add wrf sub-package

meteoinfo-lab/milconfig.xml

@@ -1,32 +1,32 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <MeteoInfo File="milconfig.xml" Type="configurefile">
-  <Path OpenPath="D:\Working\MIScript\Jython\mis\meteo\interpolation">
+  <Path OpenPath="D:\Working\MIScript\Jython\mis\traj\TrajStat">
-    <RecentFolder Folder="D:\Working\MIScript\Jython\mis\LaSW"/>
-    <RecentFolder Folder="D:\Working\MIScript\Jython\mis\meteo\wrf"/>
-    <RecentFolder Folder="D:\Working\MIScript\Jython\mis\chart"/>
-    <RecentFolder Folder="D:\Working\MIScript\Jython\mis\chart\axis"/>
-    <RecentFolder Folder="D:\Working\MIScript\Jython\mis\common_math\stats"/>
-    <RecentFolder Folder="D:\Working\MIScript\Jython\mis\common_math"/>
-    <RecentFolder Folder="D:\Working\MIScript\Jython\mis\array"/>
-    <RecentFolder Folder="D:\Working\MIScript\Jython\mis\plot_types"/>
     <RecentFolder Folder="D:\Working\MIScript\Jython\mis\plot_types\taylor"/>
     <RecentFolder Folder="D:\Working\MIScript\Jython\mis\plot_types\3d\jogl"/>
     <RecentFolder Folder="D:\Working\MIScript\Jython\mis\plot_types\3d\jogl\text"/>
     <RecentFolder Folder="D:\Working\MIScript\Jython\mis\plot_types\3d\jogl\volume"/>
-    <RecentFolder Folder="D:\Working\MIScript\Jython\mis"/>
-    <RecentFolder Folder="D:\Working\MIScript\Jython\mis\meteo"/>
     <RecentFolder Folder="D:\Working\MIScript\Jython\mis\meteo\interpolation"/>
+    <RecentFolder Folder="D:\Working\MIScript\Jython\mis\satellite"/>
+    <RecentFolder Folder="D:\Working\MIScript\Jython\mis\grads"/>
+    <RecentFolder Folder="D:\Working\MIScript\Jython\mis\satellite\himawari"/>
+    <RecentFolder Folder="D:\Working\MIScript\Jython\mis\LaSW"/>
+    <RecentFolder Folder="D:\Working\MIScript\Jython\mis\meteo\wrf"/>
+    <RecentFolder Folder="D:\Working\MIScript\Jython\mis\meteo"/>
+    <RecentFolder Folder="D:\Working\MIScript\Jython\mis\meteo\calc"/>
+    <RecentFolder Folder="D:\Working\MIScript\Jython\mis"/>
+    <RecentFolder Folder="D:\Working\MIScript\Jython\mis\traj"/>
+    <RecentFolder Folder="D:\Working\MIScript\Jython\mis\traj\TrajStat"/>
   </Path>
   <File>
     <OpenedFiles>
       <OpenedFile File="D:\Working\MIScript\Jython\mis\plot_types\3d\jogl\volume\volumeplot_perspective.py"/>
-      <OpenedFile File="D:\Working\MIScript\Jython\mis\plot_types\3d\jogl\volume\volumeplot_perspective_2.py"/>
+      <OpenedFile File="D:\Working\MIScript\Jython\mis\LaSW\typhoon_map_slice.py"/>
-      <OpenedFile File="D:\Working\MIScript\Jython\mis\meteo\interpolation\log_interpolate_1d_1.py"/>
+      <OpenedFile File="D:\Working\MIScript\Jython\mis\traj\TrajStat\plot_pscf_3d.py"/>
     </OpenedFiles>
     <RecentFiles>
       <RecentFile File="D:\Working\MIScript\Jython\mis\plot_types\3d\jogl\volume\volumeplot_perspective.py"/>
-      <RecentFile File="D:\Working\MIScript\Jython\mis\plot_types\3d\jogl\volume\volumeplot_perspective_2.py"/>
+      <RecentFile File="D:\Working\MIScript\Jython\mis\LaSW\typhoon_map_slice.py"/>
-      <RecentFile File="D:\Working\MIScript\Jython\mis\meteo\interpolation\log_interpolate_1d_1.py"/>
+      <RecentFile File="D:\Working\MIScript\Jython\mis\traj\TrajStat\plot_pscf_3d.py"/>
     </RecentFiles>
   </File>
   <Font>
@@ -34,5 +34,5 @@
   </Font>
   <LookFeel DockWindowDecorated="true" LafDecorated="true" Name="FlatDarkLaf"/>
   <Figure DoubleBuffering="true"/>
-  <Startup MainFormLocation="-7,0" MainFormSize="1417,799"/>
+  <Startup MainFormLocation="-7,0" MainFormSize="1344,736"/>
 </MeteoInfo>

meteoinfo-lab/pylib/mipylib/dataset/dimdatafile.py

@@ -119,13 +119,15 @@ class DimDataFile(object):
             return None
         v = np.array(attr.getValues())
         return v
-        
+
+    @property
     def variables(self):
         """
         Get all variables.
         """
         return self._variables
-        
+
+    @property
     def varnames(self):
         """
         Get all variable names.

meteoinfo-lab/pylib/mipylib/imagelib/filters.py

@@ -30,7 +30,7 @@ def __getimage(src):
     elif isinstance(src, Graphic):
         return src.getShape().getImage()
     elif isinstance(src, MILayer):
-        return src.layer.getImage()
+        return src._layer.getImage()
     elif isinstance(src, NDArray):
         return ImageUtil.createImage(src.asarray())
     return None
@@ -40,7 +40,7 @@ def __getreturn(src, dst):
         src.getShape().setImage(dst)
         return src
     elif isinstance(src, MILayer):
-        src.layer.setImage(dst)
+        src._layer.setImage(dst)
         return src
     elif isinstance(src, NDArray):
         r = ImageUtil.imageRead(dst)

meteoinfo-lab/pylib/mipylib/meteolib/__init__.py

@@ -1,5 +1,5 @@
 from .meteo import *
-from . import wrf
+from .wrf import *
 from . import constants
 from .calc import *
 from .interpolate import *

meteoinfo-lab/pylib/mipylib/meteolib/wrf/__init__.py

@@ -0,0 +1,11 @@
+from destag import *
+from g_slp import *
+from g_rh import *
+from g_pressure import *
+from g_geoht import *
+
+__all__ = destag.__all__
+__all__ += g_slp.__all__
+__all__ += g_rh.__all__
+__all__ += g_pressure.__all__
+__all__ += g_geoht.__all__

meteoinfo-lab/pylib/mipylib/meteolib/wrf/destag.py

@@ -0,0 +1,42 @@
+
+__all__ = ['destagger']
+
+def destagger(var, stagger_dim):
+    """
+    Return the variable data array on the unstaggered grid.
+
+    This function destaggers the variable by taking the average of the
+    values located on either side of the grid box.
+
+    :param var: (*array*) A variable on a staggered grid.
+    :param stagger_dim: (*int*) The dimension index to destagger.
+        Negative values can be used to choose dimensions referenced
+        from the right hand side (-1 is the rightmost dimension).
+
+    :returns: (*array*) The destaggered variable data array.
+    """
+    var_shape = var.shape
+    num_dims = var.ndim
+    stagger_dim_size = var_shape[stagger_dim]
+    # Dynamically building the range slices to create the appropriate
+    # number of ':'s in the array accessor lists.
+    # For example, for a 3D array, the calculation would be
+    # result = .5 * (var[:,:,0:stagger_dim_size-2]
+    #                    + var[:,:,1:stagger_dim_size-1])
+    # for stagger_dim=2.  So, full slices would be used for dims 0 and 1, but
+    # dim 2 needs the special slice.
+    full_slice = slice(None)
+    slice1 = slice(0, stagger_dim_size - 1, 1)
+    slice2 = slice(1, stagger_dim_size, 1)
+
+    # default to full slices
+    dim_ranges_1 = [full_slice] * num_dims
+    dim_ranges_2 = [full_slice] * num_dims
+
+    # for the stagger dim, insert the appropriate slice range
+    dim_ranges_1[stagger_dim] = slice1
+    dim_ranges_2[stagger_dim] = slice2
+
+    result = .5*(var[tuple(dim_ranges_1)] + var[tuple(dim_ranges_2)])
+
+    return result

meteoinfo-lab/pylib/mipylib/meteolib/wrf/g_geoht.py

@@ -0,0 +1,209 @@
+from util import either
+from destag import destagger
+from .. import constants
+import warnings
+
+__all__ = ['get_geopt', 'get_stag_geopt', 'get_height', 'get_stag_height', 'get_height_agl']
+
+def _get_geoht(wrfin, timeidx, height=True, msl=True, stag=False):
+    """Return the geopotential or geopotential height.
+
+    If *height* is False, then geopotential is returned in units of
+    [m2 s-2].  If *height* is True, then geopotential height is
+    returned in units of [m].  If *msl* is True, then geopotential height
+    is return as Mean Sea Level (MSL).  If *msl* is False, then geopotential
+    height is returned as Above Ground Level (AGL).
+    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.
+        height (:obj:`bool`, optional): Set to True to return geopotential
+            height instead of geopotential.  Default is True.
+        msl (:obj:`bool`, optional): Set to True to return geopotential height
+            as Mean Sea Level (MSL).  Set to False to return the
+            geopotential height as Above Ground Level (AGL) by subtracting
+            the terrain height.  Default is True.
+        stag (:obj:`bool`, optional): Set to True to use the vertical
+            staggered grid, rather than the mass grid. Default is False.
+
+    Returns:
+        :class:`DimArray`
+    """
+
+    varname = either("PH", "GHT")(wrfin)
+    if varname == "PH":
+        ph = wrfin["PH"][timeidx]
+        phb = wrfin["PHB"][timeidx]
+        hgt = wrfin["HGT"][timeidx]
+        geopt = ph + phb
+        if not stag:
+            geopt_unstag = destagger(geopt, -3)
+        else:
+            geopt_unstag = geopt
+    else:
+        geopt_unstag = wrfin["GHT"][timeidx] * constants.g
+        hgt = wrfin["HGT_M"][timeidx]
+
+        if stag:
+            warnings.warn("file contains no vertically staggered geopotential "
+                          "height variable, returning unstaggered result "
+                          "instead")
+    if height:
+        if msl:
+            return geopt_unstag / constants.g
+        else:
+            # Due to broadcasting with multifile/multitime, the 2D terrain
+            # array needs to be reshaped to a 3D array so the right dims
+            # line up
+            new_dims = list(hgt.shape)
+            new_dims.insert(-2, 1)
+            hgt = hgt.reshape(new_dims)
+
+            return (geopt_unstag / constants.g) - hgt
+    else:
+        return geopt_unstag
+
+def get_geopt(wrfin, timeidx=0):
+    """Return the geopotential.
+
+    The geopotential is returned in units of [m2 s-2].
+    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.
+
+    Returns:
+        :class:`DimArray`
+    """
+    return _get_geoht(wrfin, timeidx, False, True)
+
+def get_height(wrfin, timeidx=0, msl=True):
+    """Return the geopotential height.
+
+    If *msl* is True, then geopotential height is returned as Mean Sea Level
+    (MSL).  If *msl* is False, then geopotential height is returned as
+    Above Ground Level (AGL) by subtracting the terrain height.
+    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.
+        msl (:obj:`bool`, optional): Set to True to return geopotential height
+            as Mean Sea Level (MSL).  Set to False to return the
+            geopotential height as Above Ground Level (AGL) by subtracting
+            the terrain height.  Default is True.
+
+    Returns:
+        :class:`DimArray` or :class:`numpy.ndarray`: The
+        geopotential height (m).
+    """
+    return _get_geoht(wrfin, timeidx, True, msl)
+
+def get_stag_geopt(wrfin, timeidx=0):
+    """Return the geopotential for the vertically staggered grid.
+
+    The geopotential is returned in units of [m2 s-2].
+    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.
+
+    Returns:
+        :class:`DimArray` or :class:`numpy.ndarray`: The
+        geopotential (m).
+    """
+    return _get_geoht(wrfin, timeidx, False, True, stag=True)
+
+
+def get_stag_height(wrfin, timeidx=0, msl=True):
+    """Return the geopotential height for the vertically staggered grid.
+
+    If *msl* is True, then geopotential height is returned as Mean Sea Level
+    (MSL).  If *msl* is False, then geopotential height is returned as
+    Above Ground Level (AGL) by subtracting the terrain height.
+    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.
+        msl (:obj:`bool`, optional): Set to True to return geopotential height
+            as Mean Sea Level (MSL).  Set to False to return the
+            geopotential height as Above Ground Level (AGL) by subtracting
+            the terrain height.  Default is True.
+
+    Returns:
+        :class:`DimArray` or :class:`numpy.ndarray`: The
+        geopotential height (m).
+    """
+
+    return _get_geoht(wrfin, timeidx, True, msl, stag=True)
+
+
+def get_height_agl(wrfin, timeidx=0):
+    """Return the geopotential height (AGL).
+
+    The geopotential height is returned as Above Ground Level (AGL) by
+    subtracting the terrain height.
+    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.
+
+    Returns:
+        :class:`DimArray` or :class:`numpy.ndarray`: The
+        geopotential height (m).
+    """
+
+    return _get_geoht(wrfin, timeidx, True, False)

meteoinfo-lab/pylib/mipylib/meteolib/wrf/g_pressure.py

@@ -0,0 +1,19 @@
+__all__ = ['get_pressure']
+
+def get_pressure(wrfin, timeidx=0):
+    """
+    Return the pressure in the specified units.
+
+    This function extracts the necessary variables from the NetCDF file
+    object in order to perform the calculation.
+
+    :param wrfin: (*DimDataFile*) Data file.
+    :param timeidx: (*int*) Time index.
+
+    :returns: (*array*) Pressure (hPa).
+    """
+    p = wrfin['P'][timeidx]
+    pb = wrfin['PB'][timeidx]
+    pres = (p + pb) * 0.01
+
+    return pres

meteoinfo-lab/pylib/mipylib/meteolib/wrf/g_rh.py

@@ -0,0 +1,48 @@
+from .. import constants
+from ..calc.thermo import relative_humidity_from_specific_humidity, temperature_from_potential_temperature
+
+__all__ = ['get_rh', 'get_rh2m']
+
+def get_rh(wrfin, timeidx=0):
+    """
+    Return the relative humidity.
+
+    This functions extracts the necessary variables from the NetCDF file
+    object in order to perform the calculation.
+
+    :param wrfin: (*DimDataFile*) Data file.
+    :param timeidx: (*int*) Time index.
+
+    :returns: (*array*) Relative humidity.
+    """
+    t = wrfin['T'][timeidx,:,:,:]
+    p = wrfin['P'][timeidx,:,:,:]
+    pb = wrfin['PB'][timeidx,:,:,:]
+    qvapor = wrfin['QVAPOR'][timeidx,:,:,:]
+    full_t = t + constants.T_BASE
+    full_p = p + pb
+    qvapor[qvapor < 0] = 0.
+    tk = temperature_from_potential_temperature(full_p * 0.01, full_t)
+    rh = relative_humidity_from_specific_humidity(full_p * 0.01, tk, qvapor)
+
+    return rh
+
+def get_rh2m(wrfin, timeidx=0):
+    """
+    Return the 2m relative humidity.
+
+    This functions extracts the necessary variables from the NetCDF file
+    object in order to perform the calculation.
+
+    :param wrfin: (*DimDataFile*) Data file.
+    :param timeidx: (*int*) Time index.
+
+    :returns: (*array*) Relative humidity.
+    """
+    t2 = wrfin['T2'][timeidx,:,:]
+    psfc = wrfin['PSFC'][timeidx,:,:]
+    q2 = wrfin['Q2'][timeidx,:,:]
+    q2[q2 < 0] = 0.
+    rh = relative_humidity_from_specific_humidity(psfc * 0.01, t2, q2)
+
+    return rh

meteoinfo-lab/pylib/mipylib/meteolib/wrf/g_slp.py

@@ -0,0 +1,37 @@
+from org.meteoinfo.math.meteo import MeteoMath
+from mipylib.numeric.core import DimArray
+from .. import constants
+from ..calc.thermo import temperature_from_potential_temperature
+from destag import destagger
+
+__all__ = ['get_slp']
+
+def get_slp(wrfin, timeidx=0, units='hPa'):
+    """
+    Return the sea level pressure in the specified units.
+
+    This function extracts the necessary variables from the NetCDF file
+    object in order to perform the calculation.
+
+    :param wrfin: (*DimDataFile*) Data file.
+    :param timeidx: (*int*) Time index.
+    :param units: (*string*) The desired units.
+
+    :returns: (*array*) Sea level pressure.
+    """
+    t = wrfin['T'][timeidx,:,:,:]
+    p = wrfin['P'][timeidx,:,:,:]
+    pb = wrfin['PB'][timeidx,:,:,:]
+    qvapor = wrfin['QVAPOR'][timeidx,:,:,:]
+    ph = wrfin['PH'][timeidx,:,:,:]
+    phb = wrfin['PHB'][timeidx,:,:,:]
+    full_t = t + constants.T_BASE
+    full_p = p + pb
+    qvapor[qvapor < 0] = 0.
+
+    full_ph = (ph + phb) / constants.g
+    destag_ph = destagger(full_ph, -3)
+    tk = temperature_from_potential_temperature(full_p * 0.01, full_t)
+    slp = MeteoMath.calSeaPrs(destag_ph._array, tk._array, full_p._array, qvapor._array)
+
+    return DimArray(slp, dims=t.dims[1:])

meteoinfo-lab/pylib/mipylib/meteolib/wrf/util.py

@@ -0,0 +1,39 @@
+
+# Helper utilities for metadata
+class either(object):
+    """A callable class that determines which variable is present in the
+    file.
+
+    This is used in situations where the same variable type has different names
+    depending on the type of file used.  For example, in a WRF output file,
+    'P' is used for pressure, whereas in a met_em file, pressure is named
+    'PRES'.
+
+    Methods:
+        __call__(wrfin): Return the variable that is present in the file.
+            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.
+            Returns:
+                :obj:`str`: The variable name that is present in the file.
+
+    Attributes:
+        varnames (sequence): A sequence of possible variable names.
+    """
+    def __init__(self, *varnames):
+        """Initialize an :class:`either` object.
+
+        Args:
+            *varnames (sequence): A sequence of possible variable names.
+        """
+        self.varnames = varnames
+
+    def __call__(self, wrfin):
+        for varname in self.varnames:
+            if varname in wrfin.varnames:
+                return varname
+
+        raise ValueError("{} are not valid variable names".format(
+            self.varnames))

meteoinfo-lab/pylib/mipylib/meteolib/wrf/wrf.py

@@ -8,7 +8,7 @@
 from org.meteoinfo.math.meteo import MeteoMath
 from mipylib.numeric.core import NDArray, DimArray
 import constants as constants
-from .calc.thermo import relative_humidity_from_specific_humidity, temperature_from_potential_temperature
+from pylib.mipylib.meteolib.calc.thermo import relative_humidity_from_specific_humidity, temperature_from_potential_temperature
 
 __all__ = [
     'destagger','get_slp','get_rh','get_rh2m'