Fimex is a library and a program to convert gridded geospatial data between different formats and projections.
In fimex 2.0, there are some major changesd in the behaviour of ncml in fimex.
- In fimex before 2.0, the order of the dimensions for the shape of variables in ncml was reversed with respect to the ncml description. In 2.0, the dimension order in fimex and the ncml description should be the same. As both the old and new ncml text are valid, but only one of them yields useful results, this change requires manual review. This is the main reason to increase the major version number of fimex.
- There is now support for
joinNew. As part of this implementation, the behaviour ofunionandjoinExistinghas also changed and should be closer to the ncml description. Again, for the same input ncml this might produce different output compared to fimex before 2.0. - There is now support for writing to ncml, including values. This is probably only useful for small datasets, as output files might become huge for large datasets.
Fimex requires at least the following libraries to be installed for compilation
- c99/c++11 compiler
- libxml2 >= 2.6.0
- proj >= 4.4.9 and < 5.0.0 or >= 6.0.0 -- version 5 does not seem to work
- udunits2 (>= 2.1.9)
- github.com/metno/mi-cpptest
- github.com/metno/mi-programoptions
- github.com/HowardHinnant/date tested with release 2.4.1
To configure the different file formats it requires:
- NetCDF (netcdf > 3.5)
- Grib_API (grib_api > 1.4) or ecCodes
To build the python interface, it requires:
- pybind11 (>= 2.2.4)
- python numpy (for the unit tests)
Since version 0.64.0~rc1, fimex is built with cmake. The minimum required cmake version is 2.8.12.
These commands illustrate how fimex might be compiled:
SRC=/fimex/source
BLD=/fimex/build
INS=/fimex/install
GENERATOR="Unix Makefiles" # unix
GENERATOR="CodeBlocks - $GENERATOR" # for qtcreator and others
#GENERATOR="Eclipse CDT4 - $GENERATOR" # for eclipse
mkdir $BLD
cd $BLD
cmake -G"$GENERATOR" \
-DBUILD_SHARED_LIBS=ON \
-DENABLE_GRIBAPI=YES -Dgrib_api_DIR=/path/to/grib_api \
-DENABLE_THIS=YES \
-DENABLE_THAT=NO \
-DCMAKE_INSTALL_PREFIX="$INS" \
"$SRC"
make all test install
Of course, ENABLE_THIS and ENABLE_THAT should be replaced with
actual config options.
There are several ways to edit available config options
- read the top-level
CMakeLists.txtand pass values tocmakevia-D... - run
cmakewithout options, then use eitherccmake, a text-based configuration editor, orcmake-guia Qt-based configuration editor, or- some IDE editor (e.g. qtcreator)
Please note that some packages are searched via pkg-config and that
it might be necessary to have PKG_CONFIG_PATH set properly if
packages are installed in non-standard locations or if you wrote your
own .pc files.
It is recommended to build fimex outside the source directory, ie BLD != SRC in the above example.
Since Fimex makes some floating-point calculations in large loops, it is advisable to switch on SIMD/SSE operations in your compiler. On a Xeon machine with a x386 CPU and gcc, the following flags might help (those are default for x86-64)
CFLAGS='-O2 -mfpmath=sse -msse2' CXXFLAGS='-O2 -mfpmath=sse -msse2' cmake ...
Some tests require extra test data which can be downloaded from
https://wiki.met.no/fimex/download. The test data archive must be
unpacked, and the directory containing the file VERSION should be
specified to cmake
cmake ... -DTEST_EXTRADATA_DIR=/path/to/extra/test/data ...
Converting a model output from felt to NetCDF:
-
Get an overview of times, layers and grid used in the felt-file.
-
Group the parameters so that all parameters within an group use the same grid, times and the same layers (its possible to have a file with both sigma and pressure layers, but then all sigma-variables should have the same number of sigma layers and all pressure-variables should have the same number of pressure layers. Surface only variables, usually sigma=1000 felt variables, are a layer-group of their own).
-
Create a
felt2nc_variables.xmlfile for each variable group. Copy parameters from existing examples, or lookup variable and parameter names in the CF standard name documentation. If you have to generate several groups, it might be useful to split the file into axes, global attributes and variables, see, e.g.,damocles_felt2nc_variables.xml. If you have two parameters which map to the samestandard_name, make sure to give them different variable names if they are in the same group Adjust the datatype according to your data. float will always work fine, use short if you know that the variable even fits as 4-dimensional data into shorts. Use eventually acdmWriterConfig.xmlto process data as float and write the data as short. -
Validate the
felt2nc_variables.xml filewith, e.g.,xmllint --xinclude --postvalid --noout ../../share/etc/felt2nc_variables.xml -
Adjust the projection and area you want to extract in
fimex_example.cfg(or use command line arguments to fimex) -
Run
fimex -c fimex_example.cfg
To use the fimex >= 1.2 from CMake projects, please use
-Dfimex_DIR=.../lib/cmake/fimex
and
find_package(fimex "1.2" REQUIRED)
or, if you want a specific version
-Dfimex-1.0_DIR=.../lib/cmake/fimex-1.0
find_package(fimex-1.0 REQUIRED)
In both cases, include paths etc are set implicitly when using
target_link_libraries(libfimex)
This functionality is not yet supported for static fimex libraries.
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