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https://github.com/meteoinfo/MeteoInfo.git
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744 lines
26 KiB
Python
744 lines
26 KiB
Python
#-----------------------------------------------------
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# Author: Yaqiang Wang
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# Date: 2014-12-27
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# Purpose: MeteoInfo Dataset module
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# Note: Jython
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#-----------------------------------------------------
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from org.meteoinfo.ndarray import Dimension, DimensionType, Range, Array, MAMath
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from org.meteoinfo.ndarray.math import ArrayMath, ArrayUtil
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from org.meteoinfo.common import PointD
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from org.meteoinfo.projection import KnownCoordinateSystems, Reproject
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from org.meteoinfo.data.meteodata import Attribute
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from ucar.nc2 import Attribute as NCAttribute
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from ucar.ma2 import DataType as NCDataType
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from ucar.ma2 import ArrayStructure, StructureMembers
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from org.meteoinfo.data.meteodata.netcdf import NCUtil
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from org.meteoinfo.ndarray import DataType
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import mipylib.numeric as np
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import mipylib.miutil as miutil
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import datetime
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import numbers
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# Dimension variable
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class DimVariable(object):
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# variable must be org.meteoinfo.data.meteodata.Variable
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# dataset is DimDataFile
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def __init__(self, variable=None, dataset=None, ncvariable=None):
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self.variable = variable
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self.dataset = dataset
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self.ncvariable = ncvariable
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if not variable is None:
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self.name = variable.getName()
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self.dtype = np.dtype.fromjava(variable.getDataType())
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self.dims = variable.getDimensions()
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self.ndim = variable.getDimNumber()
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self.attributes = variable.getAttributes()
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self.fill_value = variable.getFillValue()
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self.scale_factor = variable.getScaleFactor()
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self.add_offset = variable.getAddOffset()
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elif not ncvariable is None:
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self.name = ncvariable.getShortName()
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self.dtype = ncvariable.getDataType()
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self.dims = ncvariable.getDimensions()
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self.ndim = len(self.dims)
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self.attributes = list(ncvariable.getAttributes())
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else:
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self.name = None
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self.dtype = None
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self.dims = None
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self.ndim = 0
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self.attributes = None
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self.proj = None if dataset is None else dataset.proj
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def __len__(self):
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len = 1
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if not self.variable is None:
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for dim in self.variable.getDimensions():
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len = len * dim.getLength()
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return len
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def __str__(self):
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r = str(self.dtype) + ' ' + 'None' if self.name is None else self.name + '('
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if self.dims is None:
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r = r + '):'
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else:
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for dim in self.dims:
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dimname = dim.getShortName()
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if dimname is None:
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dimname = 'null'
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r = r + dimname + ','
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r = r[:-1] + '):'
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if not self.attributes is None:
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for attr in self.attributes:
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r = r + '\n\t' + self.name + ': ' + attr.toString()
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return r
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def __repr__(self):
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return self.__str__()
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def __getitem__(self, indices):
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if self.variable.getDataType() in [DataType.STRUCTURE, DataType.SEQUENCE]:
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if isinstance(indices, str): #metadata
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return self.member_array(indices)
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else:
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a = self.dataset.read(self.name)
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return StructureArray(a.getArrayObject())
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if indices is None:
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inds = []
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for _ in range(self.ndim):
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inds.append(slice(None))
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indices = tuple(inds)
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if not isinstance(indices, tuple):
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indices = [indices]
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if len(indices) < self.ndim:
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indices = list(indices)
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for _ in range(self.ndim - len(indices)):
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indices.append(slice(None))
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indices = tuple(indices)
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if len(indices) != self.ndim:
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print 'indices must be ' + str(self.ndim) + ' dimensions!'
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return None
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if not self.proj is None and not self.proj.isLonLat():
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xlim = None
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ylim = None
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xidx = -1
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yidx = -1
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for i in range(0, self.ndim):
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dim = self.dims[i]
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if dim.getDimType() == DimensionType.X:
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k = indices[i]
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if isinstance(k, basestring):
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xlims = k.split(':')
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if len(xlims) == 1:
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xlim = [float(xlims[0])]
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else:
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xlim = [float(xlims[0]), float(xlims[1])]
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xidx = i
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elif dim.getDimType() == DimensionType.Y:
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k = indices[i]
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if isinstance(k, basestring):
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ylims = k.split(':')
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if len(ylims) == 1:
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ylim = [float(ylims[0])]
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else:
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ylim = [float(ylims[0]), float(ylims[1])]
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yidx = i
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if not xlim is None and not ylim is None:
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fromproj=KnownCoordinateSystems.geographic.world.WGS1984
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inpt = PointD(xlim[0], ylim[0])
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outpt1 = Reproject.reprojectPoint(inpt, fromproj, self.proj)
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if len(xlim) == 1:
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xlim = [outpt1.X]
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ylim = [outpt1.Y]
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else:
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inpt = PointD(xlim[1], ylim[1])
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outpt2 = Reproject.reprojectPoint(inpt, fromproj, self.proj)
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xlim = [outpt1.X, outpt2.X]
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ylim = [outpt1.Y, outpt2.Y]
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indices1 = []
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for i in range(0, self.ndim):
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if i == xidx:
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if len(xlim) == 1:
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indices1.append(str(xlim[0]))
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else:
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indices1.append(str(xlim[0]) + ':' + str(xlim[1]))
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elif i == yidx:
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if len(ylim) == 1:
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indices1.append(str(ylim[0]))
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else:
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indices1.append(str(ylim[0]) + ':' + str(ylim[1]))
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else:
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indices1.append(indices[i])
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indices = indices1
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origin = []
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size = []
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stride = []
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ranges = []
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dims = []
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flips = []
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onlyrange = True
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for i in range(0, self.ndim):
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isrange = True
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dimlen = self.dimlen(i)
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k = indices[i]
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sidx = 0
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eidx = 0
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step = 1
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if isinstance(k, int):
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if k < 0:
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k = self.dims[i].getLength() + k
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sidx = k
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eidx = k
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step = 1
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elif isinstance(k, slice):
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if isinstance(k.start, basestring):
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sv = float(k.start)
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sidx = self.dims[i].getValueIndex(sv)
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elif isinstance(k.start, datetime.datetime):
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sv = miutil.date2num(k.start)
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sidx = self.dims[i].getValueIndex(sv)
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else:
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sidx = 0 if k.start is None else k.start
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if sidx < 0:
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sidx = self.dimlen(i) + sidx
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if isinstance(k.stop, basestring):
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ev = float(k.stop)
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eidx = self.dims[i].getValueIndex(ev)
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elif isinstance(k.stop, datetime.datetime):
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ev = miutil.date2num(k.stop)
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eidx = self.dims[i].getValueIndex(ev)
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else:
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eidx = self.dimlen(i) if k.stop is None else k.stop
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if eidx < 0:
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eidx = self.dimlen(i) + eidx
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eidx -= 1
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if isinstance(k.step, basestring):
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nv = float(k.step) + self.dims[i].getDimValue()[0]
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nidx = self.dims[i].getValueIndex(nv)
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step = nidx - sidx
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elif isinstance(k.step, datetime.timedelta):
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nv = miutil.date2num(k.start + k.step)
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nidx = self.dims[i].getValueIndex(nv)
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step = nidx - sidx
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else:
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step = 1 if k.step is None else k.step
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elif isinstance(k, list):
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onlyrange = False
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isrange = False
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if not isinstance(k[0], datetime.datetime):
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ranges.append(k)
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else:
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tlist = []
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for tt in k:
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sv = miutil.date2num(tt)
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idx = self.dims[i].getValueIndex(sv)
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tlist.append(idx)
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ranges.append(tlist)
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k = tlist
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elif isinstance(k, basestring):
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dim = self.variable.getDimension(i)
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kvalues = k.split(':')
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sv = float(kvalues[0])
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sidx = dim.getValueIndex(sv)
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if len(kvalues) == 1:
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eidx = sidx
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step = 1
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else:
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ev = float(kvalues[1])
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eidx = dim.getValueIndex(ev)
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if len(kvalues) == 2:
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step = 1
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else:
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step = int(float(kvalues[2]) / dim.getDeltaValue())
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if sidx > eidx and step > 0:
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step = -step
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else:
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print k
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return None
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if isrange:
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if sidx >= dimlen or eidx >= dimlen:
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print('Index out of range!')
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return None
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origin.append(sidx)
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n = abs(eidx - sidx) + 1
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size.append(n)
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if n > 1:
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dim = self.variable.getDimension(i)
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#if dim.isReverse():
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# step = -step
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dim = dim.extract(sidx, eidx, step)
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#dim.setReverse(False)
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dims.append(dim)
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stride.append(step)
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if step < 0:
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#step = abs(step)
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flips.append(i)
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if sidx > eidx:
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iidx = eidx
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eidx = sidx
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sidx = iidx
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rr = Range(sidx, eidx, abs(step))
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ranges.append(rr)
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else:
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if len(k) > 1:
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dim = self.variable.getDimension(i)
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dim = dim.extract(k)
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#dim.setReverse(False)
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dims.append(dim)
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if onlyrange:
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rr = self.dataset.dataset.read(self.name, ranges)
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else:
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rr = self.dataset.dataset.take(self.name, ranges)
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if rr.getSize() == 1:
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iter = rr.getIndexIterator()
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return iter.getObjectNext()
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else:
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for i in flips:
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rr = rr.flip(i)
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rr = rr.reduce()
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ArrayMath.missingToNaN(rr, self.fill_value)
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if len(flips) > 0:
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rrr = Array.factory(rr.getDataType(), rr.getShape())
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MAMath.copy(rrr, rr)
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array = np.array(rrr)
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else:
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array = np.array(rr)
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data = np.DimArray(array, dims, self.fill_value, self.dataset.proj)
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return data
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def read(self):
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'''
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Read data array.
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:return: (*array*) Data array.
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'''
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return np.array(self.dataset.read(self.name))
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def get_members(self):
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'''
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Get structure members. Only valid for Structure data type.
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:return: Structure members.
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'''
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a = self.read()
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if a._array.getDataType() != DataType.STRUCTURE:
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print 'This method is only valid for structure array!'
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return None
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a = a._array.getArrayObject()
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return a.getMembers()
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def get_member(self, member):
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'''
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Get structure members. Only valid for Structure data type.
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:param member: (*str*) Member name.
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:return: Structure members.
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'''
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a = self.read()
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if a._array.getDataType() != DataType.STRUCTURE:
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print 'This method is only valid for structure array!'
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return None
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a = a._array.getArrayObject()
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return a.findMember(member)
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def member_array(self, member, indices=None):
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'''
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Extract member array. Only valid for Structure data type.
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:param member: (*string*) Member name.
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:param indices: (*slice*) Indices.
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:returns: (*array*) Extracted member array.
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'''
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a = self.read()
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if a._array.getDataType() != DataType.STRUCTURE:
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print 'This method is only valid for structure array!'
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return None
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a = a._array.getArrayObject()
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if isinstance(member, basestring):
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member = a.findMember(member)
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if member is None:
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raise KeyError('The member %s not exists!' % member)
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self.dataset.reopen()
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a = a.extractMemberArray(member)
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if a.getDataType() in [NCDataType.SEQUENCE, NCDataType.STRUCTURE]:
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return StructureArray(a)
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a = NCUtil.convertArray(a)
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r = np.array(a)
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if r.size == 1:
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return r[0]
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if not indices is None:
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r = r.__getitem__(indices)
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return r
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# get dimension length
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def dimlen(self, idx):
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return self.dims[idx].getLength()
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def dimvalue(self, idx, convert=False):
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'''
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Get dimension values.
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:param idx: (*int*) Dimension index.
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:param convert: (*boolean*) If convert to real values (i.e. datetime). Default
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is ``False``.
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:returns: (*array_like*) Dimension values
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'''
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dim = self.dims[idx]
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if convert:
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if dim.getDimType() == DimensionType.T:
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return miutil.nums2dates(dim.getDimValue())
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else:
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return np.array(ArrayUtil.array(self.dims[idx].getDimValue()))
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else:
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return np.array(ArrayUtil.array(self.dims[idx].getDimValue()))
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def attrvalue(self, attr):
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'''
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Get a global attribute value.
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:param attr: (*string or Attribute*) Attribute or Attribute name
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'''
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if isinstance(attr, str):
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attr = self.variable.findAttribute(attr)
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if attr is None:
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return None
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v = np.array(attr.getValues())
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return v
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def xdim(self):
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for dim in self.dims:
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if dim.getDimType() == DimensionType.X:
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return dim
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return None
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def ydim(self):
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for dim in self.dims:
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if dim.getDimType() == DimensionType.Y:
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return dim
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return None
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def zdim(self):
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for dim in self.dims:
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if dim.getDimType() == DimensionType.Z:
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return dim
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return None
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def tdim(self):
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for dim in self.dims:
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if dim.getDimType() == DimensionType.T:
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return dim
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return None
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def adddim(self, dimtype, dimvalue):
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if isinstance(dimvalue, np.NDArray):
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dimvalue = dimvalue.aslist()
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self.variable.addDimension(dimtype, dimvalue)
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self.ndim = self.variable.getDimNumber()
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def setdim(self, dimtype, dimvalue, index=None, reverse=False):
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if isinstance(dimvalue, np.NDArray):
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dimvalue = dimvalue.aslist()
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if index is None:
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self.variable.setDimension(dimtype, dimvalue, reverse)
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else:
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self.variable.setDimension(dimtype, dimvalue, reverse, index)
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self.ndim = self.variable.getDimNumber()
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def setdimrev(self, idx, reverse):
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self.dims[idx].setReverse(reverse)
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def addattr(self, attrname, attrvalue):
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if self.attributes is None:
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self.attributes = []
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if isinstance(attrvalue, Array):
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attrvalue = np.NDArray(attrvalue)
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if isinstance(attrvalue, np.NDArray):
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if attrvalue.size == 1:
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attrvalue = attrvalue[0]
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attr = Attribute(attrname, attrvalue)
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else:
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attr = Attribute(attrname, attrvalue._array)
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else:
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attr = Attribute(attrname, attrvalue)
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self.attributes.append(attr)
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if not self.ncvariable is None:
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if isinstance(attrvalue, np.NDArray):
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attrvalue = NCUtil.convertArray(attrvalue._array)
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ncattr = NCAttribute(attrname, attrvalue)
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self.ncvariable.addAttribute(ncattr)
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return attr
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class StructureArray(object):
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def __init__(self, array):
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"""
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Structure array.
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:param array: (*ArrayStructure*) NC ArrayStructure object.
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"""
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self._array = array
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@property
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def shape(self):
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"""
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Get array shape.
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:return: (*tuple of int*) Array shape.
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"""
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return tuple(self._array.getShape())
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@property
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def dtype(self):
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"""
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Get array data type.
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:return: (*DataType*) Array data type.
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"""
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return NCUtil.convertDataType(self._array.getDataType())
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def get_members(self, rec=0):
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"""
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Get structure members.
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:param rec: (*int*) Record index.
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:return: (*Member*) Structure members.
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"""
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if isinstance(self._array, ArrayStructure):
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return self._array.getMembers()
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else:
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return self._array.getObject(rec).getMembers()
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def get_member(self, member, rec=0):
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"""
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Get structure members.
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:param member: (*str*) Member name.
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:param rec: (*int*) Record index.
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:return: (*Member*) Structure members.
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"""
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if isinstance(self._array, ArrayStructure):
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return self._array.findMember(member)
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else:
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return self._array.getObject(rec).findMember(member)
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def member_array(self, member, indices=None, rec=0):
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'''
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Extract member array. Only valid for Structure data type.
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:param member: (*string*) Member name.
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:param indices: (*slice*) Indices.
|
|
:param rec: (*int*) Record index.
|
|
|
|
:returns: (*array*) Extracted member array.
|
|
'''
|
|
is_structure = isinstance(self._array, ArrayStructure)
|
|
if isinstance(member, basestring):
|
|
if is_structure:
|
|
member = self._array.findMember(member)
|
|
else:
|
|
member = self._array.getObject(rec).findMember(member)
|
|
|
|
if member is None:
|
|
raise KeyError('The member %s not exists!' % member)
|
|
|
|
if is_structure:
|
|
a = self._array.extractMemberArray(member)
|
|
else:
|
|
a = self._array.getObject(rec).extractMemberArray(member)
|
|
if a.getDataType() in [NCDataType.SEQUENCE, NCDataType.STRUCTURE]:
|
|
return StructureArray(a)
|
|
|
|
a = NCUtil.convertArray(a)
|
|
r = np.array(a)
|
|
if r.size == 1:
|
|
return r[0]
|
|
|
|
if not indices is None:
|
|
r = r.__getitem__(indices)
|
|
|
|
return r
|
|
|
|
# Variable in multiple data files (DimDataFiles) - only time dimension is different.
|
|
class TDimVariable(object):
|
|
|
|
# variable must be org.meteoinfo.data.meteodata.Variable
|
|
# dataset is DimDataFiles
|
|
def __init__(self, variable, dataset):
|
|
self.variable = variable
|
|
self.dataset = dataset
|
|
self.name = variable.getName()
|
|
self.dtype = np.dtype.fromjava(variable.getDataType())
|
|
self.ndim = variable.getDimNumber()
|
|
self.fill_value = variable.getFillValue()
|
|
self.scale_factor = variable.getScaleFactor()
|
|
self.add_offset = variable.getAddOffset()
|
|
dims = variable.getDimensions()
|
|
tdim = Dimension(DimensionType.T)
|
|
times = []
|
|
for t in self.dataset.times:
|
|
times.append(miutil.date2num(t))
|
|
tdim.setDimValues(times)
|
|
dims[0] = tdim
|
|
self.dims = dims
|
|
self.tnum = len(times)
|
|
|
|
def __str__(self):
|
|
if self.variable is None:
|
|
return 'None'
|
|
|
|
r = str(self.dtype) + ' ' + self.name + '('
|
|
for dim in self.dims:
|
|
dimname = dim.getShortName()
|
|
if dimname is None:
|
|
dimname = 'null'
|
|
r = r + dimname + ','
|
|
r = r[:-1] + '):'
|
|
attrs = self.variable.getAttributes()
|
|
for attr in attrs:
|
|
r = r + '\n\t' + self.name + ': ' + attr.toString()
|
|
return r
|
|
|
|
def __repr__(self):
|
|
return self.__str__()
|
|
|
|
def __getitem__(self, indices):
|
|
if not isinstance(indices, tuple):
|
|
indices = [indices]
|
|
|
|
if len(indices) < self.ndim:
|
|
indices = list(indices)
|
|
for _ in range(self.ndim - len(indices)):
|
|
indices.append(slice(None))
|
|
indices = tuple(indices)
|
|
|
|
if len(indices) != self.ndim:
|
|
print 'indices must be ' + str(self.ndim) + ' dimensions!'
|
|
return None
|
|
|
|
k = indices[0]
|
|
t_list = None
|
|
if isinstance(k, int):
|
|
if k < 0:
|
|
k = self.tnum + k
|
|
sidx = k
|
|
eidx = k
|
|
step = 1
|
|
elif isinstance(k, datetime.datetime):
|
|
sidx = self.dataset.timeindex(k)
|
|
eidx = sidx
|
|
step = 1
|
|
elif isinstance(k, slice):
|
|
sidx = 0 if k.start is None else k.start
|
|
if isinstance(sidx, datetime.datetime):
|
|
sidx = self.dataset.timeindex(sidx)
|
|
if sidx < 0:
|
|
sidx = self.tnum + sidx
|
|
eidx = self.tnum if k.stop is None else k.stop
|
|
if isinstance(eidx, datetime.datetime):
|
|
eidx = self.dataset.timeindex(eidx) + 1
|
|
if eidx < 0:
|
|
eidx = self.tnum + eidx
|
|
eidx -= 1
|
|
step = 1 if k.step is None else k.step
|
|
elif isinstance(k, list):
|
|
t_list = []
|
|
for t in k:
|
|
if isinstance(t, datetime.datetime):
|
|
t_list.append(self.dataset.timeindex(t))
|
|
else:
|
|
t_list.append(t)
|
|
|
|
times = []
|
|
data = None
|
|
if t_list is None:
|
|
sfidx = self.dataset.datafileindex(sidx)
|
|
si = sidx
|
|
aa = None
|
|
for i in range(sidx, eidx + 1, step):
|
|
times.append(miutil.date2num(self.dataset.gettime(i)))
|
|
fidx = self.dataset.datafileindex(i)
|
|
if fidx > sfidx:
|
|
ei = i - step
|
|
ddf = self.dataset[sfidx]
|
|
var = ddf[self.name]
|
|
ii, ssi = self.dataset.dftindex(si)
|
|
ii, eei = self.dataset.dftindex(ei)
|
|
eei += 1
|
|
nindices = list(indices)
|
|
nindices[0] = slice(ssi, eei, step)
|
|
nindices = tuple(nindices)
|
|
aa = var.__getitem__(nindices)
|
|
if si == ei:
|
|
if isinstance(aa, np.DimArray):
|
|
aa.addtdim(self.dataset.gettime(si))
|
|
else:
|
|
aa = np.array([aa])
|
|
aa = np.DimArray(aa)
|
|
aa.addtdim(self.dataset.gettime(si))
|
|
if data is None:
|
|
data = aa
|
|
else:
|
|
data = np.concatenate([data, aa])
|
|
si = i
|
|
sfidx = fidx
|
|
|
|
if si < eidx + 1:
|
|
ei = eidx + 1 - step
|
|
ddf = self.dataset[sfidx]
|
|
var = ddf[self.name]
|
|
ii, ssi = self.dataset.dftindex(si)
|
|
ii, eei = self.dataset.dftindex(ei)
|
|
eei += 1
|
|
nindices = list(indices)
|
|
nindices[0] = slice(ssi, eei, step)
|
|
nindices = tuple(nindices)
|
|
aa = var.__getitem__(nindices)
|
|
if si == ei and eidx != sidx:
|
|
if isinstance(aa, np.DimArray):
|
|
aa.addtdim(self.dataset.gettime(si))
|
|
else:
|
|
aa = np.array([aa])
|
|
aa = np.DimArray(aa)
|
|
aa.addtdim(self.dataset.gettime(si))
|
|
if data is None:
|
|
data = aa
|
|
else:
|
|
data = np.concatenate([data, aa])
|
|
|
|
if aa is None:
|
|
sfidx = self.dataset.datafileindex(sidx)
|
|
ddf = self.dataset[sfidx]
|
|
var = ddf[self.name]
|
|
ii, ssi = self.dataset.dftindex(sidx)
|
|
nindices = list(indices)
|
|
nindices[0] = slice(ssi, ssi, step)
|
|
nindices = tuple(nindices)
|
|
aa = var.__getitem__(nindices)
|
|
return aa
|
|
else:
|
|
for i in t_list:
|
|
times.append(miutil.date2num(self.dataset.gettime(i)))
|
|
fidx, ssi = self.dataset.dftindex(i)
|
|
ddf = self.dataset[fidx]
|
|
var = ddf[self.name]
|
|
nindices = list(indices)
|
|
nindices[0] = ssi
|
|
nindices = tuple(nindices)
|
|
aa = var.__getitem__(nindices)
|
|
aa.addtdim(self.dataset.gettime(i))
|
|
if data is None:
|
|
data = aa
|
|
else:
|
|
data = np.concatenate([data, aa])
|
|
|
|
if isinstance(data, np.DimArray):
|
|
return data
|
|
else:
|
|
if isinstance(aa, numbers.Number):
|
|
return aa
|
|
|
|
dims = aa.dims
|
|
dims[0].setDimValues(times)
|
|
r = np.DimArray(data, dims, aa.fill_value, aa.proj)
|
|
return r |