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import os
import numpy
import cInterface
from extraData import ExtraDataUnpacker
class UMFileException(Exception):
pass
class File(object):
"""
a class for a UM data file that gives a view of the file including sets of
PP records combined into variables
"""
def __init__(self, path,
byte_ordering = None,
word_size = None,
format = None,
parse = True):
"""
Open and parse a UM file. The following optional arguments specify
the file type. If all three are set, then this forces the file type;
otherwise, the file type is autodetected and any of them that are set
are ignored.
byte_ordering: 'little_endian' or 'big_endian'
word_size: 4 or 8
format: 'FF' or 'PP'
The default action is to open the file, store the file type from the
arguments or autodetection as described above, and then parse the
contents, giving a tree of variables and records under the File
object. However, if "parse = False" is set, then an object is
returned in which the last step is omitted, so only the file type is
stored, and there are no variables under it. Such an object can be
passed when instantiating Rec objects, and contains sufficient info
about the file type to ensure that the get_data method of those Rec
objects will work.
"""
c = cInterface.CInterface()
self._c_interface = c
self.path = path
self.fd = None
self.open_fd()
if byte_ordering and word_size and format:
self.format = format
self.byte_ordering = byte_ordering
self.word_size = word_size
else:
self._detect_file_type()
self.path = path
file_type_obj = c.create_file_type(self.format, self.byte_ordering, self.word_size)
c.set_word_size(file_type_obj)
if parse:
info = c.parse_file(self.fd, file_type_obj)
self.vars = info["vars"]
self._add_back_refs()
def open_fd(self):
"""
(Re)open the low-level file descriptor.
"""
if self.fd is None:
self.fd = os.open(self.path, os.O_RDONLY)
return self.fd
def close_fd(self):
"""
Close the low-level file descriptor.
"""
if self.fd:
os.close(self.fd)
self.fd = None
def _detect_file_type(self):
c = self._c_interface
try:
file_type_obj = c.detect_file_type(self.fd)
except:
self.close_fd()
raise IOError("File {0} has unsupported format".format(path))
d = c.file_type_obj_to_dict(file_type_obj)
self.format = d["format"]
self.byte_ordering = d["byte_ordering"]
self.word_size = d["word_size"]
def _add_back_refs(self):
"""
Add file attribute to Var objects, and both file and var attributes
to Rec objects. The important one is the file attribute in the Rec
object, as this is used when reading data. The others are provided
for extra convenience.
"""
for var in self.vars:
var.file = self
for rec in var.recs:
rec.var = var
rec.file = self
class Var(object):
"""
container for some information about variables
"""
def __init__(self, recs, nz, nt, supervar_index=None):
self.recs = recs
self.nz = nz
self.nt = nt
self.supervar_index = supervar_index
def _compare_recs_by_extra_data(self, a, b):
return cmp(a.get_extra_data(),
b.get_extra_data())
def _compare_recs_by_orig_order(self, a, b):
return cmp(self.recs.index(a), self.recs.index(b))
def group_records_by_extra_data(self):
"""
Returns a list of (sub)lists of records where each records within each
sublist has matching extra data (if any), so if the whole variable has
consistent extra data then the return value will be of length 1.
Within each group, the ordering of returned records is the same as in
self.recs
"""
compare = self._compare_recs_by_extra_data
recs = self.recs[:]
n = len(recs)
if n == 0:
# shouldn't have a var without records, but...
return []
recs.sort(compare)
# optimise simple case - if two ends of a sorted list match,
# the whole list matches
if not compare(recs[0], recs[-1]):
return [self.recs[:]]
groups = []
this_grp = []
for i, rec in enumerate(recs):
this_grp.append(rec)
if i == n - 1 or compare(rec, recs[i + 1]):
this_grp.sort(self._compare_recs_by_orig_order)
groups.append(this_grp)
this_grp = []
return groups
class Rec(object):
"""
container for some information about records
"""
def __init__(self, int_hdr, real_hdr, hdr_offset, data_offset, disk_length,
file = None):
"""
Default instantiation, which stores the supplied headers and offsets.
The 'file' argument, used to set the 'file' attribute, does not need
to be supplied, but if it is not then it will have to be set on the
returned object (to the containing File object) before calling
get_data() will work. Normally this would be done by the calling code
instantiating via File rather than directly.
"""
self.int_hdr = int_hdr
self.real_hdr = real_hdr
self.hdr_offset = hdr_offset
self.data_offset = data_offset
self.disk_length = disk_length
self._extra_data = None
if file:
self.file = file
@classmethod
def from_file_and_offsets(cls, file, hdr_offset, data_offset, disk_length):
"""
Instantiate a Rec object from the file object and the
header and data offsets. The headers are read in, and
also the record object is ready for calling get_data().
"""
c = file._c_interface
int_hdr, real_hdr = c.read_header(file.fd,
hdr_offset,
file.byte_ordering,
file.word_size)
return cls(int_hdr, real_hdr, hdr_offset, data_offset, disk_length, file=file)
def read_extra_data(self):
"""
read the extra data associated with the record
"""
c = self.file._c_interface
file = self.file
extra_data_offset, extra_data_length = \
c.get_extra_data_offset_and_length(self.int_hdr,
self.data_offset,
self.disk_length)
raw_extra_data = c.read_extra_data(file.fd,
extra_data_offset,
extra_data_length,
file.byte_ordering,
file.word_size)
edu = ExtraDataUnpacker(raw_extra_data,
file.word_size,
file.byte_ordering)
return edu.get_data()
def get_extra_data(self):
"""
get extra data associated with the record, either by
reading or using cached read
"""
if self._extra_data == None:
self._extra_data = self.read_extra_data()
return self._extra_data
def get_type_and_num_words(self):
"""
get the data type (as numpy type) and number of words as 2-tuple
"""
c = self.file._c_interface
ntype, num_words = c.get_type_and_num_words(self.int_hdr)
if ntype == 'integer':
dtype = numpy.dtype(c.file_data_int_type)
elif ntype == 'real':
dtype = numpy.dtype(c.file_data_real_type)
return dtype, num_words
def get_data(self):
"""
get the data array associated with the record
"""
c = self.file._c_interface
file = self.file
data_type, nwords = c.get_type_and_num_words(self.int_hdr)
# print "data_type = %s nwords = %s" % (data_type, nwords)
return c.read_record_data(file.fd,
self.data_offset,
self.disk_length,
file.byte_ordering,
file.word_size,
self.int_hdr,
self.real_hdr,
data_type,
nwords)
if __name__ == '__main__':
import sys
path = sys.argv[1]
f = File(path)
print f.format, f.byte_ordering, f.word_size
print "num variables: %s" % len(f.vars)
for varno, var in enumerate(f.vars):
print
print "var %s: nz = %s, nt = %s" % (varno, var.nz, var.nt)
for recno, rec in enumerate(var.recs):
print "var %s record %s" % (varno, recno)
print "hdr offset: %s" % rec.hdr_offset
print "data offset: %s" % rec.data_offset
print "disk length: %s" % rec.disk_length
print "int hdr: %s" % rec.int_hdr
print "real hdr: %s" % rec.real_hdr
print "data: %s" % rec.get_data()
print "extra_data: %s" % rec.get_extra_data()
print "type %s, num words: %s" % rec.get_type_and_num_words()
# if recno == 1:
# rec._extra_data['y'] += .01
# print "massaged_extra_data: %s" % rec.get_extra_data()
print "-----------------------"
print "all records", var.recs
print "records grouped by extra data ", var.group_records_by_extra_data()
print "==============================="
f.close_fd()
# also read a record using saved metadata
if f.vars:
format = f.format
byte_ordering = f.byte_ordering
word_size = f.word_size
myrec = f.vars[0].recs[0]
hdr_offset = myrec.hdr_offset
data_offset = myrec.data_offset
disk_length = myrec.disk_length
del(f)
fnew = File(path,
format = format,
byte_ordering = byte_ordering,
word_size = word_size,
parse = False)
rnew = Rec.from_file_and_offsets(fnew, hdr_offset, data_offset, disk_length)
print "record read using saved file type and offsets:"
print "int hdr: %s" % rnew.int_hdr
print "real hdr: %s" % rnew.real_hdr
print "data: %s" % rnew.get_data()
print "extra data: %s" % rnew.get_extra_data()
print "nx = %s" % rnew.int_hdr[18]
print "ny = %s" % rnew.int_hdr[17]
rdata = open("recdata0.txt", "w")
for value in rnew.get_data():
rdata.write("%s\n" % value)
rdata.close()
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