[R-sig-Geo] raster and oceancolor L2 netcdf data

[Warner, David]

Greetings all

I am trying to develop R code for processing L2 data (netcdf v4 files) from
the Ocean Biology Processing Group.

The data file I am working with to develop the code is at
https://github.com/dmwarn/Tethys/blob/master/A2016244185500.L2_LAC_OC.x.nc
and represents primarily Lake Michigan in the United States.  The data were
extracted from a global dataset by the oceancolor L1 and L2 data server,
not by me.

I have been using the code below to try to get the data into R and ready
for processing but am having problems with dimensions and/or
orthorectification.  The

#extent of the scene obtained using nc_open and ncvar_get
nc <- nc_open('A2016214184500.L2_LAC_OC.x.nc')
lon <- ncvar_get(nc, "navigation_data/longitude")
lat <- ncvar_get(nc, "navigation_data/latitude")
minx <- min(lon)
maxx <- max(lon)
miny <- min(lat)
maxy <- max(lat)

#create extent object
myext <- extent(-90.817, -81.92438, 40.46493, 47.14244)

#create raster
rrs.412 <- raster('A2016214184500.L2_LAC_OC.x.nc', var
="geophysical_data/Rrs_412" ,
                  ext=myext)
rrs.412
> rrs.412
class       : RasterLayer
dimensions  : 644, 528, 340032  (nrow, ncol, ncell)
resolution  : 1, 1  (x, y)
extent      : 0.5, 528.5, 0.5, 644.5  (xmin, xmax, ymin, ymax)
coord. ref. : NA
data source : /Users/dmwarner/Documents/MODIS/OC/
A2016214184500.L2_LAC_OC.x.nc
names       : Remote.sensing.reflectance.at.412.nm
zvar        : geophysical_data/Rrs_412

In spite of having tried to assign an extent, the raster extent is in rows
and columns.

Further, plotting the raster reveals that it is flipped on x axis and
somewhat rotated relative to what it should look like.  Even when flipped,
it is still not orthorectified.

How do I get the raster to have the correct extent and also get it
orthorectified?
Thanks,
Dave Warner

-- 
David Warner
Research Fisheries Biologist
U.S.G.S. Great Lakes Science Center
1451 Green Road
Ann Arbor, MI 48105
734-214-9392

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