solvcon.io.netcdf

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

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

260 """ 261 @keyword path: the file to open. 262 @type path: str 263 @keyword omode: opening mode. 264 @type omode: int 265 """ 266 from ctypes import c_char_p 267 self.lib = get_lib(libname) 268 self.ncid = None 269 # set up return type. 270 self.nc_strerror.restype = c_char_p 271 self.nc_inq_libvers.restype = c_char_p 272 # open file. 273 if path is not None: 274 self.open_file(path, omode)

275 - def __getattr__(self, key):

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

278

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

280 """ 281 Open a NetCDF file. 282 283 @keyword path: the file to open. 284 @type path: str 285 @keyword omode: opening mode. 286 @type omode: int 287 @return: ncid 288 @rtype: int 289 """ 290 from ctypes import c_int, byref 291 omode = self.NC_NOWRITE if omode is None else omode 292 if self.ncid is not None: 293 raise IOError('ncid %d has been opened'%self.ncid) 294 ncid = c_int() 295 retval = self.nc_open(path, omode, byref(ncid)) 296 if retval != self.NC_NOERR: 297 raise IOError(self.nc_strerror(retval)) 298 self.ncid = ncid.value 299 return self.ncid

300 - def close_file(self):

301 """ 302 Close the associated NetCDF file. 303 304 @return: nothing 305 """ 306 retval = self.nc_close(self.ncid) 307 if retval != self.NC_NOERR: 308 raise IOError(self.nc_strerror(retval)) 309 self.ncid = None

310

311 - def get_dim(self, name):

312 """ 313 Get the dimension of the given name. 314 315 @param name: the name of the dimension. 316 @type name: str 317 @return: the dimension (length). 318 @rtype: int 319 """ 320 from ctypes import c_int, c_long, byref 321 dimid = c_int() 322 length = c_long() 323 retval = self.nc_inq_dimid(self.ncid, name, byref(dimid)) 324 if retval != self.NC_NOERR: 325 raise IOError(self.nc_strerror(retval)) 326 retval = self.nc_inq_dimlen(self.ncid, dimid, byref(length)) 327 if retval != self.NC_NOERR: 328 raise IOError(self.nc_strerror(retval)) 329 return length.value

330

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

332 """ 333 Load ndarray from netCDF file. 334 335 @param name: the data to be loaded. 336 @type name: str 337 @param shape: the shape of ndarray. 338 @type shape: tuple 339 @param dtype: the dtype of ndarray. 340 @type dtype: str 341 @return: the loaded ndarray. 342 @rtype: numpy.ndarray 343 """ 344 from ctypes import POINTER, c_int, c_float, c_double, byref 345 from numpy import empty 346 # get value ID. 347 varid = c_int() 348 retval = self.nc_inq_varid(self.ncid, name, byref(varid)) 349 if retval != self.NC_NOERR: 350 raise IOError(self.nc_strerror(retval)) 351 # prepare array and loader. 352 arr = empty(shape, dtype=dtype) 353 if dtype == 'int32': 354 func = self.nc_get_var_int 355 elif dtype == 'float32': 356 func = self.nc_get_var_float 357 elif dtype == 'float64': 358 func = self.nc_get_var_double 359 else: 360 raise TypeError('now surrport only int, float, double, and char') 361 # load array. 362 retval = func(self.ncid, varid, arr.ctypes._as_parameter_) 363 if retval != self.NC_NOERR: 364 raise IOError(self.nc_strerror(retval)) 365 return arr

366

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

368 """ 369 Load string from netCDF file. 370 371 @param name: the data to be loaded. 372 @type name: str 373 @param shape: the shape of ndarray. Must be 1 or 2. 374 @type shape: tuple 375 @return: the loaded ndarray. 376 @rtype: numpy.ndarray 377 """ 378 from ctypes import POINTER, c_int, c_char, byref 379 from numpy import empty 380 if len(shape) > 2: 381 raise IndexError('array should have no more than two dimension') 382 # get value ID. 383 varid = c_int() 384 retval = self.nc_inq_varid(self.ncid, name, byref(varid)) 385 if retval != self.NC_NOERR: 386 raise IOError(self.nc_strerror(retval)) 387 # prepare array and loader. 388 arr = empty(shape, dtype='byte') 389 # load string data. 390 retval = self.nc_get_var_text(self.ncid, varid, 391 arr.ctypes._as_parameter_) 392 if retval != self.NC_NOERR: 393 raise IOError(self.nc_strerror(retval)) 394 # convert to string. 395 shape = (1, shape[0]) if len(shape) < 2 else shape 396 arr = arr.reshape(shape) 397 lines = [] 398 for ii in range(shape[0]): 399 for ij in range(shape[1]): 400 if arr[ii,ij] == 0: 401 lines.append(arr[ii,:ij].tostring()) 402 break 403 if len(lines) <= ii: 404 lines.append(arr[ii,:].tostring()) 405 return lines

Source Code for Module solvcon.io.netcdf