1098 lines
39 KiB
Python
1098 lines
39 KiB
Python
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"""
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NetCDF reader/writer module.
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This module is used to read and create NetCDF files. NetCDF files are
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accessed through the `netcdf_file` object. Data written to and from NetCDF
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files are contained in `netcdf_variable` objects. Attributes are given
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as member variables of the `netcdf_file` and `netcdf_variable` objects.
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This module implements the Scientific.IO.NetCDF API to read and create
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NetCDF files. The same API is also used in the PyNIO and pynetcdf
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modules, allowing these modules to be used interchangeably when working
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with NetCDF files.
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Only NetCDF3 is supported here; for NetCDF4 see
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`netCDF4-python <http://unidata.github.io/netcdf4-python/>`__,
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which has a similar API.
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"""
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from __future__ import division, print_function, absolute_import
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# TODO:
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# * properly implement ``_FillValue``.
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# * fix character variables.
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# * implement PAGESIZE for Python 2.6?
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# The Scientific.IO.NetCDF API allows attributes to be added directly to
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# instances of ``netcdf_file`` and ``netcdf_variable``. To differentiate
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# between user-set attributes and instance attributes, user-set attributes
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# are automatically stored in the ``_attributes`` attribute by overloading
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#``__setattr__``. This is the reason why the code sometimes uses
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#``obj.__dict__['key'] = value``, instead of simply ``obj.key = value``;
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# otherwise the key would be inserted into userspace attributes.
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__all__ = ['netcdf_file', 'netcdf_variable']
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import sys
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import warnings
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import weakref
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from operator import mul
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from collections import OrderedDict
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import mmap as mm
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import numpy as np
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from numpy.compat import asbytes, asstr
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from numpy import frombuffer, dtype, empty, array, asarray
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from numpy import little_endian as LITTLE_ENDIAN
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from functools import reduce
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from scipy._lib.six import integer_types, text_type, binary_type
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IS_PYPY = ('__pypy__' in sys.modules)
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ABSENT = b'\x00\x00\x00\x00\x00\x00\x00\x00'
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ZERO = b'\x00\x00\x00\x00'
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NC_BYTE = b'\x00\x00\x00\x01'
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NC_CHAR = b'\x00\x00\x00\x02'
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NC_SHORT = b'\x00\x00\x00\x03'
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NC_INT = b'\x00\x00\x00\x04'
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NC_FLOAT = b'\x00\x00\x00\x05'
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NC_DOUBLE = b'\x00\x00\x00\x06'
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NC_DIMENSION = b'\x00\x00\x00\n'
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NC_VARIABLE = b'\x00\x00\x00\x0b'
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NC_ATTRIBUTE = b'\x00\x00\x00\x0c'
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FILL_BYTE = b'\x81'
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FILL_CHAR = b'\x00'
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FILL_SHORT = b'\x80\x01'
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FILL_INT = b'\x80\x00\x00\x01'
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FILL_FLOAT = b'\x7C\xF0\x00\x00'
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FILL_DOUBLE = b'\x47\x9E\x00\x00\x00\x00\x00\x00'
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TYPEMAP = {NC_BYTE: ('b', 1),
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NC_CHAR: ('c', 1),
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NC_SHORT: ('h', 2),
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NC_INT: ('i', 4),
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NC_FLOAT: ('f', 4),
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NC_DOUBLE: ('d', 8)}
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FILLMAP = {NC_BYTE: FILL_BYTE,
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NC_CHAR: FILL_CHAR,
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NC_SHORT: FILL_SHORT,
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NC_INT: FILL_INT,
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NC_FLOAT: FILL_FLOAT,
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NC_DOUBLE: FILL_DOUBLE}
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REVERSE = {('b', 1): NC_BYTE,
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('B', 1): NC_CHAR,
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('c', 1): NC_CHAR,
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('h', 2): NC_SHORT,
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('i', 4): NC_INT,
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('f', 4): NC_FLOAT,
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('d', 8): NC_DOUBLE,
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# these come from asarray(1).dtype.char and asarray('foo').dtype.char,
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# used when getting the types from generic attributes.
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('l', 4): NC_INT,
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('S', 1): NC_CHAR}
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class netcdf_file(object):
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"""
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A file object for NetCDF data.
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A `netcdf_file` object has two standard attributes: `dimensions` and
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`variables`. The values of both are dictionaries, mapping dimension
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names to their associated lengths and variable names to variables,
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respectively. Application programs should never modify these
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dictionaries.
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All other attributes correspond to global attributes defined in the
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NetCDF file. Global file attributes are created by assigning to an
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attribute of the `netcdf_file` object.
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Parameters
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----------
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filename : string or file-like
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string -> filename
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mode : {'r', 'w', 'a'}, optional
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read-write-append mode, default is 'r'
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mmap : None or bool, optional
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Whether to mmap `filename` when reading. Default is True
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when `filename` is a file name, False when `filename` is a
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file-like object. Note that when mmap is in use, data arrays
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returned refer directly to the mmapped data on disk, and the
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file cannot be closed as long as references to it exist.
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version : {1, 2}, optional
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version of netcdf to read / write, where 1 means *Classic
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format* and 2 means *64-bit offset format*. Default is 1. See
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`here <https://www.unidata.ucar.edu/software/netcdf/docs/netcdf_introduction.html#select_format>`__
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for more info.
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maskandscale : bool, optional
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Whether to automatically scale and/or mask data based on attributes.
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Default is False.
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Notes
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-----
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The major advantage of this module over other modules is that it doesn't
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require the code to be linked to the NetCDF libraries. This module is
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derived from `pupynere <https://bitbucket.org/robertodealmeida/pupynere/>`_.
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NetCDF files are a self-describing binary data format. The file contains
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metadata that describes the dimensions and variables in the file. More
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details about NetCDF files can be found `here
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<https://www.unidata.ucar.edu/software/netcdf/docs/user_guide.html>`__. There
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are three main sections to a NetCDF data structure:
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1. Dimensions
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2. Variables
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3. Attributes
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The dimensions section records the name and length of each dimension used
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by the variables. The variables would then indicate which dimensions it
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uses and any attributes such as data units, along with containing the data
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values for the variable. It is good practice to include a
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variable that is the same name as a dimension to provide the values for
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that axes. Lastly, the attributes section would contain additional
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information such as the name of the file creator or the instrument used to
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collect the data.
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When writing data to a NetCDF file, there is often the need to indicate the
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'record dimension'. A record dimension is the unbounded dimension for a
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variable. For example, a temperature variable may have dimensions of
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latitude, longitude and time. If one wants to add more temperature data to
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the NetCDF file as time progresses, then the temperature variable should
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have the time dimension flagged as the record dimension.
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In addition, the NetCDF file header contains the position of the data in
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the file, so access can be done in an efficient manner without loading
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unnecessary data into memory. It uses the ``mmap`` module to create
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Numpy arrays mapped to the data on disk, for the same purpose.
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Note that when `netcdf_file` is used to open a file with mmap=True
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(default for read-only), arrays returned by it refer to data
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directly on the disk. The file should not be closed, and cannot be cleanly
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closed when asked, if such arrays are alive. You may want to copy data arrays
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obtained from mmapped Netcdf file if they are to be processed after the file
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is closed, see the example below.
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Examples
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--------
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To create a NetCDF file:
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>>> from scipy.io import netcdf
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>>> f = netcdf.netcdf_file('simple.nc', 'w')
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>>> f.history = 'Created for a test'
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>>> f.createDimension('time', 10)
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>>> time = f.createVariable('time', 'i', ('time',))
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>>> time[:] = np.arange(10)
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>>> time.units = 'days since 2008-01-01'
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>>> f.close()
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Note the assignment of ``arange(10)`` to ``time[:]``. Exposing the slice
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of the time variable allows for the data to be set in the object, rather
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than letting ``arange(10)`` overwrite the ``time`` variable.
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To read the NetCDF file we just created:
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>>> from scipy.io import netcdf
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>>> f = netcdf.netcdf_file('simple.nc', 'r')
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>>> print(f.history)
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b'Created for a test'
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>>> time = f.variables['time']
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>>> print(time.units)
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b'days since 2008-01-01'
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>>> print(time.shape)
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(10,)
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>>> print(time[-1])
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9
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NetCDF files, when opened read-only, return arrays that refer
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directly to memory-mapped data on disk:
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>>> data = time[:]
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>>> data.base.base
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<mmap.mmap object at 0x7fe753763180>
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If the data is to be processed after the file is closed, it needs
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to be copied to main memory:
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>>> data = time[:].copy()
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>>> f.close()
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>>> data.mean()
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4.5
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A NetCDF file can also be used as context manager:
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>>> from scipy.io import netcdf
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>>> with netcdf.netcdf_file('simple.nc', 'r') as f:
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... print(f.history)
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b'Created for a test'
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"""
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def __init__(self, filename, mode='r', mmap=None, version=1,
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maskandscale=False):
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"""Initialize netcdf_file from fileobj (str or file-like)."""
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if mode not in 'rwa':
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raise ValueError("Mode must be either 'r', 'w' or 'a'.")
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if hasattr(filename, 'seek'): # file-like
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self.fp = filename
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self.filename = 'None'
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if mmap is None:
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mmap = False
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elif mmap and not hasattr(filename, 'fileno'):
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raise ValueError('Cannot use file object for mmap')
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else: # maybe it's a string
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self.filename = filename
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omode = 'r+' if mode == 'a' else mode
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self.fp = open(self.filename, '%sb' % omode)
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if mmap is None:
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# Mmapped files on PyPy cannot be usually closed
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# before the GC runs, so it's better to use mmap=False
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# as the default.
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mmap = (not IS_PYPY)
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if mode != 'r':
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# Cannot read write-only files
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mmap = False
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self.use_mmap = mmap
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self.mode = mode
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self.version_byte = version
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self.maskandscale = maskandscale
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self.dimensions = OrderedDict()
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self.variables = OrderedDict()
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self._dims = []
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self._recs = 0
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self._recsize = 0
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self._mm = None
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self._mm_buf = None
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if self.use_mmap:
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self._mm = mm.mmap(self.fp.fileno(), 0, access=mm.ACCESS_READ)
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self._mm_buf = np.frombuffer(self._mm, dtype=np.int8)
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self._attributes = OrderedDict()
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if mode in 'ra':
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self._read()
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def __setattr__(self, attr, value):
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# Store user defined attributes in a separate dict,
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# so we can save them to file later.
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try:
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self._attributes[attr] = value
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except AttributeError:
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pass
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self.__dict__[attr] = value
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def close(self):
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"""Closes the NetCDF file."""
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if hasattr(self, 'fp') and not self.fp.closed:
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try:
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self.flush()
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finally:
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self.variables = OrderedDict()
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if self._mm_buf is not None:
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ref = weakref.ref(self._mm_buf)
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self._mm_buf = None
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if ref() is None:
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# self._mm_buf is gc'd, and we can close the mmap
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self._mm.close()
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else:
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# we cannot close self._mm, since self._mm_buf is
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# alive and there may still be arrays referring to it
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warnings.warn((
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"Cannot close a netcdf_file opened with mmap=True, when "
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"netcdf_variables or arrays referring to its data still exist. "
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"All data arrays obtained from such files refer directly to "
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"data on disk, and must be copied before the file can be cleanly "
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"closed. (See netcdf_file docstring for more information on mmap.)"
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), category=RuntimeWarning)
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self._mm = None
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self.fp.close()
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__del__ = close
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def __enter__(self):
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return self
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def __exit__(self, type, value, traceback):
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self.close()
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def createDimension(self, name, length):
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"""
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Adds a dimension to the Dimension section of the NetCDF data structure.
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Note that this function merely adds a new dimension that the variables can
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reference. The values for the dimension, if desired, should be added as
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a variable using `createVariable`, referring to this dimension.
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Parameters
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||
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----------
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name : str
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Name of the dimension (Eg, 'lat' or 'time').
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length : int
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Length of the dimension.
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See Also
|
||
|
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--------
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||
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createVariable
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"""
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||
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if length is None and self._dims:
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raise ValueError("Only first dimension may be unlimited!")
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||
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self.dimensions[name] = length
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self._dims.append(name)
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def createVariable(self, name, type, dimensions):
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||
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"""
|
||
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Create an empty variable for the `netcdf_file` object, specifying its data
|
||
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type and the dimensions it uses.
|
||
|
|
|
||
|
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Parameters
|
||
|
|
----------
|
||
|
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name : str
|
||
|
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Name of the new variable.
|
||
|
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type : dtype or str
|
||
|
|
Data type of the variable.
|
||
|
|
dimensions : sequence of str
|
||
|
|
List of the dimension names used by the variable, in the desired order.
|
||
|
|
|
||
|
|
Returns
|
||
|
|
-------
|
||
|
|
variable : netcdf_variable
|
||
|
|
The newly created ``netcdf_variable`` object.
|
||
|
|
This object has also been added to the `netcdf_file` object as well.
|
||
|
|
|
||
|
|
See Also
|
||
|
|
--------
|
||
|
|
createDimension
|
||
|
|
|
||
|
|
Notes
|
||
|
|
-----
|
||
|
|
Any dimensions to be used by the variable should already exist in the
|
||
|
|
NetCDF data structure or should be created by `createDimension` prior to
|
||
|
|
creating the NetCDF variable.
|
||
|
|
|
||
|
|
"""
|
||
|
|
shape = tuple([self.dimensions[dim] for dim in dimensions])
|
||
|
|
shape_ = tuple([dim or 0 for dim in shape]) # replace None with 0 for numpy
|
||
|
|
|
||
|
|
type = dtype(type)
|
||
|
|
typecode, size = type.char, type.itemsize
|
||
|
|
if (typecode, size) not in REVERSE:
|
||
|
|
raise ValueError("NetCDF 3 does not support type %s" % type)
|
||
|
|
|
||
|
|
data = empty(shape_, dtype=type.newbyteorder("B")) # convert to big endian always for NetCDF 3
|
||
|
|
self.variables[name] = netcdf_variable(
|
||
|
|
data, typecode, size, shape, dimensions,
|
||
|
|
maskandscale=self.maskandscale)
|
||
|
|
return self.variables[name]
|
||
|
|
|
||
|
|
def flush(self):
|
||
|
|
"""
|
||
|
|
Perform a sync-to-disk flush if the `netcdf_file` object is in write mode.
|
||
|
|
|
||
|
|
See Also
|
||
|
|
--------
|
||
|
|
sync : Identical function
|
||
|
|
|
||
|
|
"""
|
||
|
|
if hasattr(self, 'mode') and self.mode in 'wa':
|
||
|
|
self._write()
|
||
|
|
sync = flush
|
||
|
|
|
||
|
|
def _write(self):
|
||
|
|
self.fp.seek(0)
|
||
|
|
self.fp.write(b'CDF')
|
||
|
|
self.fp.write(array(self.version_byte, '>b').tostring())
|
||
|
|
|
||
|
|
# Write headers and data.
|
||
|
|
self._write_numrecs()
|
||
|
|
self._write_dim_array()
|
||
|
|
self._write_gatt_array()
|
||
|
|
self._write_var_array()
|
||
|
|
|
||
|
|
def _write_numrecs(self):
|
||
|
|
# Get highest record count from all record variables.
|
||
|
|
for var in self.variables.values():
|
||
|
|
if var.isrec and len(var.data) > self._recs:
|
||
|
|
self.__dict__['_recs'] = len(var.data)
|
||
|
|
self._pack_int(self._recs)
|
||
|
|
|
||
|
|
def _write_dim_array(self):
|
||
|
|
if self.dimensions:
|
||
|
|
self.fp.write(NC_DIMENSION)
|
||
|
|
self._pack_int(len(self.dimensions))
|
||
|
|
for name in self._dims:
|
||
|
|
self._pack_string(name)
|
||
|
|
length = self.dimensions[name]
|
||
|
|
self._pack_int(length or 0) # replace None with 0 for record dimension
|
||
|
|
else:
|
||
|
|
self.fp.write(ABSENT)
|
||
|
|
|
||
|
|
def _write_gatt_array(self):
|
||
|
|
self._write_att_array(self._attributes)
|
||
|
|
|
||
|
|
def _write_att_array(self, attributes):
|
||
|
|
if attributes:
|
||
|
|
self.fp.write(NC_ATTRIBUTE)
|
||
|
|
self._pack_int(len(attributes))
|
||
|
|
for name, values in attributes.items():
|
||
|
|
self._pack_string(name)
|
||
|
|
self._write_att_values(values)
|
||
|
|
else:
|
||
|
|
self.fp.write(ABSENT)
|
||
|
|
|
||
|
|
def _write_var_array(self):
|
||
|
|
if self.variables:
|
||
|
|
self.fp.write(NC_VARIABLE)
|
||
|
|
self._pack_int(len(self.variables))
|
||
|
|
|
||
|
|
# Sort variable names non-recs first, then recs.
|
||
|
|
def sortkey(n):
|
||
|
|
v = self.variables[n]
|
||
|
|
if v.isrec:
|
||
|
|
return (-1,)
|
||
|
|
return v._shape
|
||
|
|
variables = sorted(self.variables, key=sortkey, reverse=True)
|
||
|
|
|
||
|
|
# Set the metadata for all variables.
|
||
|
|
for name in variables:
|
||
|
|
self._write_var_metadata(name)
|
||
|
|
# Now that we have the metadata, we know the vsize of
|
||
|
|
# each record variable, so we can calculate recsize.
|
||
|
|
self.__dict__['_recsize'] = sum([
|
||
|
|
var._vsize for var in self.variables.values()
|
||
|
|
if var.isrec])
|
||
|
|
# Set the data for all variables.
|
||
|
|
for name in variables:
|
||
|
|
self._write_var_data(name)
|
||
|
|
else:
|
||
|
|
self.fp.write(ABSENT)
|
||
|
|
|
||
|
|
def _write_var_metadata(self, name):
|
||
|
|
var = self.variables[name]
|
||
|
|
|
||
|
|
self._pack_string(name)
|
||
|
|
self._pack_int(len(var.dimensions))
|
||
|
|
for dimname in var.dimensions:
|
||
|
|
dimid = self._dims.index(dimname)
|
||
|
|
self._pack_int(dimid)
|
||
|
|
|
||
|
|
self._write_att_array(var._attributes)
|
||
|
|
|
||
|
|
nc_type = REVERSE[var.typecode(), var.itemsize()]
|
||
|
|
self.fp.write(asbytes(nc_type))
|
||
|
|
|
||
|
|
if not var.isrec:
|
||
|
|
vsize = var.data.size * var.data.itemsize
|
||
|
|
vsize += -vsize % 4
|
||
|
|
else: # record variable
|
||
|
|
try:
|
||
|
|
vsize = var.data[0].size * var.data.itemsize
|
||
|
|
except IndexError:
|
||
|
|
vsize = 0
|
||
|
|
rec_vars = len([v for v in self.variables.values()
|
||
|
|
if v.isrec])
|
||
|
|
if rec_vars > 1:
|
||
|
|
vsize += -vsize % 4
|
||
|
|
self.variables[name].__dict__['_vsize'] = vsize
|
||
|
|
self._pack_int(vsize)
|
||
|
|
|
||
|
|
# Pack a bogus begin, and set the real value later.
|
||
|
|
self.variables[name].__dict__['_begin'] = self.fp.tell()
|
||
|
|
self._pack_begin(0)
|
||
|
|
|
||
|
|
def _write_var_data(self, name):
|
||
|
|
var = self.variables[name]
|
||
|
|
|
||
|
|
# Set begin in file header.
|
||
|
|
the_beguine = self.fp.tell()
|
||
|
|
self.fp.seek(var._begin)
|
||
|
|
self._pack_begin(the_beguine)
|
||
|
|
self.fp.seek(the_beguine)
|
||
|
|
|
||
|
|
# Write data.
|
||
|
|
if not var.isrec:
|
||
|
|
self.fp.write(var.data.tostring())
|
||
|
|
count = var.data.size * var.data.itemsize
|
||
|
|
self._write_var_padding(var, var._vsize - count)
|
||
|
|
else: # record variable
|
||
|
|
# Handle rec vars with shape[0] < nrecs.
|
||
|
|
if self._recs > len(var.data):
|
||
|
|
shape = (self._recs,) + var.data.shape[1:]
|
||
|
|
# Resize in-place does not always work since
|
||
|
|
# the array might not be single-segment
|
||
|
|
try:
|
||
|
|
var.data.resize(shape)
|
||
|
|
except ValueError:
|
||
|
|
var.__dict__['data'] = np.resize(var.data, shape).astype(var.data.dtype)
|
||
|
|
|
||
|
|
pos0 = pos = self.fp.tell()
|
||
|
|
for rec in var.data:
|
||
|
|
# Apparently scalars cannot be converted to big endian. If we
|
||
|
|
# try to convert a ``=i4`` scalar to, say, '>i4' the dtype
|
||
|
|
# will remain as ``=i4``.
|
||
|
|
if not rec.shape and (rec.dtype.byteorder == '<' or
|
||
|
|
(rec.dtype.byteorder == '=' and LITTLE_ENDIAN)):
|
||
|
|
rec = rec.byteswap()
|
||
|
|
self.fp.write(rec.tostring())
|
||
|
|
# Padding
|
||
|
|
count = rec.size * rec.itemsize
|
||
|
|
self._write_var_padding(var, var._vsize - count)
|
||
|
|
pos += self._recsize
|
||
|
|
self.fp.seek(pos)
|
||
|
|
self.fp.seek(pos0 + var._vsize)
|
||
|
|
|
||
|
|
def _write_var_padding(self, var, size):
|
||
|
|
encoded_fill_value = var._get_encoded_fill_value()
|
||
|
|
num_fills = size // len(encoded_fill_value)
|
||
|
|
self.fp.write(encoded_fill_value * num_fills)
|
||
|
|
|
||
|
|
def _write_att_values(self, values):
|
||
|
|
if hasattr(values, 'dtype'):
|
||
|
|
nc_type = REVERSE[values.dtype.char, values.dtype.itemsize]
|
||
|
|
else:
|
||
|
|
types = [(t, NC_INT) for t in integer_types]
|
||
|
|
types += [
|
||
|
|
(float, NC_FLOAT),
|
||
|
|
(str, NC_CHAR)
|
||
|
|
]
|
||
|
|
# bytes index into scalars in py3k. Check for "string" types
|
||
|
|
if isinstance(values, text_type) or isinstance(values, binary_type):
|
||
|
|
sample = values
|
||
|
|
else:
|
||
|
|
try:
|
||
|
|
sample = values[0] # subscriptable?
|
||
|
|
except TypeError:
|
||
|
|
sample = values # scalar
|
||
|
|
|
||
|
|
for class_, nc_type in types:
|
||
|
|
if isinstance(sample, class_):
|
||
|
|
break
|
||
|
|
|
||
|
|
typecode, size = TYPEMAP[nc_type]
|
||
|
|
dtype_ = '>%s' % typecode
|
||
|
|
# asarray() dies with bytes and '>c' in py3k. Change to 'S'
|
||
|
|
dtype_ = 'S' if dtype_ == '>c' else dtype_
|
||
|
|
|
||
|
|
values = asarray(values, dtype=dtype_)
|
||
|
|
|
||
|
|
self.fp.write(asbytes(nc_type))
|
||
|
|
|
||
|
|
if values.dtype.char == 'S':
|
||
|
|
nelems = values.itemsize
|
||
|
|
else:
|
||
|
|
nelems = values.size
|
||
|
|
self._pack_int(nelems)
|
||
|
|
|
||
|
|
if not values.shape and (values.dtype.byteorder == '<' or
|
||
|
|
(values.dtype.byteorder == '=' and LITTLE_ENDIAN)):
|
||
|
|
values = values.byteswap()
|
||
|
|
self.fp.write(values.tostring())
|
||
|
|
count = values.size * values.itemsize
|
||
|
|
self.fp.write(b'\x00' * (-count % 4)) # pad
|
||
|
|
|
||
|
|
def _read(self):
|
||
|
|
# Check magic bytes and version
|
||
|
|
magic = self.fp.read(3)
|
||
|
|
if not magic == b'CDF':
|
||
|
|
raise TypeError("Error: %s is not a valid NetCDF 3 file" %
|
||
|
|
self.filename)
|
||
|
|
self.__dict__['version_byte'] = frombuffer(self.fp.read(1), '>b')[0]
|
||
|
|
|
||
|
|
# Read file headers and set data.
|
||
|
|
self._read_numrecs()
|
||
|
|
self._read_dim_array()
|
||
|
|
self._read_gatt_array()
|
||
|
|
self._read_var_array()
|
||
|
|
|
||
|
|
def _read_numrecs(self):
|
||
|
|
self.__dict__['_recs'] = self._unpack_int()
|
||
|
|
|
||
|
|
def _read_dim_array(self):
|
||
|
|
header = self.fp.read(4)
|
||
|
|
if header not in [ZERO, NC_DIMENSION]:
|
||
|
|
raise ValueError("Unexpected header.")
|
||
|
|
count = self._unpack_int()
|
||
|
|
|
||
|
|
for dim in range(count):
|
||
|
|
name = asstr(self._unpack_string())
|
||
|
|
length = self._unpack_int() or None # None for record dimension
|
||
|
|
self.dimensions[name] = length
|
||
|
|
self._dims.append(name) # preserve order
|
||
|
|
|
||
|
|
def _read_gatt_array(self):
|
||
|
|
for k, v in self._read_att_array().items():
|
||
|
|
self.__setattr__(k, v)
|
||
|
|
|
||
|
|
def _read_att_array(self):
|
||
|
|
header = self.fp.read(4)
|
||
|
|
if header not in [ZERO, NC_ATTRIBUTE]:
|
||
|
|
raise ValueError("Unexpected header.")
|
||
|
|
count = self._unpack_int()
|
||
|
|
|
||
|
|
attributes = OrderedDict()
|
||
|
|
for attr in range(count):
|
||
|
|
name = asstr(self._unpack_string())
|
||
|
|
attributes[name] = self._read_att_values()
|
||
|
|
return attributes
|
||
|
|
|
||
|
|
def _read_var_array(self):
|
||
|
|
header = self.fp.read(4)
|
||
|
|
if header not in [ZERO, NC_VARIABLE]:
|
||
|
|
raise ValueError("Unexpected header.")
|
||
|
|
|
||
|
|
begin = 0
|
||
|
|
dtypes = {'names': [], 'formats': []}
|
||
|
|
rec_vars = []
|
||
|
|
count = self._unpack_int()
|
||
|
|
for var in range(count):
|
||
|
|
(name, dimensions, shape, attributes,
|
||
|
|
typecode, size, dtype_, begin_, vsize) = self._read_var()
|
||
|
|
# https://www.unidata.ucar.edu/software/netcdf/docs/user_guide.html
|
||
|
|
# Note that vsize is the product of the dimension lengths
|
||
|
|
# (omitting the record dimension) and the number of bytes
|
||
|
|
# per value (determined from the type), increased to the
|
||
|
|
# next multiple of 4, for each variable. If a record
|
||
|
|
# variable, this is the amount of space per record. The
|
||
|
|
# netCDF "record size" is calculated as the sum of the
|
||
|
|
# vsize's of all the record variables.
|
||
|
|
#
|
||
|
|
# The vsize field is actually redundant, because its value
|
||
|
|
# may be computed from other information in the header. The
|
||
|
|
# 32-bit vsize field is not large enough to contain the size
|
||
|
|
# of variables that require more than 2^32 - 4 bytes, so
|
||
|
|
# 2^32 - 1 is used in the vsize field for such variables.
|
||
|
|
if shape and shape[0] is None: # record variable
|
||
|
|
rec_vars.append(name)
|
||
|
|
# The netCDF "record size" is calculated as the sum of
|
||
|
|
# the vsize's of all the record variables.
|
||
|
|
self.__dict__['_recsize'] += vsize
|
||
|
|
if begin == 0:
|
||
|
|
begin = begin_
|
||
|
|
dtypes['names'].append(name)
|
||
|
|
dtypes['formats'].append(str(shape[1:]) + dtype_)
|
||
|
|
|
||
|
|
# Handle padding with a virtual variable.
|
||
|
|
if typecode in 'bch':
|
||
|
|
actual_size = reduce(mul, (1,) + shape[1:]) * size
|
||
|
|
padding = -actual_size % 4
|
||
|
|
if padding:
|
||
|
|
dtypes['names'].append('_padding_%d' % var)
|
||
|
|
dtypes['formats'].append('(%d,)>b' % padding)
|
||
|
|
|
||
|
|
# Data will be set later.
|
||
|
|
data = None
|
||
|
|
else: # not a record variable
|
||
|
|
# Calculate size to avoid problems with vsize (above)
|
||
|
|
a_size = reduce(mul, shape, 1) * size
|
||
|
|
if self.use_mmap:
|
||
|
|
data = self._mm_buf[begin_:begin_+a_size].view(dtype=dtype_)
|
||
|
|
data.shape = shape
|
||
|
|
else:
|
||
|
|
pos = self.fp.tell()
|
||
|
|
self.fp.seek(begin_)
|
||
|
|
data = frombuffer(self.fp.read(a_size), dtype=dtype_
|
||
|
|
).copy()
|
||
|
|
data.shape = shape
|
||
|
|
self.fp.seek(pos)
|
||
|
|
|
||
|
|
# Add variable.
|
||
|
|
self.variables[name] = netcdf_variable(
|
||
|
|
data, typecode, size, shape, dimensions, attributes,
|
||
|
|
maskandscale=self.maskandscale)
|
||
|
|
|
||
|
|
if rec_vars:
|
||
|
|
# Remove padding when only one record variable.
|
||
|
|
if len(rec_vars) == 1:
|
||
|
|
dtypes['names'] = dtypes['names'][:1]
|
||
|
|
dtypes['formats'] = dtypes['formats'][:1]
|
||
|
|
|
||
|
|
# Build rec array.
|
||
|
|
if self.use_mmap:
|
||
|
|
rec_array = self._mm_buf[begin:begin+self._recs*self._recsize].view(dtype=dtypes)
|
||
|
|
rec_array.shape = (self._recs,)
|
||
|
|
else:
|
||
|
|
pos = self.fp.tell()
|
||
|
|
self.fp.seek(begin)
|
||
|
|
rec_array = frombuffer(self.fp.read(self._recs*self._recsize),
|
||
|
|
dtype=dtypes).copy()
|
||
|
|
rec_array.shape = (self._recs,)
|
||
|
|
self.fp.seek(pos)
|
||
|
|
|
||
|
|
for var in rec_vars:
|
||
|
|
self.variables[var].__dict__['data'] = rec_array[var]
|
||
|
|
|
||
|
|
def _read_var(self):
|
||
|
|
name = asstr(self._unpack_string())
|
||
|
|
dimensions = []
|
||
|
|
shape = []
|
||
|
|
dims = self._unpack_int()
|
||
|
|
|
||
|
|
for i in range(dims):
|
||
|
|
dimid = self._unpack_int()
|
||
|
|
dimname = self._dims[dimid]
|
||
|
|
dimensions.append(dimname)
|
||
|
|
dim = self.dimensions[dimname]
|
||
|
|
shape.append(dim)
|
||
|
|
dimensions = tuple(dimensions)
|
||
|
|
shape = tuple(shape)
|
||
|
|
|
||
|
|
attributes = self._read_att_array()
|
||
|
|
nc_type = self.fp.read(4)
|
||
|
|
vsize = self._unpack_int()
|
||
|
|
begin = [self._unpack_int, self._unpack_int64][self.version_byte-1]()
|
||
|
|
|
||
|
|
typecode, size = TYPEMAP[nc_type]
|
||
|
|
dtype_ = '>%s' % typecode
|
||
|
|
|
||
|
|
return name, dimensions, shape, attributes, typecode, size, dtype_, begin, vsize
|
||
|
|
|
||
|
|
def _read_att_values(self):
|
||
|
|
nc_type = self.fp.read(4)
|
||
|
|
n = self._unpack_int()
|
||
|
|
|
||
|
|
typecode, size = TYPEMAP[nc_type]
|
||
|
|
|
||
|
|
count = n*size
|
||
|
|
values = self.fp.read(int(count))
|
||
|
|
self.fp.read(-count % 4) # read padding
|
||
|
|
|
||
|
|
if typecode != 'c':
|
||
|
|
values = frombuffer(values, dtype='>%s' % typecode).copy()
|
||
|
|
if values.shape == (1,):
|
||
|
|
values = values[0]
|
||
|
|
else:
|
||
|
|
values = values.rstrip(b'\x00')
|
||
|
|
return values
|
||
|
|
|
||
|
|
def _pack_begin(self, begin):
|
||
|
|
if self.version_byte == 1:
|
||
|
|
self._pack_int(begin)
|
||
|
|
elif self.version_byte == 2:
|
||
|
|
self._pack_int64(begin)
|
||
|
|
|
||
|
|
def _pack_int(self, value):
|
||
|
|
self.fp.write(array(value, '>i').tostring())
|
||
|
|
_pack_int32 = _pack_int
|
||
|
|
|
||
|
|
def _unpack_int(self):
|
||
|
|
return int(frombuffer(self.fp.read(4), '>i')[0])
|
||
|
|
_unpack_int32 = _unpack_int
|
||
|
|
|
||
|
|
def _pack_int64(self, value):
|
||
|
|
self.fp.write(array(value, '>q').tostring())
|
||
|
|
|
||
|
|
def _unpack_int64(self):
|
||
|
|
return frombuffer(self.fp.read(8), '>q')[0]
|
||
|
|
|
||
|
|
def _pack_string(self, s):
|
||
|
|
count = len(s)
|
||
|
|
self._pack_int(count)
|
||
|
|
self.fp.write(asbytes(s))
|
||
|
|
self.fp.write(b'\x00' * (-count % 4)) # pad
|
||
|
|
|
||
|
|
def _unpack_string(self):
|
||
|
|
count = self._unpack_int()
|
||
|
|
s = self.fp.read(count).rstrip(b'\x00')
|
||
|
|
self.fp.read(-count % 4) # read padding
|
||
|
|
return s
|
||
|
|
|
||
|
|
|
||
|
|
class netcdf_variable(object):
|
||
|
|
"""
|
||
|
|
A data object for netcdf files.
|
||
|
|
|
||
|
|
`netcdf_variable` objects are constructed by calling the method
|
||
|
|
`netcdf_file.createVariable` on the `netcdf_file` object. `netcdf_variable`
|
||
|
|
objects behave much like array objects defined in numpy, except that their
|
||
|
|
data resides in a file. Data is read by indexing and written by assigning
|
||
|
|
to an indexed subset; the entire array can be accessed by the index ``[:]``
|
||
|
|
or (for scalars) by using the methods `getValue` and `assignValue`.
|
||
|
|
`netcdf_variable` objects also have attribute `shape` with the same meaning
|
||
|
|
as for arrays, but the shape cannot be modified. There is another read-only
|
||
|
|
attribute `dimensions`, whose value is the tuple of dimension names.
|
||
|
|
|
||
|
|
All other attributes correspond to variable attributes defined in
|
||
|
|
the NetCDF file. Variable attributes are created by assigning to an
|
||
|
|
attribute of the `netcdf_variable` object.
|
||
|
|
|
||
|
|
Parameters
|
||
|
|
----------
|
||
|
|
data : array_like
|
||
|
|
The data array that holds the values for the variable.
|
||
|
|
Typically, this is initialized as empty, but with the proper shape.
|
||
|
|
typecode : dtype character code
|
||
|
|
Desired data-type for the data array.
|
||
|
|
size : int
|
||
|
|
Desired element size for the data array.
|
||
|
|
shape : sequence of ints
|
||
|
|
The shape of the array. This should match the lengths of the
|
||
|
|
variable's dimensions.
|
||
|
|
dimensions : sequence of strings
|
||
|
|
The names of the dimensions used by the variable. Must be in the
|
||
|
|
same order of the dimension lengths given by `shape`.
|
||
|
|
attributes : dict, optional
|
||
|
|
Attribute values (any type) keyed by string names. These attributes
|
||
|
|
become attributes for the netcdf_variable object.
|
||
|
|
maskandscale : bool, optional
|
||
|
|
Whether to automatically scale and/or mask data based on attributes.
|
||
|
|
Default is False.
|
||
|
|
|
||
|
|
|
||
|
|
Attributes
|
||
|
|
----------
|
||
|
|
dimensions : list of str
|
||
|
|
List of names of dimensions used by the variable object.
|
||
|
|
isrec, shape
|
||
|
|
Properties
|
||
|
|
|
||
|
|
See also
|
||
|
|
--------
|
||
|
|
isrec, shape
|
||
|
|
|
||
|
|
"""
|
||
|
|
def __init__(self, data, typecode, size, shape, dimensions,
|
||
|
|
attributes=None,
|
||
|
|
maskandscale=False):
|
||
|
|
self.data = data
|
||
|
|
self._typecode = typecode
|
||
|
|
self._size = size
|
||
|
|
self._shape = shape
|
||
|
|
self.dimensions = dimensions
|
||
|
|
self.maskandscale = maskandscale
|
||
|
|
|
||
|
|
self._attributes = attributes or OrderedDict()
|
||
|
|
for k, v in self._attributes.items():
|
||
|
|
self.__dict__[k] = v
|
||
|
|
|
||
|
|
def __setattr__(self, attr, value):
|
||
|
|
# Store user defined attributes in a separate dict,
|
||
|
|
# so we can save them to file later.
|
||
|
|
try:
|
||
|
|
self._attributes[attr] = value
|
||
|
|
except AttributeError:
|
||
|
|
pass
|
||
|
|
self.__dict__[attr] = value
|
||
|
|
|
||
|
|
def isrec(self):
|
||
|
|
"""Returns whether the variable has a record dimension or not.
|
||
|
|
|
||
|
|
A record dimension is a dimension along which additional data could be
|
||
|
|
easily appended in the netcdf data structure without much rewriting of
|
||
|
|
the data file. This attribute is a read-only property of the
|
||
|
|
`netcdf_variable`.
|
||
|
|
|
||
|
|
"""
|
||
|
|
return bool(self.data.shape) and not self._shape[0]
|
||
|
|
isrec = property(isrec)
|
||
|
|
|
||
|
|
def shape(self):
|
||
|
|
"""Returns the shape tuple of the data variable.
|
||
|
|
|
||
|
|
This is a read-only attribute and can not be modified in the
|
||
|
|
same manner of other numpy arrays.
|
||
|
|
"""
|
||
|
|
return self.data.shape
|
||
|
|
shape = property(shape)
|
||
|
|
|
||
|
|
def getValue(self):
|
||
|
|
"""
|
||
|
|
Retrieve a scalar value from a `netcdf_variable` of length one.
|
||
|
|
|
||
|
|
Raises
|
||
|
|
------
|
||
|
|
ValueError
|
||
|
|
If the netcdf variable is an array of length greater than one,
|
||
|
|
this exception will be raised.
|
||
|
|
|
||
|
|
"""
|
||
|
|
return self.data.item()
|
||
|
|
|
||
|
|
def assignValue(self, value):
|
||
|
|
"""
|
||
|
|
Assign a scalar value to a `netcdf_variable` of length one.
|
||
|
|
|
||
|
|
Parameters
|
||
|
|
----------
|
||
|
|
value : scalar
|
||
|
|
Scalar value (of compatible type) to assign to a length-one netcdf
|
||
|
|
variable. This value will be written to file.
|
||
|
|
|
||
|
|
Raises
|
||
|
|
------
|
||
|
|
ValueError
|
||
|
|
If the input is not a scalar, or if the destination is not a length-one
|
||
|
|
netcdf variable.
|
||
|
|
|
||
|
|
"""
|
||
|
|
if not self.data.flags.writeable:
|
||
|
|
# Work-around for a bug in NumPy. Calling itemset() on a read-only
|
||
|
|
# memory-mapped array causes a seg. fault.
|
||
|
|
# See NumPy ticket #1622, and SciPy ticket #1202.
|
||
|
|
# This check for `writeable` can be removed when the oldest version
|
||
|
|
# of numpy still supported by scipy contains the fix for #1622.
|
||
|
|
raise RuntimeError("variable is not writeable")
|
||
|
|
|
||
|
|
self.data.itemset(value)
|
||
|
|
|
||
|
|
def typecode(self):
|
||
|
|
"""
|
||
|
|
Return the typecode of the variable.
|
||
|
|
|
||
|
|
Returns
|
||
|
|
-------
|
||
|
|
typecode : char
|
||
|
|
The character typecode of the variable (eg, 'i' for int).
|
||
|
|
|
||
|
|
"""
|
||
|
|
return self._typecode
|
||
|
|
|
||
|
|
def itemsize(self):
|
||
|
|
"""
|
||
|
|
Return the itemsize of the variable.
|
||
|
|
|
||
|
|
Returns
|
||
|
|
-------
|
||
|
|
itemsize : int
|
||
|
|
The element size of the variable (eg, 8 for float64).
|
||
|
|
|
||
|
|
"""
|
||
|
|
return self._size
|
||
|
|
|
||
|
|
def __getitem__(self, index):
|
||
|
|
if not self.maskandscale:
|
||
|
|
return self.data[index]
|
||
|
|
|
||
|
|
data = self.data[index].copy()
|
||
|
|
missing_value = self._get_missing_value()
|
||
|
|
data = self._apply_missing_value(data, missing_value)
|
||
|
|
scale_factor = self._attributes.get('scale_factor')
|
||
|
|
add_offset = self._attributes.get('add_offset')
|
||
|
|
if add_offset is not None or scale_factor is not None:
|
||
|
|
data = data.astype(np.float64)
|
||
|
|
if scale_factor is not None:
|
||
|
|
data = data * scale_factor
|
||
|
|
if add_offset is not None:
|
||
|
|
data += add_offset
|
||
|
|
|
||
|
|
return data
|
||
|
|
|
||
|
|
def __setitem__(self, index, data):
|
||
|
|
if self.maskandscale:
|
||
|
|
missing_value = (
|
||
|
|
self._get_missing_value() or
|
||
|
|
getattr(data, 'fill_value', 999999))
|
||
|
|
self._attributes.setdefault('missing_value', missing_value)
|
||
|
|
self._attributes.setdefault('_FillValue', missing_value)
|
||
|
|
data = ((data - self._attributes.get('add_offset', 0.0)) /
|
||
|
|
self._attributes.get('scale_factor', 1.0))
|
||
|
|
data = np.ma.asarray(data).filled(missing_value)
|
||
|
|
if self._typecode not in 'fd' and data.dtype.kind == 'f':
|
||
|
|
data = np.round(data)
|
||
|
|
|
||
|
|
# Expand data for record vars?
|
||
|
|
if self.isrec:
|
||
|
|
if isinstance(index, tuple):
|
||
|
|
rec_index = index[0]
|
||
|
|
else:
|
||
|
|
rec_index = index
|
||
|
|
if isinstance(rec_index, slice):
|
||
|
|
recs = (rec_index.start or 0) + len(data)
|
||
|
|
else:
|
||
|
|
recs = rec_index + 1
|
||
|
|
if recs > len(self.data):
|
||
|
|
shape = (recs,) + self._shape[1:]
|
||
|
|
# Resize in-place does not always work since
|
||
|
|
# the array might not be single-segment
|
||
|
|
try:
|
||
|
|
self.data.resize(shape)
|
||
|
|
except ValueError:
|
||
|
|
self.__dict__['data'] = np.resize(self.data, shape).astype(self.data.dtype)
|
||
|
|
self.data[index] = data
|
||
|
|
|
||
|
|
def _default_encoded_fill_value(self):
|
||
|
|
"""
|
||
|
|
The default encoded fill-value for this Variable's data type.
|
||
|
|
"""
|
||
|
|
nc_type = REVERSE[self.typecode(), self.itemsize()]
|
||
|
|
return FILLMAP[nc_type]
|
||
|
|
|
||
|
|
def _get_encoded_fill_value(self):
|
||
|
|
"""
|
||
|
|
Returns the encoded fill value for this variable as bytes.
|
||
|
|
|
||
|
|
This is taken from either the _FillValue attribute, or the default fill
|
||
|
|
value for this variable's data type.
|
||
|
|
"""
|
||
|
|
if '_FillValue' in self._attributes:
|
||
|
|
fill_value = np.array(self._attributes['_FillValue'],
|
||
|
|
dtype=self.data.dtype).tostring()
|
||
|
|
if len(fill_value) == self.itemsize():
|
||
|
|
return fill_value
|
||
|
|
else:
|
||
|
|
return self._default_encoded_fill_value()
|
||
|
|
else:
|
||
|
|
return self._default_encoded_fill_value()
|
||
|
|
|
||
|
|
def _get_missing_value(self):
|
||
|
|
"""
|
||
|
|
Returns the value denoting "no data" for this variable.
|
||
|
|
|
||
|
|
If this variable does not have a missing/fill value, returns None.
|
||
|
|
|
||
|
|
If both _FillValue and missing_value are given, give precedence to
|
||
|
|
_FillValue. The netCDF standard gives special meaning to _FillValue;
|
||
|
|
missing_value is just used for compatibility with old datasets.
|
||
|
|
"""
|
||
|
|
|
||
|
|
if '_FillValue' in self._attributes:
|
||
|
|
missing_value = self._attributes['_FillValue']
|
||
|
|
elif 'missing_value' in self._attributes:
|
||
|
|
missing_value = self._attributes['missing_value']
|
||
|
|
else:
|
||
|
|
missing_value = None
|
||
|
|
|
||
|
|
return missing_value
|
||
|
|
|
||
|
|
@staticmethod
|
||
|
|
def _apply_missing_value(data, missing_value):
|
||
|
|
"""
|
||
|
|
Applies the given missing value to the data array.
|
||
|
|
|
||
|
|
Returns a numpy.ma array, with any value equal to missing_value masked
|
||
|
|
out (unless missing_value is None, in which case the original array is
|
||
|
|
returned).
|
||
|
|
"""
|
||
|
|
|
||
|
|
if missing_value is None:
|
||
|
|
newdata = data
|
||
|
|
else:
|
||
|
|
try:
|
||
|
|
missing_value_isnan = np.isnan(missing_value)
|
||
|
|
except (TypeError, NotImplementedError):
|
||
|
|
# some data types (e.g., characters) cannot be tested for NaN
|
||
|
|
missing_value_isnan = False
|
||
|
|
|
||
|
|
if missing_value_isnan:
|
||
|
|
mymask = np.isnan(data)
|
||
|
|
else:
|
||
|
|
mymask = (data == missing_value)
|
||
|
|
|
||
|
|
newdata = np.ma.masked_where(mymask, data)
|
||
|
|
|
||
|
|
return newdata
|
||
|
|
|
||
|
|
|
||
|
|
NetCDFFile = netcdf_file
|
||
|
|
NetCDFVariable = netcdf_variable
|