* Added writing facility. Still largely untested.

master
wirawan 15 years ago
parent 15baf746f9
commit 69592e9a8f
  1. 152
      iofmt/fortbin.py

@ -1,4 +1,4 @@
# $Id: fortbin.py,v 1.1 2010-02-08 21:49:54 wirawan Exp $
# $Id: fortbin.py,v 1.2 2010-02-19 18:39:17 wirawan Exp $
#
# wpylib.iofmt.fortbin module
# Created: 20100208
@ -15,28 +15,40 @@ import sys
from wpylib.sugar import ifelse
class fortran_bin_file(object):
"""A tool for reading Fortran binary files."""
def __init__(self, filename=None):
self.record_marker_type = numpy.uint32
self.debug = 100
"""A tool for reading Fortran binary files.
Caveat: On 64-bit systems, typical Fortran implementations still have int==int32
(i.e. the LP64 programming model), unless "-i8" kind of option is enabled.
To use 64-bit default integer, set the default_int attribute to numpy.int64 .
"""
record_marker_type = numpy.uint32
default_int = numpy.int32
default_float = numpy.float64
default_str = numpy.str_
def __init__(self, filename=None, mode="r"):
self.debug = 0
if filename:
self.open(filename)
self.open(filename, mode)
def open(self, filename):
self.F = open(filename, "rb")
def open(self, filename, mode="r"):
self.F = open(filename, mode+"b")
def read(self, *fields, **opts):
"""Reads a Fortran record.
The description of the fields are given as
(name, dtype, length) tuples."""
from numpy import fromfile as rd
if self.debug:
if self.debug or opts.get("debug"):
dbg = lambda msg : sys.stderr.write(msg)
else:
dbg = lambda msg : None
def fld_count(f):
if len(f) > 2:
return f[2]
if isinstance(f[2], (list,tuple)):
return numpy.product(f[2])
else:
return f[2]
else:
return 1
@ -52,6 +64,8 @@ class fortran_bin_file(object):
if "out" in opts:
rslt = opts["out"]
elif "dest" in opts:
rslt = opts["dest"]
else:
rslt = {}
@ -67,7 +81,14 @@ class fortran_bin_file(object):
if len(f) > 2:
(name,Dtyp,Len) = f
dtyp = numpy.dtype(Dtyp)
setval(rslt, name, numpy.fromfile(self.F, dtyp, Len))
Len2 = fld_count(f)
if isinstance(f[2], list) or isinstance(f[2], tuple):
# Special handling for shaped arrays
arr = numpy.fromfile(self.F, dtyp, Len2)
setval(rslt, name, arr.reshape(tuple(Len), order='F'))
else:
setval(rslt, name, numpy.fromfile(self.F, dtyp, Len2))
else:
# Special handling for scalars
name = f[0]
@ -87,3 +108,112 @@ class fortran_bin_file(object):
return rslt
def writevals(self, *vals, **opts):
"""Writes a Fortran record.
Only values need to be given, because the types are known.
This is a direct converse of read subroutine."""
if self.debug:
dbg = lambda msg : sys.stderr.write(msg)
else:
dbg = lambda msg : None
vals0 = vals
vals = []
for v in vals0:
if isinstance(v, int):
v2 = self.default_int(v)
if v2 != v:
raise OverflowError, \
"Integer too large to represent by default int: %d" % v
vals.append(v2)
elif isinstance(v, float):
v2 = self.default_float(v)
# FIXME: check for overflow error like in integer conversion above
vals.append(v2)
elif isinstance(v, str):
v2 = self.default_str(v)
vals.append(v2)
elif "itemsize" in dir(v):
vals.append(v)
else:
raise NotImplementedError, \
"Unsupported object of type %s of value %s" \
(str(type(v)), str(v))
reclen = numpy.sum([ v.size * v.itemsize for v in vals ], \
dtype=self.record_marker_type)
dbg("Record length = %d\n" % reclen)
dbg("Item count = %d\n" % len(vals))
reclen.tofile(self.F)
for v in vals:
if isinstance(v, numpy.ndarray):
# Always store in "Fortran" format, i.e. column major
# Since tofile() always write in the row major format,
# we will transpose it before writing:
v.T.tofile(self.F)
else:
v.tofile(self.F)
reclen.tofile(self.F)
def writefields(self, src, *fields, **opts):
if (issubclass(src.__class__, dict) and issubclass(dict, src.__class__)) \
or "__getitem__" in dir(src):
def getval(d, k):
return d[k]
else:
# Assume we can use getattr method:
getval = getattr
vals = []
for f in fields:
if isinstance(f, str):
vals.append(getval(src, f))
elif isinstance(f, (list, tuple)):
v = getval(src, f[0])
# FIXME: check datatype and do necessary conversion if f[1] exists
# Exception: if a string spec is found, we will retrofit the string
# to that kind of object. Strings that are too long are silently
# truncated and those that are too short will have whitespaces
# (ASCII 32) appended.
if len(f) > 1:
dtyp = numpy.dtype(f[1])
if dtyp.char == 'S':
strlen = dtyp.itemsize
v = self.default_str("%-*s" % (strlen, v[:strlen]))
# FIXME: check dimensionality if f[2] exists
vals.append(v)
else:
raise ValueError, "Invalid field type: %s" % str(type(f))
def array_major_dim(arr):
"""Tests whether a numpy array is column or row major.
It will return the following:
-1 : row major
+1 : column major
0 : unknown (e.g. no indication one way or the other)
In the case of inconsistent order, we will raise an exception."""
if len(arr.shape) <= 1:
return 0
elif arr.flags['C_CONTIGUOUS']:
return -1
elif arr.flags['F_CONTIGUOUS']:
return +1
# In case of noncontiguous array, we will have to test it
# based on the strides
else:
Lstrides = numpy.array(arr.shape[:-1])
Rstrides = numpy.array(arr.shape[1:])
if numpy.all(Lstrides >= Rstrides):
# Categorizes equal consecutive strides to "row major" as well
return -1
elif numpy.all(Lstrides <= Rstrides):
return +1
else:
raise RuntimeError, \
"Unable to determine whether this is a row or column major object."

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