File: cInterface.py

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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)