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43b0a1251b Oliv* #!/usr/bin/env python3
ae10cb9ac4 Oliv* # -*- coding: utf-8 -*-
7621b5d564 Oliv* """Usage: gluemncbig [-2] [-q] [--verbose] [--help] [--many] [-v <vars>] -o <outfile> <files>
ae10cb9ac4 Oliv* 
                  -v <vars>  comma-separated list of variable names or glob patterns
3c7f3cce62 Oliv*  -2         write a NetCDF version 2 (64-Bit Offset) file allowing for large records
692071215d Oliv*  --many     many tiles: assemble only along x in memory; less efficient
                             on some filesystems, but opens fewer files simultaneously and
                             uses less memory
ae10cb9ac4 Oliv*  -q         suppress progress messages
                  --verbose  report variables
7621b5d564 Oliv*  --help     show this help text
ae10cb9ac4 Oliv* 
                 All files must have the same variables.
                 Each variable (or 1 record of it) must fit in memory.
692071215d Oliv* With --many, only a row of tiles along x must fit in memory.
ae10cb9ac4 Oliv* 
                 Examples:
                 
                 gluemncbig -o ptr.nc mnc_*/ptr_tave.*.nc
                 gluemncbig -o BIO.nc -v 'BIO_*' mnc_*/ptr_tave.*.nc
                 """
8b8576185f Mart* from __future__ import print_function
ae10cb9ac4 Oliv* 
                 # NetCDF reader/writer module modified from pupynere,
                 # https://bitbucket.org/robertodealmeida/pupynere/
                 # to allow delayed reading/writing of variable data.
                 # MIT license
                 
                 moduledoc = u"""
                 NetCDF reader/writer module.
                 
                 This module is used to read and create NetCDF files. NetCDF files are
                 accessed through the `netcdf_file` object. Data written to and from NetCDF
                 files are contained in `netcdf_variable` objects. Attributes are given
                 as member variables of the `netcdf_file` and `netcdf_variable` objects.
                 
                 Notes
                 -----
                 NetCDF files are a self-describing binary data format. The file contains
                 metadata that describes the dimensions and variables in the file. More
                 details about NetCDF files can be found `here
                 <http://www.unidata.ucar.edu/software/netcdf/docs/netcdf.html>`_. There
                 are three main sections to a NetCDF data structure:
                 
                 1. Dimensions
                 2. Variables
                 3. Attributes
                 
                 The dimensions section records the name and length of each dimension used
                 by the variables. The variables would then indicate which dimensions it
                 uses and any attributes such as data units, along with containing the data
                 values for the variable. It is good practice to include a
                 variable that is the same name as a dimension to provide the values for
                 that axes. Lastly, the attributes section would contain additional
                 information such as the name of the file creator or the instrument used to
                 collect the data.
                 
                 When writing data to a NetCDF file, there is often the need to indicate the
                 'record dimension'. A record dimension is the unbounded dimension for a
                 variable. For example, a temperature variable may have dimensions of
                 latitude, longitude and time. If one wants to add more temperature data to
                 the NetCDF file as time progresses, then the temperature variable should
                 have the time dimension flagged as the record dimension.
                 
                 This module implements the Scientific.IO.NetCDF API to read and create
                 NetCDF files. The same API is also used in the PyNIO and pynetcdf
                 modules, allowing these modules to be used interchangeably when working
                 with NetCDF files. The major advantage of this module over other
                 modules is that it doesn't require the code to be linked to the NetCDF
                 libraries.
                 
                 In addition, the NetCDF file header contains the position of the data in
                 the file, so access can be done in an efficient manner without loading
                 unnecessary data into memory. It uses the ``mmap`` module to create
                 Numpy arrays mapped to the data on disk, for the same purpose.
                 
                 Examples
                 --------
                 
                 To create a NetCDF file:
                 
                     >>> f = netcdf_file('simple.nc', 'w')
                     >>> f.history = 'Created for a test'
                
** Warning **
Wide character in print at /usr/local/share/lxr/source line 1030, <$git> line 86.


     >>> f.location = u'北京'
                     >>> f.createDimension('time', 10)
                     >>> time = f.createVariable('time', 'i', ('time',))
                     >>> time[:] = range(10)
                     >>> time.units = u'µs since 2008-01-01'
                     >>> f.close()
                 
                 Note the assignment of ``range(10)`` to ``time[:]``.  Exposing the slice
                 of the time variable allows for the data to be set in the object, rather
                 than letting ``range(10)`` overwrite the ``time`` variable.
                 
                 To read the NetCDF file we just created:
                 
                     >>> f = netcdf_file('simple.nc', 'r')
4d634188c7 Mart*     >>> print(f.history)
ae10cb9ac4 Oliv*     Created for a test
4d634188c7 Mart*     >>> print(f.location)
ae10cb9ac4 Oliv*
** Warning **
Wide character in print at /usr/local/share/lxr/source line 1030, <$git> line 103.


     北京
                     >>> time = f.variables['time']
4d634188c7 Mart*     >>> print(time.units)
ae10cb9ac4 Oliv*     µs since 2008-01-01
4d634188c7 Mart*     >>> print(time.shape)
ae10cb9ac4 Oliv*     (10,)
4d634188c7 Mart*     >>> print(time[-1])
ae10cb9ac4 Oliv*     9
                     >>> f.close()
                 
                 TODO:
                  * properly implement ``_FillValue``.
                  * implement Jeff Whitaker's patch for masked variables.
                  * fix character variables.
                  * implement PAGESIZE for Python 2.6?
                 """
                 
                 __all__ = ['netcdf_file']
                 
                 
                 from operator import mul
                 try:
                     from collections import OrderedDict
                 except ImportError:
                     OrderedDict = dict
                 from mmap import mmap, ACCESS_READ
                 
                 import numpy as np
7621b5d564 Oliv* from numpy import frombuffer, ndarray, dtype, empty, array, asarray
ae10cb9ac4 Oliv* from numpy import little_endian as LITTLE_ENDIAN
                 
                 import sys
                 
1e6e2cc1e4 Oliv* # the following are mostly from numpy.compat.py3k
                 
ae10cb9ac4 Oliv* if sys.version_info[0] >= 3:
42a4453aaf Mart*     from functools import reduce
ae10cb9ac4 Oliv*     def asbytes(s):
                         if isinstance(s, bytes):
                             return s
                         return str(s).encode('latin1')
                 
                     def asstr(s):
                         if isinstance(s, bytes):
                             return s.decode('latin1')
                         return str(s)
42a4453aaf Mart* 
                     long = int
                     unicode = str
1e6e2cc1e4 Oliv*     basestring = str
ae10cb9ac4 Oliv* else:
42a4453aaf Mart*     # python 2
ae10cb9ac4 Oliv*     asbytes = str
                     asstr = str
42a4453aaf Mart*     long = long
                     unicode = unicode
                     basestring = basestring
ae10cb9ac4 Oliv* 
e1e3780d86 Oliv* ABSENT       = b'\x00\x00\x00\x00\x00\x00\x00\x00'
                 ZERO         = b'\x00\x00\x00\x00'
                 NC_BYTE      = b'\x00\x00\x00\x01'
                 NC_CHAR      = b'\x00\x00\x00\x02'
                 NC_SHORT     = b'\x00\x00\x00\x03'
                 NC_INT       = b'\x00\x00\x00\x04'
                 NC_FLOAT     = b'\x00\x00\x00\x05'
                 NC_DOUBLE    = b'\x00\x00\x00\x06'
                 NC_DIMENSION = b'\x00\x00\x00\n'
                 NC_VARIABLE  = b'\x00\x00\x00\x0b'
                 NC_ATTRIBUTE = b'\x00\x00\x00\x0c'
ae10cb9ac4 Oliv* 
                 
                 TYPEMAP = { NC_BYTE:   dtype(np.byte),
                             NC_CHAR:   dtype('c'),
                             NC_SHORT:  dtype(np.int16).newbyteorder('>'),
                             NC_INT:    dtype(np.int32).newbyteorder('>'),
                             NC_FLOAT:  dtype(np.float32).newbyteorder('>'),
                             NC_DOUBLE: dtype(np.float64).newbyteorder('>'),
                             }
                 
                 REVERSE = { dtype(np.byte):    NC_BYTE,
                             dtype('c'):        NC_CHAR,
                             dtype(np.int16):   NC_SHORT,
                             dtype(np.int32):   NC_INT,
                             dtype(np.int64):   NC_INT,  # will be converted to int32
                             dtype(np.float32): NC_FLOAT,
                             dtype(np.float64): NC_DOUBLE,
                             }
                 
                 
                 class NetCDFError(Exception):
                     pass
                 
                 
                 class unmapped_array(object):
                     def __init__(self, shape, dtype_):
d44462b8a9 Oliv*         self.shape = tuple(int(_) for _ in shape)
ae10cb9ac4 Oliv*         self.dtype = dtype(dtype_)
                 
                     @property
                     def itemsize(self):
                         return self.dtype.itemsize
                 
                     @property
                     def size(self):
                         return reduce(mul, self.shape, 1)
                 
                     @property
                     def nbytes(self):
                         return self.size * self.itemsize
                 
                     def __len__(self):
                         return self.shape[0]
                 
                     def __getitem__(self, indx):
                         raise NetCDFError('netcdf_file: delay is True, use read_var or read_recvar to read variable data')
                 
                     def __setitem__(self, indx, val):
                         raise NetCDFError('netcdf_file: delay is True, use write_var or write_recvar to assign variable data')
                 
                 
                 class netcdf_file(object):
                     """
                     A file object for NetCDF data.
                 
                     A `netcdf_file` object has two standard attributes: `dimensions` and
                     `variables`. The values of both are dictionaries, mapping dimension
                     names to their associated lengths and variable names to variables,
                     respectively. Application programs should never modify these
                     dictionaries.
                 
                     All other attributes correspond to global attributes defined in the
                     NetCDF file. Global file attributes are created by assigning to an
                     attribute of the `netcdf_file` object.
                 
                     If delay is True, variable data is only read/written on demand.
                     In this case, if mode="w", write_metadata() needs to be called after
                     all dimensions, variables and attributes have been defined, but before
                     any variable data is written.
                 
                     Parameters
                     ----------
                     filename : string or file-like
                         string -> filename
                     mode : {'r', 'w'}, optional
                         read-write mode, default is 'r'
                     mmap : None or bool, optional
                         Whether to mmap `filename` when reading.  Default is True
                         when `filename` is a file name, False when `filename` is a
                         file-like object
                     delay : bool, optional
                         Whether to delay reading of variable data.  Default is False.
                         This is an alternative to mmap for more efficient reading.
                     version : {1, 2}, optional
                         version of netcdf to read / write, where 1 means *Classic
                         format* and 2 means *64-bit offset format*.  Default is 1.  See
                         `here <http://www.unidata.ucar.edu/software/netcdf/docs/netcdf/Which-Format.html>`_
                         for more info.
                 
                     """
                     def __init__(self, filename, mode='r', mmap=None, version=1, delay=False):
                         """Initialize netcdf_file from fileobj (str or file-like)."""
                         if delay:
                             if mmap is None:
                                 mmap = False
                             else:
                                 raise ValueError('Cannot delay variables for mmap')
                         if hasattr(filename, 'seek'):  # file-like
                             self.fp = filename
                             self.filename = 'None'
                             if mmap is None:
                                 mmap = False
                             elif mmap and not hasattr(filename, 'fileno'):
                                 raise ValueError('Cannot use file object for mmap')
                         else:  # string?
                             self.filename = filename
                             self.fp = open(self.filename, '%sb' % mode)
                             if mmap is None:
                                 mmap = True
                         self.use_mmap = mmap
                         self.version_byte = version
                         self.delay = delay
                 
                         if not mode in 'rw':
                             raise ValueError("Mode must be either 'r' or 'w'.")
                         self.mode = mode
                 
                         self.dimensions = OrderedDict()
                         self.variables = OrderedDict()
                 
                         self._dims = []
                         self._recs = 0
                         self._recsize = 0
                 
                         self._mapped = False
                         self._begins = OrderedDict()
                 
                         self._attributes = OrderedDict()
                 
                         if mode == 'r':
                             self._read()
                 
                     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 close(self):
                         """Closes the NetCDF file."""
                         try:
                             closed = self.fp.closed
                         except AttributeError:
                             pass
                         else:
                             if not closed:
                                 try:
                                     self.flush()
                                 finally:
                                     self.fp.close()
                     __del__ = close
                 
                     def createDimension(self, name, length):
                         """
                         Adds a dimension to the Dimension section of the NetCDF data structure.
                 
                         Note that this function merely adds a new dimension that the variables can
                         reference.  The values for the dimension, if desired, should be added as
                         a variable using `createVariable`, referring to this dimension.
                 
                         Parameters
                         ----------
                         name : str
                             Name of the dimension (Eg, 'lat' or 'time').
                         length : int
                             Length of the dimension.
                 
                         See Also
                         --------
                         createVariable
                 
                         """
                         self.dimensions[name] = length
                         self._dims.append(name)
                 
                     def createVariable(self, name, type, dimensions):
                         """
                         Create an empty variable for the `netcdf_file` object, specifying its data
                         type and the dimensions it uses.
                 
                         Parameters
                         ----------
                         name : str
                             Name of the new variable.
                         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
                 
                         if not isinstance(type, dtype): type = dtype(type)
                         if type.newbyteorder('=') not in REVERSE:
                             raise ValueError("NetCDF 3 does not support type %s" % type)
                 
                         if self.delay:
                             data = unmapped_array(shape_, type)
                         else:
                             data = empty(shape_, type)
                         self.variables[name] = netcdf_variable(data, type, shape, dimensions)
                         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
                 
                         """
9a1526c006 Oliv*         if getattr(self, 'mode', None) == 'w':
ae10cb9ac4 Oliv*             if self.delay:
                                 if not self._mapped:
                                     self._map()
                                 self.update_numrecs(self._recs)
                             else:
                                 self._write()
                     sync = flush
                 
                     def write_metadata(self):
                         '''This needs to be called before assigning any data to variables!'''
                         if self.delay:
                             self._map()
                         else:
                             raise UserWarning('write_metadata is void unless delay is True')
                 
                     def _map(self):
                         self.fp.seek(0)
e1e3780d86 Oliv*         self.fp.write(b'CDF')
9a1526c006 Oliv*         self.fp.write(array(self.version_byte, '>b').tobytes())
ae10cb9ac4 Oliv* 
                         # Write headers
                         self._write_numrecs()
                         self._write_dim_array()
                         self._write_gatt_array()
                         self._map_var_array()
                         self._mapped = True
                 
                     def _map_var_array(self):
                         if self.variables:
                             self.fp.write(NC_VARIABLE)
                             self._pack_int(len(self.variables))
                 
                             # Separate record variables from non-record ones, keep order
                             nonrec_vars = [ k for k,v in self.variables.items() if not v.isrec ]
                             rec_vars = [ k for k,v in self.variables.items() if v.isrec ]
                 
                             # Set the metadata for all variables.
                             for name in nonrec_vars + rec_vars:
                                 self._map_var_metadata(name)
                 
                             # Now that we have the metadata, we know the vsize of
                             # each variable, so we can calculate their position in the file
                 
                             pos0 = pos = self.fp.tell()
                 
                             # set file pointers for all variables.
                             for name in nonrec_vars:
                                 var = self.variables[name]
                                 # Set begin in file header.
                                 self.fp.seek(var._begin)
                                 self._pack_begin(pos)
                                 self._begins[name] = pos
                                 pos += var._vsize
                 
                             recstart = pos
                 
                             for name in rec_vars:
                                 var = self.variables[name]
                                 # Set begin in file header.
                                 self.fp.seek(var._begin)
                                 self._pack_begin(pos)
                                 self._begins[name] = pos
                                 pos += var._vsize
                 
                             self.__dict__['_recsize'] = pos - recstart
                 
                             # first var
                             self.fp.seek(pos0)
                         else:
                             self.fp.write(ABSENT)
                 
                     def _map_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.dtype.newbyteorder('=')]
                         self.fp.write(asbytes(nc_type))
                 
                         if not var.isrec:
                             vsize = var.data.size * var.data.itemsize
                             vsize += -vsize % 4
                         else:  # record variable
                             if 1:  #var.data.shape[0]:
                                 size = reduce(mul, var.data.shape[1:], 1)
                                 vsize = size * var.data.itemsize
                             else:
                                 vsize = 0
                             rec_vars = len([var for var in self.variables.values()
                                     if var.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)
                 
                     @property
                     def numrecs(self):
                         return self._recs
                 
                     @property
                     def attributes(self):
                         return self._attributes
                 
                     @property
                     def begins(self):
                         return [(name,pos,self.variables[name].isrec) for name,pos in self._begins.items()]
                 
692071215d Oliv*     def write_var(self, name, val, j0=None, iY=-2):
ae10cb9ac4 Oliv*         if not self.delay:
                             raise NetCDFError('netcdf_file: delay is False, need to assign to variables')
                         if not self._mapped:
                             raise NetCDFError('netcdf_file: need to call write_metadata first')
                         pos = self._begins[name]
692071215d Oliv*         var = self.variables[name]
ae10cb9ac4 Oliv*         count = var.data.size * var.data.itemsize
692071215d Oliv*         if j0 is not None:
                             if iY == 0:
                                 idxs = [()]
                             else:
                                 idxs = np.ndindex(*var.data.shape[:iY])
                             for idx in idxs:
                                 ii = idx + (j0,) + len(var.data.shape[iY+1:])*(0,)
                                 offset = np.ravel_multi_index(ii, var.data.shape)*var.data.itemsize
                                 end = offset + val[idx].size*var.data.itemsize
                                 if end > count:
                                     raise NetCDFError('array too large: {} > {}'.format(end, count))
                                 self.fp.seek(pos+offset)
                                 np.asanyarray(val[idx], var.data.dtype.newbyteorder('>')).tofile(self.fp)
                         else:
                             end = val.size*var.data.itemsize
                             if end != count:
                                 raise NetCDFError('array too large: {} > {}'.format(end, count))
                             self.fp.seek(pos)
                             np.asanyarray(val, var.data.dtype.newbyteorder('>')).tofile(self.fp)
                             # pad
e1e3780d86 Oliv*             self.fp.write(b'\x00' * (var._vsize - count))
ae10cb9ac4 Oliv* 
692071215d Oliv*     def write_recvar(self, name, rec, val, j0=None, iY=-2):
ae10cb9ac4 Oliv*         if not self.delay:
                             raise NetCDFError('netcdf_file: delay is False, need to assign to variables')
                         if not self._mapped:
                             raise NetCDFError('netcdf_file: need to call write_metadata first')
                         pos = self._begins[name] + rec*self._recsize
692071215d Oliv*         var = self.variables[name]
ae10cb9ac4 Oliv*         count = reduce(mul, var.data.shape[1:], 1) * var.data.itemsize
692071215d Oliv*         if j0 is not None:
                             if iY == 0:
                                 idxs = [()]
                             else:
                                 idxs = np.ndindex(*var.data.shape[1:iY])
                             for idx in idxs:
                                 ii = idx + (j0,) + len(var.data.shape[iY+1:])*(0,)
                                 offset = np.ravel_multi_index(ii, var.data.shape[1:])*var.data.itemsize
                                 end = offset + val[idx].size*var.data.itemsize
                                 if end > count:
                                     raise NetCDFError('array too large: {} > {}'.format(end, count))
                                 self.fp.seek(pos+offset)
                                 np.asanyarray(val[idx], var.data.dtype.newbyteorder('>')).tofile(self.fp)
                         else:
                             end = val.size*var.data.itemsize
                             if end != count:
                                 raise ValueError('netcdf_file.write_recvar: array too large')
                             self.fp.seek(pos)
                             np.asanyarray(val, var.data.dtype.newbyteorder('>')).tofile(self.fp)
                             # pad
e1e3780d86 Oliv*             self.fp.write(b'\x00' * (var._vsize - count))
ae10cb9ac4 Oliv*         if rec >= self._recs:
                             self.__dict__['_recs'] = rec + 1
                 
                     def _write(self):
                         self.fp.seek(0)
e1e3780d86 Oliv*         self.fp.write(b'CDF')
9a1526c006 Oliv*         self.fp.write(array(self.version_byte, '>b').tobytes())
ae10cb9ac4 Oliv* 
                         # 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.__dict__['_numrecs_begin'] = self.fp.tell()
                         self._pack_int(self._recs)
                 
                     def update_numrecs(self, numrecs):
                         self.__dict__['_recs'] = numrecs
                         self.fp.seek(self._numrecs_begin)
                         self._pack_int(numrecs)
                 
                     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_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 variables non-recs first, then recs. We use a DSU
                 #            # since some people use pupynere with Python 2.3.x.
                 #            deco = [ (v._shape and not v.isrec, k) for (k, v) in self.variables.items() ]
                 #            deco.sort()
                 #            variables = [ k for (unused, k) in deco ][::-1]
                             # Separate record variables from non-record ones, keep order
                             nonrec_vars = [ k for k,v in self.variables.items() if not v.isrec ]
                             rec_vars = [ k for k,v in self.variables.items() if v.isrec ]
                             variables = nonrec_vars + rec_vars
                 
                             # 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.dtype.newbyteorder('=')]
                         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([var for var in self.variables.values()
                                     if var.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:
                             if (var.data.dtype.byteorder == '<' or 
                                     (var.data.dtype.byteorder == '=' and LITTLE_ENDIAN)):
                                 var.data = var.data.byteswap()
9a1526c006 Oliv*             self.fp.write(var.data.tobytes())
ae10cb9ac4 Oliv*             count = var.data.size * var.data.itemsize
e1e3780d86 Oliv*             self.fp.write(b'\x00' * (var._vsize - count))
ae10cb9ac4 Oliv*         else:  # record variable
                             # Handle rec vars with shape[0] < nrecs.
                             if self._recs > len(var.data):
                                 shape = (self._recs,) + var.data.shape[1:]
                                 var.data.resize(shape)
                 
                             pos0 = pos = self.fp.tell()
                             for rec in var.data:
                                 if (rec.dtype.byteorder == '<' or 
                                         (rec.dtype.byteorder == '=' and LITTLE_ENDIAN)):
                                     rec = rec.byteswap()
9a1526c006 Oliv*                 self.fp.write(rec.tobytes())
ae10cb9ac4 Oliv*                 # Padding
                                 count = rec.size * rec.itemsize
e1e3780d86 Oliv*                 self.fp.write(b'\x00' * (var._vsize - count))
ae10cb9ac4 Oliv*                 pos += self._recsize
                                 self.fp.seek(pos)
                             self.fp.seek(pos0 + var._vsize)
                 
                     def _write_values(self, values):
                         if hasattr(values, 'dtype'):
                             nc_type = REVERSE[values.dtype.newbyteorder('=')]
                         else:
                             types = [
                                     (int, NC_INT),
42a4453aaf Mart*                     (long, NC_INT),
ae10cb9ac4 Oliv*                     (float, NC_FLOAT),
42a4453aaf Mart*                     (basestring, NC_CHAR),
ae10cb9ac4 Oliv*                     ]
                             try:
                                 sample = values[0]
                             except (IndexError, TypeError):
                                 sample = values
42a4453aaf Mart*             if isinstance(sample, unicode):
                                 if not isinstance(values, unicode):
                                     raise ValueError(
                                         "NetCDF requires that text be encoded as UTF-8")
a97439910f Oliv*                 values = values.encode('utf-8')
ae10cb9ac4 Oliv*             for class_, nc_type in types:
                                 if isinstance(sample, class_): break
                 
a97439910f Oliv*         if nc_type == NC_CHAR:
                             if len(values) == 0:
                                 # only this can represent zero-length strings
                                 dtype_ = dtype('c')
                             else:
                                 # this avoids double encoding in python 3
                                 dtype_ = dtype('S')
                         else:
                             dtype_ = TYPEMAP[nc_type]
                 
                         values = asarray(values, dtype_)
ae10cb9ac4 Oliv* 
                         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()
9a1526c006 Oliv*         self.fp.write(values.tobytes())
ae10cb9ac4 Oliv*         count = values.size * values.itemsize
e1e3780d86 Oliv*         self.fp.write(b'\x00' * (-count % 4))  # pad
ae10cb9ac4 Oliv* 
                     def _read(self):
                         # Check magic bytes and version
                         magic = self.fp.read(3)
e1e3780d86 Oliv*         if not magic == b'CDF':
ae10cb9ac4 Oliv*             raise TypeError("Error: %s is not a valid NetCDF 3 file" %
                                             self.filename)
7621b5d564 Oliv*         self.__dict__['version_byte'] = frombuffer(self.fp.read(1), '>b')[0]
ae10cb9ac4 Oliv* 
                         # 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 not header 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 not header 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_values()
                         return attributes
                 
                     def _read_var_array(self):
                         header = self.fp.read(4)
                         if not header in [ZERO, NC_VARIABLE]:
                             raise ValueError("Unexpected header.")
                 
                         begin = 0
                         dtypes = {'names': [], 'formats': []}
                         rec_vars = []
                         count = self._unpack_int()
3c7f3cce62 Oliv*         rec_vsizes = []
ae10cb9ac4 Oliv*         for var in range(count):
                             name, dimensions, shape, attributes, type, begin_, vsize = self._read_var()
                             # http://www.unidata.ucar.edu/software/netcdf/docs/netcdf.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
3c7f3cce62 Oliv*                 rec_vsizes.append(vsize)
ae10cb9ac4 Oliv*                 if begin == 0: begin = begin_
                                 dtypes['names'].append(name)
                                 dtypes['formats'].append(str(shape[1:]) + '>' + type.char)
                 
                                 # Handle padding with a virtual variable.
                                 if type.char in 'bch':
                                     actual_size = reduce(mul, (1,) + shape[1:]) * type.itemsize
                                     padding = -actual_size % 4
                                     if padding:
                                         dtypes['names'].append('_padding_%d' % var)
                                         dtypes['formats'].append('(%d,)>b' % padding)
                 
                                 # Data will be set later.
                                 if self.delay:
                                     self._begins[name] = begin_
                                     data = unmapped_array((self._recs,)+shape[1:], type)
                                 else:
                                     data = None
                             else:  # not a record variable
                                 # Calculate size to avoid problems with vsize (above)
                                 a_size = reduce(mul, shape, 1) * type.itemsize
                                 pos = self.fp.tell()
                                 if self.use_mmap:
                                     mm = mmap(self.fp.fileno(), begin_+a_size, access=ACCESS_READ)
                                     data = ndarray.__new__(ndarray, shape, dtype=type,
                                             buffer=mm, offset=begin_, order=0)
                                 elif self.delay:
                                     self._begins[name] = begin_
                                     data = unmapped_array(shape, type)
                                 else:
                                     self.fp.seek(begin_)
7621b5d564 Oliv*                     data = frombuffer(self.fp.read(a_size), type)
ae10cb9ac4 Oliv*                     data.shape = shape
                                 self.fp.seek(pos)
                 
                             # Add variable.
                             self.variables[name] = netcdf_variable(data, type, shape, dimensions, attributes)
                 
                         if rec_vars and not self.delay:
                             dtypes['formats'] = [f.replace('()', '').replace(' ', '') for f in dtypes['formats']]
                             # 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.
                             pos = self.fp.tell()
3c7f3cce62 Oliv*             rec_arrays = []
ae10cb9ac4 Oliv*             if self.use_mmap:
                                 mm = mmap(self.fp.fileno(), begin+self._recs*self._recsize, access=ACCESS_READ)
3c7f3cce62 Oliv*                 if self._recsize >= 1<<31:
                                     # need to work around limitation of numpy.dtype.itemsize to 32 bit
                                     i = 0
                                     while i < len(rec_vsizes):
                                         ends = np.cumsum(rec_vsizes[i:])
                                         n = np.searchsorted(ends, 1<<31)
                                         dtype1 = dict(names=dtypes['names'][i:i+n], formats=dtypes['formats'][i:i+n])
                                         rec_array = ndarray.__new__(ndarray, (self._recs,), dtype=dtype1,
                                                 buffer=mm, offset=begin, order=0)
                                         rec_arrays.append(rec_array)
                                         begin += ends[n-1]
                                         i += n
                                 else:
                                     rec_array = ndarray.__new__(ndarray, (self._recs,), dtype=dtypes,
                                             buffer=mm, offset=begin, order=0)
                                     rec_arrays = [ rec_array ]
ae10cb9ac4 Oliv*             else:
                                 self.fp.seek(begin)
7621b5d564 Oliv*                 rec_array = frombuffer(self.fp.read(self._recs*self._recsize), dtype=dtypes)
ae10cb9ac4 Oliv*                 rec_array.shape = (self._recs,)
3c7f3cce62 Oliv*                 rec_arrays = [ rec_array ]
ae10cb9ac4 Oliv*             self.fp.seek(pos)
                 
3c7f3cce62 Oliv*             for rec_array in rec_arrays:
                                 for var in rec_array.dtype.names:
                                     self.variables[var].__dict__['data'] = rec_array[var]
ae10cb9ac4 Oliv* 
                     def read_var(self, name):
                         var = self.variables[name]
                         pos = self._begins[name]
                         self.fp.seek(pos)
7621b5d564 Oliv*         data = frombuffer(self.fp.read(var.data.nbytes), dtype=var.data.dtype)
ae10cb9ac4 Oliv*         data.shape = var.data.shape
                         return data
                 
                     def read_recvar(self, name, rec):
                         var = self.variables[name]
                         pos = self._begins[name] + rec*self._recsize
                         self.fp.seek(pos)
                         count = reduce(mul, var.data.shape[1:], 1) * var.data.itemsize
7621b5d564 Oliv*         data = frombuffer(self.fp.read(count), dtype=var.data.dtype)
ae10cb9ac4 Oliv*         data.shape = var.data.shape[1:]
                         return data
                 
                     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]()
                         type = TYPEMAP[nc_type]
                 
                         return name, dimensions, shape, attributes, type, begin, vsize
                 
                     def _read_values(self):
                         nc_type = self.fp.read(4)
                         n = self._unpack_int()
                 
                         type = TYPEMAP[nc_type]
                 
                         count = n*type.itemsize
                         values = self.fp.read(int(count))
                         self.fp.read(-count % 4)  # read padding
                 
9a1526c006 Oliv*         if type.char != 'c':
7621b5d564 Oliv*             values = frombuffer(values, type)
ae10cb9ac4 Oliv*             if values.shape == (1,): values = values[0]
                         else:
                             ## text values are encoded via UTF-8, per NetCDF standard
e1e3780d86 Oliv*             values = values.rstrip(b'\x00').decode('utf-8', 'replace')
ae10cb9ac4 Oliv*         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):
9a1526c006 Oliv*         self.fp.write(array(value, '>i').tobytes())
ae10cb9ac4 Oliv*     _pack_int32 = _pack_int
                 
                     def _unpack_int(self):
7621b5d564 Oliv*         return int(frombuffer(self.fp.read(4), '>i')[0])
ae10cb9ac4 Oliv*     _unpack_int32 = _unpack_int
                 
                     def _pack_int64(self, value):
9a1526c006 Oliv*         self.fp.write(array(value, '>q').tobytes())
ae10cb9ac4 Oliv* 
                     def _unpack_int64(self):
7621b5d564 Oliv*         return frombuffer(self.fp.read(8), '>q')[0]
ae10cb9ac4 Oliv* 
                     def _pack_string(self, s):
                         count = len(s)
                         self._pack_int(count)
                         self.fp.write(asbytes(s))
e1e3780d86 Oliv*         self.fp.write(b'\x00' * (-count % 4))  # pad
ae10cb9ac4 Oliv* 
                     def _unpack_string(self):
                         count = self._unpack_int()
e1e3780d86 Oliv*         s = self.fp.read(count).rstrip(b'\x00')
ae10cb9ac4 Oliv*         self.fp.read(-count % 4)  # read padding
                         return s
                 
                 
                 class netcdf_variable(object):
                     """
                     A data object for the `netcdf` module.
                 
                     `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.
                     type: numpy dtype
                         Desired data-type 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.
                 
                 
                     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, type, shape, dimensions, attributes=None):
                         self.data = data
                         self.dtype = type
                         self._shape = shape
                         self.dimensions = dimensions
                 
                         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
                 
                     @property
                     def attributes(self):
                         return self._attributes
                 
                     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 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.dtype.char
                 
                     def itemsize(self):
                         """
                         Return the itemsize of the variable.
                 
                         Returns
                         -------
                         itemsize : int
                             The element size of the variable (eg, 8 for float64).
                 
                         """
                         return self.dtype.itemsize
                 
                     def __getitem__(self, index):
                         return self.data[index]
                 
                     def __setitem__(self, index, 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:]
                                 self.data.resize(shape)
                         self.data[index] = data
                 
                 
                 NetCDFFile = netcdf_file
                 NetCDFVariable = netcdf_variable
                 
                 # End of NetCDF reader/writer module
                 
                 
                 if __name__ == '__main__':
                     import sys
                     import os
692071215d Oliv*     import errno
ae10cb9ac4 Oliv*     import re
                     import glob
                     import fnmatch
                     from getopt import gnu_getopt as getopt
a23974bf3e Oliv*     from getopt import GetoptError
ae10cb9ac4 Oliv*     try:
                         from collections import OrderedDict
                     except ImportError:
                         OrderedDict = dict
                     import numpy as np
                 
692071215d Oliv*     tilepatt = re.compile(r'\.t([0-9]{3}[0-9]*)\.nc$')
ae10cb9ac4 Oliv*     iterpatt = re.compile(r'(\.[0-9]{10})$')
                 
                     # parse command-line arguments
                     try:
7621b5d564 Oliv*         optlist,fnames = getopt(sys.argv[1:], '2qho:v:', ['many', 'verbose', 'help'])
a23974bf3e Oliv*     except GetoptError as e:
                         sys.exit('Error: ' + str(e) + '\n\n' + __doc__)
ae10cb9ac4 Oliv* 
7621b5d564 Oliv*     opts = dict(optlist)
                 
                     if '--help' in opts or '-h' in opts:
                         print(__doc__)
                         sys.exit()
                 
a23974bf3e Oliv*     if not fnames:
                         sys.exit('You need to specify at least one input file.')
                 
ae10cb9ac4 Oliv*     outname = opts.get('-o')
3c7f3cce62 Oliv*     version = '-2' in opts and 2 or 1
ae10cb9ac4 Oliv*     progress = '-q' not in opts
                     verbose = '--verbose' in opts
692071215d Oliv*     manytiles = '--many' in opts
ae10cb9ac4 Oliv*     tname = 'T'
                 
a23974bf3e Oliv*     if outname is None:
                         sys.exit('You need to specify an output file using the -o option.')
                 
ae10cb9ac4 Oliv*     # turn into list of compiled regular expressions
                     varpatt = opts.get('-v', '').split(',')
                     varpatt = [ re.compile(fnmatch.translate(patt.strip())) for patt in varpatt ]
                 
                     readopts = dict(delay=True)
3c7f3cce62 Oliv*     writeopts = dict(delay=True, version=version)
ae10cb9ac4 Oliv* 
                     if len(fnames) == 1 and sum(s in fnames[0] for s in '*?[]'):
                         globpatt = fnames[0]
                         fnames = glob.glob(globpatt)
                         if len(fnames) == 0:
03f05d3ffd Oliv*             raise IOError('No files matching {0}', globpatt)
ae10cb9ac4 Oliv* 
                     fnames.sort()
                 
                     # Get list of iterations
                     itfiles = {}
692071215d Oliv*     # files without iteration number
1dcbcd7847 Oliv*     files0 = {}
ae10cb9ac4 Oliv*     for fname in fnames:
1dcbcd7847 Oliv*         tn = tilepatt.search(fname).group(1)
ae10cb9ac4 Oliv*         base = tilepatt.sub('', fname)
                         m = iterpatt.search(base)
                         if m:
1dcbcd7847 Oliv*             it = m.group(1)
                             itfiles.setdefault(it, {})[tn] = fname
692071215d Oliv*         else:
1dcbcd7847 Oliv*             files0[tn] = fname
                 
                     files0 = [v for k,v in sorted(files0.items())]
ae10cb9ac4 Oliv* 
8b8576185f Mart*     its = sorted(itfiles.keys())
ae10cb9ac4 Oliv*     for it in its:
1dcbcd7847 Oliv*         itfiles[it] = [v for k,v in sorted(itfiles[it].items())]
ae10cb9ac4 Oliv* 
                     filess = [ itfiles[it] for it in its ]
692071215d Oliv*     if len(files0) and len(filess):
                         sys.exit('Both files with and without iteration number present.  Aborting.')
                     elif len(filess):
ae10cb9ac4 Oliv*         files0 = filess[0]
692071215d Oliv*     else:
                         filess = [files0]
ae10cb9ac4 Oliv* 
                     if verbose:
4d634188c7 Mart*         print('Files to be read:')
ae10cb9ac4 Oliv*         for files in filess:
4d634188c7 Mart*             print(files[0], '... (%d)' % (len(files)))
ae10cb9ac4 Oliv* 
                     nc = netcdf_file(files0[0], 'r', **readopts)
                     gatt = OrderedDict(nc.attributes)
                     #gatt['tile_number'] = 1
                     #gatt['bi'] = 1
                     #gatt['bj'] = 1
                     del gatt['tile_number']
                     del gatt['bi']
                     del gatt['bj']
111bdbd545 Oliv*     for k in list(gatt):
ae10cb9ac4 Oliv*         if k.startswith('exch2_'):
                             del gatt[k]
                 
                     sNx = gatt['sNx']
                     sNy = gatt['sNy']
                     Nx = gatt['Nx']
                     Ny = gatt['Ny']
                     ntx = gatt['nSx']*gatt['nPx']
                     nty = gatt['nSy']*gatt['nPy']
                     ntiles = ntx*nty
                 
                     for it in its:
                         if len(itfiles[it]) != ntiles:
                             raise ValueError('Error: found %d tiles for iteration %s, need %d' % (
                                              len(itfiles[it]), it[1:], ntiles))
                 
                     Xslice = []
                     Yslice = []
                     for tn in range(ntx*nty):
                         bj,bi = divmod(tn, ntx)
                         ie = sNx*(bi+1-ntx) or None
                         je = sNy*(bj+1-nty) or None
                         Xslice.append(slice(sNx*bi, ie))
                         Yslice.append(slice(sNy*bj, je))
                 
                     dims = OrderedDict()
                     for k,n in nc.dimensions.items():
                         if k[0] == 'X':
                             n += Nx - sNx
                         elif k[0] == 'Y':
                             n += Ny - sNy
                         dims[k] = n
                 
4d634188c7 Mart*     print('Tiled dimensions:',
                           ' '.join([k for k in nc.dimensions if k[0] in 'XY']))
ae10cb9ac4 Oliv* 
                     havetime = tname in dims
                     if havetime:
                         assert dims[tname] is None
                         nrec = nc.numrecs
4d634188c7 Mart*         print('Record dimension:', tname)
ae10cb9ac4 Oliv*     else:
                         assert len(its) <= 1
                         nrec = None
                 
                     if verbose:
4d634188c7 Mart*         print('Variables:')
ae10cb9ac4 Oliv* 
                     varprops = OrderedDict()
                     for name,var in nc.variables.items():
                         if name in dims or sum(patt.search(name) is not None for patt in varpatt) or len(varpatt) == 0:
                             varprops[name] = {}
                             varprops[name]['dtype'] = var.data.dtype
                             varprops[name]['dimensions'] = var.dimensions
                             varprops[name]['ncattrs'] = OrderedDict(var.attributes)
                             iX = None
                             iY = None
                             for i,dim in enumerate(var.dimensions):
                                 if dim[0] == 'X':
                                     iX = i
                                 elif dim[0] == 'Y':
                                     iY = i
                             varprops[name]['iX'] = iX
                             varprops[name]['iY'] = iY
                             dimstrs = len(var.dimensions)*[':']
                             if tname in var.dimensions: dimstrs[list(var.dimensions).index(tname)] = tname
                             if iX is not None: dimstrs[iX] = var.dimensions[iX]
                             if iY is not None: dimstrs[iY] = var.dimensions[iY]
4d634188c7 Mart*             if verbose:
                                 print( '%s %s(%s)' % (var.typecode(), name, ','.join(dimstrs)))
ae10cb9ac4 Oliv* 
                     ######################################################################
                     # create global netcdf file
                     ncout = netcdf_file(outname, 'w', **writeopts)
                 
                     try:
                         # global attributes
                         for name,att in gatt.items():
                             setattr(ncout, name, att)
                 
                         # create dimensions
                         for name,n in dims.items():
                             ncout.createDimension(name, n)
                 
                         # create variables with attributes
                         vars = {}
                         for name,var in varprops.items():
                             dtype_ = np.dtype(var['dtype']).newbyteorder('>')
4d634188c7 Mart*         #    if verbose: print('Creating variable', name, dtype_, var['dimensions'])
ae10cb9ac4 Oliv*             vars[name] = ncout.createVariable(name, dtype_, var['dimensions'])
                             for attname,att in var['ncattrs'].items():
                                 setattr(vars[name], attname, att)
                 
                         ncout.write_metadata()
                 
3c7f3cce62 Oliv*         if version == 1:
                             for sz in ncout._begins.values():
                                 if sz >= 1<<31:
                                     sys.exit('ERROR: Variables too big for NetCDF version 1, try "-2" option.')
                 
692071215d Oliv*         if manytiles:
                             # open only files along x-slice of tiles simultaneously
                             # will have to jump around output file a bit...
                 
                             # easier this way; have to reopen many files anyway
                             nc.close()
                 
                             nyslice = sNy
                 
                             # sort tiles into x-slices
                             iterslices = []
ae10cb9ac4 Oliv*             for fnames in filess:
692071215d Oliv*                 myslicefiles = [[] for _ in range(nty)]
                                 for fname in fnames:
                                     m = tilepatt.search(fname)
                                     if m is None:
                                         sys.exit('Could not extract tile number from file name: {0}'.format(fname))
                                     tn = int(m.group(1)) - 1
                                     bj,bi = divmod(tn, ntx)
                                     myslicefiles[bj].append(fname)
                                 iterslices.append(myslicefiles)
                 
                             irec = 0
                             for tileslices in iterslices:
                                 for bj in range(nty):
                                     if len(tileslices[bj]) != ntx:
                                         raise ValueError('found %d tiles for bj = %d, need %d' % (
                                                          len(tileslices[bj]), bj+1, ntx))
                                     # open files
1dcbcd7847 Oliv*                     ncs = []
692071215d Oliv*                     for fname in tileslices[bj]:
                                         try:
                                             nc = netcdf_file(fname, 'r', **readopts)
                                         except IOError as e:
                                             if e.errno == errno.EMFILE:
                                                 sys.exit('ERROR: Too many open files.  Ask developer to improve script ;)')
                                             raise
1dcbcd7847 Oliv*                         ncs.append(nc)
692071215d Oliv* 
                                     if irec == 0:
                                         # assemble non-record variable data
                                         if bj == 0 and progress and not verbose:
                                             sys.stderr.write('Writing non-record variables\n')
                                         indstrings = {}
                                         for name,pos,isrec in ncout.begins:
                                             if not isrec:
4d634188c7 Mart*                                 if verbose: print(name)
692071215d Oliv*                                 prop = varprops[name]
                                                 vardims = prop['dimensions']
                                                 var = vars[name]
                                                 indx = len(vardims)*[slice(None)]
                                                 iX = prop['iX']
                                                 iY = prop['iY']
                                                 shape = list(var.shape)
                                                 if iY is not None:
                                                     # this is needed for V and vorticity point fields that have Ny+1
                                                     shape[iY] = shape[iY] - Ny + nyslice
                                                     j0 = bj*nyslice
                                                 else:
                                                     j0 = None
                                                 data = np.empty(shape, var.data.dtype.newbyteorder('>'))
1dcbcd7847 Oliv*                                 for nc in ncs:
692071215d Oliv*                                     tn = nc.tile_number - 1
                                                     if iX is not None: indx[iX] = Xslice[tn]
                                                     data[tuple(indx)] = nc.read_var(name)
                 
                                                 ncout.write_var(name, data, j0, iY)
                                                 del data
                                             else:  # isrec
                                                 if not havetime:
                                                     raise ValueError('record variables, but no time')
                 
                                     # assemble record variable data
                                     if havetime:
                                         # any of the ncs
                                         nrec = nc.numrecs
                                         if bj == 0 and progress and not verbose:
                                             sys.stderr.write('Writing {0} records: '.format(nrec))
                                         for irecin in range(nrec):
                                             if bj == 0 and progress and not verbose:
                                                 sys.stderr.write('.')
                                             for name,pos,isrec in ncout.begins:
                                                 if isrec:
4d634188c7 Mart*                                     if verbose: print(irec+irecin, name)
692071215d Oliv*                                     prop = varprops[name]
                                                     vardims = prop['dimensions'][1:]
                                                     var = vars[name]
                                                     indx = len(vardims)*[slice(None)]
                                                     iX = prop['iX']
                                                     iY = prop['iY']
                                                     shape = list(var.data.shape)
                                                     if iY is not None:
                                                         shape[iY] = shape[iY] - Ny + nyslice
                                                         j0 = bj*nyslice
                                                     else:
                                                         j0 = None
                                                     data = np.empty(shape[1:], var.data.dtype.newbyteorder('>'))
1dcbcd7847 Oliv*                                     for nc in ncs:
692071215d Oliv*                                         tn = nc.tile_number - 1
                                                         if iX is not None: indx[iX-1] = Xslice[tn]
                                                         data[tuple(indx)] = nc.read_recvar(name, irecin)
                 
                                                     ncout.write_recvar(name, irec+irecin, data, j0, iY)
                                                     del data
                 
                                         if bj == 0 and progress and not verbose:
                                             sys.stderr.write('\n')
                 
1dcbcd7847 Oliv*                     for nc in ncs:
692071215d Oliv*                         nc.close()
                 
                                     if progress and not verbose:
                                         if bj == 0 and nty > 1:
                                             sys.stderr.write('Writing {0} more slices: '.format(nty-1))
                                         else:
                                             sys.stderr.write('.')
                 
                                 if nty > 1 and progress and not verbose:
                                     sys.stderr.write('\n')
                 
                                 if havetime:
                                     irec += nrec
                 
                         else:
1dcbcd7847 Oliv*             ncs = [nc]
                             for fname in files0[1:]:
                                 try:
                                     nc = netcdf_file(fname, 'r', **readopts)
                                 except IOError as e:
                                     if e.errno == errno.EMFILE:
                                         sys.exit('ERROR: Too many open files.  Try again with --many or increase the limit on open files.')
                                     raise
                                 ncs.append(nc)
692071215d Oliv* 
                             # assemble non-record variable data
                             if progress and not verbose: sys.stderr.write('Writing non-record variables\n')
                             indstrings = {}
                             for name,pos,isrec in ncout.begins:
                                 if not isrec:
4d634188c7 Mart*                     if verbose: print(name)
692071215d Oliv*                     prop = varprops[name]
                                     vardims = prop['dimensions']
                                     var = vars[name]
                                     indx = len(vardims)*[slice(None)]
                                     iX = prop['iX']
                                     iY = prop['iY']
                                     data = np.empty(var.shape, var.data.dtype.newbyteorder('>'))
1dcbcd7847 Oliv*                     for nc in ncs:
692071215d Oliv*                         tn = nc.tile_number - 1
                                         if iX is not None: indx[iX] = Xslice[tn]
                                         if iY is not None: indx[iY] = Yslice[tn]
                                         data[tuple(indx)] = nc.read_var(name)
                 
                                     ncout.write_var(name, data)
                                     del data
                                 else:  # isrec
                                     if not havetime:
                                         raise ValueError('record variables, but no time')
                 
                             # assemble record variable data
                             if havetime:
                                 irec = 0
                                 for fnames in filess:
                                     if irec:
1dcbcd7847 Oliv*                         ncs = []
692071215d Oliv*                         for fname in fnames:
1dcbcd7847 Oliv*                             nc = netcdf_file(fname, 'r', **readopts)
                                             ncs.append(nc)
692071215d Oliv* 
                                     nrec = nc.numrecs
                                     if progress and not verbose: sys.stderr.write('Writing {0} records: '.format(nrec))
                                     for irecin in range(nrec):
                                         if progress and not verbose: sys.stderr.write('.')
                                         for name,pos,isrec in ncout.begins:
                                             if isrec:
4d634188c7 Mart*                                 if verbose: print(irec+irecin, name)
692071215d Oliv*                                 prop = varprops[name]
                                                 vardims = prop['dimensions'][1:]
                                                 var = vars[name]
                                                 indx = len(vardims)*[slice(None)]
                                                 iX = prop['iX']
                                                 iY = prop['iY']
                                                 data = np.empty(var.data.shape[1:], var.data.dtype.newbyteorder('>'))
1dcbcd7847 Oliv*                                 for nc in ncs:
692071215d Oliv*                                     tn = nc.tile_number - 1
                                                     if iX is not None: indx[iX-1] = Xslice[tn]
                                                     if iY is not None: indx[iY-1] = Yslice[tn]
                                                     data[tuple(indx)] = nc.read_recvar(name, irecin)
                 
                                                 ncout.write_recvar(name, irec+irecin, data)
                                                 del data
                 
                                     irec += nrec
                 
1dcbcd7847 Oliv*                     for nc in ncs:
692071215d Oliv*                         nc.close()
                 
                                     if progress and not verbose: sys.stderr.write('\n')
ae10cb9ac4 Oliv* 
                     finally:
                         ncout.close()
                 

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