Unpack.bat

@REM This script will
@REM  1) Unzip the dredge data
@REM  2) Create the necessary subdirectories
@REM  3) Pull out the initial state and recruit data from the dredge survey file.
@REM  4) Compile the source code
@REM  5) Run the sim to create the growth data
@REM  6) Run the UK to interpolate the results to the region grid locations, does this separately for MA and GB
@REM  7)Call Octave to plot the data and produce pdf output files located in the Results subdirectory
@REM    - Lat_Lon_Grid_AAAA_DN_YYYY_scale.pdf
@REM      -- AAAA is
@REM        EBMS: exploitable biomass in metric tons
@REM        LAND: landings by number
@REM        LPUE: Landings per Unit Effort
@REM        FEFF: Fishing Effort
@REM        RECR: Recruits
@REM      -- DN is MA or GB
@REM      -- YYYY is the year 2005 - 2008
@REM      -- Scale is the maximum value shown. The final plot is scaled to show the range 0 to 50
@REM    - Lat_Lon_Surv_AAAA_DN_YYYY_scale.pdf
@REM       same as above shows the original data plotted at the survey locations.

@echo off

if "'%DredgeFile%'" EQU "''" (
    echo Env Variable Not Set
    echo "For example > set DredgeFile=dredgetowbysize7917"
    exit /b 10
)

if "'%HabCamFile%'" EQU "''" (
    @echo Env Variable Not Set
    @echo "For example > set HabCamFile=Habcam_BySegment_2000_2014-2020"
    exit /b 10
)

set argCount=0
for %%x in (%*) do (
   set /A argCount+=1
   set "argVec[!argCount!]=%%~x"
)

if %argCount% NEQ 5 goto args_count_wrong
goto args_count_ok

:args_count_wrong
    @echo Missing arguments
    @echo "Expecting: Unpack.bat  ReferenceYr RecrYrStrt RecrYrStop Domain [M|O]"
    @REM                             %1           %2         %3       %4     %5
    @echo "Domain"
    @echo "    MA"
    @echo "    GB"
    @echo "    ALL, both MA and GB"
    @echo "[M|O]"
    @echo "    M: Use Matlab for numerical processing"
    @echo "    O: Use Octave for numerical processing"
    exit /b 11

:args_count_ok
if "%4" EQU "MA" goto check_math_arg
if "%4" EQU "GB" goto check_math_arg
if "%4" EQU "AL" goto check_math_arg
:domain_wrong
    @echo Invalid Domain Arg:  %4
    @echo "Domain"
    @echo "    MA"
    @echo "    GB"
    @echo "    AL, both MA and GB"
    exit /b 13

:check_math_arg
if "%5" EQU "M" goto continue
if "%5" EQU "O" goto continue
:math_arg_wrong
    @echo Invalid Math Arg:  %5
    @echo "Math Arg"
    @echo "    M EQU> Use Matlab"
    @echo "    O EQU> Use Octave"
    exit /b 14

:continue
@REM Unzip both survey files
@REM unzip dredge data
@echo %DredgeFile%
if "%DredgeFile%" NEQ "NONE" (
if not exist OriginalData\%DredgeFile%.csv (
    cd OriginalData
    "C:\Program Files\7-Zip\7z" e %DredgeFile%.zip
    cd ..
)
)

@REM unzip HabCam data
if not exist OriginalData\%HabCamFile%.csv (
    cd OriginalData
    "C:\Program Files\7-Zip\7z" e %HabCamFile%.zip
    cd ..
)

@REM Create Directories used by GeoSAMS
if not exist Data\ (
    mkdir Data\
)
if not exist GrowthOutput\ (
    mkdir GrowthOutput\
)
if not exist Results\ (
    mkdir Results\
)
if not exist RecruitField\ (
    mkdir RecruitField\
)
if not exist RecruitEstimates\ (
    mkdir RecruitEstimates\
)
if not exist Analysis\ (
    mkdir Analysis\
)
if not exist MFigures\ (
    mkdir MFigures\
)
if not exist MFigures\Results (
    mkdir MFigures\Results
)

@REM Make GeoSam executables
cd SRC
if not exist mod\ (
    mkdir mod\
)
if not exist obj\ (
    mkdir obj\
)
make

@REM Make UK executables
cd ..\UKsrc
attrib -R IORoutines.f90
attrib -R Globals.f90
copy ..\SRC\IORoutines.f90 .
copy ..\SRC\Globals.f90 .
@REM prevent modification of these file in this directory
attrib +R .\IORoutines.f90
attrib +R Globals.f90

if not exist mod\ (
    mkdir mod\
)
if not exist obj\ (
    mkdir obj\
)
make

@REM finish with preprocessing
cd ..

@REM Pull Out Survey Data --------------------------------------------------------------
@REM Always pull dregde data
@REM if "%5" EQU "M" if "%6" EQU "D" (
if "%5" EQU "M" (
    @echo matlab.exe -batch "TrawlData5mmbin(%1, '%4'); exit;"
    matlab.exe -batch "TrawlData5mmbin(%1, '%4'); exit;"
    IF ERRORLEVEL 1 (
        @echo Error in MATLAB TrawlData5mmbin. Stopping
        exit 1/b
    )

    @echo matlab.exe -batch "HabCamData5mmbin(%1, '%4', 'T'); exit;"
    matlab.exe -batch "HabCamData5mmbin(%1, '%4', 'T'); exit;"
    IF ERRORLEVEL 1 (
        @echo Error in MATLAB HabCamData5mmbin. Stopping
        exit 1/b
    )
)

@REM Always pull dredge data
@REM if "%5" EQU "O" if "%6" EQU "D" (
if "%5" EQU "O" (
    @echo octave PreProcess/TrawlData5mmbin.m $1 $4
    octave PreProcess/TrawlData5mmbin.m $1 $4
    IF ERRORLEVEL 1 (
        @echo Error in Octave TrawlData5mmbin. Stopping
        exit 1/b
    )

    @REM Alwyas pull HabCam data and append to dredge data
    @REM if "%5" EQU "O" if "%6" EQU "H" (
    @echo octave PreProcess/HabCamData5mmbin.m $1 $4 'T'
    octave PreProcess/HabCamData5mmbin.m $1 $4 'T'
    IF ERRORLEVEL 1 (
        @echo Error in Octave TrawlData5mmbin. Stopping
        exit 1/b
    )
)

@REM Process Recruit Data --------------------------------------------------------------
if "%5" EQU "M" (
    @echo matlab.exe -batch "PullOutProcessRecruitData(%2, %3, '%4'); exit;"
    matlab.exe -batch "PullOutProcessRecruitData(%2, %3, '%4'); exit;"
)
if "%5" EQU "O" (
    @echo PreProcess/PullOutProcessRecruitData.m %2 %3 %4
    octave PreProcess/PullOutProcessRecruitData.m %2 %3 %4 
)
IF ERRORLEVEL 1 (
    @echo Error in MATLAB PullOutProcessRecruitData. Stopping
    exit 3/b
)

@REM Expand Nearest Neighbor to first year Survey Grid----------------------------------
if "%5" EQU "M" matlab.exe -batch "NearestNeighborRecInterp(%2, %3, '%4', %1); exit;"
if "%5" EQU "O" octave mfiles/NearestNeighborRecInterp.m %2 %3 %4 %1
IF ERRORLEVEL 1 (
    @echo Error in MATLAB NearestNeighborRecInterp. Stopping
    exit 4/b
)