solvcon.io.netcdf

42 """ 43 Wrapper for the netCDF library by using ctypes. Mainly designed for 44 reading. Native functions remains to be nc_*. NC_* are class members for 45 constants defined in the header file. 46 """ 47 48 # netcdf external data types 49 NC_NAT = 0 # Not A Type. 50 NC_BYTE = 1 # signed 1 byte integer. 51 NC_CHAR = 2 # ISO/ASCII character. 52 NC_SHORT = 3 # signed 2 byte integer. 53 NC_INT = 4 # signed 4 byte integer. 54 NC_LONG = NC_INT # deprecated, but required for backward compatibility. 55 NC_FLOAT = 5 # single precision floating point number. 56 NC_DOUBLE = 6 # double precision floating point number. 57 NC_UBYTE = 7 # unsigned 1 byte int. 58 NC_USHORT = 8 # unsigned 2-byte int. 59 NC_UINT = 9 # unsigned 4-byte int. 60 NC_INT64 = 10 # signed 8-byte int. 61 NC_UINT64 = 11 # unsigned 8-byte int. 62 NC_STRING = 12 # string. 63 # used internally in support of user-defines types. They are also the class 64 # returned by nc_inq_user_type. 65 NC_VLEN = 13 # used internally for vlen types. 66 NC_OPAQUE = 14 # used internally for opaque types. 67 NC_ENUM = 15 # used internally for enum types. 68 NC_COMPOUND = 16 # used internally for compound types. 69 70 # Default fill values. 71 NC_FILL_BYTE = -127 72 NC_FILL_CHAR = 0 73 NC_FILL_SHORT = -32767 74 NC_FILL_INT = -2147483647L 75 NC_FILL_FLOAT = 9.9692099683868690e+36 # near 15 * 2^119. 76 NC_FILL_DOUBLE = 9.9692099683868690e+36 77 NC_FILL_UBYTE = 255 78 NC_FILL_USHORT = 65535 79 NC_FILL_UINT = 4294967295 80 NC_FILL_INT64 = -9223372036854775806 81 NC_FILL_UINT64 = 18446744073709551614 82 NC_FILL_STRING = '' 83 84 # max and min. 85 NC_MAX_BYTE = 127 86 NC_MIN_BYTE = -NC_MAX_BYTE - 1 87 NC_MAX_CHAR = 255 88 NC_MAX_SHORT = 32767 89 NC_MIN_SHORT = -NC_MAX_SHORT - 1 90 NC_MAX_INT = 2147483647 91 NC_MIN_INT = -NC_MAX_INT - 1 92 NC_MAX_FLOAT = 3.402823466e+38 93 NC_MIN_FLOAT = -NC_MAX_FLOAT 94 NC_MAX_DOUBLE = 1.7976931348623157e+308 95 NC_MIN_DOUBLE = -NC_MAX_DOUBLE 96 NC_MAX_UBYTE = NC_MAX_CHAR 97 NC_MAX_USHORT = 65535 98 NC_MAX_UINT = 4294967295 99 NC_MAX_INT64 = 9223372036854775807 100 NC_MIN_INT64 = -9223372036854775807 - 1 101 NC_MAX_UINT64 = 18446744073709551615 102 X_INT64_MAX = 9223372036854775807 103 X_INT64_MIN = -X_INT64_MAX - 1 104 X_UINT64_MAX = 18446744073709551615 105 106 # for fill. 107 _FillValue = '_FillValue' 108 NC_FILL = 0 109 NC_NOFILL = 0x100 110 111 # mode for nc_open 112 NC_NOWRITE = 0 # default read-only. 113 NC_WRITE = 0x0001 # read and write. 114 # mode for nc_create 115 NC_CLOBBER = 0 116 NC_NOCLOBBER = 0x0004 # don't descroy existing file. 117 NC_64BIT_OFFSET = 0x0200 # use 64-bit (large) file offsets. 118 NC_NETCDF4 = 0x1000 # use netCDF-4/HDF5 format. 119 NC_CLASSICAL_MODE = 0x0100 # enforce classic model with NC_NETCDF4. 120 # mode for both nc_open and nc_create. 121 NC_SHARE = 0x0800 # share updates, limit cache. 122 NC_MPIIO = 0x2000 123 NC_MPIPOSIX = 0x4000 124 NC_PNETXCDF = 0x8000 125 # future mode for nc_open and nc_create 126 NC_LOCK = 0x0400 127 128 # formats; there are more than one format since 3.6. 129 NC_FORMAT_CLASSIC = 1 130 NC_FORMAT_64BIT = 2 131 NC_FORMAT_NETCDF4 = 3 132 NC_FORMAT_NETCDF4_CLASSIC = 4 133 134 # for nc__open and nc__create. 135 NC_SIZEHINT_DEFAULT = 0 136 137 # in nc__enddef, align to chunk size. 138 NC_ALIGN_CHUNK = -1 139 140 # size argument to ncdimdef for unlimit. 141 NC_UNLIMITED = 0 142 143 # attribute ID for global attributes. 144 NC_GLOBAL = -1 145 146 # interfacial max; nothing to do with netCDF internal implementation. 147 NC_MAX_DIMS = 1024 # max dimensions per file. 148 NC_MAX_ATTRS = 8192 # max global or per variable attributes. 149 NC_MAX_VARS = 8192 # max variables per file. 150 NC_MAX_NAME = 256 # max length of a name. 151 NC_MAX_VAR_DIMS = NC_MAX_DIMS # max per variable dimensions. 152 153 # endianness for HDF5 files. 154 NC_ENDIAN_NATIVE = 0 155 NC_ENDIAN_LITTLE = 1 156 NC_ENDIAN_BIG = 2 157 # chunk or continuous for HDF5 files. 158 NC_CHUNKED = 0 159 NC_CONTIGUOUS = 1 160 # checksum for HDF5 files. 161 NC_NOCHECKSUM = 0 162 NC_FLETCHER32 = 1 163 # shuffle for HDF5 files. 164 NC_NOSHUFFLE = 0 165 NC_SHUFFLE = 1 166 167 # errors. 168 NC_NOERR = 0 # no error. 169 170 NC2_ERR = -1 # for all errors in the v2 API. 171 NC_EBADID = -33 # Not a netcdf id. 172 NC_ENFILE = -34 # Too many netcdfs open. 173 NC_EEXIST = -35 # netcdf file exists && NC_NOCLOBBER. 174 NC_EINVAL = -36 # Invalid Argument. 175 NC_EPERM = -37 # Write to read only. 176 NC_ENOTINDEFINE = -38 # Operation not allowed in data mode. 177 NC_EINDEFINE = -39 # Operation not allowed in define mode. 178 NC_EINVALCOORDS = -40 # Index exceeds dimension bound. 179 NC_EMAXDIMS = -41 # NC_MAX_DIMS exceeded. 180 NC_ENAMEINUSE = -42 # String match to name in use. 181 NC_ENOTATT = -43 # Attribute not found. 182 NC_EMAXATTS = -44 # NC_MAX_ATTRS exceeded. 183 NC_EBADTYPE = -45 # Not a netcdf data type. 184 NC_EBADDIM = -46 # Invalid dimension id or name. 185 NC_EUNLIMPOS = -47 # NC_UNLIMITED in the wrong index. 186 NC_EMAXVARS = -48 # NC_MAX_VARS exceeded. 187 NC_ENOTVAR = -49 # Variable not found. 188 NC_EGLOBAL = -50 # Action prohibited on NC_GLOBAL varid. 189 NC_ENOTNC = -51 # Not a netcdf file. 190 NC_ESTS = -52 # In Fortran, string too short. 191 NC_EMAXNAME = -53 # NC_MAX_NAME exceeded. 192 NC_EUNLIMIT = -54 # NC_UNLIMITED size already in use. 193 NC_ENORECVARS = -55 # nc_rec op when there are no record vars. 194 NC_ECHAR = -56 # Attempt to convert between text & numbers. 195 NC_EEDGE = -57 # Start+count exceeds dimension bound. 196 NC_ESTRIDE = -58 # Illegal stride. 197 NC_EBADNAME = -59 # Attribute or variable name contains illegal 198 # characters. 199 200 # following must match value in ncx.h 201 NC_ERANGE = -60 # Math result not representable. 202 NC_ENOMEM = -61 # Memory allocation (malloc) failure. 203 NC_EVARSIZE = -62 # One or more variable sizes violate format 204 # constraints. 205 NC_EDIMSIZE = -63 # Invalid dimension size. 206 NC_ETRUNC = -64 # File likely truncated or possibly corrupted. 207 NC_EAXISTYPE = -65 # Unknown axis type. 208 209 # following errors are added for DAP. 210 NC_EDAP = -66 # Generic DAP error. 211 NC_ECURL = -67 # Generic libcurl error. 212 NC_EIO = -68 # Generic IO error. 213 NC_ENODATA = -69 # Attempt to access variable with no data. 214 NC_EDAPSVC = -70 # DAP Server side error. 215 NC_EDAS = -71 # Malformed or inaccessible DAS. 216 NC_EDDS = -72 # Malformed or inaccessible DDS. 217 NC_EDATADDS = -73 # Malformed or inaccessible DATADDS. 218 NC_EDAPURL = -74 # Malformed DAP URL. 219 NC_EDAPCONSTRAINT = -75 # Malformed DAP Constraint. 220 221 # following was added in support of netcdf-4. Make all netcdf-4 error codes 222 # < -100 so that errors can be added to netcdf-3 if needed. 223 NC4_FIRST_ERROR = -100 224 NC_EHDFERR = -101 # Error at HDF5 layer. 225 NC_ECANTREAD = -102 # Can't read. 226 NC_ECANTWRITE = -103 # Can't write. 227 NC_ECANTCREATE = -104 # Can't create. 228 NC_EFILEMETA = -105 # Problem with file metadata. 229 NC_EDIMMETA = -106 # Problem with dimension metadata. 230 NC_EATTMETA = -107 # Problem with attribute metadata. 231 NC_EVARMETA = -108 # Problem with variable metadata. 232 NC_ENOCOMPOUND = -109 # Not a compound type. 233 NC_EATTEXISTS = -110 # Attribute already exists. 234 NC_ENOTNC4 = -111 # Attempting netcdf-4 operation on netcdf-3 file. 235 NC_ESTRICTNC3 = -112 # Attempting netcdf-4 operation on strict nc3 236 # netcdf-4 file. 237 NC_ENOTNC3 = -113 # Attempting netcdf-3 operation on netcdf-4 file. 238 NC_ENOPAR = -114 # Parallel operation on file opened for non-parallel 239 # access. 240 NC_EPARINIT = -115 # Error initializing for parallel access. 241 NC_EBADGRPID = -116 # Bad group ID. 242 NC_EBADTYPID = -117 # Bad type ID. 243 NC_ETYPDEFINED = -118 # Type has already been defined and may not be 244 # edited. 245 NC_EBADFIELD = -119 # Bad field ID. 246 NC_EBADCLASS = -120 # Bad class. 247 NC_EMAPTYPE = -121 # Mapped access for atomic types only. 248 NC_ELATEFILL = -122 # Attempt to define fill value when data already 249 # exists. 250 NC_ELATEDEF = -123 # Attempt to define var properties, like deflate, after 251 # enddef. 252 NC_EDIMSCALE = -124 # Probem with HDF5 dimscales. 253 NC_ENOGRP = -125 # No group found. 254 NC_ESTORAGE = -126 # Can't specify both contiguous and chunking. 255 NC_EBADCHUNK = -127 # Bad chunksize. 256 NC_ENOTBUILT = -128 # Attempt to use feature that was not turned on when 257 # netCDF was built. 258 NC4_LAST_ERROR = -128 259

260 - def __init__(self, path=None, omode=None, libname='libnetcdf.so'):

261 """ 262 @keyword path: the file to open. 263 @type path: str 264 @keyword omode: opening mode. 265 @type omode: int 266 """ 267 from ctypes import c_char_p 268 self.lib = get_lib(libname) 269 self.ncid = None 270 # set up return type. 271 self.nc_strerror.restype = c_char_p 272 self.nc_inq_libvers.restype = c_char_p 273 # open file. 274 if path is not None: 275 self.open_file(path, omode)

276 - def __getattr__(self, key):

277 if key.startswith('nc_'): 278 return getattr(self.lib, key)

279

280 - def open_file(self, path, omode=None):

281 """ 282 Open a NetCDF file. 283 284 @keyword path: the file to open. 285 @type path: str 286 @keyword omode: opening mode. 287 @type omode: int 288 @return: ncid 289 @rtype: int 290 """ 291 from ctypes import c_int, byref 292 omode = self.NC_NOWRITE if omode is None else omode 293 if self.ncid is not None: 294 raise IOError('ncid %d has been opened'%self.ncid) 295 ncid = c_int() 296 retval = self.nc_open(path, omode, byref(ncid)) 297 if retval != self.NC_NOERR: 298 raise IOError(self.nc_strerror(retval)) 299 self.ncid = ncid.value 300 return self.ncid

301 - def close_file(self):

302 """ 303 Close the associated NetCDF file. 304 305 @return: nothing 306 """ 307 retval = self.nc_close(self.ncid) 308 if retval != self.NC_NOERR: 309 raise IOError(self.nc_strerror(retval)) 310 self.ncid = None

311

312 - def get_dim(self, name):

313 """ 314 Get the dimension of the given name. 315 316 @param name: the name of the dimension. 317 @type name: str 318 @return: the dimension (length). 319 @rtype: int 320 """ 321 from ctypes import c_int, c_long, byref 322 dimid = c_int() 323 length = c_long() 324 retval = self.nc_inq_dimid(self.ncid, name, byref(dimid)) 325 if retval != self.NC_NOERR: 326 raise IOError(self.nc_strerror(retval)) 327 retval = self.nc_inq_dimlen(self.ncid, dimid, byref(length)) 328 if retval != self.NC_NOERR: 329 raise IOError(self.nc_strerror(retval)) 330 return length.value

331

332 - def get_array(self, name, shape, dtype):

333 """ 334 Load ndarray from netCDF file. 335 336 @param name: the data to be loaded. 337 @type name: str 338 @param shape: the shape of ndarray. 339 @type shape: tuple 340 @param dtype: the dtype of ndarray. 341 @type dtype: str 342 @return: the loaded ndarray. 343 @rtype: numpy.ndarray 344 """ 345 from ctypes import POINTER, c_int, c_float, c_double, byref 346 from numpy import empty 347 # get value ID. 348 varid = c_int() 349 retval = self.nc_inq_varid(self.ncid, name, byref(varid)) 350 if retval != self.NC_NOERR: 351 raise IOError(self.nc_strerror(retval)) 352 # prepare array and loader. 353 arr = empty(shape, dtype=dtype) 354 if dtype == 'int32': 355 func = self.nc_get_var_int 356 elif dtype == 'float32': 357 func = self.nc_get_var_float 358 elif dtype == 'float64': 359 func = self.nc_get_var_double 360 else: 361 raise TypeError('now surrport only int, float, double, and char') 362 # load array. 363 retval = func(self.ncid, varid, arr.ctypes._as_parameter_) 364 if retval != self.NC_NOERR: 365 raise IOError(self.nc_strerror(retval)) 366 return arr

367

368 - def get_lines(self, name, shape):

369 """ 370 Load string from netCDF file. 371 372 @param name: the data to be loaded. 373 @type name: str 374 @param shape: the shape of ndarray. Must be 1 or 2. 375 @type shape: tuple 376 @return: the loaded ndarray. 377 @rtype: numpy.ndarray 378 """ 379 from ctypes import POINTER, c_int, c_char, byref 380 from numpy import empty 381 if len(shape) > 2: 382 raise IndexError('array should have no more than two dimension') 383 # get value ID. 384 varid = c_int() 385 retval = self.nc_inq_varid(self.ncid, name, byref(varid)) 386 if retval != self.NC_NOERR: 387 raise IOError(self.nc_strerror(retval)) 388 # prepare array and loader. 389 arr = empty(shape, dtype='byte') 390 # load string data. 391 retval = self.nc_get_var_text(self.ncid, varid, 392 arr.ctypes._as_parameter_) 393 if retval != self.NC_NOERR: 394 raise IOError(self.nc_strerror(retval)) 395 # convert to string. 396 shape = (1, shape[0]) if len(shape) < 2 else shape 397 arr = arr.reshape(shape) 398 lines = [] 399 for ii in range(shape[0]): 400 for ij in range(shape[1]): 401 if arr[ii,ij] == 0: 402 lines.append(arr[ii,:ij].tostring()) 403 break 404 if len(lines) <= ii: 405 lines.append(arr[ii,:].tostring()) 406 return lines

Source Code for Module solvcon.io.netcdf