## README for Imaginex Data examples on MODATA
# 5/7/20 khudson@udel.edu - Written by Katie Hudson
# 12/18/20 khudson@udel.edu - Calibration equations for each glider added plus some formatting changes

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########## DECODING 853 DATA AND EXAMPLES ###################################
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imagenex2csv_v2.jar decodes raw imaginex files (.853) and converts to .csv with the first column being the time stamp for each ping and the remaining columns are the 200 bins measured by the imaginex. 

The Imaginex853 records data up to 100m below the glider, so each bin is 0.5 m

imagenex2csv_v2.jar can be run from terminal with the following syntax:
java -jar /filepath/imagenex2csv_v2.jar --file=FILENAME.853 --output=DESIREDCSVNAME.csv
#####java needs to be up to date for this to work! ####

Three examples of .853 files and their corresponding .csvs are provided at http://modata.ceoe.udel.edu/public/Antarctica_2020/imaginex_examples
Raw .853 files are stored in the LOGS folder on the SCIENCE bay in the gliders

glider_imaginex_merged_UDsubset.csv is an EXAMPLE of how I merged the glider and imaginex data by timestamp ONLY (no calculation of depth of returns or consideration of pitch/roll). Here, timestamp from the pings is matched to the timestamp from the merged glider data (compiled by dbdmerge, etc)

Imaginex853 data is appended to the glider data with bins still in columns, so that one row = one ping. Raw depth of the returns (in meters) can be calculated using gliderDepth + BinNumber * 0.5 for visualization as needed. See below for pitch correction. 

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##### APPLYING CALIBRATION AND DEPTH CORRECTIONS TO CALCULATE SV ############
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Data from the Imagenex853 calibrations at NOAA SWFSC in July 2020 in conjunction with a calibration spreadsheet provided by Damien Guihen were used to generate a calibration coefficient C (contact the author for a copy). Offsets from the manufacturer gave unique RR and SL values for each instrument. All other values were kept constant between the two instruments. 

The equation to calculate Sv is Equation 1 from Guihen et al 2014: 
Sv = RBV + 20*log10(range) + (2 * a * range) - (RR + SL) - (10 * log10((sound.vel * tau)/2)) - (10*log10(EBA)) - C - gain

RBV is equal to 20 * log10(signal) where signal is the raw voltage returns from the 853. 

Variables kept constant for BOTH Gliders: 
    a <- 0.0423
    range <- 100
    sound.vel <- 1518.4
    tau <- .0001 #(us to s)
    EBA <- 17.65720842
    gain <- 40

UD746 Constants: 
    RR <- -180.5
    SL <- 212.5
    C <- 13.9264021

UAF507 Constants: 
    RR <- -181.7
    SL <- 212.9
    C <- 23.08747648

### DEPTH CORRECTION ###
Depth was corrected using the glider pitch, which was interpolated as needed, using the following equation provided by R. Cutter: 
correctedDepth = (BinNumber * 0.5) * cos(gliderPitch - 22) + gliderDepth