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import os
import numpy
import numpy.ctypeslib
import ctypes as CT
import umfile
_len_real_hdr = 19
_len_int_hdr = 45
class File_type(CT.Structure):
_fields_ = [("format", CT.c_int),
("byte_ordering", CT.c_int),
("word_size", CT.c_int)]
def _get_ctypes_array(dtype, size=None):
"""
get ctypes corresponding to a numpy array of a given type;
the size should not be necessary unless the storage for the array
is allocated in the C code
"""
kwargs = {'dtype': dtype,
'ndim': 1,
'flags': ('C_CONTIGUOUS', 'WRITEABLE')}
if size:
kwargs['shape'] = (size,)
return numpy.ctypeslib.ndpointer(**kwargs)
def _gen_rec_class(int_type, float_type):
class Rec(CT.Structure):
"""
ctypes object corresponding to the Rec object in the C code,
"""
_fields_ = [("int_hdr", _get_ctypes_array(int_type, _len_int_hdr)),
("real_hdr", _get_ctypes_array(float_type, _len_real_hdr)),
("header_offset", CT.c_size_t),
("data_offset", CT.c_size_t),
("disk_length", CT.c_size_t),
("_internp", CT.c_void_p)]
return Rec
Rec32 = _gen_rec_class(numpy.int32, numpy.float32)
Rec64 = _gen_rec_class(numpy.int64, numpy.float64)
def _gen_var_class(rec_class):
class Var(CT.Structure):
"""
ctypes object corresponding to the Var object in the C code
"""
_fields_ = [("recs", CT.POINTER(CT.POINTER(rec_class))),
("nz", CT.c_int),
("nt", CT.c_int),
("supervar_index", CT.c_int),
("_internp", CT.c_void_p)]
return Var
Var32 = _gen_var_class(Rec32)
Var64 = _gen_var_class(Rec64)
def _gen_file_class(var_class):
class File(CT.Structure):
"""
ctypes object corresponding to the File object in the C code
"""
_fields_ = [("fd", CT.c_int),
("file_type", File_type),
("nvars", CT.c_int),
("vars", CT.POINTER(CT.POINTER(var_class))),
("_internp", CT.c_void_p)]
return File
File32 = _gen_file_class(Var32)
File64 = _gen_file_class(Var64)
class Enum(object):
def __init__(self, *names):
self.names = names
def as_name(self, val):
if isinstance(val, str):
return val
else:
return self.names[val]
def as_index(self, val):
if isinstance(val, int):
return val
return self.names.index(val)
enum_file_format = Enum("PP", "FF")
enum_byte_ordering = Enum("little_endian", "big_endian")
enum_data_type = Enum("integer", "real")
class CInterface(object):
"""
Interface to the C shared library functions
"""
def __init__(self, lib_name = "umfile.so"):
lib_dir = os.path.join(os.path.dirname(__file__) or ".",
"c-lib")
lib_path = os.path.join(lib_dir, lib_name)
self.lib = CT.CDLL(lib_path)
def _is_null_pointer(self, ptr):
try:
ptr.contents
return False
except ValueError:
return True
def detect_file_type(self, fd):
"""
auto-detect file type; returns a File_type ctypes object
that can be passed to file_parse(), or
raises an exception if file type cannot be detected
"""
file_type = File_type()
rv = self.lib.detect_file_type(fd, CT.pointer(file_type))
if rv != 0:
raise umfile.UMFileException("File type could not be detected")
return file_type
def file_type_obj_to_dict(self, file_type):
"""
converts a FileType object returned by detect_file_type()
into a dictionary that include meaningful string
values in place of the integers that derive from the C enum
statments, specifically:
'format': 'PP' or 'FF'
'byte_ordering': 'little_endian' or 'big_endian'
and also
'word_size': 4 or 8
"""
format = enum_file_format.as_name(file_type.format)
byte_ordering = enum_byte_ordering.as_name(file_type.byte_ordering)
word_size = file_type.word_size
return {
'format': format,
'byte_ordering': byte_ordering,
'word_size': word_size
}
def create_file_type(self, format, byte_ordering, word_size):
"""
takes string input values:
'format': 'PP' or 'FF'
'byte_ordering': 'little_endian' or 'big_endian'
'word_size': 4 or 8
and returns a FileType object (ctypes structure containing integer
values) that can be passed to file_parse()
"""
return File_type(format = enum_file_format.as_index(format),
byte_ordering = enum_byte_ordering.as_index(byte_ordering),
word_size = word_size)
def set_word_size(self, val):
"""
Sets the word size used to interpret returned pointers from subsequent
calls, in particular the pointers to PP headers embedded in the tree of
objects returned by file_parse() and the data array that is populated
by read_record_data().
the 'val' argument contains either just the word_size value to use or a
file_type object from which it is to be extracted
"""
if isinstance(val, File_type):
word_size = val.word_size
else:
word_size = val
if word_size == 4:
self.file_class = File32
self.file_data_int_type = numpy.int32
self.file_data_real_type = numpy.float32
elif word_size == 8:
self.file_class = File64
self.file_data_int_type = numpy.int64
self.file_data_real_type = numpy.float64
else:
raise ValueError("word size must be 4 or 8 (not %s)" % word_size)
def _get_ctypes_int_array(self, size=None):
return _get_ctypes_array(self.file_data_int_type, size)
def _get_ctypes_real_array(self, size=None):
return _get_ctypes_array(self.file_data_real_type, size)
def _get_empty_real_array(self, size):
"""
get empty numpy real array according to word size previously
set with set_word_size()
"""
return numpy.empty(size, dtype = self.file_data_real_type)
def _get_empty_int_array(self, size):
"""
as _get_empty_real_array but for int
"""
return numpy.empty(size, dtype = self.file_data_int_type)
def parse_file(self, fh, file_type):
"""
Given an open file handle, work out information from the file, and
return this in a dictionary, of which currently the only key actually
implemented is 'vars', containing a list of variables, as that is all
that the caller requires.
arguments: fh - low-level file handle (integer)
file_type - File_type object as returned by detect_file_type() or
create_file_type()
"""
func = self.lib.file_parse
file_p_type = CT.POINTER(self.file_class)
func.restype = file_p_type
file_p = func(fh, file_type)
if self._is_null_pointer(file_p):
raise umfile.UMFileException("file parsing failed")
file = file_p.contents
c_vars = file.vars[:file.nvars]
rv = {'vars': map(self.c_var_to_py_var, c_vars)}
# now that we have copied all the data into python objects for the
# caller, free any memory allocated in the C code before returning
free_func = self.lib.file_free
free_func._fields_ = file_p_type
free_func(file_p)
return rv
def c_var_to_py_var(self, c_var_p):
"""
create a umfile.Var object from a ctypes object corresponding to 'Var*'
in the C code
"""
c_var = c_var_p.contents
nz = c_var.nz
nt = c_var.nt
svi = c_var.supervar_index
if svi < 0:
svi = None
c_recs = c_var.recs
recs = [self.c_rec_to_py_rec(c_recs[recid]) for recid in range(nz * nt)]
return umfile.Var(recs, nz, nt, svi)
def c_rec_to_py_rec(self, c_rec_p):
"""
create a umfile.Rec object from a ctypes object corresponding to 'Rec*'
in the C code
"""
c_rec = c_rec_p.contents
# numpy.copy used here so we can go back and free the memory allocated
# by C without affecting the python object
int_hdr = numpy.copy(numpy.ctypeslib.as_array(c_rec.int_hdr))
real_hdr = numpy.copy(numpy.ctypeslib.as_array(c_rec.real_hdr))
header_offset = c_rec.header_offset
data_offset = c_rec.data_offset
disk_length = c_rec.disk_length
return umfile.Rec(int_hdr, real_hdr, header_offset, data_offset, disk_length)
def get_type_and_num_words(self, int_hdr):
"""
from integer header, work out data type and number of words to read
(read_record_data requires this)
returns 2-tuple of:
data type: 'integer' or 'real'
number of words
"""
word_size = int_hdr.itemsize
self.lib.get_type_and_num_words.argtypes = [ CT.c_int,
self._get_ctypes_int_array(),
CT.POINTER(CT.c_int),
CT.POINTER(CT.c_size_t) ]
data_type = CT.c_int()
num_words = CT.c_size_t()
rv = self.lib.get_type_and_num_words(word_size,
int_hdr,
CT.pointer(data_type),
CT.pointer(num_words))
if rv != 0:
raise umfile.UMFileException("error determining data type and size from integer header")
return enum_data_type.as_name(data_type.value), num_words.value
def get_extra_data_offset_and_length(self, int_hdr, data_offset, disk_length):
"""
from integer header, gets offset and length of extra data
returns 2-tuple (offset, length), both in units of BYTES
"""
word_size = int_hdr.itemsize
func = self.lib.get_extra_data_offset_and_length
func.argtypes = [ CT.c_int,
self._get_ctypes_int_array(),
CT.c_size_t,
CT.c_size_t,
CT.POINTER(CT.c_size_t),
CT.POINTER(CT.c_size_t) ]
extra_data_offset = CT.c_size_t()
extra_data_length = CT.c_size_t()
rv = func(word_size, int_hdr, data_offset, disk_length,
CT.pointer(extra_data_offset), CT.pointer(extra_data_length))
if rv != 0:
raise umfile.UMFileException("error determining extra data length from integer header")
return extra_data_offset.value, extra_data_length.value
def read_header(self,
fd,
header_offset,
byte_ordering,
word_size):
"""
reads header from open file, returning as 2-tuple (int_hdr, real_hdr) of numpy arrays
"""
self.lib.read_header.argtypes = [ CT.c_int,
CT.c_size_t,
CT.c_int,
CT.c_int,
self._get_ctypes_int_array(),
self._get_ctypes_real_array()]
int_hdr = self._get_empty_int_array(_len_int_hdr)
real_hdr = self._get_empty_real_array(_len_real_hdr)
rv = self.lib.read_header(fd,
header_offset,
enum_byte_ordering.as_index(byte_ordering),
word_size,
int_hdr,
real_hdr)
if rv != 0:
raise umfile.UMFileException("error reading header data")
return int_hdr, real_hdr
def read_extra_data(self,
fd,
extra_data_offset,
extra_data_length,
byte_ordering,
word_size):
"""
reads record data from open file
inputs:
fd - integer low-level file descriptor
extra_data_offset - offset in bytes
extra_disk_length - disk length of extra data in bytes
byte_ordering - 'little_endian' or 'big_endian'
word_size - 4 or 8
returns: extra data as string)
"""
extra_data = "\0" * extra_data_length
self.lib.read_extra_data.argtypes = [ CT.c_int,
CT.c_size_t,
CT.c_size_t,
CT.c_int,
CT.c_int,
CT.c_char_p ]
rv = self.lib.read_extra_data(fd,
extra_data_offset,
extra_data_length,
enum_byte_ordering.as_index(byte_ordering),
word_size,
extra_data)
if rv != 0:
raise umfile.UMFileException("error reading extra data")
return extra_data
def read_record_data(self,
fd,
data_offset,
disk_length,
byte_ordering,
word_size,
int_hdr,
real_hdr,
data_type,
nwords):
"""
reads record data from open file
inputs:
fd - integer low-level file descriptor
data_offset - offset in words
disk_length - disk length of data record in words
byte_ordering - 'little_endian' or 'big_endian'
word_size - 4 or 8
int_hdr - integer PP headers (numpy array)
real_hdr - real PP headers (numpy array)
data_type - 'integer' or 'real'
nwords - number of words to read
type and nwords should have been returned by get_type_and_num_words()
"""
if data_type == 'integer':
data = self._get_empty_int_array(nwords)
ctypes_data = self._get_ctypes_int_array()
elif data_type == 'real':
data = self._get_empty_real_array(nwords)
ctypes_data = self._get_ctypes_real_array()
else:
raise ValueError("data_type must be 'integer' or 'real'")
self.lib.read_record_data.argtypes = [ CT.c_int,
CT.c_size_t,
CT.c_size_t,
CT.c_int,
CT.c_int,
self._get_ctypes_int_array(),
self._get_ctypes_real_array(),
CT.c_size_t,
ctypes_data ]
rv = self.lib.read_record_data(fd,
data_offset,
disk_length,
enum_byte_ordering.as_index(byte_ordering),
word_size,
int_hdr,
real_hdr,
nwords,
data)
if rv != 0:
raise umfile.UMFileException("error reading record data")
return data
if __name__ == "__main__":
import sys
c = CInterface()
fd = os.open(sys.argv[1], os.O_RDONLY)
file_type = c.detect_file_type(fd)
print c.file_type_obj_to_dict(file_type)
c.set_word_size(file_type)
info = c.parse_file(fd, file_type)
for var in info['vars']:
print "nz = %s, nt = %s" % (var.nz, var.nt)
for rec in var.recs:
print rec.hdr_offset
print "data offset", rec.data_offset
print "disk length", rec.disk_length
print "int hdr", rec.int_hdr
print "real hdr", rec.real_hdr
data_type, nwords = c.get_type_and_num_words(rec.int_hdr)
print "data_type = %s nwords = %s" % (data_type, nwords)
data = c.read_record_data(fd,
rec.data_offset,
rec.disk_length,
file_type.byte_ordering,
file_type.word_size,
rec.int_hdr,
rec.real_hdr,
data_type,
nwords)
print "data (%s values): %s ... %s" % (len(data), data[:10], data[-10:])
extra_data_offset, extra_data_length = \
c.get_extra_data_offset_and_length(rec.int_hdr,
rec.data_offset,
rec.disk_length)
print "extra data offset: %s" % extra_data_offset
print "extra data length: %s" % extra_data_length
extra_data = c.read_extra_data(fd,
extra_data_offset,
extra_data_length,
file_type.byte_ordering,
file_type.word_size)
print "extra data (%s bytes) read" % (len(extra_data))
print c.read_header(fd,
info['vars'][0].recs[0].hdr_offset,
file_type.byte_ordering,
file_type.word_size)
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