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emodnet-chemistry's Issues

Compressing the product netCDF files?

Shall we apply compression on the netCDF files?

Example

ncks -7 -L 1 --baa=4 --ppc default=3 Water_body_chlorophyll-a.4Danl.nc Water_body_chlorophyll-a.4Danl_compressed.nc

Initial size: 4.0G
Final size: 237M

Command explanation

  • -7 (equivalent to --fl_fmt=netcdf4_classic): format to netCDF4 (probably not required in our case)
  • -L 1: set deflation level to 1 (should be between 1 and 9).
  • --baa=4: Bit Adjustment Algorithms is set to Granular BitRound
  • --ppc: Precision Preserving Compression: preserve three significant digits (value should be adapted)

New products not properly rendered in OceanBrowser

Problem

The new products (v2023) cannot be viewer on OceanBrowser. Example here with chlorophyll-a.
Screenshot from 2023-08-14 11-55-26

Origin of the problem

Possibly linked to Unidata/netcdf-c#2591.

root@ddb75bc7a870:/var/www/data/Tests/By_sea_regions/Arctic_Ocean# python3
Python 3.6.9 (default, Oct  8 2020, 12:12:24)
[GCC 8.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import netCDF4
>>> ds = netCDF4.Dataset("Water_body_dissolved_oxygen_concentration.4Danl.nc")
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "netCDF4/_netCDF4.pyx", line 2015, in netCDF4._netCDF4.Dataset.__init__
  File "netCDF4/_netCDF4.pyx", line 1636, in netCDF4._netCDF4._ensure_nc_success
OSError: [Errno -101] NetCDF: HDF error: b'Water_body_dissolved_oxygen_concentration.4Danl.nc'
>>> netCDF4.__version__
'1.3.1'

So could be due to "checksum" / flectcher32 in the files.

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