rr.prd -p new_l1_rr.prd -R -x 2 -loop -fbk spectrum.txt -mom @liste
 

with 'liste' file containing:
mom0.ncd
mom1.ncd
mom2.ncd

with 'spectrum.txt' file containing:
412.500 0.3
442.500 0.3
490.000 0.3
510.000 0.3
560.000 0.3
620.000 0.3
665.000 0.3
681.250 0.3
705.000 0.3
753.750 0.3
760.625 0.3
775.000 0.3
865.000 0.3
885.000 0.3
900.000 0.3

with containt of the WVL variable in the MOM files:
dimension WVL=1
value WVL= 753.75

will produce a file named new_l1_rr.prd w/ same size and geometry as file l1_rr.prd. First and second frame (-x 2 option) will we computed using mom0.ncd for the 753.75 nm band, and from a 0.3 reflectance for the other bands ( -fbk option), the solar flux that will be used is retrieved from the l1_rr.prd file ( -R option). Third and fourth frames are computed using mom1.ncd, fifth and sixth frames using mom2.ncd, seventh and eighth frames using using mom0.ncd (-loop option), etc.

Notes :

1) VERY IMPORTANT .....
 You must have a L1b product which will be used as a skeleton; it will specify the resolution, the size, the geometry and the annotations of the product file.

 2) make sure to define the MEGS_HOME environment variable to specify where the index_#.txa and database.db will be found, if you do not wish to specify this variable make sure to copy the files index_a.txa or index_3.txa (respectively for a L1b RR or FR product) and a database.db file.

3) the indexing convention for the azimuth difference angles Df in MOM is reversed in MEGS (and 5S-6S ...), in other words:
- specular reflexion :  Df=0° in MOM corresponds to Df=180° in MEGS
- backscattering      :  Df=180° in MOM corresponds to Df=0° in MEGS

(installed under /megs_test/validation/tools; Last Modified: 26/11/1999)

---

SimulMeris: gathers and extends the MomToMerss and oceanTdsMom functionalities. In addition, SimulMeris can take into account the position on the map to compute radiances above water or land, and to take into account pressure and ozone retrieved from ECMWF maps.
 
Syntaxe : SimulMeris [-tl %d] [-format %s] [-fmto %s] -m|-i[n] %s -p|-o[ut] %s [-nf %d] [-map] [-wat] [-land] [-x %d] [-loop] [-R] [-L] -mom %s -lmom %s [-wv %s] [-wvmom %s] [-x900 %lf] [-ox %s] [-P %s] [-x760 %lf] [-oz %s] [-xcl %d] [-ycl %d] [-wcl %d] [-hcl %d] [-cmom %s] [-fbk %s] [-rcl %lf] [-kwl %s] [-kts %s] [-ktv %s] [-kdf %s] [-klu %s] [-fanal %s]
 
Options for checking the data flow:
[-tl 0]                    trace level (0: no tracing, 1: major steps, 2: +each frame, 3: +each band)

Options for input/output configuration:
[-format %s]   model file and product file format. The argument can be either "merss", "iomap" or "megs".

merss: the model file (-m option or -i[n]) is a ASCII file with the MERIS geometry exported by MERSS. The output file (-p option or-o[ut]) is a radiance ASCII file which can be imported  by MERSS. This option allows a processing equivalent to MomToMerss. See SPDL document for format description.
iomap: the model file is a geometric file with MERSS internal format. The output file is a radiance file with MERSS internal format. See SPDL document for format description.
megs: the model file and the output file are files following the format of the Level 1B MERIS product. This option allows a processing equivalent to oceanTdsMom. See IODD document for format description.
[-fmto %s]    output file format, if different from input file format. The argument can be either "merss" or "iomap".
If  the model has a L1b format (option -m megs), the output format is obligatory L1b.
-m|-i[n] %s    model file name
-p|-o[ut] %s  output file name
[-nf -1]          number of frames of the output file, if it must be different from the one of the model file.

Options for the terrestrial surface model:
[-map]            if selected, an atlas determines the surface type (water or land) from the geographical position of each pixel. The atlas must be in the Coastline/Land/ocean MERIS auxiliary file ./files/clo.prd. The MEGS_HOME variable must specify the path of a valid MEGS arborescence.
[-wat]             if -m option is not selected, all the pixels will be of "water" type.
[-land]            if -m option is not selected, all the pixels will be of "land" type.

Options for the radiance model: (see  above)
[-x 0]            repeat factor
[-loop]          mom loop switch
[-R]               reflectance input
[-L]               radiance input
-mom %s       water MOM simulation filename (or list of simulations)
-lmom %s      land MOM simulation filename (or list of simulations)

The -x and -loop options apply also above water and land.


Options for the gaz absorption model:
[-wv %s]     water vapour absorption bands. The argument can be either "none", "abso" (default) or "all"

none: no water vapour absorption is applied.
abso: water vapour absorption is applied to the 900 nm band.
all: water vapour absorption is applied to all bands.

The reference band is 885 nm (radiance retrieved from the water or land MOM file).  To compute L900, the ratio L900/L885 is determined (see below) and L900 = L885 * (L900 /L995).  If option is "-wv all", the ratio L900/L885 is used to calculate the transmission of water vapour in other bands, using the polynomial of the algorithm of the MEGS level 2. This transmission is then applied to radiances.

[-wvmom %s]    water vapour MOM simulation filename

If option -wv abso" or -wv all is selected, the 900/885 radiance ratio is computed from this file according to the geometry of each pixel.
[-x900 1.0]     If option -wv abso or -wv all is selected, and "-wvmom" absent, 900/885 radiance ratio.
[-ox abso]      absorption bands of oxygen. The argument can be either "none", "abso" (default) or "all"
none: no oxygen absorption is applied.
abso: oxygen absorption is applied to the 760 nm band.
all: oxygen absorption is applied to 760 and 775 nm bands.

The reference band is 753 nm (radiance read in the water or land mom file).  To compute L760, the ratio L760/L753 is determined and L760 = L753 * (L760 /L753).  If pressure is specified by option -P, the ratio L760/L753 is determined by the reverse of the polynomial  mP2=f(L760/L753), of the algorithm of  the MERIS level 2. Otherwise it is fixed by option -x760.  If option is -ox all, the ratio L760/L753 is used to calculate the transmission of oxygen in the 775 nm band, using the polynomial of the algorithm of the MEGS level 2. This transmission is then applied to radiances.

[-P 1013.25]    pressure- The argument can be either "ecmwf" or a number.

ecmwf: surface pressure is read from the pressure mapin the file "files/press.prd" according to the position of each pixel.
nombre: surface pressure is fixed.
[-x760 1.0]    If option -P is absent, fix the ratio 760/753.
[-oz 350.0]    ozone- The argument can be either "ecmwf" or a number.
ecmwf: total ozone is read from ozone map in the file "files/ozone.prd" according to the position of each pixel.
nombre: total ozone is fixed.
The transmission of ozone calculated with the algorithm of MERIS level 2  from its optical thicknessin each band and according to the geometry of each pixel.


Options for the cloud model:
[-xcl -1]        cloud first column (MERIS convention)
[-ycl -1]        cloud first line (MERIS convention)
[-wcl -1]       cloud width
[-hcl -1]        cloud height
[-cmom %s]  cloud mom simulations file name
[-fbk %s]      file of backup reflectance spectrum (see above).
[-rcl 0.7]       cloud reflectance if options -cmom and -fbk are not set.

Options for reading the MOM files:
[-kwl WVL]                    see above
[-kts SLR_ZNT]
[-ktv PRP_ZNT_ATM]
[-kdf AZM_DFF]
[-klu L_UP_ATM]
[-fanal /megs_test/validation/tools/AnalyseMom.awk]

(installed under /megs_test/validation/tools; Last Modified: 07/12/1999)

---

solflux : computes the solar flux in any band from a file holding the solar flux spectrum. The flux is expressed in the unit system of the flux file. Bands need to be specified in this system. Flux values are interpolated and corrected according to the day.
 

Syntax : solflux [-f %s] [-i %s] [-o %s] [-d %lg] [-m %d] [-s %d] [-wl] [-tee] [-csv] [-nohead] [-p %8.3f]

 [-f /megs_test/validation/tools/solflux.dat]: solar flux file
 [-i %s]           : input file
 [-o %s]          : output file
 [-d 95.0]        : Julian day
 [-m 0]            : mode
 [-s 0]             : input sampling mode
 [-wl]              : switch to print wavelength
 [-tee]             : switch to repeat input values
 [-csv]             : switch to output in CSV format (separator ;)
 [-nohead]       : switch to disable the printing of a header
 [-p %8.3f]      : printing format (according to the syntax of the C-language printf() function)

If the -o option is omitted, flux values are written on the standart output (format "8.3f").

The -d option allows to specify the day for which the flux is computed, for correction relative to the reference day (number 95).

The -m option allows to specify the band specification mode:
   0: specify on each line the central wavelength and bandwidth
   1: specify on each line the minimum and maximum wavelength

The -s option allows to specify the flux interpolation mode:
   0: integration using the rectangles method
   1: integration using the trapeze method
   2: interpolation at the central wavelength
   3: interpolation at the closest central wavelength

If the -wl option is specified, the central wavelengths are written with solar flux in the output file
 (column 1: wavelength, column 2: flux).

If the -tee option is specified, central wavelengths and bandwiths are written with solar flux in columns 1 and 2 of output file.

By default, a line starting w/ character # is printed at the head of the output file. This line is inhibited by the option -nohead.

Format of the "flux" file:
ASCII, delimiter: spaces, column 1: wavelength, column 2: solar flux

(installed under /megs_test/validation/tools)
 

---

RefModel: computation of the water leaving reflectance; r'_w = p.L_w/E_d(0+) are computed either with the ref_model and iop_model routines or w/ the PML tables (using the pml_model routines).

Syntax : RefModel [-W %g] [-ffq %s] [-fiq %s] [-fk %s] [-fr %s] [-fg %s] [-fi %s] [-fw %s] [-faw %s] [-fachl %s] [-fased %s] [-fpchl %s] [-fpsed %s] [-fcase1 %s] [-fcase2 %s] [-xbc %lf %lf %lf %lf] [-xbs %lf %lf %lf %lf] [-xay %lf %lf] [-xay2 %lf %lf] [-xkay %lf %lf] [-pml] [-kd] [-pf] [-psm] [-bbt] [-lsp] [-prod] [-i[n] %s] [-o[ut] %s] [-tl %d] [-csv] [-tee] [-p %s]

- Options used for the configuration :
 

[-pml]	uses the PML tables
[-prod]	uses the MERIS auxiliary products whenever possible
[-i[n] <filename>]	input filename (standard input if not specified)
[-o[ut] <filename>]	output filename (standard output if not specified)
[-tl <int>]	trace level (0: none; 1: major steps; 2: major functions; 3: all functions)  NOTE: trace messages are written to the standard error stream.
[-csv]	output format is Comma Separated Variable (w/ delimiter: ";") (only used in conjunction w/ the -format line option)
[-tee]	repeats in the output the input values (only used in conjunction w/ the -format line option)
[-p  <code>]	format used for printing numerical values (according to the syntax of the C-language printf() function)

- Options used for the water reflectance model :
 

[-ffq <filename>]	ASCII file holding the f/Q table  /megs_test/validation/tools/OceanModel/f_upon_Q.dat.MOM
[-fiq <filename> ]	ASCII file used for indexing the f/Q table  /megs_test/validation/tools/OceanModel/INDEX_FoverQ  NOTE: if the -prod option is specified than none of the two files above are used and MERIS auxiliary product file case1.prd is used instead.
[-fk <filename>]	file w/ Kd values (used in conjunction w/ the -kd option)  /megs_test/validation/tools/OceanModel/TAB_COEFS_KD
[-fr <filename>]	ASCII file holding the Rgothic table  /megs_test/validation/tools/OceanModel/TAB_RGOTH  NOTE: if the -prod option is specified than this file is not used and Rgothic is retrieved from MERIS auxiliary product file case1.prd instead.
[-fg <filename>]	ASCII file holding the IOP table (used in conjunction w/ the -pml option)  /megs_test/validation/tools/OceanModel/GOP.txt
[-fi <filename>]	ASCII file used for indexing the reflectance table (used in conjunction w/ the -pml option)  /megs_test/validation/tools/OceanModel/IOP_H.txt
[-fw <filename>]	file giving reflectances versus IOP (used in conjunction w/ the -pml option)  /megs_test/validation/tools/OceanModel/IOP.dat  NOTE: if the -prod option is specified than none of the three files above are used and MERIS auxiliary product file case2.prd is used instead.
[-faw <filename>]	ASCII file holding the water absorption table  /megs_test/validation/tools/OceanModel/WATER_ABSORPTION
[-fachl <filename>]	ASCII file holding the chlorophyll absorption table /megs_test/validation/tools/OceanModel/CHL_ABSORPTION  NOTE: if the -kd option is specified than none of the two files above are used
[-fased <filename>]	ASCII file holding the sediment absorption table /megs_test/validation/tools/OceanModel/SED_ABSORPTION
[-fpchl <filename>]	ASCII file holding the phytoplancton volume scattering function (used in conjunction w/ the -pf option)  /megs_test/validation/tools/OceanModel/PHASE_FUNC_CHL
[-fpsed <filename>]	ASCII file holding the sediment volume scattering function (used in conjunction w/ the -pf option)  /megs_test/validation/tools/OceanModel/PHASE_FUNC_SED
[-fcase1 <filename>]	case1 MERIS auxiliary product filename (used in conjunction w/ the -prod option)  /megs_aux/products/pt_ocean1/case1.10.00.prd  NOTE: this file also affects the glint
[-fcase2 <filename>]	case2 MERIS auxiliary product filename (used in conjunction w/ the -prod and -pml options)  /megs_aux/products/pu_ocean2/case2.11.00.prd
[-W 0.]	wind speed (m.s-1)
[-xbc <x1> <x2> <x3> <x4>]	coefficients for the following equation: bchl = x1.(chl)x2.(l/x3)x4 0.416 0.766 550. -1
[-xbs <x1> <x2> <x3> <x4>]	coefficients for the following equation: bspm = x1.(spm)x2.(l/x3)x4 0.8 1. 550. -0.812
[-xay <x1> <x2>]	coefficients for the following equation: ay = a(440).exp[x1.(l - x2)]
[-xay2 <x1> <x2>]	coefficients for the following equation: ay2 = a(440).exp[x1.(l - x2)]
[-xkay <x1> <x2>]	coefficients for the following equation: a(440)=[x1 + x2.log(chl)].[aw + achl]
[-kd]	specifies the Kd model to use for the absorption (Morel&Antoine 1994) (by default water and chlorophyll absorption values are tabulated)
[-pf]	computes bb~ using the phase function (by default bb~ = 0.02)
[-psm]	selects the bb/(a + bb) model for the reflectance computation (by default the bb/a model is used)
[-bbt]	forces bb~ to decrease wrt Chl according to the Morel 1988 model (by default it is constant)
[-lsp]	specifies that bspm should be linearely interpolated wrt l

Input file format:
ASCII formated file, read line by line w/ the following columns:
  thetas   sun zenith angle (degrees)
  thetav   viewing zenith angle (degrees)
  delta    azimuth difference angle (degrees)
  <chl>    chlorophyll (mg.m^-3)
  <spm>    sediment (g.m^-3)
            <Y>      yellow substance (m^-1)

Output file format:

ASCII formated file, written line by line w/ the following columns:
  tag of input file (if the -tee option is specified)
  reflectance for bands 412, 442, 490, 510, 560, 620, 665, 705, 775, 865 nm
If the -csv option is specified than the columns will be separated with ";" and the first line give the tag names for each column.
The "-p" option specifies the format used for printing numerical values (following the printf() syntax).


(installed under /megs_test/validation/tools; Last Modified: 02/11/1999)

 

---

TOAModel: computes TOA reflectances above water;  rho = p.L_t/[F₀.cos(q_s)] are computed w/ the functions ref_model, iop_model, pml_model, glint_model, atm_model.

    rho = gazeous_transmittance * [(direct_transmittance * rho_g) + rho_path + (diffuse_transmittance * rho_w)]

with:

       rho_g         : specular reflectance
        rho_path    : atmospheric reflectance (Rayleigh+aerosol)
        rho_w        : water laving reflectance

Syntax :
TOAModel [-nowat] [-nosky] [-nogli] [-pathonly] [-pml] [-prod]
[-nwl %d] [-wl %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf] [-i[n] %s] [-o[ut] %s] [-tl %d] [-csv] [-tee] [-nohead] [-p %s] [-format %s] [-ffq %s] [-fiq %s] [-fk %s] [-fr %s] [-fg %s] [-fi %s]
[-fw %s] [-faw %s] [-fachl %s] [-fased %s] [-fpchl %s] [-fpsed %s] [-fot %s] [-ffa %s] [-fomega %s] [-fspa %s] [-ftaubl %s] [-fpath %s] [-fcase1 %s] [-fcase2 %s] [-fatm %s] [-faer %s] [-C %lf] [-s %lf] [-y %lf] [-W %lf] [-xbc %lf %lf %lf %lf] [-xbs %lf %lf %lf %lf] [-xay %lf %lf] [-xay2 %lf %lf] [-xkay1 %lf %lf] [-kd] [-pf] [-psm] [-bbt] [-lsp] [-aer %d] [-taua %lf] [-press %lf] [-ozone %lf] [-wvap %lf] [-iso] [-wc] [-khi %lf] [-tgpol] [-x760 %lf] [-x900 %lf]

NOTE: because of the numerous options, it is highly recommended to use this tool through a shell script.

Options :

- General options:
 

[-nowat]	inhibits the water leaving reflectance model (rho_w: 0)
[-nosky]	inhibits the atmospheric model  (reflectance: 0, transmittance 1)
[-nogli]	inhibits the glint model (rho_g: 0)
[-pathonly]	inhibits the computation of the atmospheric reflectance (reflectance: 0)  NOTE: useful for computing the maritime signal TOArho_w
[-pml]	if set then the PML model is used for rho_w
[-prod]	if set then MERIS auxiliary products are used whenever possible
[-nwl <int>]	number of bands (15)
[-wl <x1> ... <x_nwl>]	wavelengths of output bands (nm)  [412.500 442.500 490.000 510.000 560.000 620.000 665.000 681.250 705.000 753.750 761.250 775.000 865.000 885.000 900.000]  NOTE: there must be as many wavelengths as given by the -nwl option
[-i[n] <fichier>]	input filename (by default standard input)
[-o[ut] <fichier>]	output filename (by default standard output)
[-tl <int>]	trace level (0: none; 1: major steps 2: major functions; 3: all functions)  NOTE: all trace messages are written to the standard error stream
[-csv]	output in Comma Separated Variable format (delimiter is ";") (only used in conjunction w/ the -format line option)
[-tee]	repeats the input values in the output (only used in conjunction w/ the -format line option)
[-nohead]	inhibits the writing of the header line (only used in conjunction w/ the -format line option)
[-p  <code>]	format used for printing numerical values (according to the syntax of the C-language printf() function)
[-format <code>]	format of the output file  The recognized formats are line (default format), mom, bomem. In the line format, the values are specified and computed line by line; the output format is the same as for RefModel described above. The MOM format is described here and the bomem name is reserved for a future update.

- Options for the water reflectance model:
 

[-ffq <filename>]	ASCII file for the f/Q table  /megs_test/validation/tools/OceanModel/f_upon_Q.dat.MOM
[-fiq <filename> ]	ASCII file for indexing f/Q table  /megs_test/validation/tools/OceanModel/INDEX_FoverQ  NOTE: if the -prod option is specified than none of the two files above are used and MERIS auxiliary product file case1.prd is used instead.
[-fk <filename>]	ASCII file for the Kd table (used in conjunction w/ the -kd option)  /megs_test/validation/tools/OceanModel/TAB_COEFS_KD
[-fr <filename>]	ASCII file for the Rgothic table /megs_test/validation/tools/OceanModel/TAB_RGOTH  NOTE: if the -prod option is set then Rgothic is retrieved from the MERIS case1 auxiliary product
[-fg <filename>]	ASCII file for the IOP table (used in conjunction w/ the -pml option)  /megs_test/validation/tools/OceanModel/GOP.txt
[-fi <filename>]	ASCII file used for indexing the reflectance table (used in conjunction w/ the -pml option)  /megs_test/validation/tools/OceanModel/IOP_H.txt
[-fw <filename>]	ASCII file for the reflectance versus IOP table (used in conjunction w/ the -pml option)  /megs_test/validation/tools/OceanModel/IOP.dat  NOTE: if the -prod option is specified than none of the three files above are used and MERIS auxiliary product file case2.prd is used instead.
[-faw <filename>]	ASCII file for the water absorption table /megs_test/validation/tools/OceanModel/WATER_ABSORPTION
[-fachl <filename>]	ASCII file for the chlorophyll absorption table  /megs_test/validation/tools/OceanModel/CHL_ABSORPTION  NOTE: if the -kd option is set then the two above files are not used
[-fased <filename>]	ASCII file for the SPM absorption table  /megs_test/validation/tools/OceanModel/SED_ABSORPTION
[-fpchl <filename>]	ASCII file holding the phytoplancton volume scattering function (used in conjunction w/ the -pf option)  /megs_test/validation/tools/OceanModel/PHASE_FUNC_CHL
[-fpsed <filename>]	ASCII file holding the sediment volume scattering function (used in conjunction w/ the -pf option)  /megs_test/validation/tools/OceanModel/PHASE_FUNC_SED
[-fcase1 <filename>]	case1 MERIS auxiliary product filename (used in conjunction w/ the -prod option)  /megs_aux/products/pt_ocean1/case1.10.00.prd  NOTE: this file also affects the glint model
[-fcase2 <filename>]	case2 MERIS auxiliary product filename (used in conjunction w/ the -prod and -pml options)  /megs_aux/products/pu_ocean2/case2.11.00.prd
[-C 0.]	Chl concentration (in mg.m-3) (used in conjunction w/ the -format mom or -format bomem options)
[-s 0.]	SPM concentration (in g.m-3) (used in conjunction w/ the -format mom or -format bomem options)
[-y 0.]	yellow substance absorption at 440nm (in m-1) (used in conjunction w/ the -format mom or -format bomem options)
[-W 0.]	wind speed (m/s)  NOTE: this option also affects the atmospheric and glint models
[-xbc <x1> <x2> <x3> <x4>]	coefficients for the following equation: bchl = x1.(chl)x2.(l/x3)x4 0.416 0.766 550. -1
[-xbs <x1> <x2> <x3> <x4>]	coefficients for the following equation: bspm = x1.(spm)x2.(l/x3)x4 0.8 1. 550. -0.812
[-xay <x1> <x2>]	coefficients for the following equation: ay = a(440).exp[x1.(l - x2)]
[-xay2 <x1> <x2>]	coefficients for the following equation: ay2 = a(440).exp[x1.(l - x2)]
[-xkay1 <x1> <x2>]	coefficients for the following equation: a(440)=[x1 + x2.log(chl)].[aw + achl]
[-kd]	specifies the Kd model to use for the absorption (Morel&Antoine 1994) (by default water and chlorophyll absorption values are tabulated)
[-pf]	computes bb~ using the phase function (by default bb~ = 0.02)
[-psm]	selects the bb/(a + bb) model for the reflectance computation (by default the bb/a model is used)
[-bbt]	forces bb~ to decrease wrt Chl according to the Morel 1988 model (by default it is constant)
[-lsp]	specifies that bspm should be linearely interpolated wrt l

- Options for the atmospheric model:
 

[-fot <filename>]	ASCII file holding atmospheric optical thickness /megs_test/validation/tools/OceanModel/OPTICAL_THICKNESSES_MOM  NOTE: if the -prod option is specified than the MERIS auxiliary product file atmosphere.prd is used instead.
[-ffa <filename>]	ASCII file holding forward to total scattering ratio /megs_aux/proto/lpcm/LUTS_MARS98/FATAB_MOMNEW
[-fomega <filename>]	ASCII file holding single scattering albedo  /megs_test/validation/tools/OceanModel/OMEGA_FILE
[-fspa <filename>]	ASCII file holding spectral optical thickness /megs_aux/proto/lpcm.3/new_specdep.dat
[-ftaubl <filename>]	ASCII file used for indexing optical thickness /megs_aux/proto/lpcm.3/new_taubl_865.dat  NOTE: if the -prod option is specified than none of the four files above are used and MERIS auxiliary product file atmosphere.prd is used instead.
[-fpath <filename>]	ASCII file (following the MOM  or Bomem format) holding atmospheric reflectances no default value!!!! NOTE: if the -prod option is specified than parameters are retrieved from the MERIS auxiliary product files atmosphere.prd and aerosol.prd.
[-fatm <filename>]	atmosphere MERIS auxiliary product filename (in conjunction w/ the -prod option)  /megs_aux/products/pp_atmosphere/atmosphere.10.00.prd
[-faer <filename>]	aerosol MERIS auxiliary product filename (in conjunction w/ the -prod option)  /megs_aux/products/pr_ocean_aerosol/oceanaero.10.00.prd
[-aer <int>]	aerosol model number (from 0 to 32) (by default 0)  NOTE: this number must be consistent w/ the atmospheric reflectance file
[-taua 0]	aerosol optical thickness at 560 nm (in conjunction w/ the -prod option)
[-press 1013.25]	atmospheric pressure (in hPa)
[-ozone 350.0]	ozone (in DU)
[-wvap 2.0]	water vapour (in g.cm-2)
[-tgpol]	selects a polynomial model for the gazeous transmission
[-x760 1.0]	760/753 band ratio (in conjunction w/ the -prod and -tgpol options)
[-x900 1.0]	900/885 band ratio (in conjunction w/ the -prod and -tgpol options)

- Options for the glint model:
 

[-iso]	computes the glint using an isotropic model (by default it is anisotropic)
[-wc]	corrects the glint for water foam (by default it is not corrected)  NOTE: if the -prod option is specified than the two above parameters are read from the MERIS auxiliary product case1.prd.
[-khi 0.]	azimuth difference angle between wind and sun directions

Correspondence with AddTrhowToMom options:

TOAModel writes only one file at a time; the -r option of AddTrhowToMom_new corresponds to a second execution of TOAModel with the -nosky option.

The compatibility of TOAModel with AddTrhowToMom_new is limited : results may slightly differ because of the AddTrhowToMom limitations corrected with TOAModel.
 

AddTrhowToMom_new option	TOAModel option(s)	AddTrhowToMom_new option	TOAModel option(s)
-m 0	-kd -xbc "0.30 0.62 550. -1."	-p	-pml
-m 1	-xbc "0.30 0.62 550. -1."	-o	-xbc "0.30 0.62 550. -1."
-m 2	-kd
-m 3
-m 4	-psm -kd -xbc "0.30 0.62 550. -1."
-m 5	-psm -xbc "0.30 0.62 550. -1."
-m 6	-psm -kd
-m 7	-psm
-m 8	-pml

The following TOAModel options must be selected to insure compatibility with AddTrhowToMom_new:
-format mom, -nogli, -bbt.

The other options of AddTrhowToMom_new have the same meaning as for TOAModel.

Input file format:
with the -format line option (which is the default), the input file is identical to the one used for RefModel (see above); with the other options (-format mom or -format bomem), there is no input file.

Output file format:
with the -format line option (which is the default), the output file holds in columns the bands specified to TOAModel (by default the 15 MERIS bands; see the -nwl and -wl options above) and a single line header (starting with #) is printed by default - this header line may be suppressed with the -nohead option. The -tee et -csv options have the same meaning as for RefModel.

Improvements wrt AddTrhoToMom_new:

• the computations may be fully in line w/ those of MEGS (w/ the -prod option);
• the aerosol optical thickness is related to wavelength;
• the Sun glint may be accounted for (w/ the -glint option);
• the chlorophyll backscattering is related to wavelength according to Morel (1988) (w/ the -bbt option);
• the computation precision has been improved (all computations are now performed in double precision);
• all models are now fully configurable;
• the input/output formats allow to lower the number of MOM files needed.


(installed under /megs_test/validation/tools; Last Modified: 23/11/1999)

---

AerosolTau: computes aerosol optical thickness values for all bands.
 
Syntax :
AerosolTau [-prod] [-nwl %d] [-wl %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf]
[-o[ut] %s] [-tl %d] [-csv] [-tee] [-nohead] [-p %s] [-fspa %s] [-ftaubl %s] [-fpath %s] [-faer %s]
[-aer %d] [-taua %lf]

Options :
 

[-prod]	uses MERIS auxiliary products whenever possible
[-nwl <int>]	number of bands (15)
[-wl <x1> ... <x_nwl>]	band wavelengths (nm)  [412.500 442.500 490.000 510.000 560.000 620.000 665.000 681.250 705.000 753.750 761.250 775.000 865.000 885.000 900.000]  NOTE: there must be as many wavelengths as given by the -nwl option
[-o[ut] <filename>]	output filename (otherwise results are sent to the standard output)
[-tl <int>]	trace level (0: none; 1: main steps; 2: main functions; 3: all functions)  NOTE: trace messages are sent to the standard error
[-csv]	if set, then the output is CSV formatted (columns delimited w/ ;) (only used in conjunction w/ the -format line option)
[-tee]	if set, then input values are repeated in the output (only used in conjunction w/ the -format line option)
[-nohead]	supresses the header line (only used in conjunction w/ the -format line option)
[-p  <code>]	format used for writing numerical values (according to the syntax of the C-language printf() function)
[-fspa <filename>]	name of the ASCII file giving the optical thickness spectrum  by default: /megs_aux/proto/lpcm.3/new_specdep.dat
[-ftaubl <filename>]	name of the ASCII file giving optical thickness indexation by default: /megs_aux/proto/lpcm.3/new_taubl_865.dat  NOTE: when the -prod option is set, none of the 2 above files are used and values retrieved from the aerosol auxiliary product are used instead
[-fpath <filename>]	filename (ASCII, MOM format or Bomem) holding atmospheric de reflectances  no default value!  NOTE: when the -prod option is set the file given here is not used and the parameters are retrieved from the atmosphere and aerosol auxiliary products instead.
[-faer <filename>]	filename specifying the aerosol auxiliary product (only when the -prod option is set)  by default: /megs_aux/products/pr_ocean_aerosol/oceanaero.10.00.prd
[-fatm <filename>]	filename specifying the atmosphere auxiliary product (only when the -prod option is set)  by default: /megs_aux/products/pp_atmosphere/atmosphere.10.00.prd
[-aer <int>]	aerosol model number (from 0 to 32) (default value: 0)  NOTE: this number must be consistent w/ the file holding the atmospheric reflectance values
[-taua 0]	aerosol optical thickness at 560 nm (only when the -prod option is set)


 

Examples:
aer=2; taua=0.2
AerosolTau -prod -o aerosol_tau.txt -tl 2 -faer files/oceanaer.prd -fatm files/atmosphere.prd -aer $aer -taua $taua
AerosolTau -prod -o aerosol_tau.txt -tl 2 -faer files/oceanaer.prd -fatm files/atmosphere.prd -aer $aer -taua $taua -nohead
AerosolTau -prod                            -tl 2 -faer files/oceanaer.prd -fatm files/atmosphere.prd -aer $aer -taua $taua -nohead  >  aerosol_tau.txt

Format of the output file:
The output file holds in columns the bands specified as input (by default the 15 MERIS bands, see the -nwl and -wl options above). The -tee and -csv options have the same meaning as for RefModel.

Two header lines (starting w/ #) are printed, they may be suppressed w/ the -nohead option.

(installed under /megs_test/validation/tools; Last Modified: 12/11/1999)
 

---

AbsorptionBands: modifies the values of the absorption bands (760.625 et 900 nm) of a MOM file from other MOM files or given values.
rho (mom1, absorption band) = rho (mom1, reference) * ratio
or
rho (mom2, absorption band) = rho (mom1, reference) * [rho(mom2, absorption) / rho(mom2, reference)]
Syntax :
AbsorptionBands -i[n] %s [-o[ut] %s] [-tl %d] [-p %s] [-format %s] [-fo2 %s] [-fh2o %s] [-x760 %lf] [-x900 %lf]
 
Options :
- General Options:
 

-i[n] <filename>	input filename (compolsary !)
[-o[ut] <filename>]	output filename (otherwise results are sent to the standard output stream)
[-tl <int>]	trace level (0: none; 1: major steps; 2: main functions; 3: all functions)  NOTE: trace messages are sent to the standard error stream
[-p  <code>]	format used for printing numerical values (according to the syntax of the C-language printf() function)
[-format <code>]	format of the output file (only mom is currently recognized)

- Options for the absorption model:
 

[-fh2o <filename>]	file following the MOM format for bands 885 and 900 (not available)
[-fo2 <filename>]	file following the MOM format for bands 753 et 760 (not available)
[-x760 1.0]	760/753 band ratio
[-x900 1.0]	900/885 band ratio

(installed under /megs_test/validation/tools; Last Modified: 23/11/1999)