# WRF-Python Internals¶

WRF-Python is a collection of diagnostic and interpolation routines for WRF-ARW data. The API is kept to a minimal set of functions, since we’ve found this to be the easiest to teach to new programmers, students, and scientists. Future plans include adopting the Pangeo xarray/dask model, along with an object oriented API, but this is not currently supported as of this user guide.

A typical use case for a WRF-Python user is to:

1. Open a WRF data file (or sequence of files) using NetCDF4-python or PyNIO.
2. Compute a WRF diagnostic using wrf.getvar().
3. Perform any additional computations using methods outside of WRF-Python.
4. Create a plot of the output using matplotlib (basemap or cartopy) or PyNGL.

The purpose of this guide is to explain the internals of item (2) so that users can help contribute or support the computational diagnostic routines.

## Overview of a wrf.getvar() Diagnostic Computation¶

A diagnostic computed using the wrf.getvar() function consists of the following steps:

1. Call the appropriate ‘getter’ function based on the specified diagnostic label. This step occurs in the wrf.getvar() routine in routines.py.
2. Extract the required variables from the NetCDF data file (or files).
3. Compute the diagnostic using a wrapped Fortran, C, or Python routine.
4. Convert to the desired units (if applicable).
5. Set the metadata (if desired) and return the result as an xarray.DataArray, or return a numpy.ndarray if no metadata is required.

In the source directory, the wrf.getvar() ‘getter’ routines have a “g_” prefix for the naming convention (the “g” is for “get”).

The unit conversion is handled by a wrapt decorator that can be found in decorators.py. The setting of the metadata is handled using a wrapt decorator, which can be found in the metadecorators.py file.

## Overview of Compiled Computational Routines¶

Currently, the compiled computational routines are written in Fortran 90 and exposed the Python using f2py. The routines have been aquired over decades, originated from NCL’s Fortran77 codebase, the WRF model itself, or other tools like RIP (Read Interpolate Plot), and do not necessarily conform to a common programming mindset (e.g. 1D arrays, 2D arrays, etc).

The raw Fortran routines are compiled in to the wrf._wrffortran extension module, but are not particularly useful for applications in their raw form. These routines are imported in the extension.py module, where additional functionality is added to make the routines more user friendly.

The typical behavior for a fully exported Fortran routine in extension.py is:

1. Verify that the supplied arguments are valid in shape. Although f2py does this as well, the errors thrown by f2py are confusing to users, so this step helps provide better error messages.
2. Allocate an ouput array based on the output shape of the algorithm, number of “leftmost”[1] dimensions, and size of the data.
3. Iterate over the leftmost [1] dimensions and compute output for argument data slices that are of the same dimensionality as the compiled algorithm.
4. Cast the argument arrays (or array slices) in to the dtype used in the compiled routine. For WRF data, the conversion is usually from a 4-byte float to an 8-byte double.
5. Extract the argument arrays out of xarray in to numpy arrays (if applicable) and transpose them in to Fortran ordering. Note that this does not actually do any copying of the data, it simply reorders the shape tuple for the data and sets the Fortran ordering flag. This allows data pointers from the output array slices to be passed directly to the Fortran routine, which eliminates the need to copy the result to the output array.

The steps described above are handled in wrapt decorators that can be found in decorators.py. For some routines that produce multiple outputs or have atypical behavior, the special case decorators are located in specialdec.py.

 [1] (1, 2) If the Fortran algorithm is written for a 2-dimensional array, and a users passes in a 5-dimensional array, there are 3 “leftmost” dimensions.

## Example¶

The above overviews are better explained by an example. Although there are a few exceptions (e.g. ll_to_xy), many of the routines in WRF-Python behave this way.

For this example, let’s make a routine that adds a variable’s base state to its perturbation. This is the kind of thing that you’d normally use numpy for (e.g. Ptot = PB + P), but you could do this if you wanted concurrency for this operation via OpenMP rather than using dask (in a future release of WRF-Python, both OpenMP and dask will be available).

### Fortran Code¶

Below is the Fortran 90 code, which will be written to a file called example.f90.

SUBROUTINE pert_add(base, pert, total, nx, ny)

!f2py intent(in,out) :: result

REAL(KIND=8), INTENT(IN), DIMENSION(nx, ny) :: base, pert
REAL(KIND=8), INTENT(OUT), DIMENSION(nx, ny) :: total
INTEGER, INTENT(IN) :: nx, ny

INTEGER :: i

!$OMP PARALLEL DO COLLAPSE(2) SCHEDULE(runtime) DO j=1, ny DO i=1, nx total(i, j) = base(i, j) + pert(i, j) END DO END DO !$OMP END PARALLEL DO



This code adds the 2D base and perturbation variables and stores the result in a 2D output array. (For this example, we’re using a 2D array to help illustrate leftmost indexing below, but it could have been written using a 1D or 3D array).

At the top, there are these two f2py directives:

!f2py threadsafe
!f2py intent(in,out) :: total


The threadsafe directive tells f2py to release Python’s Global Interpreter Lock (GIL) before calling the Fortran routine. The Fortran code no longer uses Python variables, so you should relese the GIL before running the computation. This way, Python threads will contine to run, which may be important if you are using this in a webserver or in some other threaded environment like dask’s threaded scheduler.

The intent(in,out) f2py directive is used because we will be supplying a slice of the output array directly to this routine and don’t want to have to copy the result from Fortran back in to the result array. By specifying intent(in,out), we’re telling f2py to use the pointer to our output array directly.

Finally, for the OpenMP directive, the scheduler is set to use runtime scheduling via SCHEDULE(runtime). By using runtime scheduling, users can set the scheduling type within Python, but for most users the default is sufficient.

#### Building the Fortran Code¶

To build the Fortran code, the example.f90 source code should be placed in the fortran directory of the source tree.

Next, we need to update the numpy.distutils.core.Extension section of setup.py in the root directory of the source tree.

ext1 = numpy.distutils.core.Extension(
name="wrf._wrffortran",
sources=["fortran/wrf_constants.f90",
"fortran/wrf_testfunc.f90",
"fortran/wrf_user.f90",
"fortran/rip_cape.f90",
"fortran/wrf_cloud_fracf.f90",
"fortran/wrf_fctt.f90",
"fortran/wrf_user_dbz.f90",
"fortran/wrf_relhl.f90",
"fortran/calc_uh.f90",
"fortran/wrf_user_latlon_routines.f90",
"fortran/wrf_pvo.f90",
"fortran/eqthecalc.f90",
"fortran/wrf_rip_phys_routines.f90",
"fortran/wrf_pw.f90",
"fortran/wrf_vinterp.f90",
"fortran/wrf_wind.f90",
"fortran/omp.f90",
"fortran/example.f90 # New file added here
]
)


The easiest way to build your code is to use one of the build scripts located in the build_scripts directory of the source tree. These scripts contain variants for compiling with or without OpenMP support. Unless you are debugging a problem, building with OpenMP is recommended.

For this example, we’re going to assume you already followed how to Setting Up Your Development Environment. Below are the build instructions for compiling with OpenMP enabled on GCC (Linux or Mac):

pip uninstall wrf-python
cd build_scripts
sh ./gnu_omp.sh


The above command will build and install the new routine, along with the other Fortran routines. If you recieve errors, then your code failed to build sucessfully. Otherwise, your new routine can be called as wrf._wrffortran.pert_add().

### Creating a Thin Python Wrapper¶

The new Fortran pert_add routine will work well for a 2D slice of data. However, if you want to extend the functionality to work with any dimensional array, you’ll need to add a thin wrapper with some extra functionality that make use of wrapt decorators.

First, let’s start by creating a very thin wrapper in Python in extension.py.

from wrf._wrffortran import pert_add

.
.
.

Located in example.f90.

"""
if outview is None:
outview = np.empty(base.shape[0:2], base.dtype, order="F")

pert,
outview)

return result


Despite being only a few lines of code, there is quite a bit going on in the wrapper. The first thing to note is the arguments to the wrapper function. The only arguments that we need for the wrapper are the inputs to the function and an “outview” keyword argument. At this point in the call chain, the arguments are assumed to be Fortran-ordered, in that the Fortran ordering flag is set and the shape is transposed from a usual C-ordered numpy array (the data itself remains in the same order that it was created). By passing numpy arrays with the Fortran order flag set, f2py will pass the pointer directly through to the Fortran routine.

The outview keyword argument is used during leftmost dimension indexing to send slices of the output array to the Fortran routine to be filled. If there are no leftmost dimensions (e.g. this routine is called with 2D data), then the outview argument will be None and an outview variable will be created with the same number of dimensions as the base argument. It should be created with Fortran ordering so that the pointer is directly passed to the Fortran routine.

When the actual wrf._wrffortran.pert_add() Fortran routine is called, the nx and ny arguments are ommitted because f2py will supply this for us based on the shape of the numpy arrays we are supplying as input arguments. F2py also likes to return an array as a result, so even though we supplied outview as an array to be filled by the Fortran routine, we will still get a result from the function call that is pointing to the same thing as outview. (We could have chosen to ignore the result and return outview instead).

### Extract and Transpose¶

The arrays that are being passed to the _pert_add thin wrapper need to be numpy arrays in Fortran ordering, but they won’t come this way from users. They will come in as either numpy.ndarray or xarray.DataArray and will be C-ordered. So, we need to make sure that a Fortran-ordered numpy.ndarray is what is passed to the thin wrapper.

Since this type of operation is repeated for many diagnostic functions, a decorator has been written in decorators.py for this purpose. Let’s decorate our thin wrapper with this function.

@extract_and_transpose()

Located in example.f90.

"""
if outview is None:
outview = np.empty(base.shape[0:2], base.dtype, order="F")

pert,
outview)

return result


The extract_and_transpose() decorator converts any argument to _pert_add that are of type xarray.DataArray to numpy.ndarray, and then gets the numpy.ndarray.T attribute, and passes this on to the _pert_add wrapper.

Following the computation, we want the result to be returned back as the same C-ordered array types that went in as arguments, so this decorator takes the result of the computation and returns the numpy.ndarray.T from the Fortran-ordered result. This result gets passed back up the decorator chain.

### Cast to Fortran Array Types¶

The Fortran routine expects a specific data type for the arrays (usually REAL(KIND=8)). WRF files typically store their data as 4-byte floating point numbers to save space. The arrays being passed to the wrf.decorators.extract_and_transpose() decorator need to be converted to the type used in the Fortran routine (e.g. double), then converted back to the original type (e.g. float) after the computation is finished. This is handled by the wrf.decorators.cast_type() decorator function in decorators.py.

@cast_type(arg_idxs=(0, 1))
@extract_and_transpose()

Located in example.f90.

"""
if outview is None:
outview = np.empty(base.shape[0:2], base.dtype, order="F")

pert,
outview)

return result


The wrf.decorators.cast_type() decorator function takes an arg_idxs argument to specify which positional arguments need to be cast to the Fortran algorithm type, in this case arguments 0 and 1 (base and pert).

Following the computation, the result will be cast back to the original type for the input arguments (usually float), and passed back up the decorator chain.

### Leftmost Dimension Indexing¶

The WRF-Python algorithms written in Fortran are usually written for fixed size arrays of 1, 2, or 3 dimensions. If your input arrays have more than the number of dimensions specified for the Fortran algorithm, then we need to do the following:

1. Determine how many leftmost dimensions are used.
2. Create an output array that has a shape that contains the leftmost dimensions concatenated with the shape of the result from the Fortran algorithm.
3. Iterate over the leftmost dimensions and send slices of the input arrays to the Fortran algorithm.
4. Along with the input arrays above, send a slice of the output array to be filled by the Fortran algorithm.
5. Return the fully calculated output array.

The wrf.decorators.left_iteration() is general purpose decorator contained in decorators.py to handle most leftmost index iteration cases. (Note: Some products, like cape_2d, return multiple products in the output and don’t fall in to this generic category, so those decorators can be found in specialdec.py)

Let’s look at how this is used below.

@left_iteration(2, 2, ref_var_idx=0)
@cast_type(arg_idxs=(0, 1))
@extract_and_transpose()

Located in example.f90.

"""
if outview is None:
outview = np.empty(base.shape[0:2], base.dtype, order="F")

pert,
outview)

return result


The wrf.decorators.left_iteration() decorator handles many different use cases with its arguments, but this example is one of the more common cases. The 0th positional argument tells the decorator that the “reference” input variable should provide at least two dimensions. This should be set to the same number of dimensions as in the Fortran algorithm, which is two in this case. Dimensions to the left of these two dimensions are considered “leftmost” dimensions.

The next positional argument (value of 2) tells the decorator that the newly created output variable should retain the shape of the reference variable’s right two dimensions. This only applies when your output has less dimensions than the reference variable (e.g. sea level pressure uses geopotential height for the reference but produces 2D output). Since we are not reducing the output dimensions, it should be set to the same value as the previous argument.

The final keyword argument of ref_ver_idx tells the decorator to use positional argument 0 (for the _pert_add function) as the reference variable.

The result of this decorator will be the fully computed output array, which gets passed back up the chain.

### Checking Argument Shapes¶

Before any computations can be performed, the argument shapes are checked to verify their sizes. Although f2py will catch problems at the entry point to the Fortran routine, the error thrown is confusing to users.

The wrf.decorators.check_args() decorator is used to verify that the arguments are the correct size before proceeding.

Here is how it is used:

@check_args(0, 2, (2, 2))
@left_iteration(2, 2, ref_var_idx=0)
@cast_type(arg_idxs=(0, 1))
@extract_and_transpose()

Located in example.f90.

"""
if outview is None:
outview = np.empty(base.shape[0:2], base.dtype, order="F")

pert,
outview)

return result


The 0th positional argument (value of 0), tells wrf.decorators.check_args() that the 0th positional argument of _pert_add is the reference variable.

The next postional argument (value of 2) tells wrf.decorators.check_args() that it should expect at least 2 dimensions for the reference variable. This should be set to the number of dimensions used in the Fortran algorithm, which is two in this case.

The final positional argument is a tuple with the number of dimensions that are expected for each array argument. Again, this should be set to the same number of dimensions expected in the Fortran routine for each positional argument. If an argument to your wrapped function is not an array type, you can use None in the tuple to ignore it, but that is not applicable for this example.

### Putting It All Together¶

The previous sections showed how the decorator chain was built up from the _pert_add function. However, when you actually make a call to _pert_add, the decorators are called from top to bottom. This means check_args is called first, then left_iteration, then cast_type, then extract_and_transpose, and finally _pert_add. After _pert_add is finished, the result is passed back up the chain and back to the user.

Now that we have a fully wrapped compiled routine, how might we use this?

Let’s make a new wrf.getvar() diagnostic called ‘total_pressure’. A similar diagnostic already exists in WRF-Python, but this is just for illustration of how to use our newly wrapped Fortran routine.

#### Make a ‘getter’ Function¶

First, we need a ‘getter’ routine that extracts the required input variables from the WRF NetCDF file(s) to perform the computation. In this case, the variables are P and PB.

The current naming convention in WRF-Python is to prefix the ‘getter’ functions with a ‘g_’, so let’s call this file g_totalpres.py and make a function get_total_pressure inside of it.

The contents of this file will be:

# g_totalpres.py

from .util import extract_vars

description="total pressure",
units="Pa")
def get_total_pressure(wrfin, timeidx=0, method="cat", squeeze=True,
cache=None, meta=True, _key=None):

This functions extracts the necessary variables from the NetCDF file
object in order to perform the calculation.

Args:

wrfin (:class:netCDF4.Dataset, :class:Nio.NioFile, or an \
iterable): WRF-ARW NetCDF
data as a :class:netCDF4.Dataset, :class:Nio.NioFile
or an iterable sequence of the aforementioned types.

timeidx (:obj:int or :data:wrf.ALL_TIMES, optional): The
desired time index. This value can be a positive integer,
negative integer, or
:data:wrf.ALL_TIMES (an alias for None) to return
all times in the file or sequence. The default is 0.

method (:obj:str, optional): The aggregation method to use for
sequences.  Must be either 'cat' or 'join'.
'cat' combines the data along the Time dimension.
'join' creates a new dimension for the file index.
The default is 'cat'.

squeeze (:obj:bool, optional): Set to False to prevent dimensions
with a size of 1 from being automatically removed from the
shape of the output. Default is True.

cache (:obj:dict, optional): A dictionary of (varname, ndarray)
that can be used to supply pre-extracted NetCDF variables to
the computational routines.  It is primarily used for internal
purposes, but can also be used to improve performance by
eliminating the need to repeatedly extract the same variables
used in multiple diagnostics calculations, particularly when
using large sequences of files.
Default is None.

meta (:obj:bool, optional): Set to False to disable metadata and
return :class:numpy.ndarray instead of
:class:xarray.DataArray.  Default is True.

_key (:obj:int, optional): A caching key. This is used for
internal purposes only.  Default is None.

Returns:
:class:xarray.DataArray or :class:numpy.ndarray: Omega.
If xarray is
enabled and the *meta* parameter is True, then the result will be a
:class:xarray.DataArray object.  Otherwise, the result will be a
:class:numpy.ndarray object with no metadata.

"""

# Get the base and perturbation pressures
varnames = ("PB", "P")
ncvars = extract_vars(wrfin, timeidx, varnames, method, squeeze, cache,
meta=False, _key=_key)

pb = ncvars["PB"]
p = ncvars["P"]



This getter function extracts the PB and P (base and pertrubation pressure) variables and calls the _pert_add function and returns the result. The arguments wrfin, timeidx, method, squeeze, cache, meta, and _key are used for every getter function and you can read what they do in the docstring.

The getter function is also decorated with a wrf.decorators.copy_and_set_metadata() decorator. This is a general purpose decorator that is used for copying metadata from an input variable to the result. In this case, the variable to copy is ‘P’. The name parameter specifies that the xarray.DataArray.name attribute for the variable (the name that will be written to a NetCDF variable). The description is a brief description for variable that will be placed in the xarray.DataArray.attrs dictionary along with the units parameter.

#### Make Your New Diagnostic Available in wrf.getvar()¶

The final step is to make the new ‘total_pressure’ diagnostic available from wrf.getvar(). To do this, modifications need to be made to routines.py.

First, import your new getter routine at the top of routines.py.

from __future__ import (absolute_import, division, print_function)

from .util import (get_iterable, is_standard_wrf_var, extract_vars,
viewkeys, get_id)
from .g_cape import (get_2dcape, get_3dcape, get_cape2d_only,
get_cin2d_only, get_lcl, get_lfc, get_3dcape_only,
get_3dcin_only)
.
.
.
from .g_cloudfrac import (get_cloudfrac, get_low_cloudfrac,
get_mid_cloudfrac, get_high_cloudfrac)
from .g_totalpres import get_total_pressure


Next, update _FUNC_MAP to map your diagnostic label (‘total_pressure’) to the getter routine (get_total_pres).

_FUNC_MAP = {"cape2d": get_2dcape,
"cape3d": get_3dcape,
.
.
.
"high_cloudfrac": get_high_cloudfrac,
"total_pressure": get_total_pressure
}


Finally, update _VALID_KARGS to inform wrf.getvar() of any additional keyword argument names that this routine might use. The wrf.getvar() routine will check keyword arguments and throws an error when it gets any that are not declared in this map.

In this case, there aren’t any addtional keyword arguments, so we’ll just supply an empty list.

_VALID_KARGS = {"cape2d": ["missing"],
"cape3d": ["missing"],
"dbz": ["do_variant", "do_liqskin"],
"maxdbz": ["do_variant", "do_liqskin"],
.
.
.
"high_cloudfrac": ["vert_type", "low_thresh",
"mid_thresh", "high_thresh"],
"total_pressure": []
}


After this is complete, your new routine is now available for use from wrf.getvar().